{ "cells": [ { "cell_type": "markdown", "metadata": { "tags": [] }, "source": [ "# __Let's doing the same mapping with each sample sequenced in illumina__\n", "We have 18 samples in the SHORT_READS directory. For each sample, we want to perform all the steps to obtain the last bam used to call SNPs.\n", "\n", "The trick here is to use a __`for` loop in bash__, in which all the unique commands to be carried out for a sample are grouped together. And if we have 3 samples, these commands will be executed 3 times, for example. We cans\n", "\n", "We will use a for loop : \n", "* first with two samples\n", "* secondly with the 18 samples : 1613 1868 4752 5417 685 716 A1 A8 B1 B218 B8 C218 C2 D119 E2 E318 G11 H44\n", " \n", " \n", "### Before starting, remove all the files generated in the results directory" ] }, { "cell_type": "code", "execution_count": 6, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "1613.flagstat 1868.flagstat\n", "1613.onlymappedpaired.bam 1868.onlymappedpaired.bam\n", "1613.onlymappedpaired.bam.bai 1868.onlymappedpaired.bam.bai\n", "1613.sorted.bam 1868.onlymappedpaired.flagstat\n", "1616_1868.bcf 1868.sorted.bam\n", "1616_1868.vcf\n" ] } ], "source": [ "cd /home/jovyan/SV_DATA/RESULTS\n", "ls" ] }, { "cell_type": "code", "execution_count": 8, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "rm: cannot remove '*bam*': No such file or directory\n", "rm: cannot remove '*flagstat': No such file or directory\n", "1616_1868.bcf 1616_1868.vcf\n" ] } ], "source": [ "rm *bam* *flagstat\n", "ls" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Let's try our first for loop" ] }, { "cell_type": "code", "execution_count": 17, "metadata": { "tags": [] }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "1613\n", "1868\n" ] } ], "source": [ "for sample in 1613 1868 \n", " do\n", " echo \"$sample\"\n", " done;" ] }, { "cell_type": "code", "execution_count": 18, "metadata": { "tags": [] }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "---> I can start a series of instructions for the same sample :\n", "\t Here the sample **1613** \n", "\n", "---> I can start a series of instructions for the same sample :\n", "\t Here the sample **1868** \n", "\n" ] } ], "source": [ "for sample in 1613 1868 \n", " do\n", " echo \"---> I can start a series of instructions for the same sample :\"\n", " echo -e \"\\t Here the sample **${sample}** \\n\"\n", " done;" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### Gradually add each analysis step:\n", "* mapping with `bwa mem`\n", "* then running `samtools flagstat` \n", "* then filtering with `samtools view` and `samtools index`" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "tags": [] }, "outputs": [], "source": [ "for sample in 1613 1868\n", " do\n", " echo -e \"###################### ${sample} \"\n", " \n", " echo -e \"#### Mapping \"\n", " # PUT BWA MEM COMMAND\n", " bwa-mem2 mem -t 8 -R \"@RG\\tID:${sample}\\tSM:${sample}\" ../REF/GCA_002220235.1_ASM222023v1_genomic.fna ../SHORT_READS/${sample}_R1.fastq.gz ../SHORT_READS/${sample}_R2.fastq.gz |\n", " samtools sort -@ 8 -o ./${sample}.sorted.bam\n", " \n", " echo -e \"### Stat \"\n", " # PUT SAMTOOLS FLAGSTAT COMMAND\n", " samtools flagstat ./${sample}.sorted.bam > ./${sample}.flagstat \n", " \n", " # PUT SAMTOOLS VIEW TO FILTER BAM\n", " echo -e \"### Filtering\"\n", " samtools view -bh -@8 -f 0x02 -o ./${sample}.mappedpaired.bam ./${sample}.sorted.bam\n", " \n", " # PUT SAMTOOLS INDEX\n", " echo -e \"### Indexing bam\n", " samtools index ./${sample}.mappedpaired.bam\n", " \n", "\n", " done;" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### List the content of the `RESULTS` directory - `ls -lht`" ] }, { "cell_type": "code", "execution_count": 48, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "total 660M\n", "drwxr-sr-x 2 jovyan users 4.0K Oct 3 20:00 3_bam_filtered\n", "drwxr-sr-x 3 jovyan users 4.0K Oct 3 20:00 2_bam_flagstat\n", "drwxr-sr-x 2 jovyan users 4.0K Oct 3 20:00 1_bam_raw\n", "-rw-r--r-- 1 jovyan users 46K Oct 3 19:39 1868.mappedpaired.bam.bai\n", "-rw-r--r-- 1 jovyan users 137M Oct 3 19:39 1868.mappedpaired.bam\n", "-rw-r--r-- 1 jovyan users 519 Oct 3 19:39 1868.flagstat\n", "-rw-r--r-- 1 jovyan users 158M Oct 3 19:39 1868.sorted.bam\n", "-rw-r--r-- 1 jovyan users 46K Oct 3 19:38 1613.mappedpaired.bam.bai\n", "-rw-r--r-- 1 jovyan users 154M Oct 3 19:38 1613.mappedpaired.bam\n", "-rw-r--r-- 1 jovyan users 521 Oct 3 19:38 1613.flagstat\n", "-rw-r--r-- 1 jovyan users 167M Oct 3 19:38 1613.sorted.bam\n", "-rw-r--r-- 1 jovyan users 36M Oct 3 15:34 1616_1868.vcf\n", "-rw-r--r-- 1 jovyan users 8.8M Oct 3 15:01 1616_1868.bcf\n" ] } ], "source": [ "ls -lht /home/jovyan/SV_DATA/RESULTS" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "-----------\n", "#### __BONUS__... only if you have the time to write more \"complex\" code... \n", "We want to group all the files generated by the same software for each sample in a single :\n", "* the `1_bam_raw` directory that contains all bam files\n", "* the `2_bam_flagstat` directory that contains all files generated by `samtools flagstat`\n", "* the `3_bam_filtered` directory that contains all filtered bam files" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "#### ADDING FILE TREE\n", "res_dir=\"/home/jovyan/SV_DATA/RESULTS\"\n", "bam_raw_dir=\"${res_dir}/1_bam_raw\"\n", "bam_stat_dir=\"${res_dir}/2_bam_flagstat\"\n", "bam_filtered_dir=\"${res_dir}/3_bam_filtered\"\n", "\n", "data_dir=\"/home/jovyan/SV_DATA\"\n", "ref=\"${data_dir}/REF/GCA_002220235.1_ASM222023v1_genomic.fna\"\n", "\n", "cd $res_dir\n", "mkdir -p $bam_raw_dir\n", "mkdir -p $bam_stat_dir\n", "mkdir -p $bam_filtered_dir\n", "\n", "for sample in 1613 1868\n", " do\n", " \n", " fq1=\"${data_dir}/SHORT_READS/${sample}_R1.fastq.gz\"\n", " fq2=\"${data_dir}/SHORT_READS/${sample}_R2.fastq.gz\"\n", " \n", " echo -e \"######################\\n Mapping ${sample} \"\n", " # PUT BWA MEM CDE ADAPTED\n", " bwa-mem2 mem -t 8 -R \"@RG\\tID:${sample}\\tSM:${sample}\" ${ref} ${fq1} ${fq2} | samtools sort -@ 8 -o ${bam_raw_dir}/${sample}.sorted.bam\n", " \n", " echo -e \"######################\\nFlagstat ${sample} \"\n", " # PUT FLAGSTAT\n", " samtools flagstat ${bam_raw_dir}/${sample}.sorted.bam > ${bam_stat_dir}/${sample}.flagstat \n", " \n", " # PUT FILTER\n", " echo -e \"######################\\n Filtering ${sample} \"\n", " samtools view -bh -@8 -f 0x02 -o ${bam_filtered_dir}/${sample}.mappedpaired.bam ${bam_raw_dir}/${sample}.sorted.bam\n", " \n", " # PUT INDEX\n", " samtools index ${bam_filtered_dir}/${sample}.mappedpaired.bam\n", " \n", " done;" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### List recursively the content of the `RESULTS` directory - `ls -R`" ] }, { "cell_type": "code", "execution_count": 43, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/home/jovyan/SV_DATA/RESULTS:\n", "total 660M\n", "-rw-r--r-- 1 jovyan users 521 Oct 3 19:38 1613.flagstat\n", "-rw-r--r-- 1 jovyan users 154M Oct 3 19:38 1613.mappedpaired.bam\n", "-rw-r--r-- 1 jovyan users 46K Oct 3 19:38 1613.mappedpaired.bam.bai\n", "-rw-r--r-- 1 jovyan users 167M Oct 3 19:38 1613.sorted.bam\n", "-rw-r--r-- 1 jovyan users 8.8M Oct 3 15:01 1616_1868.bcf\n", "-rw-r--r-- 1 jovyan users 36M Oct 3 15:34 1616_1868.vcf\n", "-rw-r--r-- 1 jovyan users 519 Oct 3 19:39 1868.flagstat\n", "-rw-r--r-- 1 jovyan users 137M Oct 3 19:39 1868.mappedpaired.bam\n", "-rw-r--r-- 1 jovyan users 46K Oct 3 19:39 1868.mappedpaired.bam.bai\n", "-rw-r--r-- 1 jovyan users 158M Oct 3 19:39 1868.sorted.bam\n", "drwxr-sr-x 2 jovyan users 4.0K Oct 3 19:40 1_bam_raw\n", "drwxr-sr-x 3 jovyan users 4.0K Oct 3 19:42 2_bam_flagstat\n", "drwxr-sr-x 2 jovyan users 4.0K Oct 3 19:41 3_bam_filtered\n", "\n", "/home/jovyan/SV_DATA/RESULTS/1_bam_raw:\n", "total 324M\n", "-rw-r--r-- 1 jovyan users 167M Oct 3 19:40 1613.sorted.bam\n", "-rw-r--r-- 1 jovyan users 158M Oct 3 19:41 1868.sorted.bam\n", "\n", "/home/jovyan/SV_DATA/RESULTS/2_bam_flagstat:\n", "total 8.0K\n", "-rw-r--r-- 1 jovyan users 521 Oct 3 19:40 1613.flagstat\n", "-rw-r--r-- 1 jovyan users 0 Oct 3 19:35 1615.flagstat\n", "-rw-r--r-- 1 jovyan users 519 Oct 3 19:41 1868.flagstat\n", "\n", "/home/jovyan/SV_DATA/RESULTS/3_bam_filtered:\n", "total 291M\n", "-rw-r--r-- 1 jovyan users 154M Oct 3 19:40 1613.mappedpaired.bam\n", "-rw-r--r-- 1 jovyan users 46K Oct 3 19:40 1613.mappedpaired.bam.bai\n", "-rw-r--r-- 1 jovyan users 137M Oct 3 19:41 1868.mappedpaired.bam\n", "-rw-r--r-- 1 jovyan users 46K Oct 3 19:41 1868.mappedpaired.bam.bai\n" ] } ], "source": [ "ls -lRh /home/jovyan/SV_DATA/RESULTS " ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Let's try our previous loop on all the samples" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "bcftools mpileup --threads 8 -f ../REF/GCA_002220235.1_ASM222023v1_genomic.fna *paired.bam | bcftools call --threads 8 -cv -Oz -o 1613_1868.bcfls -lRh /home/jovyan/SV_DATA/RESULTS " ] }, { "cell_type": "code", "execution_count": 45, "metadata": { "tags": [] }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "######################\n", " Mapping 1613 \n", "-----------------------------\n", "Executing in AVX2 mode!!\n", "-----------------------------\n", "Ref file: /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna\n", "Entering FMI_search\n", "reference seq len = 30148641\n", "count\n", "0,\t1\n", "1,\t7834026\n", "2,\t15074321\n", "3,\t22314616\n", "4,\t30148641\n", "\n", "Reading other elements of the index from files /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna\n", "prefix: /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna\n", "[M::bwa_idx_load_ele] read 0 ALT contigs\n", "Done reading Index!!\n", "Reading reference genome..\n", "Binary seq file = /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna.0123\n", "Reference genome size: 30148640 bp\n", "Done readng reference genome !!\n", "\n", "[0000] 1: Calling process()\n", "\n", "Threads used (compute): 8\n", "Info: projected #read in a task: 529811\n", "------------------------------------------\n", "Memory pre-allocation for chaining: 1114.7223 MB\n", "Memory pre-allocation for BSW: 1916.9362 MB\n", "Memory pre-allocation for BWT: 618.5134 MB\n", "------------------------------------------\n", "No. of pipeline threads: 2\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000217, nseq: 320478\n", "\t[0000][ M::kt_pipeline] read 320478 sequences (80000217 bp)...\n", "[0000] 2. Calling mem_process_seqs.., task: 0\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000178, nseq: 320478\n", "\t[0000][ M::kt_pipeline] read 320478 sequences (80000178 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 320478\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (6, 146360, 9, 7)\n", "[M::mem_pestat] skip orientation FF as there are not enough pairs\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (228, 278, 344)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 576)\n", "[M::mem_pestat] mean and std.dev: (290.09, 87.34)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 692)\n", "[M::mem_pestat] skip orientation RF as there are not enough pairs\n", "[M::mem_pestat] skip orientation RR as there are not enough pairs\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 320478 reads in 46.573 CPU sec, 5.827 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 1\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000142, nseq: 320476\n", "\t[0000][ M::kt_pipeline] read 320476 sequences (80000142 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 320478\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (7, 146471, 14, 7)\n", "[M::mem_pestat] skip orientation FF as there are not enough pairs\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (227, 277, 343)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 575)\n", "[M::mem_pestat] mean and std.dev: (289.75, 87.63)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 691)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (60, 334, 2198)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 6474)\n", "[M::mem_pestat] mean and std.dev: (1083.00, 1224.54)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 8612)\n", "[M::mem_pestat] skip orientation RR as there are not enough pairs\n", "[M::mem_pestat] skip orientation RF\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 320478 reads in 45.432 CPU sec, 5.637 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 2\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000457, nseq: 320478\n", "\t[0000][ M::kt_pipeline] read 320478 sequences (80000457 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 320476\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (13, 146615, 11, 9)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3706, 4374, 7453)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 14947)\n", "[M::mem_pestat] mean and std.dev: (4598.31, 2463.35)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 18694)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (227, 277, 343)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 575)\n", "[M::mem_pestat] mean and std.dev: (289.61, 87.35)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 691)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (156, 217, 2198)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 6282)\n", "[M::mem_pestat] mean and std.dev: (1123.36, 1223.29)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 8324)\n", "[M::mem_pestat] skip orientation RR as there are not enough pairs\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 320476 reads in 45.501 CPU sec, 5.625 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 3\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 47353187, nseq: 189696\n", "\t[0000][ M::kt_pipeline] read 189696 sequences (47353187 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 320478\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (6, 146206, 5, 5)\n", "[M::mem_pestat] skip orientation FF as there are not enough pairs\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (227, 276, 342)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 572)\n", "[M::mem_pestat] mean and std.dev: (288.48, 86.88)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 687)\n", "[M::mem_pestat] skip orientation RF as there are not enough pairs\n", "[M::mem_pestat] skip orientation RR as there are not enough pairs\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 320478 reads in 45.614 CPU sec, 5.696 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 4\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 0, nseq: 0\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 189696\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 86576, 7, 5)\n", "[M::mem_pestat] skip orientation FF as there are not enough pairs\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (227, 277, 343)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 575)\n", "[M::mem_pestat] mean and std.dev: (289.32, 87.35)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 691)\n", "[M::mem_pestat] skip orientation RF as there are not enough pairs\n", "[M::mem_pestat] skip orientation RR as there are not enough pairs\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 189696 reads in 26.823 CPU sec, 3.414 real sec\n", "[0000] read_chunk: 80000000, work_chunk_size: 0, nseq: 0\n", "[0000] Computation ends..\n", "No. of OMP threads: 8\n", "Processor is runnig @2295.112426 MHz\n", "Runtime profile:\n", "\n", "\t Time taken for main_mem function: 27.71 Sec\n", "\n", "\tIO times (sec) :\n", "\tReading IO time (reads) avg: 4.95, (4.95, 4.95)\n", "\tWriting IO time (SAM) avg: 2.03, (2.03, 2.03)\n", "\tReading IO time (Reference Genome) avg: 0.02, (0.02, 0.02)\n", "\tIndex read time avg: 0.21, (0.21, 0.21)\n", "\n", "\tOverall time (sec) (Excluding Index reading time):\n", "\tPROCESS() (Total compute time + (read + SAM) IO time) : 27.48\n", "\tMEM_PROCESS_SEQ() (Total compute time (Kernel + SAM)), avg: 26.19, (26.19, 26.19)\n", "\n", "\t SAM Processing time (sec):\n", "\t--WORKER_SAM avg: 3.84, (3.84, 3.84)\n", "\n", "\tKernels' compute time (sec):\n", "\tTotal kernel (smem+sal+bsw) time avg: 22.02, (22.02, 22.02)\n", "\t\tSMEM compute avg: 7.94, (7.99, 7.86)\n", "\t\tSAL compute avg: 0.85, (0.93, 0.80)\n", "\t\tBSW time, avg: 12.73, (12.76, 12.63)\n", "\n", "\tTotal allocs: 1941303 = 1941303 out total requests: 2368737, Rate: 0.82\n", "\n", "Important parameter settings: \n", "\tBATCH_SIZE: 512\n", "\tMAX_SEQ_LEN_REF: 256\n", "\tMAX_SEQ_LEN_QER: 128\n", "\tMAX_SEQ_LEN8: 128\n", "\tSEEDS_PER_READ: 500\n", "\tSIMD_WIDTH8 X: 32\n", "\tSIMD_WIDTH16 X: 16\n", "\tAVG_SEEDS_PER_READ: 64\n", "[bam_sort_core] merging from 0 files and 4 in-memory blocks...\n", "######################\n", "Flagstat 1613 \n", "######################\n", " Filtering 1613 \n", "######################\n", " Mapping 1868 \n", "-----------------------------\n", "Executing in AVX2 mode!!\n", "-----------------------------\n", "Ref file: /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna\n", "Entering FMI_search\n", "reference seq len = 30148641\n", "count\n", "0,\t1\n", "1,\t7834026\n", "2,\t15074321\n", "3,\t22314616\n", "4,\t30148641\n", "\n", "Reading other elements of the index from files /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna\n", "prefix: /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna\n", "[M::bwa_idx_load_ele] read 0 ALT contigs\n", "Done reading Index!!\n", "Reading reference genome..\n", "Binary seq file = /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna.0123\n", "Reference genome size: 30148640 bp\n", "Done readng reference genome !!\n", "\n", "[0000] 1: Calling process()\n", "\n", "Threads used (compute): 8\n", "Info: projected #read in a task: 529811\n", "------------------------------------------\n", "Memory pre-allocation for chaining: 1114.7223 MB\n", "Memory pre-allocation for BSW: 1916.9362 MB\n", "Memory pre-allocation for BWT: 618.5134 MB\n", "------------------------------------------\n", "No. of pipeline threads: 2\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000378, nseq: 320474\n", "\t[0000][ M::kt_pipeline] read 320474 sequences (80000378 bp)...\n", "[0000] 2. Calling mem_process_seqs.., task: 0\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000317, nseq: 320476\n", "\t[0000][ M::kt_pipeline] read 320476 sequences (80000317 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 320474\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 140082, 4, 2)\n", "[M::mem_pestat] skip orientation FF as there are not enough pairs\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (215, 256, 308)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (29, 494)\n", "[M::mem_pestat] mean and std.dev: (264.14, 71.38)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 587)\n", "[M::mem_pestat] skip orientation RF as there are not enough pairs\n", "[M::mem_pestat] skip orientation RR as there are not enough pairs\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 320474 reads in 38.487 CPU sec, 4.829 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 1\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000454, nseq: 320474\n", "\t[0000][ M::kt_pipeline] read 320474 sequences (80000454 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 320476\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (6, 139952, 4, 2)\n", "[M::mem_pestat] skip orientation FF as there are not enough pairs\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (215, 256, 308)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (29, 494)\n", "[M::mem_pestat] mean and std.dev: (264.15, 71.74)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 587)\n", "[M::mem_pestat] skip orientation RF as there are not enough pairs\n", "[M::mem_pestat] skip orientation RR as there are not enough pairs\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 320476 reads in 38.779 CPU sec, 4.757 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 2\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000276, nseq: 320476\n", "\t[0000][ M::kt_pipeline] read 320476 sequences (80000276 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 320474\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 139828, 5, 6)\n", "[M::mem_pestat] skip orientation FF as there are not enough pairs\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (214, 255, 308)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (26, 496)\n", "[M::mem_pestat] mean and std.dev: (263.87, 72.06)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 590)\n", "[M::mem_pestat] skip orientation RF as there are not enough pairs\n", "[M::mem_pestat] skip orientation RR as there are not enough pairs\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 320474 reads in 38.082 CPU sec, 4.695 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 3\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 24368032, nseq: 97618\n", "\t[0000][ M::kt_pipeline] read 97618 sequences (24368032 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 320476\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 139969, 5, 2)\n", "[M::mem_pestat] skip orientation FF as there are not enough pairs\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (215, 256, 307)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (31, 491)\n", "[M::mem_pestat] mean and std.dev: (263.51, 71.18)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 583)\n", "[M::mem_pestat] skip orientation RF as there are not enough pairs\n", "[M::mem_pestat] skip orientation RR as there are not enough pairs\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 320476 reads in 37.491 CPU sec, 4.684 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 4\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 0, nseq: 0\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 97618\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 42657, 1, 0)\n", "[M::mem_pestat] skip orientation FF as there are not enough pairs\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (214, 256, 307)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (28, 493)\n", "[M::mem_pestat] mean and std.dev: (263.48, 71.13)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 586)\n", "[M::mem_pestat] skip orientation RF as there are not enough pairs\n", "[M::mem_pestat] skip orientation RR as there are not enough pairs\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 97618 reads in 12.080 CPU sec, 1.533 real sec\n", "[0000] read_chunk: 80000000, work_chunk_size: 0, nseq: 0\n", "[0000] Computation ends..\n", "No. of OMP threads: 8\n", "Processor is runnig @2295.111872 MHz\n", "Runtime profile:\n", "\n", "\t Time taken for main_mem function: 21.91 Sec\n", "\n", "\tIO times (sec) :\n", "\tReading IO time (reads) avg: 4.62, (4.62, 4.62)\n", "\tWriting IO time (SAM) avg: 2.03, (2.03, 2.03)\n", "\tReading IO time (Reference Genome) avg: 0.02, (0.02, 0.02)\n", "\tIndex read time avg: 0.18, (0.18, 0.18)\n", "\n", "\tOverall time (sec) (Excluding Index reading time):\n", "\tPROCESS() (Total compute time + (read + SAM) IO time) : 21.71\n", "\tMEM_PROCESS_SEQ() (Total compute time (Kernel + SAM)), avg: 20.49, (20.49, 20.49)\n", "\n", "\t SAM Processing time (sec):\n", "\t--WORKER_SAM avg: 2.50, (2.50, 2.50)\n", "\n", "\tKernels' compute time (sec):\n", "\tTotal kernel (smem+sal+bsw) time avg: 17.77, (17.77, 17.77)\n", "\t\tSMEM compute avg: 7.18, (7.23, 7.15)\n", "\t\tSAL compute avg: 0.74, (0.77, 0.71)\n", "\t\tBSW time, avg: 9.39, (9.47, 9.28)\n", "\n", "\tTotal allocs: 1640189 = 1640189 out total requests: 1975792, Rate: 0.83\n", "\n", "Important parameter settings: \n", "\tBATCH_SIZE: 512\n", "\tMAX_SEQ_LEN_REF: 256\n", "\tMAX_SEQ_LEN_QER: 128\n", "\tMAX_SEQ_LEN8: 128\n", "\tSEEDS_PER_READ: 500\n", "\tSIMD_WIDTH8 X: 32\n", "\tSIMD_WIDTH16 X: 16\n", "\tAVG_SEEDS_PER_READ: 64\n", "[bam_sort_core] merging from 0 files and 4 in-memory blocks...\n", "######################\n", "Flagstat 1868 \n", "######################\n", " Filtering 1868 \n", "######################\n", " Mapping 4752 \n", "-----------------------------\n", "Executing in AVX2 mode!!\n", "-----------------------------\n", "Ref file: /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna\n", "Entering FMI_search\n", "reference seq len = 30148641\n", "count\n", "0,\t1\n", "1,\t7834026\n", "2,\t15074321\n", "3,\t22314616\n", "4,\t30148641\n", "\n", "Reading other elements of the index from files /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna\n", "prefix: /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna\n", "[M::bwa_idx_load_ele] read 0 ALT contigs\n", "Done reading Index!!\n", "Reading reference genome..\n", "Binary seq file = /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna.0123\n", "Reference genome size: 30148640 bp\n", "Done readng reference genome !!\n", "\n", "[0000] 1: Calling process()\n", "\n", "Threads used (compute): 8\n", "Info: projected #read in a task: 529811\n", "------------------------------------------\n", "Memory pre-allocation for chaining: 1114.7223 MB\n", "Memory pre-allocation for BSW: 1916.9362 MB\n", "Memory pre-allocation for BWT: 618.5134 MB\n", "------------------------------------------\n", "No. of pipeline threads: 2\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000288, nseq: 320480\n", "\t[0000][ M::kt_pipeline] read 320480 sequences (80000288 bp)...\n", "[0000] 2. Calling mem_process_seqs.., task: 0\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000294, nseq: 320482\n", "\t[0000][ M::kt_pipeline] read 320482 sequences (80000294 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 320480\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (7, 106323, 11, 5)\n", "[M::mem_pestat] skip orientation FF as there are not enough pairs\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (208, 256, 317)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 535)\n", "[M::mem_pestat] mean and std.dev: (264.81, 84.17)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 644)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (90, 94, 138)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 234)\n", "[M::mem_pestat] mean and std.dev: (96.22, 25.16)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 282)\n", "[M::mem_pestat] skip orientation RR as there are not enough pairs\n", "[M::mem_pestat] skip orientation RF\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 320480 reads in 38.875 CPU sec, 4.913 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 1\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000435, nseq: 320480\n", "\t[0000][ M::kt_pipeline] read 320480 sequences (80000435 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 320482\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 106230, 16, 6)\n", "[M::mem_pestat] skip orientation FF as there are not enough pairs\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (208, 256, 317)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 535)\n", "[M::mem_pestat] mean and std.dev: (265.22, 83.78)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 644)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (34, 110, 133)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 331)\n", "[M::mem_pestat] mean and std.dev: (69.15, 48.68)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 430)\n", "[M::mem_pestat] skip orientation RR as there are not enough pairs\n", "[M::mem_pestat] skip orientation RF\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 320482 reads in 38.677 CPU sec, 4.757 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 2\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000402, nseq: 320482\n", "\t[0000][ M::kt_pipeline] read 320482 sequences (80000402 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 320480\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 106337, 17, 5)\n", "[M::mem_pestat] skip orientation FF as there are not enough pairs\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (208, 256, 316)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 532)\n", "[M::mem_pestat] mean and std.dev: (264.21, 83.53)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 640)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (46, 115, 1118)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3262)\n", "[M::mem_pestat] mean and std.dev: (154.07, 271.30)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 4334)\n", "[M::mem_pestat] skip orientation RR as there are not enough pairs\n", "[M::mem_pestat] skip orientation RF\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 320480 reads in 38.320 CPU sec, 4.735 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 3\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 16220815, nseq: 64980\n", "\t[0000][ M::kt_pipeline] read 64980 sequences (16220815 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 320482\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 106579, 10, 4)\n", "[M::mem_pestat] skip orientation FF as there are not enough pairs\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (208, 256, 315)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 529)\n", "[M::mem_pestat] mean and std.dev: (264.30, 83.55)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 636)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (27, 76, 125)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 321)\n", "[M::mem_pestat] mean and std.dev: (67.89, 43.26)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 419)\n", "[M::mem_pestat] skip orientation RR as there are not enough pairs\n", "[M::mem_pestat] skip orientation RF\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 320482 reads in 37.876 CPU sec, 4.744 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 4\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] 3. Calling kt_for - worker_aln\n", "[0000] read_chunk: 80000000, work_chunk_size: 0, nseq: 0\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 64980\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 21580, 1, 1)\n", "[M::mem_pestat] skip orientation FF as there are not enough pairs\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (208, 255, 317)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 535)\n", "[M::mem_pestat] mean and std.dev: (264.44, 84.54)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 644)\n", "[M::mem_pestat] skip orientation RF as there are not enough pairs\n", "[M::mem_pestat] skip orientation RR as there are not enough pairs\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 64980 reads in 8.380 CPU sec, 1.049 real sec\n", "[0000] read_chunk: 80000000, work_chunk_size: 0, nseq: 0\n", "[0000] Computation ends..\n", "No. of OMP threads: 8\n", "Processor is runnig @2295.158576 MHz\n", "Runtime profile:\n", "\n", "\t Time taken for main_mem function: 21.61 Sec\n", "\n", "\tIO times (sec) :\n", "\tReading IO time (reads) avg: 4.54, (4.54, 4.54)\n", "\tWriting IO time (SAM) avg: 1.83, (1.83, 1.83)\n", "\tReading IO time (Reference Genome) avg: 0.02, (0.02, 0.02)\n", "\tIndex read time avg: 0.20, (0.20, 0.20)\n", "\n", "\tOverall time (sec) (Excluding Index reading time):\n", "\tPROCESS() (Total compute time + (read + SAM) IO time) : 21.39\n", "\tMEM_PROCESS_SEQ() (Total compute time (Kernel + SAM)), avg: 20.19, (20.19, 20.19)\n", "\n", "\t SAM Processing time (sec):\n", "\t--WORKER_SAM avg: 2.65, (2.65, 2.65)\n", "\n", "\tKernels' compute time (sec):\n", "\tTotal kernel (smem+sal+bsw) time avg: 17.28, (17.28, 17.28)\n", "\t\tSMEM compute avg: 7.77, (7.83, 7.73)\n", "\t\tSAL compute avg: 0.60, (0.62, 0.58)\n", "\t\tBSW time, avg: 8.51, (8.53, 8.49)\n", "\n", "\tTotal allocs: 1263990 = 1263990 out total requests: 1630989, Rate: 0.77\n", "\n", "Important parameter settings: \n", "\tBATCH_SIZE: 512\n", "\tMAX_SEQ_LEN_REF: 256\n", "\tMAX_SEQ_LEN_QER: 128\n", "\tMAX_SEQ_LEN8: 128\n", "\tSEEDS_PER_READ: 500\n", "\tSIMD_WIDTH8 X: 32\n", "\tSIMD_WIDTH16 X: 16\n", "\tAVG_SEEDS_PER_READ: 64\n", "[bam_sort_core] merging from 0 files and 4 in-memory blocks...\n", "######################\n", "Flagstat 4752 \n", "######################\n", " Filtering 4752 \n", "######################\n", " Mapping 5417 \n", "-----------------------------\n", "Executing in AVX2 mode!!\n", "-----------------------------\n", "Ref file: /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna\n", "Entering FMI_search\n", "reference seq len = 30148641\n", "count\n", "0,\t1\n", "1,\t7834026\n", "2,\t15074321\n", "3,\t22314616\n", "4,\t30148641\n", "\n", "Reading other elements of the index from files /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna\n", "prefix: /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna\n", "[M::bwa_idx_load_ele] read 0 ALT contigs\n", "Done reading Index!!\n", "Reading reference genome..\n", "Binary seq file = /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna.0123\n", "Reference genome size: 30148640 bp\n", "Done readng reference genome !!\n", "\n", "[0000] 1: Calling process()\n", "\n", "Threads used (compute): 8\n", "Info: projected #read in a task: 529811\n", "------------------------------------------\n", "Memory pre-allocation for chaining: 1114.7223 MB\n", "Memory pre-allocation for BSW: 1916.9362 MB\n", "Memory pre-allocation for BWT: 618.5134 MB\n", "------------------------------------------\n", "No. of pipeline threads: 2\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000094, nseq: 320484\n", "\t[0000][ M::kt_pipeline] read 320484 sequences (80000094 bp)...\n", "[0000] 2. Calling mem_process_seqs.., task: 0\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000380, nseq: 320482\n", "\t[0000][ M::kt_pipeline] read 320482 sequences (80000380 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 320484\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (16, 130401, 10, 9)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3685, 4303, 7719)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 15787)\n", "[M::mem_pestat] mean and std.dev: (5413.12, 2250.12)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 19821)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (242, 304, 392)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 692)\n", "[M::mem_pestat] mean and std.dev: (322.82, 112.92)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 842)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (168, 6769, 7457)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 22035)\n", "[M::mem_pestat] mean and std.dev: (4321.30, 3444.03)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 29324)\n", "[M::mem_pestat] skip orientation RR as there are not enough pairs\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 320484 reads in 56.958 CPU sec, 7.146 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 1\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000397, nseq: 320482\n", "\t[0000][ M::kt_pipeline] read 320482 sequences (80000397 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 320482\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (14, 130543, 11, 10)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3576, 4814, 5140)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (448, 8268)\n", "[M::mem_pestat] mean and std.dev: (4464.00, 1301.20)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 9832)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (242, 303, 392)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 692)\n", "[M::mem_pestat] mean and std.dev: (322.19, 112.39)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 842)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (79, 2567, 6436)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 19150)\n", "[M::mem_pestat] mean and std.dev: (3544.18, 3421.54)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 25507)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2792, 4592, 7388)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 16580)\n", "[M::mem_pestat] mean and std.dev: (4821.60, 2711.84)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 21176)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 320482 reads in 56.741 CPU sec, 7.033 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 2\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000238, nseq: 320480\n", "\t[0000][ M::kt_pipeline] read 320480 sequences (80000238 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 320482\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (17, 130153, 11, 11)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2728, 3792, 4967)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 9445)\n", "[M::mem_pestat] mean and std.dev: (3989.71, 1815.69)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 11684)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (241, 304, 391)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 691)\n", "[M::mem_pestat] mean and std.dev: (322.12, 112.56)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 841)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (61, 78, 5789)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 17245)\n", "[M::mem_pestat] mean and std.dev: (2443.82, 3362.74)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 22973)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3615, 4201, 4662)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1521, 6756)\n", "[M::mem_pestat] mean and std.dev: (4268.70, 663.66)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (474, 7803)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 320482 reads in 57.053 CPU sec, 7.081 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 3\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 69011090, nseq: 276460\n", "\t[0000][ M::kt_pipeline] read 276460 sequences (69011090 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 320480\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (14, 130351, 11, 15)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3629, 4072, 5554)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 9404)\n", "[M::mem_pestat] mean and std.dev: (4571.93, 2013.13)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 12624)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (241, 302, 388)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 682)\n", "[M::mem_pestat] mean and std.dev: (320.37, 111.28)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 829)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (107, 976, 7236)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 21494)\n", "[M::mem_pestat] mean and std.dev: (3563.09, 3747.72)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 28623)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3932, 4729, 5210)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1376, 7766)\n", "[M::mem_pestat] mean and std.dev: (4321.31, 796.33)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (98, 9044)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 320480 reads in 55.157 CPU sec, 6.853 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 4\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 0, nseq: 0\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 276460\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (13, 112307, 5, 14)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3592, 4542, 5246)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (284, 8554)\n", "[M::mem_pestat] mean and std.dev: (4654.54, 1641.58)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 11221)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (241, 302, 390)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 688)\n", "[M::mem_pestat] mean and std.dev: (320.89, 111.75)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 837)\n", "[M::mem_pestat] skip orientation RF as there are not enough pairs\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2824, 3946, 4754)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 8614)\n", "[M::mem_pestat] mean and std.dev: (4194.14, 1635.77)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 10737)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 276460 reads in 47.921 CPU sec, 6.043 real sec\n", "[0000] read_chunk: 80000000, work_chunk_size: 0, nseq: 0\n", "[0000] Computation ends..\n", "No. of OMP threads: 8\n", "Processor is runnig @2295.080884 MHz\n", "Runtime profile:\n", "\n", "\t Time taken for main_mem function: 35.84 Sec\n", "\n", "\tIO times (sec) :\n", "\tReading IO time (reads) avg: 5.18, (5.18, 5.18)\n", "\tWriting IO time (SAM) avg: 2.28, (2.28, 2.28)\n", "\tReading IO time (Reference Genome) avg: 0.02, (0.02, 0.02)\n", "\tIndex read time avg: 0.18, (0.18, 0.18)\n", "\n", "\tOverall time (sec) (Excluding Index reading time):\n", "\tPROCESS() (Total compute time + (read + SAM) IO time) : 35.64\n", "\tMEM_PROCESS_SEQ() (Total compute time (Kernel + SAM)), avg: 34.15, (34.15, 34.15)\n", "\n", "\t SAM Processing time (sec):\n", "\t--WORKER_SAM avg: 6.29, (6.29, 6.29)\n", "\n", "\tKernels' compute time (sec):\n", "\tTotal kernel (smem+sal+bsw) time avg: 27.55, (27.55, 27.55)\n", "\t\tSMEM compute avg: 9.45, (9.48, 9.41)\n", "\t\tSAL compute avg: 0.86, (0.87, 0.83)\n", "\t\tBSW time, avg: 16.60, (16.68, 16.52)\n", "\n", "\tTotal allocs: 1948029 = 1948029 out total requests: 2705604, Rate: 0.72\n", "\n", "Important parameter settings: \n", "\tBATCH_SIZE: 512\n", "\tMAX_SEQ_LEN_REF: 256\n", "\tMAX_SEQ_LEN_QER: 128\n", "\tMAX_SEQ_LEN8: 128\n", "\tSEEDS_PER_READ: 500\n", "\tSIMD_WIDTH8 X: 32\n", "\tSIMD_WIDTH16 X: 16\n", "\tAVG_SEEDS_PER_READ: 64\n", "[bam_sort_core] merging from 0 files and 4 in-memory blocks...\n", "######################\n", "Flagstat 5417 \n", "######################\n", " Filtering 5417 \n", "######################\n", " Mapping 685 \n", "-----------------------------\n", "Executing in AVX2 mode!!\n", "-----------------------------\n", "Ref file: /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna\n", "Entering FMI_search\n", "reference seq len = 30148641\n", "count\n", "0,\t1\n", "1,\t7834026\n", "2,\t15074321\n", "3,\t22314616\n", "4,\t30148641\n", "\n", "Reading other elements of the index from files /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna\n", "prefix: /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna\n", "[M::bwa_idx_load_ele] read 0 ALT contigs\n", "Done reading Index!!\n", "Reading reference genome..\n", "Binary seq file = /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna.0123\n", "Reference genome size: 30148640 bp\n", "Done readng reference genome !!\n", "\n", "[0000] 1: Calling process()\n", "\n", "Threads used (compute): 8\n", "Info: projected #read in a task: 529811\n", "------------------------------------------\n", "Memory pre-allocation for chaining: 1114.7223 MB\n", "Memory pre-allocation for BSW: 1916.9362 MB\n", "Memory pre-allocation for BWT: 618.5134 MB\n", "------------------------------------------\n", "No. of pipeline threads: 2\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000058, nseq: 320490\n", "\t[0000][ M::kt_pipeline] read 320490 sequences (80000058 bp)...\n", "[0000] 2. Calling mem_process_seqs.., task: 0\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000025, nseq: 320492\n", "\t[0000][ M::kt_pipeline] read 320492 sequences (80000025 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 320490\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 104381, 11, 5)\n", "[M::mem_pestat] skip orientation FF as there are not enough pairs\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (223, 271, 335)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 559)\n", "[M::mem_pestat] mean and std.dev: (283.08, 84.79)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 671)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (209, 469, 1263)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3371)\n", "[M::mem_pestat] mean and std.dev: (766.91, 823.60)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 4425)\n", "[M::mem_pestat] skip orientation RR as there are not enough pairs\n", "[M::mem_pestat] skip orientation RF\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 320490 reads in 41.324 CPU sec, 5.193 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 1\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000250, nseq: 320490\n", "\t[0000][ M::kt_pipeline] read 320490 sequences (80000250 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 320492\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 104360, 10, 7)\n", "[M::mem_pestat] skip orientation FF as there are not enough pairs\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (223, 271, 333)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (3, 553)\n", "[M::mem_pestat] mean and std.dev: (282.11, 84.01)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 663)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (6, 660, 1311)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3921)\n", "[M::mem_pestat] mean and std.dev: (852.20, 827.51)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 5226)\n", "[M::mem_pestat] skip orientation RR as there are not enough pairs\n", "[M::mem_pestat] skip orientation RF\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 320492 reads in 40.258 CPU sec, 4.955 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 2\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000270, nseq: 320496\n", "\t[0000][ M::kt_pipeline] read 320496 sequences (80000270 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 320490\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (6, 104006, 13, 6)\n", "[M::mem_pestat] skip orientation FF as there are not enough pairs\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (223, 271, 333)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (3, 553)\n", "[M::mem_pestat] mean and std.dev: (281.68, 83.67)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 663)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (170, 480, 1180)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3200)\n", "[M::mem_pestat] mean and std.dev: (693.15, 580.11)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 4210)\n", "[M::mem_pestat] skip orientation RR as there are not enough pairs\n", "[M::mem_pestat] skip orientation RF\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 320490 reads in 40.265 CPU sec, 4.959 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 3\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 41372116, nseq: 165742\n", "\t[0000][ M::kt_pipeline] read 165742 sequences (41372116 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 320496\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 104316, 13, 3)\n", "[M::mem_pestat] skip orientation FF as there are not enough pairs\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (223, 270, 332)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (5, 550)\n", "[M::mem_pestat] mean and std.dev: (281.18, 83.44)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 659)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (37, 142, 901)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2629)\n", "[M::mem_pestat] mean and std.dev: (281.00, 364.36)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 3493)\n", "[M::mem_pestat] skip orientation RR as there are not enough pairs\n", "[M::mem_pestat] skip orientation RF\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 320496 reads in 40.603 CPU sec, 5.071 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 4\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 0, nseq: 0\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 165742\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 54172, 7, 2)\n", "[M::mem_pestat] skip orientation FF as there are not enough pairs\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (223, 270, 333)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (3, 553)\n", "[M::mem_pestat] mean and std.dev: (281.89, 83.86)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 663)\n", "[M::mem_pestat] skip orientation RF as there are not enough pairs\n", "[M::mem_pestat] skip orientation RR as there are not enough pairs\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 165742 reads in 20.777 CPU sec, 2.624 real sec\n", "[0000] read_chunk: 80000000, work_chunk_size: 0, nseq: 0\n", "[0000] Computation ends..\n", "No. of OMP threads: 8\n", "Processor is runnig @2295.046316 MHz\n", "Runtime profile:\n", "\n", "\t Time taken for main_mem function: 24.30 Sec\n", "\n", "\tIO times (sec) :\n", "\tReading IO time (reads) avg: 4.88, (4.88, 4.88)\n", "\tWriting IO time (SAM) avg: 1.89, (1.89, 1.89)\n", "\tReading IO time (Reference Genome) avg: 0.02, (0.02, 0.02)\n", "\tIndex read time avg: 0.17, (0.17, 0.17)\n", "\n", "\tOverall time (sec) (Excluding Index reading time):\n", "\tPROCESS() (Total compute time + (read + SAM) IO time) : 24.11\n", "\tMEM_PROCESS_SEQ() (Total compute time (Kernel + SAM)), avg: 22.80, (22.80, 22.80)\n", "\n", "\t SAM Processing time (sec):\n", "\t--WORKER_SAM avg: 3.13, (3.13, 3.13)\n", "\n", "\tKernels' compute time (sec):\n", "\tTotal kernel (smem+sal+bsw) time avg: 19.40, (19.40, 19.40)\n", "\t\tSMEM compute avg: 8.45, (8.48, 8.40)\n", "\t\tSAL compute avg: 0.63, (0.65, 0.61)\n", "\t\tBSW time, avg: 9.86, (9.89, 9.83)\n", "\n", "\tTotal allocs: 1436378 = 1436378 out total requests: 1799935, Rate: 0.80\n", "\n", "Important parameter settings: \n", "\tBATCH_SIZE: 512\n", "\tMAX_SEQ_LEN_REF: 256\n", "\tMAX_SEQ_LEN_QER: 128\n", "\tMAX_SEQ_LEN8: 128\n", "\tSEEDS_PER_READ: 500\n", "\tSIMD_WIDTH8 X: 32\n", "\tSIMD_WIDTH16 X: 16\n", "\tAVG_SEEDS_PER_READ: 64\n", "[bam_sort_core] merging from 0 files and 4 in-memory blocks...\n", "######################\n", "Flagstat 685 \n", "######################\n", " Filtering 685 \n", "######################\n", " Mapping 716 \n", "-----------------------------\n", "Executing in AVX2 mode!!\n", "-----------------------------\n", "Ref file: /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna\n", "Entering FMI_search\n", "reference seq len = 30148641\n", "count\n", "0,\t1\n", "1,\t7834026\n", "2,\t15074321\n", "3,\t22314616\n", "4,\t30148641\n", "\n", "Reading other elements of the index from files /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna\n", "prefix: /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna\n", "[M::bwa_idx_load_ele] read 0 ALT contigs\n", "Done reading Index!!\n", "Reading reference genome..\n", "Binary seq file = /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna.0123\n", "Reference genome size: 30148640 bp\n", "Done readng reference genome !!\n", "\n", "[0000] 1: Calling process()\n", "\n", "Threads used (compute): 8\n", "Info: projected #read in a task: 529811\n", "------------------------------------------\n", "Memory pre-allocation for chaining: 1114.7223 MB\n", "Memory pre-allocation for BSW: 1916.9362 MB\n", "Memory pre-allocation for BWT: 618.5134 MB\n", "------------------------------------------\n", "No. of pipeline threads: 2\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000085, nseq: 320472\n", "\t[0000][ M::kt_pipeline] read 320472 sequences (80000085 bp)...\n", "[0000] 2. Calling mem_process_seqs.., task: 0\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000154, nseq: 320472\n", "\t[0000][ M::kt_pipeline] read 320472 sequences (80000154 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 320472\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 36711, 12, 0)\n", "[M::mem_pestat] skip orientation FF as there are not enough pairs\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (139, 217, 287)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 583)\n", "[M::mem_pestat] mean and std.dev: (218.77, 108.53)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 731)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (95, 305, 2811)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 8243)\n", "[M::mem_pestat] mean and std.dev: (1172.58, 1941.99)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 10959)\n", "[M::mem_pestat] skip orientation RR as there are not enough pairs\n", "[M::mem_pestat] skip orientation RF\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 320472 reads in 50.326 CPU sec, 6.299 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 1\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000138, nseq: 320470\n", "\t[0000][ M::kt_pipeline] read 320470 sequences (80000138 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 320472\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 36613, 9, 0)\n", "[M::mem_pestat] skip orientation FF as there are not enough pairs\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (139, 215, 286)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 580)\n", "[M::mem_pestat] mean and std.dev: (218.14, 107.72)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 727)\n", "[M::mem_pestat] skip orientation RF as there are not enough pairs\n", "[M::mem_pestat] skip orientation RR as there are not enough pairs\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 320472 reads in 49.305 CPU sec, 6.090 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 2\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000423, nseq: 320470\n", "\t[0000][ M::kt_pipeline] read 320470 sequences (80000423 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 320470\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 36696, 7, 3)\n", "[M::mem_pestat] skip orientation FF as there are not enough pairs\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (139, 215, 286)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 580)\n", "[M::mem_pestat] mean and std.dev: (218.03, 107.96)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 727)\n", "[M::mem_pestat] skip orientation RF as there are not enough pairs\n", "[M::mem_pestat] skip orientation RR as there are not enough pairs\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 320470 reads in 49.535 CPU sec, 6.112 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 3\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 24533199, nseq: 98278\n", "\t[0000][ M::kt_pipeline] read 98278 sequences (24533199 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 320470\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 36940, 11, 2)\n", "[M::mem_pestat] skip orientation FF as there are not enough pairs\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (140, 215, 285)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 575)\n", "[M::mem_pestat] mean and std.dev: (217.20, 106.99)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 720)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (50, 174, 3013)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 8939)\n", "[M::mem_pestat] mean and std.dev: (860.10, 1425.22)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 11902)\n", "[M::mem_pestat] skip orientation RR as there are not enough pairs\n", "[M::mem_pestat] skip orientation RF\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 320470 reads in 48.296 CPU sec, 6.063 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 4\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 0, nseq: 0\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 98278\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 11246, 3, 0)\n", "[M::mem_pestat] skip orientation FF as there are not enough pairs\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (141, 218, 288)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 582)\n", "[M::mem_pestat] mean and std.dev: (219.49, 107.78)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 729)\n", "[M::mem_pestat] skip orientation RF as there are not enough pairs\n", "[M::mem_pestat] skip orientation RR as there are not enough pairs\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 98278 reads in 15.312 CPU sec, 1.941 real sec\n", "[0000] read_chunk: 80000000, work_chunk_size: 0, nseq: 0\n", "[0000] Computation ends..\n", "No. of OMP threads: 8\n", "Processor is runnig @2295.107264 MHz\n", "Runtime profile:\n", "\n", "\t Time taken for main_mem function: 27.92 Sec\n", "\n", "\tIO times (sec) :\n", "\tReading IO time (reads) avg: 4.59, (4.59, 4.59)\n", "\tWriting IO time (SAM) avg: 1.57, (1.57, 1.57)\n", "\tReading IO time (Reference Genome) avg: 0.02, (0.02, 0.02)\n", "\tIndex read time avg: 0.18, (0.18, 0.18)\n", "\n", "\tOverall time (sec) (Excluding Index reading time):\n", "\tPROCESS() (Total compute time + (read + SAM) IO time) : 27.71\n", "\tMEM_PROCESS_SEQ() (Total compute time (Kernel + SAM)), avg: 26.50, (26.50, 26.50)\n", "\n", "\t SAM Processing time (sec):\n", "\t--WORKER_SAM avg: 8.50, (8.50, 8.50)\n", "\n", "\tKernels' compute time (sec):\n", "\tTotal kernel (smem+sal+bsw) time avg: 17.77, (17.77, 17.77)\n", "\t\tSMEM compute avg: 9.46, (9.48, 9.40)\n", "\t\tSAL compute avg: 0.27, (0.30, 0.24)\n", "\t\tBSW time, avg: 7.56, (7.59, 7.53)\n", "\n", "\tTotal allocs: 650317 = 650317 out total requests: 3102554, Rate: 0.21\n", "\n", "Important parameter settings: \n", "\tBATCH_SIZE: 512\n", "\tMAX_SEQ_LEN_REF: 256\n", "\tMAX_SEQ_LEN_QER: 128\n", "\tMAX_SEQ_LEN8: 128\n", "\tSEEDS_PER_READ: 500\n", "\tSIMD_WIDTH8 X: 32\n", "\tSIMD_WIDTH16 X: 16\n", "\tAVG_SEEDS_PER_READ: 64\n", "[bam_sort_core] merging from 0 files and 4 in-memory blocks...\n", "######################\n", "Flagstat 716 \n", "######################\n", " Filtering 716 \n", "######################\n", " Mapping A1 \n", "-----------------------------\n", "Executing in AVX2 mode!!\n", "-----------------------------\n", "Ref file: /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna\n", "Entering FMI_search\n", "reference seq len = 30148641\n", "count\n", "0,\t1\n", "1,\t7834026\n", "2,\t15074321\n", "3,\t22314616\n", "4,\t30148641\n", "\n", "Reading other elements of the index from files /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna\n", "prefix: /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna\n", "[M::bwa_idx_load_ele] read 0 ALT contigs\n", "Done reading Index!!\n", "Reading reference genome..\n", "Binary seq file = /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna.0123\n", "Reference genome size: 30148640 bp\n", "Done readng reference genome !!\n", "\n", "[0000] 1: Calling process()\n", "\n", "Threads used (compute): 8\n", "Info: projected #read in a task: 529811\n", "------------------------------------------\n", "Memory pre-allocation for chaining: 1114.7223 MB\n", "Memory pre-allocation for BSW: 1916.9362 MB\n", "Memory pre-allocation for BWT: 618.5134 MB\n", "------------------------------------------\n", "No. of pipeline threads: 2\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "Reallocating initial memory allocations!!\n", "[0000] 2. Calling mem_process_seqs.., task: 0\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (26, 223942, 52, 25)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (1077, 3786, 4331)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 10839)\n", "[M::mem_pestat] mean and std.dev: (3494.65, 2560.85)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 14093)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (291, 333, 375)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (123, 543)\n", "[M::mem_pestat] mean and std.dev: (333.31, 63.04)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (39, 627)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2315, 2410, 2708)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1529, 3494)\n", "[M::mem_pestat] mean and std.dev: (2453.15, 149.69)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1136, 3887)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2102, 4645, 6858)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 16370)\n", "[M::mem_pestat] mean and std.dev: (4452.08, 2291.82)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 21126)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 31.840 CPU sec, 4.117 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 1\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (16, 223974, 36, 26)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3535, 4580, 6858)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 13504)\n", "[M::mem_pestat] mean and std.dev: (4407.81, 2576.51)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 16827)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (291, 332, 374)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (125, 540)\n", "[M::mem_pestat] mean and std.dev: (332.39, 62.72)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (42, 623)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2300, 2386, 2501)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1898, 2903)\n", "[M::mem_pestat] mean and std.dev: (2398.82, 105.35)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1697, 3104)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (480, 3599, 7413)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 21279)\n", "[M::mem_pestat] mean and std.dev: (3517.77, 2916.34)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 28212)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 30.149 CPU sec, 3.720 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 2\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (27, 223974, 45, 16)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2104, 3720, 5649)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 12739)\n", "[M::mem_pestat] mean and std.dev: (3987.96, 2421.47)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 16284)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (291, 333, 374)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (125, 540)\n", "[M::mem_pestat] mean and std.dev: (332.60, 62.62)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (42, 623)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (1266, 2381, 2523)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 5037)\n", "[M::mem_pestat] mean and std.dev: (1885.22, 896.31)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 6294)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (1125, 2366, 4194)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 10332)\n", "[M::mem_pestat] mean and std.dev: (2970.69, 2359.28)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 13401)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 30.171 CPU sec, 3.726 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 3\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (29, 223211, 27, 19)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2804, 4227, 7377)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 16523)\n", "[M::mem_pestat] mean and std.dev: (4374.45, 2789.37)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 21096)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (289, 331, 373)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (121, 541)\n", "[M::mem_pestat] mean and std.dev: (331.33, 62.76)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (37, 625)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (667, 1200, 2403)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 5875)\n", "[M::mem_pestat] mean and std.dev: (1354.12, 1323.76)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 7611)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3668, 4401, 6942)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 13490)\n", "[M::mem_pestat] mean and std.dev: (4831.84, 2593.15)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 16764)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 30.868 CPU sec, 3.804 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 4\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (16, 223859, 40, 21)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3505, 3917, 6858)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 13564)\n", "[M::mem_pestat] mean and std.dev: (3827.44, 2557.10)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 16917)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (290, 332, 373)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (124, 539)\n", "[M::mem_pestat] mean and std.dev: (331.90, 62.47)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (41, 622)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (1146, 2261, 2432)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 5004)\n", "[M::mem_pestat] mean and std.dev: (1638.38, 757.65)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 6290)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2376, 3880, 7756)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 18516)\n", "[M::mem_pestat] mean and std.dev: (4263.14, 2749.53)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 23896)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 30.225 CPU sec, 3.727 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 5\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (25, 223948, 30, 16)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3659, 3719, 5464)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (49, 9074)\n", "[M::mem_pestat] mean and std.dev: (3989.52, 2109.01)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 12426)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (291, 333, 374)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (125, 540)\n", "[M::mem_pestat] mean and std.dev: (332.95, 62.80)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (42, 623)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2369, 2419, 2486)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (2135, 2720)\n", "[M::mem_pestat] mean and std.dev: (2423.14, 70.34)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (2018, 2837)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2065, 3841, 7907)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 19591)\n", "[M::mem_pestat] mean and std.dev: (4351.81, 2798.50)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 25433)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 30.774 CPU sec, 3.802 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 6\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (25, 223799, 31, 26)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (472, 4732, 7966)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 22954)\n", "[M::mem_pestat] mean and std.dev: (4165.36, 2973.08)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 30448)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (291, 333, 374)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (125, 540)\n", "[M::mem_pestat] mean and std.dev: (333.20, 62.72)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (42, 623)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (742, 2366, 2818)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 6970)\n", "[M::mem_pestat] mean and std.dev: (2284.74, 1722.10)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 9173)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3798, 7183, 7790)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 15774)\n", "[M::mem_pestat] mean and std.dev: (5822.96, 2295.74)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 19766)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 30.280 CPU sec, 3.745 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 7\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (17, 224231, 22, 24)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (249, 2142, 3643)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 10431)\n", "[M::mem_pestat] mean and std.dev: (2176.76, 2224.65)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 13825)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (292, 334, 375)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (126, 541)\n", "[M::mem_pestat] mean and std.dev: (333.62, 62.74)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (43, 624)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (1067, 2368, 2409)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 5093)\n", "[M::mem_pestat] mean and std.dev: (1750.55, 791.67)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 6435)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2122, 3852, 5267)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 11557)\n", "[M::mem_pestat] mean and std.dev: (3604.92, 2226.42)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 14702)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 29.844 CPU sec, 3.705 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 8\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (24, 224469, 36, 29)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2192, 3885, 4848)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 10160)\n", "[M::mem_pestat] mean and std.dev: (3789.21, 2510.48)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 13831)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (291, 333, 374)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (125, 540)\n", "[M::mem_pestat] mean and std.dev: (332.77, 62.62)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (42, 623)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2290, 2374, 2432)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (2006, 2716)\n", "[M::mem_pestat] mean and std.dev: (2399.37, 77.86)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1864, 2858)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2050, 3696, 4332)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 8896)\n", "[M::mem_pestat] mean and std.dev: (3626.69, 2311.58)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 12873)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 30.260 CPU sec, 3.731 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 9\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (22, 223825, 24, 14)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (334, 3875, 7535)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 21937)\n", "[M::mem_pestat] mean and std.dev: (3856.73, 2890.69)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 29138)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (292, 333, 375)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (126, 541)\n", "[M::mem_pestat] mean and std.dev: (333.36, 62.73)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (43, 624)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2286, 2395, 2447)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1964, 2769)\n", "[M::mem_pestat] mean and std.dev: (2415.06, 62.79)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1803, 2930)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3664, 4646, 7745)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 15907)\n", "[M::mem_pestat] mean and std.dev: (5003.71, 2012.13)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 19988)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 30.307 CPU sec, 3.725 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 10\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (21, 221002, 35, 21)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2050, 2663, 4769)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 10207)\n", "[M::mem_pestat] mean and std.dev: (3113.29, 2189.61)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 12926)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (292, 333, 375)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (126, 541)\n", "[M::mem_pestat] mean and std.dev: (333.47, 62.47)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (43, 624)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (1144, 2358, 2426)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 4990)\n", "[M::mem_pestat] mean and std.dev: (1861.82, 934.80)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 6272)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2300, 3910, 6798)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 15794)\n", "[M::mem_pestat] mean and std.dev: (4140.71, 2156.74)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 20292)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 32.192 CPU sec, 3.996 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 11\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (17, 222048, 43, 25)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3701, 4911, 7837)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 16109)\n", "[M::mem_pestat] mean and std.dev: (5301.59, 2278.33)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 20245)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (291, 333, 374)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (125, 540)\n", "[M::mem_pestat] mean and std.dev: (332.53, 62.53)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (42, 623)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2289, 2375, 2423)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (2021, 2691)\n", "[M::mem_pestat] mean and std.dev: (2402.87, 67.88)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1887, 2825)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2019, 3724, 7478)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 18396)\n", "[M::mem_pestat] mean and std.dev: (4149.60, 2864.93)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 23855)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 31.216 CPU sec, 3.854 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 12\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (23, 223081, 31, 28)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3531, 4051, 7332)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 14934)\n", "[M::mem_pestat] mean and std.dev: (4690.78, 2292.71)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 18735)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (291, 332, 374)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (125, 540)\n", "[M::mem_pestat] mean and std.dev: (332.27, 62.52)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (42, 623)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (1216, 2365, 2458)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 4942)\n", "[M::mem_pestat] mean and std.dev: (1922.97, 950.59)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 6184)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3713, 4134, 6858)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 13148)\n", "[M::mem_pestat] mean and std.dev: (4547.50, 2039.38)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 16293)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 30.535 CPU sec, 3.767 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 13\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (18, 223113, 31, 25)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2091, 3790, 4795)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 10203)\n", "[M::mem_pestat] mean and std.dev: (3532.67, 1988.51)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 12907)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (290, 333, 373)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (124, 539)\n", "[M::mem_pestat] mean and std.dev: (332.39, 62.57)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (41, 622)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (1140, 2277, 2434)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 5022)\n", "[M::mem_pestat] mean and std.dev: (1807.55, 849.87)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 6316)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2809, 4308, 7523)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 16951)\n", "[M::mem_pestat] mean and std.dev: (4576.56, 2449.59)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 21665)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 30.719 CPU sec, 3.779 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 14\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (22, 223578, 67, 26)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (300, 3873, 6858)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 19974)\n", "[M::mem_pestat] mean and std.dev: (3790.59, 3028.41)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 26532)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (292, 333, 375)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (126, 541)\n", "[M::mem_pestat] mean and std.dev: (333.39, 62.70)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (43, 624)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2408, 2462, 2735)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1754, 3389)\n", "[M::mem_pestat] mean and std.dev: (2479.80, 104.57)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1427, 3716)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2164, 3734, 4939)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 10489)\n", "[M::mem_pestat] mean and std.dev: (3907.50, 2502.65)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 13918)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 31.281 CPU sec, 3.860 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 15\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (27, 223420, 23, 20)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2113, 3692, 5013)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 10813)\n", "[M::mem_pestat] mean and std.dev: (3814.48, 2480.08)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 13735)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (293, 334, 375)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (129, 539)\n", "[M::mem_pestat] mean and std.dev: (334.31, 62.44)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (47, 621)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2248, 2407, 2454)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1836, 2866)\n", "[M::mem_pestat] mean and std.dev: (2384.87, 169.17)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1630, 3072)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (1135, 2099, 4005)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 9745)\n", "[M::mem_pestat] mean and std.dev: (2764.15, 2028.74)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 12615)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 30.526 CPU sec, 3.763 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 16\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (26, 223754, 34, 19)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3617, 4730, 6845)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 13301)\n", "[M::mem_pestat] mean and std.dev: (4452.69, 2466.91)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 16529)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (293, 335, 376)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (127, 542)\n", "[M::mem_pestat] mean and std.dev: (334.87, 62.52)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (44, 625)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2277, 2408, 2469)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1893, 2853)\n", "[M::mem_pestat] mean and std.dev: (2429.96, 106.31)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1701, 3045)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2377, 3762, 5447)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 11587)\n", "[M::mem_pestat] mean and std.dev: (3750.89, 2453.14)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 14657)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 29.963 CPU sec, 3.821 real sec\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 2. Calling mem_process_seqs.., task: 17\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 73979400, nseq: 493196\n", "\t[0000][ M::kt_pipeline] read 493196 sequences (73979400 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (18, 223277, 39, 32)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2118, 3442, 3937)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 7575)\n", "[M::mem_pestat] mean and std.dev: (2696.06, 1713.48)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 9550)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (293, 334, 376)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (127, 542)\n", "[M::mem_pestat] mean and std.dev: (334.30, 62.63)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (44, 625)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2343, 2425, 2596)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1837, 3102)\n", "[M::mem_pestat] mean and std.dev: (2437.56, 118.33)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1584, 3355)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2271, 3736, 5533)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 12057)\n", "[M::mem_pestat] mean and std.dev: (3993.88, 2699.53)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 15319)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 30.888 CPU sec, 3.883 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 18\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 0, nseq: 0\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 493196\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (24, 206660, 39, 24)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (1957, 3657, 3829)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 7573)\n", "[M::mem_pestat] mean and std.dev: (2818.83, 1384.03)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 9445)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (292, 334, 375)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (126, 541)\n", "[M::mem_pestat] mean and std.dev: (334.12, 62.85)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (43, 624)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (1234, 2378, 2436)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 4840)\n", "[M::mem_pestat] mean and std.dev: (1898.59, 795.58)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 6042)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3778, 4261, 7724)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 15616)\n", "[M::mem_pestat] mean and std.dev: (5043.12, 2785.36)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 19562)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 493196 reads in 27.596 CPU sec, 3.530 real sec\n", "[0000] read_chunk: 80000000, work_chunk_size: 0, nseq: 0\n", "[0000] Computation ends..\n", "No. of OMP threads: 8\n", "Processor is runnig @2295.072260 MHz\n", "Runtime profile:\n", "\n", "\t Time taken for main_mem function: 76.52 Sec\n", "\n", "\tIO times (sec) :\n", "\tReading IO time (reads) avg: 19.07, (19.07, 19.07)\n", "\tWriting IO time (SAM) avg: 16.07, (16.07, 16.07)\n", "\tReading IO time (Reference Genome) avg: 0.02, (0.02, 0.02)\n", "\tIndex read time avg: 0.19, (0.19, 0.19)\n", "\n", "\tOverall time (sec) (Excluding Index reading time):\n", "\tPROCESS() (Total compute time + (read + SAM) IO time) : 76.31\n", "\tMEM_PROCESS_SEQ() (Total compute time (Kernel + SAM)), avg: 72.04, (72.04, 72.04)\n", "\n", "\t SAM Processing time (sec):\n", "\t--WORKER_SAM avg: 11.48, (11.48, 11.48)\n", "\n", "\tKernels' compute time (sec):\n", "\tTotal kernel (smem+sal+bsw) time avg: 58.45, (58.45, 58.45)\n", "\t\tSMEM compute avg: 30.96, (31.03, 30.84)\n", "\t\tSAL compute avg: 3.38, (3.46, 3.32)\n", "\t\tBSW time, avg: 22.78, (22.81, 22.73)\n", "\n", "\tTotal allocs: 10247593 = 10247593 out total requests: 12491096, Rate: 0.82\n", "\n", "Important parameter settings: \n", "\tBATCH_SIZE: 512\n", "\tMAX_SEQ_LEN_REF: 256\n", "\tMAX_SEQ_LEN_QER: 128\n", "\tMAX_SEQ_LEN8: 128\n", "\tSEEDS_PER_READ: 500\n", "\tSIMD_WIDTH8 X: 32\n", "\tSIMD_WIDTH16 X: 16\n", "\tAVG_SEEDS_PER_READ: 64\n", "[bam_sort_core] merging from 4 files and 4 in-memory blocks...\n", "######################\n", "Flagstat A1 \n", "######################\n", " Filtering A1 \n", "######################\n", " Mapping A8 \n", "-----------------------------\n", "Executing in AVX2 mode!!\n", "-----------------------------\n", "Ref file: /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna\n", "Entering FMI_search\n", "reference seq len = 30148641\n", "count\n", "0,\t1\n", "1,\t7834026\n", "2,\t15074321\n", "3,\t22314616\n", "4,\t30148641\n", "\n", "Reading other elements of the index from files /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna\n", "prefix: /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna\n", "[M::bwa_idx_load_ele] read 0 ALT contigs\n", "Done reading Index!!\n", "Reading reference genome..\n", "Binary seq file = /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna.0123\n", "Reference genome size: 30148640 bp\n", "Done readng reference genome !!\n", "\n", "[0000] 1: Calling process()\n", "\n", "Threads used (compute): 8\n", "Info: projected #read in a task: 529811\n", "------------------------------------------\n", "Memory pre-allocation for chaining: 1114.7223 MB\n", "Memory pre-allocation for BSW: 1916.9362 MB\n", "Memory pre-allocation for BWT: 618.5134 MB\n", "------------------------------------------\n", "No. of pipeline threads: 2\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000357, nseq: 320486\n", "\t[0000][ M::kt_pipeline] read 320486 sequences (80000357 bp)...\n", "[0000] 2. Calling mem_process_seqs.., task: 0\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000080, nseq: 320488\n", "\t[0000][ M::kt_pipeline] read 320488 sequences (80000080 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 320486\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (10, 141054, 2, 13)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3733, 5121, 7028)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 13618)\n", "[M::mem_pestat] mean and std.dev: (4761.60, 2231.94)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 16913)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (251, 315, 403)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 707)\n", "[M::mem_pestat] mean and std.dev: (333.55, 111.48)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 859)\n", "[M::mem_pestat] skip orientation RF as there are not enough pairs\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2424, 3623, 5580)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 11892)\n", "[M::mem_pestat] mean and std.dev: (3998.54, 1807.09)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 15048)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 320486 reads in 38.733 CPU sec, 4.856 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 1\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000230, nseq: 320486\n", "\t[0000][ M::kt_pipeline] read 320486 sequences (80000230 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 320488\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (17, 141054, 4, 11)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2797, 3390, 5603)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 11215)\n", "[M::mem_pestat] mean and std.dev: (3660.53, 2683.62)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 14395)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (251, 315, 403)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 707)\n", "[M::mem_pestat] mean and std.dev: (333.62, 111.78)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 859)\n", "[M::mem_pestat] skip orientation RF as there are not enough pairs\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2531, 2930, 4403)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 8147)\n", "[M::mem_pestat] mean and std.dev: (3044.50, 1296.84)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 10019)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 320488 reads in 38.092 CPU sec, 4.697 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 2\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000269, nseq: 320486\n", "\t[0000][ M::kt_pipeline] read 320486 sequences (80000269 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 320486\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (7, 141293, 3, 5)\n", "[M::mem_pestat] skip orientation FF as there are not enough pairs\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (251, 314, 401)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 701)\n", "[M::mem_pestat] mean and std.dev: (332.33, 110.76)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 851)\n", "[M::mem_pestat] skip orientation RF as there are not enough pairs\n", "[M::mem_pestat] skip orientation RR as there are not enough pairs\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 320486 reads in 38.101 CPU sec, 4.711 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 3\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 76486907, nseq: 306410\n", "\t[0000][ M::kt_pipeline] read 306410 sequences (76486907 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 320486\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (11, 141295, 1, 12)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2663, 3720, 4873)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 9293)\n", "[M::mem_pestat] mean and std.dev: (2977.64, 1868.12)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 11503)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (250, 314, 401)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 703)\n", "[M::mem_pestat] mean and std.dev: (332.34, 110.69)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 854)\n", "[M::mem_pestat] skip orientation RF as there are not enough pairs\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (4885, 5474, 7464)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 12622)\n", "[M::mem_pestat] mean and std.dev: (5921.25, 1687.13)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 15201)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 320486 reads in 38.549 CPU sec, 4.768 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 4\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 0, nseq: 0\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 306410\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (7, 135208, 2, 6)\n", "[M::mem_pestat] skip orientation FF as there are not enough pairs\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (251, 314, 401)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 701)\n", "[M::mem_pestat] mean and std.dev: (331.91, 110.20)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 851)\n", "[M::mem_pestat] skip orientation RF as there are not enough pairs\n", "[M::mem_pestat] skip orientation RR as there are not enough pairs\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 306410 reads in 36.002 CPU sec, 4.554 real sec\n", "[0000] read_chunk: 80000000, work_chunk_size: 0, nseq: 0\n", "[0000] Computation ends..\n", "No. of OMP threads: 8\n", "Processor is runnig @2295.054684 MHz\n", "Runtime profile:\n", "\n", "\t Time taken for main_mem function: 25.36 Sec\n", "\n", "\tIO times (sec) :\n", "\tReading IO time (reads) avg: 5.40, (5.40, 5.40)\n", "\tWriting IO time (SAM) avg: 2.27, (2.27, 2.27)\n", "\tReading IO time (Reference Genome) avg: 0.02, (0.02, 0.02)\n", "\tIndex read time avg: 0.22, (0.22, 0.22)\n", "\n", "\tOverall time (sec) (Excluding Index reading time):\n", "\tPROCESS() (Total compute time + (read + SAM) IO time) : 25.12\n", "\tMEM_PROCESS_SEQ() (Total compute time (Kernel + SAM)), avg: 23.58, (23.58, 23.58)\n", "\n", "\t SAM Processing time (sec):\n", "\t--WORKER_SAM avg: 3.36, (3.36, 3.36)\n", "\n", "\tKernels' compute time (sec):\n", "\tTotal kernel (smem+sal+bsw) time avg: 19.87, (19.87, 19.87)\n", "\t\tSMEM compute avg: 8.04, (8.12, 7.93)\n", "\t\tSAL compute avg: 0.89, (0.93, 0.85)\n", "\t\tBSW time, avg: 10.47, (10.52, 10.41)\n", "\n", "\tTotal allocs: 1889396 = 1889396 out total requests: 2261941, Rate: 0.84\n", "\n", "Important parameter settings: \n", "\tBATCH_SIZE: 512\n", "\tMAX_SEQ_LEN_REF: 256\n", "\tMAX_SEQ_LEN_QER: 128\n", "\tMAX_SEQ_LEN8: 128\n", "\tSEEDS_PER_READ: 500\n", "\tSIMD_WIDTH8 X: 32\n", "\tSIMD_WIDTH16 X: 16\n", "\tAVG_SEEDS_PER_READ: 64\n", "[bam_sort_core] merging from 0 files and 4 in-memory blocks...\n", "######################\n", "Flagstat A8 \n", "######################\n", " Filtering A8 \n", "######################\n", " Mapping B1 \n", "-----------------------------\n", "Executing in AVX2 mode!!\n", "-----------------------------\n", "Ref file: /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna\n", "Entering FMI_search\n", "reference seq len = 30148641\n", "count\n", "0,\t1\n", "1,\t7834026\n", "2,\t15074321\n", "3,\t22314616\n", "4,\t30148641\n", "\n", "Reading other elements of the index from files /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna\n", "prefix: /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna\n", "[M::bwa_idx_load_ele] read 0 ALT contigs\n", "Done reading Index!!\n", "Reading reference genome..\n", "Binary seq file = /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna.0123\n", "Reference genome size: 30148640 bp\n", "Done readng reference genome !!\n", "\n", "[0000] 1: Calling process()\n", "\n", "Threads used (compute): 8\n", "Info: projected #read in a task: 529811\n", "------------------------------------------\n", "Memory pre-allocation for chaining: 1114.7223 MB\n", "Memory pre-allocation for BSW: 1916.9362 MB\n", "Memory pre-allocation for BWT: 618.5134 MB\n", "------------------------------------------\n", "No. of pipeline threads: 2\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000190, nseq: 320492\n", "\t[0000][ M::kt_pipeline] read 320492 sequences (80000190 bp)...\n", "[0000] 2. Calling mem_process_seqs.., task: 0\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000068, nseq: 320492\n", "\t[0000][ M::kt_pipeline] read 320492 sequences (80000068 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 320492\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (6, 145362, 7, 8)\n", "[M::mem_pestat] skip orientation FF as there are not enough pairs\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (249, 309, 393)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 681)\n", "[M::mem_pestat] mean and std.dev: (326.94, 106.24)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 825)\n", "[M::mem_pestat] skip orientation RF as there are not enough pairs\n", "[M::mem_pestat] skip orientation RR as there are not enough pairs\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 320492 reads in 38.757 CPU sec, 4.898 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 1\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000043, nseq: 320488\n", "\t[0000][ M::kt_pipeline] read 320488 sequences (80000043 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 320492\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (9, 145493, 14, 8)\n", "[M::mem_pestat] skip orientation FF as there are not enough pairs\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (250, 309, 393)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 679)\n", "[M::mem_pestat] mean and std.dev: (326.85, 105.91)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 822)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (836, 5557, 9647)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 27269)\n", "[M::mem_pestat] mean and std.dev: (4454.36, 3840.87)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 36080)\n", "[M::mem_pestat] skip orientation RR as there are not enough pairs\n", "[M::mem_pestat] skip orientation RF\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 320492 reads in 37.876 CPU sec, 4.685 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 2\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000367, nseq: 320490\n", "\t[0000][ M::kt_pipeline] read 320490 sequences (80000367 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 320488\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (6, 145316, 13, 8)\n", "[M::mem_pestat] skip orientation FF as there are not enough pairs\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (249, 309, 392)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 678)\n", "[M::mem_pestat] mean and std.dev: (326.45, 106.04)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 821)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (24, 3189, 5636)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 16860)\n", "[M::mem_pestat] mean and std.dev: (2648.38, 2365.89)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 22472)\n", "[M::mem_pestat] skip orientation RR as there are not enough pairs\n", "[M::mem_pestat] skip orientation RF\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 320488 reads in 38.764 CPU sec, 4.770 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 3\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 77196989, nseq: 309260\n", "\t[0000][ M::kt_pipeline] read 309260 sequences (77196989 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 320490\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (12, 145475, 14, 9)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2568, 3870, 4030)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 6954)\n", "[M::mem_pestat] mean and std.dev: (2957.90, 1184.78)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 8416)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (249, 308, 391)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 675)\n", "[M::mem_pestat] mean and std.dev: (325.75, 105.61)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 817)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (28, 119, 5715)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 17089)\n", "[M::mem_pestat] mean and std.dev: (2149.43, 3117.57)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 22776)\n", "[M::mem_pestat] skip orientation RR as there are not enough pairs\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 320490 reads in 38.238 CPU sec, 4.747 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 4\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 0, nseq: 0\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 309260\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (7, 140335, 7, 5)\n", "[M::mem_pestat] skip orientation FF as there are not enough pairs\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (249, 308, 391)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 675)\n", "[M::mem_pestat] mean and std.dev: (325.90, 105.82)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 817)\n", "[M::mem_pestat] skip orientation RF as there are not enough pairs\n", "[M::mem_pestat] skip orientation RR as there are not enough pairs\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 309260 reads in 35.886 CPU sec, 4.523 real sec\n", "[0000] read_chunk: 80000000, work_chunk_size: 0, nseq: 0\n", "[0000] Computation ends..\n", "No. of OMP threads: 8\n", "Processor is runnig @2295.094458 MHz\n", "Runtime profile:\n", "\n", "\t Time taken for main_mem function: 25.32 Sec\n", "\n", "\tIO times (sec) :\n", "\tReading IO time (reads) avg: 5.48, (5.48, 5.48)\n", "\tWriting IO time (SAM) avg: 2.23, (2.23, 2.23)\n", "\tReading IO time (Reference Genome) avg: 0.03, (0.03, 0.03)\n", "\tIndex read time avg: 0.24, (0.24, 0.24)\n", "\n", "\tOverall time (sec) (Excluding Index reading time):\n", "\tPROCESS() (Total compute time + (read + SAM) IO time) : 25.06\n", "\tMEM_PROCESS_SEQ() (Total compute time (Kernel + SAM)), avg: 23.62, (23.62, 23.62)\n", "\n", "\t SAM Processing time (sec):\n", "\t--WORKER_SAM avg: 3.29, (3.29, 3.29)\n", "\n", "\tKernels' compute time (sec):\n", "\tTotal kernel (smem+sal+bsw) time avg: 20.01, (20.01, 20.01)\n", "\t\tSMEM compute avg: 7.92, (7.99, 7.83)\n", "\t\tSAL compute avg: 0.89, (0.94, 0.84)\n", "\t\tBSW time, avg: 10.64, (10.69, 10.57)\n", "\n", "\tTotal allocs: 1982296 = 1982296 out total requests: 2371015, Rate: 0.84\n", "\n", "Important parameter settings: \n", "\tBATCH_SIZE: 512\n", "\tMAX_SEQ_LEN_REF: 256\n", "\tMAX_SEQ_LEN_QER: 128\n", "\tMAX_SEQ_LEN8: 128\n", "\tSEEDS_PER_READ: 500\n", "\tSIMD_WIDTH8 X: 32\n", "\tSIMD_WIDTH16 X: 16\n", "\tAVG_SEEDS_PER_READ: 64\n", "[bam_sort_core] merging from 0 files and 4 in-memory blocks...\n", "######################\n", "Flagstat B1 \n", "######################\n", " Filtering B1 \n", "######################\n", " Mapping B218 \n", "-----------------------------\n", "Executing in AVX2 mode!!\n", "-----------------------------\n", "Ref file: /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna\n", "Entering FMI_search\n", "reference seq len = 30148641\n", "count\n", "0,\t1\n", "1,\t7834026\n", "2,\t15074321\n", "3,\t22314616\n", "4,\t30148641\n", "\n", "Reading other elements of the index from files /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna\n", "prefix: /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna\n", "[M::bwa_idx_load_ele] read 0 ALT contigs\n", "Done reading Index!!\n", "Reading reference genome..\n", "Binary seq file = /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna.0123\n", "Reference genome size: 30148640 bp\n", "Done readng reference genome !!\n", "\n", "[0000] 1: Calling process()\n", "\n", "Threads used (compute): 8\n", "Info: projected #read in a task: 529811\n", "------------------------------------------\n", "Memory pre-allocation for chaining: 1114.7223 MB\n", "Memory pre-allocation for BSW: 1916.9362 MB\n", "Memory pre-allocation for BWT: 618.5134 MB\n", "------------------------------------------\n", "No. of pipeline threads: 2\n", "[W::bseq_read_orig] the 2nd file has fewer sequences.\n", "[0000] read_chunk: 80000000, work_chunk_size: 0, nseq: 0\n", "[W::bseq_read_orig] the 2nd file has fewer sequences.\n", "[0000] read_chunk: 80000000, work_chunk_size: 0, nseq: 0\n", "[0000] Computation ends..\n", "No. of OMP threads: 8\n", "Processor is runnig @2295.106338 MHz\n", "Runtime profile:\n", "\n", "\t Time taken for main_mem function: 0.85 Sec\n", "\n", "\tIO times (sec) :\n", "\tReading IO time (reads) avg: 0.62, (0.62, 0.62)\n", "\tWriting IO time (SAM) avg: 0.00, (0.00, 0.00)\n", "\tReading IO time (Reference Genome) avg: 0.02, (0.02, 0.02)\n", "\tIndex read time avg: 0.20, (0.20, 0.20)\n", "\n", "\tOverall time (sec) (Excluding Index reading time):\n", "\tPROCESS() (Total compute time + (read + SAM) IO time) : 0.62\n", "\tMEM_PROCESS_SEQ() (Total compute time (Kernel + SAM)), avg: 0.00, (0.00, 0.00)\n", "\n", "\t SAM Processing time (sec):\n", "\t--WORKER_SAM avg: 0.00, (0.00, 0.00)\n", "\n", "\tKernels' compute time (sec):\n", "\tTotal kernel (smem+sal+bsw) time avg: 0.00, (0.00, 0.00)\n", "\t\tSMEM compute avg: 0.00, (0.00, 0.00)\n", "\t\tSAL compute avg: 0.00, (0.00, 0.00)\n", "\t\tBSW time, avg: 0.00, (0.00, 0.00)\n", "\n", "\tTotal allocs: 0 = 0 out total requests: 0, Rate: -nan\n", "\n", "Important parameter settings: \n", "\tBATCH_SIZE: 512\n", "\tMAX_SEQ_LEN_REF: 256\n", "\tMAX_SEQ_LEN_QER: 128\n", "\tMAX_SEQ_LEN8: 128\n", "\tSEEDS_PER_READ: 500\n", "\tSIMD_WIDTH8 X: 32\n", "\tSIMD_WIDTH16 X: 16\n", "\tAVG_SEEDS_PER_READ: 64\n", "######################\n", "Flagstat B218 \n", "######################\n", " Filtering B218 \n", "######################\n", " Mapping B8 \n", "-----------------------------\n", "Executing in AVX2 mode!!\n", "-----------------------------\n", "Ref file: /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna\n", "Entering FMI_search\n", "reference seq len = 30148641\n", "count\n", "0,\t1\n", "1,\t7834026\n", "2,\t15074321\n", "3,\t22314616\n", "4,\t30148641\n", "\n", "Reading other elements of the index from files /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna\n", "prefix: /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna\n", "[M::bwa_idx_load_ele] read 0 ALT contigs\n", "Done reading Index!!\n", "Reading reference genome..\n", "Binary seq file = /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna.0123\n", "Reference genome size: 30148640 bp\n", "Done readng reference genome !!\n", "\n", "[0000] 1: Calling process()\n", "\n", "Threads used (compute): 8\n", "Info: projected #read in a task: 529811\n", "------------------------------------------\n", "Memory pre-allocation for chaining: 1114.7223 MB\n", "Memory pre-allocation for BSW: 1916.9362 MB\n", "Memory pre-allocation for BWT: 618.5134 MB\n", "------------------------------------------\n", "No. of pipeline threads: 2\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000388, nseq: 320480\n", "\t[0000][ M::kt_pipeline] read 320480 sequences (80000388 bp)...\n", "[0000] 2. Calling mem_process_seqs.., task: 0\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000455, nseq: 320480\n", "\t[0000][ M::kt_pipeline] read 320480 sequences (80000455 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 320480\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (14, 139975, 10, 14)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (202, 2328, 4516)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 13144)\n", "[M::mem_pestat] mean and std.dev: (3191.29, 2912.96)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 17458)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (238, 301, 393)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 703)\n", "[M::mem_pestat] mean and std.dev: (322.44, 113.22)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 858)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (94, 3911, 5637)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 16723)\n", "[M::mem_pestat] mean and std.dev: (3058.40, 2441.67)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 22266)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (426, 3559, 4636)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 13056)\n", "[M::mem_pestat] mean and std.dev: (3136.64, 2381.73)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 17266)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 320480 reads in 37.605 CPU sec, 4.757 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 1\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000464, nseq: 320480\n", "\t[0000][ M::kt_pipeline] read 320480 sequences (80000464 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 320480\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (8, 140072, 7, 17)\n", "[M::mem_pestat] skip orientation FF as there are not enough pairs\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (238, 301, 393)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 703)\n", "[M::mem_pestat] mean and std.dev: (322.43, 112.73)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 858)\n", "[M::mem_pestat] skip orientation RF as there are not enough pairs\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (1661, 2746, 3666)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 7676)\n", "[M::mem_pestat] mean and std.dev: (2604.88, 1669.36)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 9681)\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 320480 reads in 36.954 CPU sec, 4.576 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 2\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000045, nseq: 320476\n", "\t[0000][ M::kt_pipeline] read 320476 sequences (80000045 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 320480\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (11, 140001, 8, 18)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (1652, 3705, 4281)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 9539)\n", "[M::mem_pestat] mean and std.dev: (3518.73, 2462.38)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 13368)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (238, 300, 391)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 697)\n", "[M::mem_pestat] mean and std.dev: (321.33, 112.34)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 850)\n", "[M::mem_pestat] skip orientation RF as there are not enough pairs\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2119, 3702, 7757)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 19033)\n", "[M::mem_pestat] mean and std.dev: (4188.56, 2893.38)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 24671)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 320480 reads in 36.774 CPU sec, 4.541 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 3\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000315, nseq: 320480\n", "\t[0000][ M::kt_pipeline] read 320480 sequences (80000315 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 320476\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (20, 140172, 7, 9)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (1675, 3524, 4185)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 9205)\n", "[M::mem_pestat] mean and std.dev: (3129.20, 2377.86)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 12641)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (237, 300, 390)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 696)\n", "[M::mem_pestat] mean and std.dev: (320.37, 111.94)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 849)\n", "[M::mem_pestat] skip orientation RF as there are not enough pairs\n", "[M::mem_pestat] skip orientation RR as there are not enough pairs\n", "[M::mem_pestat] skip orientation FF\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 320476 reads in 37.051 CPU sec, 4.577 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 4\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 15180980, nseq: 60814\n", "\t[0000][ M::kt_pipeline] read 60814 sequences (15180980 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 320480\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (12, 140222, 11, 9)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2336, 4015, 7683)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 18377)\n", "[M::mem_pestat] mean and std.dev: (4228.50, 2823.83)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 23724)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (237, 299, 390)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 696)\n", "[M::mem_pestat] mean and std.dev: (320.23, 111.81)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 849)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (126, 570, 5690)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 16818)\n", "[M::mem_pestat] mean and std.dev: (2812.00, 3204.54)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 22382)\n", "[M::mem_pestat] skip orientation RR as there are not enough pairs\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 320480 reads in 36.455 CPU sec, 4.607 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 5\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] 3. Calling kt_for - worker_aln\n", "[0000] read_chunk: 80000000, work_chunk_size: 0, nseq: 0\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 60814\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 26516, 1, 2)\n", "[M::mem_pestat] skip orientation FF as there are not enough pairs\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (237, 300, 389)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 693)\n", "[M::mem_pestat] mean and std.dev: (320.06, 111.28)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 845)\n", "[M::mem_pestat] skip orientation RF as there are not enough pairs\n", "[M::mem_pestat] skip orientation RR as there are not enough pairs\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 60814 reads in 7.621 CPU sec, 0.938 real sec\n", "[0000] read_chunk: 80000000, work_chunk_size: 0, nseq: 0\n", "[0000] Computation ends..\n", "No. of OMP threads: 8\n", "Processor is runnig @2295.084660 MHz\n", "Runtime profile:\n", "\n", "\t Time taken for main_mem function: 25.43 Sec\n", "\n", "\tIO times (sec) :\n", "\tReading IO time (reads) avg: 5.66, (5.66, 5.66)\n", "\tWriting IO time (SAM) avg: 2.40, (2.40, 2.40)\n", "\tReading IO time (Reference Genome) avg: 0.02, (0.02, 0.02)\n", "\tIndex read time avg: 0.20, (0.20, 0.20)\n", "\n", "\tOverall time (sec) (Excluding Index reading time):\n", "\tPROCESS() (Total compute time + (read + SAM) IO time) : 25.21\n", "\tMEM_PROCESS_SEQ() (Total compute time (Kernel + SAM)), avg: 23.99, (23.99, 23.99)\n", "\n", "\t SAM Processing time (sec):\n", "\t--WORKER_SAM avg: 3.22, (3.22, 3.22)\n", "\n", "\tKernels' compute time (sec):\n", "\tTotal kernel (smem+sal+bsw) time avg: 20.33, (20.33, 20.33)\n", "\t\tSMEM compute avg: 8.46, (8.53, 8.40)\n", "\t\tSAL compute avg: 0.93, (0.96, 0.90)\n", "\t\tBSW time, avg: 10.46, (10.51, 10.40)\n", "\n", "\tTotal allocs: 1964366 = 1964366 out total requests: 2350718, Rate: 0.84\n", "\n", "Important parameter settings: \n", "\tBATCH_SIZE: 512\n", "\tMAX_SEQ_LEN_REF: 256\n", "\tMAX_SEQ_LEN_QER: 128\n", "\tMAX_SEQ_LEN8: 128\n", "\tSEEDS_PER_READ: 500\n", "\tSIMD_WIDTH8 X: 32\n", "\tSIMD_WIDTH16 X: 16\n", "\tAVG_SEEDS_PER_READ: 64\n", "[bam_sort_core] merging from 0 files and 4 in-memory blocks...\n", "######################\n", "Flagstat B8 \n", "######################\n", " Filtering B8 \n", "######################\n", " Mapping C218 \n", "-----------------------------\n", "Executing in AVX2 mode!!\n", "-----------------------------\n", "Ref file: /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna\n", "Entering FMI_search\n", "reference seq len = 30148641\n", "count\n", "0,\t1\n", "1,\t7834026\n", "2,\t15074321\n", "3,\t22314616\n", "4,\t30148641\n", "\n", "Reading other elements of the index from files /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna\n", "prefix: /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna\n", "[M::bwa_idx_load_ele] read 0 ALT contigs\n", "Done reading Index!!\n", "Reading reference genome..\n", "Binary seq file = /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna.0123\n", "Reference genome size: 30148640 bp\n", "Done readng reference genome !!\n", "\n", "[0000] 1: Calling process()\n", "\n", "Threads used (compute): 8\n", "Info: projected #read in a task: 529811\n", "------------------------------------------\n", "Memory pre-allocation for chaining: 1114.7223 MB\n", "Memory pre-allocation for BSW: 1916.9362 MB\n", "Memory pre-allocation for BWT: 618.5134 MB\n", "------------------------------------------\n", "No. of pipeline threads: 2\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "Reallocating initial memory allocations!!\n", "[0000] 2. Calling mem_process_seqs.., task: 0\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (23, 171203, 26, 36)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2454, 3571, 4984)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 10044)\n", "[M::mem_pestat] mean and std.dev: (3597.57, 2019.29)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 12574)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (281, 323, 365)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (113, 533)\n", "[M::mem_pestat] mean and std.dev: (323.11, 62.97)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (29, 617)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (178, 2601, 5915)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 17389)\n", "[M::mem_pestat] mean and std.dev: (3640.42, 3577.49)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 23126)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2186, 3815, 5294)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 11510)\n", "[M::mem_pestat] mean and std.dev: (3504.56, 1715.18)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 14618)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 42.773 CPU sec, 5.445 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 1\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (33, 170438, 27, 26)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (1354, 4484, 5420)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 13552)\n", "[M::mem_pestat] mean and std.dev: (3822.97, 2657.69)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 17618)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (280, 322, 364)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (112, 532)\n", "[M::mem_pestat] mean and std.dev: (322.17, 62.94)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (28, 616)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (126, 319, 4720)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 13908)\n", "[M::mem_pestat] mean and std.dev: (2618.78, 3303.62)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 18502)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2942, 3854, 4758)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 8390)\n", "[M::mem_pestat] mean and std.dev: (3827.56, 1943.85)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 11603)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 41.637 CPU sec, 5.161 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 2\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (35, 170258, 28, 20)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (452, 3542, 4724)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 13268)\n", "[M::mem_pestat] mean and std.dev: (3319.11, 2353.58)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 17540)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (280, 322, 364)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (112, 532)\n", "[M::mem_pestat] mean and std.dev: (322.19, 62.85)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (28, 616)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (118, 767, 5867)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 17365)\n", "[M::mem_pestat] mean and std.dev: (2891.04, 3542.90)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 23114)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2765, 4691, 5500)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 10970)\n", "[M::mem_pestat] mean and std.dev: (4395.45, 2462.27)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 14245)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 41.798 CPU sec, 5.168 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 3\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (41, 169940, 16, 34)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2721, 3711, 6067)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 12759)\n", "[M::mem_pestat] mean and std.dev: (4071.07, 2494.19)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 16105)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (279, 321, 362)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (113, 528)\n", "[M::mem_pestat] mean and std.dev: (321.20, 62.63)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (30, 611)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (214, 2646, 9718)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 28726)\n", "[M::mem_pestat] mean and std.dev: (3726.50, 3984.17)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 38230)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3618, 4283, 6060)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 10944)\n", "[M::mem_pestat] mean and std.dev: (4900.44, 2474.86)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 14800)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 42.065 CPU sec, 5.198 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 4\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (25, 170166, 25, 28)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3413, 3924, 5502)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 9680)\n", "[M::mem_pestat] mean and std.dev: (4357.32, 2257.45)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 13387)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (280, 322, 363)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (114, 529)\n", "[M::mem_pestat] mean and std.dev: (321.59, 62.77)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (31, 612)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (154, 848, 5882)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 17338)\n", "[M::mem_pestat] mean and std.dev: (2799.84, 3206.14)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 23066)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (1589, 2774, 5465)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 13217)\n", "[M::mem_pestat] mean and std.dev: (3567.04, 2531.98)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 17093)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 42.573 CPU sec, 5.254 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 5\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (28, 170836, 22, 20)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2735, 3809, 4984)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 9482)\n", "[M::mem_pestat] mean and std.dev: (3726.37, 2148.74)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 12321)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (281, 323, 365)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (113, 533)\n", "[M::mem_pestat] mean and std.dev: (323.02, 62.82)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (29, 617)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (199, 627, 6324)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 18574)\n", "[M::mem_pestat] mean and std.dev: (2993.91, 3322.78)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 24699)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3492, 4021, 6049)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 11163)\n", "[M::mem_pestat] mean and std.dev: (4449.20, 2110.31)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 13720)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 42.461 CPU sec, 5.244 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 6\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (35, 170305, 23, 25)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2808, 4390, 7416)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 16632)\n", "[M::mem_pestat] mean and std.dev: (4741.37, 3000.13)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 21240)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (281, 323, 365)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (113, 533)\n", "[M::mem_pestat] mean and std.dev: (323.19, 62.72)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (29, 617)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (150, 2710, 7551)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 22353)\n", "[M::mem_pestat] mean and std.dev: (3796.43, 3776.41)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 29754)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3037, 3731, 4827)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 8407)\n", "[M::mem_pestat] mean and std.dev: (3605.82, 1431.05)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 10197)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 42.012 CPU sec, 5.186 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 7\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (18, 170712, 22, 29)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2896, 3923, 4748)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 8452)\n", "[M::mem_pestat] mean and std.dev: (3567.29, 1366.84)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 10304)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (282, 324, 365)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (116, 531)\n", "[M::mem_pestat] mean and std.dev: (323.57, 62.82)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (33, 614)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (130, 3422, 6175)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 18265)\n", "[M::mem_pestat] mean and std.dev: (3320.18, 3025.20)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 24310)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3858, 4384, 5035)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1504, 7389)\n", "[M::mem_pestat] mean and std.dev: (4220.00, 661.11)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (327, 8566)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 41.251 CPU sec, 5.116 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 8\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (35, 170802, 25, 26)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3645, 4430, 5661)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 9693)\n", "[M::mem_pestat] mean and std.dev: (4405.67, 2138.93)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 12961)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (281, 323, 364)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (115, 530)\n", "[M::mem_pestat] mean and std.dev: (322.77, 62.71)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (32, 613)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (134, 2594, 7500)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 22232)\n", "[M::mem_pestat] mean and std.dev: (3024.36, 3282.18)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 29598)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3250, 4963, 5853)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 11059)\n", "[M::mem_pestat] mean and std.dev: (4818.31, 2757.79)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 15849)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 42.574 CPU sec, 5.251 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 9\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (32, 168886, 24, 27)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3052, 3800, 4314)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (528, 6838)\n", "[M::mem_pestat] mean and std.dev: (3860.04, 894.67)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 8100)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (281, 323, 364)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (115, 530)\n", "[M::mem_pestat] mean and std.dev: (322.86, 62.96)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (32, 613)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (342, 3265, 7654)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 22278)\n", "[M::mem_pestat] mean and std.dev: (3984.25, 3763.12)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 29590)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3258, 3943, 5455)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 9849)\n", "[M::mem_pestat] mean and std.dev: (4092.23, 2161.00)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 12736)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 42.385 CPU sec, 5.244 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 10\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (35, 168790, 24, 24)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3464, 3724, 5235)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 8777)\n", "[M::mem_pestat] mean and std.dev: (3991.74, 2043.78)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 12167)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (282, 324, 365)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (116, 531)\n", "[M::mem_pestat] mean and std.dev: (323.54, 62.43)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (33, 614)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (169, 2669, 7570)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 22372)\n", "[M::mem_pestat] mean and std.dev: (3398.92, 3665.62)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 29773)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3635, 4523, 5688)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 9794)\n", "[M::mem_pestat] mean and std.dev: (4117.52, 1676.64)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 11847)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 42.620 CPU sec, 5.271 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 11\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (33, 168718, 25, 41)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3283, 3733, 4701)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (447, 7537)\n", "[M::mem_pestat] mean and std.dev: (3609.68, 1310.37)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 8955)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (281, 323, 364)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (115, 530)\n", "[M::mem_pestat] mean and std.dev: (322.55, 62.32)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (32, 613)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (166, 767, 5812)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 17104)\n", "[M::mem_pestat] mean and std.dev: (2085.08, 2725.01)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 22750)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3490, 4141, 5792)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 10396)\n", "[M::mem_pestat] mean and std.dev: (4002.73, 2262.53)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 13053)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 42.637 CPU sec, 5.271 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 12\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (29, 169521, 24, 28)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (546, 3721, 5474)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 15330)\n", "[M::mem_pestat] mean and std.dev: (3547.97, 2280.38)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 20258)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (280, 322, 363)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (114, 529)\n", "[M::mem_pestat] mean and std.dev: (322.06, 62.70)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (31, 612)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (162, 194, 5795)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 17061)\n", "[M::mem_pestat] mean and std.dev: (2317.00, 3247.67)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 22694)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3057, 3835, 4586)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 7644)\n", "[M::mem_pestat] mean and std.dev: (3556.52, 1352.44)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 9173)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 41.909 CPU sec, 5.167 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 13\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (23, 169248, 41, 26)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3320, 3727, 4292)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1376, 6236)\n", "[M::mem_pestat] mean and std.dev: (3813.68, 889.05)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (257, 7370)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (281, 323, 364)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (115, 530)\n", "[M::mem_pestat] mean and std.dev: (322.56, 62.75)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (32, 613)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (135, 352, 7515)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 22275)\n", "[M::mem_pestat] mean and std.dev: (2729.37, 3277.67)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 29655)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2073, 3014, 3681)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 6897)\n", "[M::mem_pestat] mean and std.dev: (2861.77, 1409.83)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 8505)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 42.182 CPU sec, 5.225 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 14\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (25, 170366, 32, 28)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2032, 3606, 4258)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 8710)\n", "[M::mem_pestat] mean and std.dev: (3107.38, 2172.80)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 11799)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (282, 324, 365)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (116, 531)\n", "[M::mem_pestat] mean and std.dev: (323.59, 62.61)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (33, 614)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (142, 1423, 5853)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 17275)\n", "[M::mem_pestat] mean and std.dev: (2998.66, 3114.60)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 22986)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2444, 4562, 5663)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 12101)\n", "[M::mem_pestat] mean and std.dev: (4341.04, 2553.42)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 15320)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 42.159 CPU sec, 5.201 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 15\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (36, 169233, 18, 27)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (1424, 3678, 5043)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 12281)\n", "[M::mem_pestat] mean and std.dev: (3547.69, 2269.89)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 15900)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (282, 324, 366)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (114, 534)\n", "[M::mem_pestat] mean and std.dev: (324.20, 62.98)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (30, 618)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (1525, 3804, 7557)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 19621)\n", "[M::mem_pestat] mean and std.dev: (4457.11, 3290.79)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 25653)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3607, 4145, 5255)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (311, 8551)\n", "[M::mem_pestat] mean and std.dev: (4254.83, 1224.05)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 10199)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 42.353 CPU sec, 5.259 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 16\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (38, 170360, 23, 27)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3868, 4448, 5424)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (756, 8536)\n", "[M::mem_pestat] mean and std.dev: (4306.13, 969.55)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 10092)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (283, 325, 366)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (117, 532)\n", "[M::mem_pestat] mean and std.dev: (324.74, 62.75)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (34, 615)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (124, 849, 7638)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 22666)\n", "[M::mem_pestat] mean and std.dev: (3443.09, 4064.32)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 30180)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3546, 4236, 6158)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 11382)\n", "[M::mem_pestat] mean and std.dev: (4533.52, 2116.83)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 13994)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 41.752 CPU sec, 5.304 real sec\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 2. Calling mem_process_seqs.., task: 17\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 41882100, nseq: 279214\n", "\t[0000][ M::kt_pipeline] read 279214 sequences (41882100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (26, 169634, 30, 26)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3620, 4366, 5413)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (34, 8999)\n", "[M::mem_pestat] mean and std.dev: (4386.23, 2247.24)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 13375)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (282, 324, 366)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (114, 534)\n", "[M::mem_pestat] mean and std.dev: (324.20, 62.78)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (30, 618)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (153, 2786, 5831)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 17187)\n", "[M::mem_pestat] mean and std.dev: (3155.37, 3138.66)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 22865)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3154, 4274, 5113)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 9031)\n", "[M::mem_pestat] mean and std.dev: (4395.35, 2244.61)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 13374)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 40.895 CPU sec, 5.156 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 18\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 0, nseq: 0\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 279214\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (14, 88969, 10, 10)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (531, 4440, 4954)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 13800)\n", "[M::mem_pestat] mean and std.dev: (3715.36, 2417.50)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 18223)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (282, 324, 365)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (116, 531)\n", "[M::mem_pestat] mean and std.dev: (323.65, 62.78)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (33, 614)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (52, 152, 172)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 412)\n", "[M::mem_pestat] mean and std.dev: (95.12, 55.29)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 532)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3184, 3684, 5239)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 9349)\n", "[M::mem_pestat] mean and std.dev: (4291.90, 1816.83)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 11559)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 279214 reads in 21.942 CPU sec, 2.752 real sec\n", "[0000] read_chunk: 80000000, work_chunk_size: 0, nseq: 0\n", "[0000] Computation ends..\n", "No. of OMP threads: 8\n", "Processor is runnig @2295.062368 MHz\n", "Runtime profile:\n", "\n", "\t Time taken for main_mem function: 99.68 Sec\n", "\n", "\tIO times (sec) :\n", "\tReading IO time (reads) avg: 18.40, (18.40, 18.40)\n", "\tWriting IO time (SAM) avg: 15.45, (15.45, 15.45)\n", "\tReading IO time (Reference Genome) avg: 0.02, (0.02, 0.02)\n", "\tIndex read time avg: 0.19, (0.19, 0.19)\n", "\n", "\tOverall time (sec) (Excluding Index reading time):\n", "\tPROCESS() (Total compute time + (read + SAM) IO time) : 99.47\n", "\tMEM_PROCESS_SEQ() (Total compute time (Kernel + SAM)), avg: 96.85, (96.85, 96.85)\n", "\n", "\t SAM Processing time (sec):\n", "\t--WORKER_SAM avg: 20.24, (20.24, 20.24)\n", "\n", "\tKernels' compute time (sec):\n", "\tTotal kernel (smem+sal+bsw) time avg: 74.64, (74.64, 74.64)\n", "\t\tSMEM compute avg: 38.35, (38.41, 38.31)\n", "\t\tSAL compute avg: 2.79, (2.85, 2.74)\n", "\t\tBSW time, avg: 32.00, (32.04, 31.94)\n", "\n", "\tTotal allocs: 8321109 = 8321109 out total requests: 13519246, Rate: 0.62\n", "\n", "Important parameter settings: \n", "\tBATCH_SIZE: 512\n", "\tMAX_SEQ_LEN_REF: 256\n", "\tMAX_SEQ_LEN_QER: 128\n", "\tMAX_SEQ_LEN8: 128\n", "\tSEEDS_PER_READ: 500\n", "\tSIMD_WIDTH8 X: 32\n", "\tSIMD_WIDTH16 X: 16\n", "\tAVG_SEEDS_PER_READ: 64\n", "[bam_sort_core] merging from 4 files and 4 in-memory blocks...\n", "######################\n", "Flagstat C218 \n", "######################\n", " Filtering C218 \n", "######################\n", " Mapping C2 \n", "-----------------------------\n", "Executing in AVX2 mode!!\n", "-----------------------------\n", "Ref file: /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna\n", "Entering FMI_search\n", "reference seq len = 30148641\n", "count\n", "0,\t1\n", "1,\t7834026\n", "2,\t15074321\n", "3,\t22314616\n", "4,\t30148641\n", "\n", "Reading other elements of the index from files /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna\n", "prefix: /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna\n", "[M::bwa_idx_load_ele] read 0 ALT contigs\n", "Done reading Index!!\n", "Reading reference genome..\n", "Binary seq file = /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna.0123\n", "Reference genome size: 30148640 bp\n", "Done readng reference genome !!\n", "\n", "[0000] 1: Calling process()\n", "\n", "Threads used (compute): 8\n", "Info: projected #read in a task: 529811\n", "------------------------------------------\n", "Memory pre-allocation for chaining: 1114.7223 MB\n", "Memory pre-allocation for BSW: 1916.9362 MB\n", "Memory pre-allocation for BWT: 618.5134 MB\n", "------------------------------------------\n", "No. of pipeline threads: 2\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000097, nseq: 320492\n", "\t[0000][ M::kt_pipeline] read 320492 sequences (80000097 bp)...\n", "[0000] 2. Calling mem_process_seqs.., task: 0\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000200, nseq: 320492\n", "\t[0000][ M::kt_pipeline] read 320492 sequences (80000200 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 320492\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (10, 141733, 22, 7)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (4468, 7331, 7812)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 14500)\n", "[M::mem_pestat] mean and std.dev: (5904.40, 2321.19)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 17844)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (254, 319, 412)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 728)\n", "[M::mem_pestat] mean and std.dev: (340.14, 115.43)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 886)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (182, 1648, 2407)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 6857)\n", "[M::mem_pestat] mean and std.dev: (1290.10, 1066.96)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 9082)\n", "[M::mem_pestat] skip orientation RR as there are not enough pairs\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 320492 reads in 38.345 CPU sec, 4.816 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 1\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000224, nseq: 320490\n", "\t[0000][ M::kt_pipeline] read 320490 sequences (80000224 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 320492\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 142050, 15, 12)\n", "[M::mem_pestat] skip orientation FF as there are not enough pairs\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (254, 319, 411)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 725)\n", "[M::mem_pestat] mean and std.dev: (339.56, 115.46)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 882)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2331, 2357, 2584)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1825, 3090)\n", "[M::mem_pestat] mean and std.dev: (2454.73, 152.27)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1572, 3343)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3621, 3845, 7618)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 15612)\n", "[M::mem_pestat] mean and std.dev: (4881.75, 2657.17)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 19609)\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 320492 reads in 37.563 CPU sec, 4.639 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 2\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000297, nseq: 320492\n", "\t[0000][ M::kt_pipeline] read 320492 sequences (80000297 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 320490\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (7, 141750, 16, 7)\n", "[M::mem_pestat] skip orientation FF as there are not enough pairs\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (254, 319, 411)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 725)\n", "[M::mem_pestat] mean and std.dev: (339.37, 114.77)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 882)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (198, 2038, 2659)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 7581)\n", "[M::mem_pestat] mean and std.dev: (1180.79, 1121.83)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 10042)\n", "[M::mem_pestat] skip orientation RR as there are not enough pairs\n", "[M::mem_pestat] skip orientation RF\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 320490 reads in 37.467 CPU sec, 4.622 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 3\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 65220309, nseq: 261280\n", "\t[0000][ M::kt_pipeline] read 261280 sequences (65220309 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 320492\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (7, 141640, 21, 7)\n", "[M::mem_pestat] skip orientation FF as there are not enough pairs\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (253, 318, 410)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 724)\n", "[M::mem_pestat] mean and std.dev: (338.57, 114.59)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 881)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (719, 2262, 2605)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 6377)\n", "[M::mem_pestat] mean and std.dev: (1756.80, 983.48)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 8263)\n", "[M::mem_pestat] skip orientation RR as there are not enough pairs\n", "[M::mem_pestat] skip orientation RF\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 320492 reads in 37.204 CPU sec, 4.621 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 4\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 0, nseq: 0\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 261280\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 115685, 12, 8)\n", "[M::mem_pestat] skip orientation FF as there are not enough pairs\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (253, 318, 409)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 721)\n", "[M::mem_pestat] mean and std.dev: (338.01, 114.38)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 877)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (457, 2229, 2428)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 6370)\n", "[M::mem_pestat] mean and std.dev: (1377.50, 1042.58)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 8341)\n", "[M::mem_pestat] skip orientation RR as there are not enough pairs\n", "[M::mem_pestat] skip orientation RF\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 261280 reads in 29.972 CPU sec, 3.796 real sec\n", "[0000] read_chunk: 80000000, work_chunk_size: 0, nseq: 0\n", "[0000] Computation ends..\n", "No. of OMP threads: 8\n", "Processor is runnig @2295.087906 MHz\n", "Runtime profile:\n", "\n", "\t Time taken for main_mem function: 24.17 Sec\n", "\n", "\tIO times (sec) :\n", "\tReading IO time (reads) avg: 5.35, (5.35, 5.35)\n", "\tWriting IO time (SAM) avg: 1.91, (1.91, 1.91)\n", "\tReading IO time (Reference Genome) avg: 0.02, (0.02, 0.02)\n", "\tIndex read time avg: 0.21, (0.21, 0.21)\n", "\n", "\tOverall time (sec) (Excluding Index reading time):\n", "\tPROCESS() (Total compute time + (read + SAM) IO time) : 23.93\n", "\tMEM_PROCESS_SEQ() (Total compute time (Kernel + SAM)), avg: 22.49, (22.49, 22.49)\n", "\n", "\t SAM Processing time (sec):\n", "\t--WORKER_SAM avg: 3.18, (3.18, 3.18)\n", "\n", "\tKernels' compute time (sec):\n", "\tTotal kernel (smem+sal+bsw) time avg: 18.96, (18.96, 18.96)\n", "\t\tSMEM compute avg: 7.73, (7.76, 7.69)\n", "\t\tSAL compute avg: 0.80, (0.84, 0.76)\n", "\t\tBSW time, avg: 9.96, (10.02, 9.91)\n", "\n", "\tTotal allocs: 1854630 = 1854630 out total requests: 2196178, Rate: 0.84\n", "\n", "Important parameter settings: \n", "\tBATCH_SIZE: 512\n", "\tMAX_SEQ_LEN_REF: 256\n", "\tMAX_SEQ_LEN_QER: 128\n", "\tMAX_SEQ_LEN8: 128\n", "\tSEEDS_PER_READ: 500\n", "\tSIMD_WIDTH8 X: 32\n", "\tSIMD_WIDTH16 X: 16\n", "\tAVG_SEEDS_PER_READ: 64\n", "[bam_sort_core] merging from 0 files and 4 in-memory blocks...\n", "######################\n", "Flagstat C2 \n", "######################\n", " Filtering C2 \n", "######################\n", " Mapping D119 \n", "-----------------------------\n", "Executing in AVX2 mode!!\n", "-----------------------------\n", "Ref file: /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna\n", "Entering FMI_search\n", "reference seq len = 30148641\n", "count\n", "0,\t1\n", "1,\t7834026\n", "2,\t15074321\n", "3,\t22314616\n", "4,\t30148641\n", "\n", "Reading other elements of the index from files /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna\n", "prefix: /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna\n", "[M::bwa_idx_load_ele] read 0 ALT contigs\n", "Done reading Index!!\n", "Reading reference genome..\n", "Binary seq file = /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna.0123\n", "Reference genome size: 30148640 bp\n", "Done readng reference genome !!\n", "\n", "[0000] 1: Calling process()\n", "\n", "Threads used (compute): 8\n", "Info: projected #read in a task: 529811\n", "------------------------------------------\n", "Memory pre-allocation for chaining: 1114.7223 MB\n", "Memory pre-allocation for BSW: 1916.9362 MB\n", "Memory pre-allocation for BWT: 618.5134 MB\n", "------------------------------------------\n", "No. of pipeline threads: 2\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "Reallocating initial memory allocations!!\n", "[0000] 2. Calling mem_process_seqs.., task: 0\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (52, 218506, 33, 47)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3098, 3810, 5500)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 10304)\n", "[M::mem_pestat] mean and std.dev: (4123.42, 2540.97)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 14287)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (309, 355, 401)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (125, 585)\n", "[M::mem_pestat] mean and std.dev: (355.38, 69.44)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (33, 677)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (98, 1169, 5760)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 17084)\n", "[M::mem_pestat] mean and std.dev: (2251.24, 2777.37)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 22746)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3695, 4476, 7230)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 14300)\n", "[M::mem_pestat] mean and std.dev: (4864.34, 2963.28)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 17835)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 49.079 CPU sec, 6.299 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 1\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (55, 218335, 29, 56)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2369, 3788, 4665)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 9257)\n", "[M::mem_pestat] mean and std.dev: (3519.37, 2053.32)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 11733)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (309, 355, 400)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (127, 582)\n", "[M::mem_pestat] mean and std.dev: (354.87, 69.20)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (36, 673)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (124, 1586, 5777)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 17083)\n", "[M::mem_pestat] mean and std.dev: (2883.76, 2764.17)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 22736)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3603, 4095, 4786)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1237, 7152)\n", "[M::mem_pestat] mean and std.dev: (4130.58, 848.53)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (54, 8335)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 47.482 CPU sec, 5.891 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 2\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (46, 217946, 28, 54)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3550, 4552, 5493)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 9379)\n", "[M::mem_pestat] mean and std.dev: (4508.60, 2140.69)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 13071)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (309, 355, 401)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (125, 585)\n", "[M::mem_pestat] mean and std.dev: (355.14, 69.28)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (33, 677)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (167, 1141, 1640)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 4586)\n", "[M::mem_pestat] mean and std.dev: (936.83, 848.20)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 6059)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3523, 4329, 5718)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 10108)\n", "[M::mem_pestat] mean and std.dev: (4703.89, 2343.23)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 14077)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 48.013 CPU sec, 5.972 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 3\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (57, 218237, 45, 46)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3623, 4426, 5500)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 9254)\n", "[M::mem_pestat] mean and std.dev: (4370.40, 2400.33)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 13972)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (309, 355, 401)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (125, 585)\n", "[M::mem_pestat] mean and std.dev: (355.10, 69.36)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (33, 677)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (158, 1134, 2833)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 8183)\n", "[M::mem_pestat] mean and std.dev: (2051.40, 2451.38)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 11857)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3454, 3962, 5215)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 8737)\n", "[M::mem_pestat] mean and std.dev: (3954.43, 1587.11)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 10498)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 47.524 CPU sec, 5.888 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 4\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (52, 218141, 51, 59)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3325, 4064, 4832)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (311, 7846)\n", "[M::mem_pestat] mean and std.dev: (3960.84, 1430.44)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 9683)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (309, 355, 401)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (125, 585)\n", "[M::mem_pestat] mean and std.dev: (355.13, 69.17)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (33, 677)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (137, 958, 3297)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 9617)\n", "[M::mem_pestat] mean and std.dev: (2022.88, 2594.03)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 12777)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3542, 4349, 5616)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 9764)\n", "[M::mem_pestat] mean and std.dev: (4645.88, 2225.37)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 13547)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 47.760 CPU sec, 5.945 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 5\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (67, 217899, 39, 60)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2265, 4029, 5051)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 10623)\n", "[M::mem_pestat] mean and std.dev: (3833.12, 2501.80)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 13840)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (309, 355, 401)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (125, 585)\n", "[M::mem_pestat] mean and std.dev: (354.93, 69.42)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (33, 677)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (377, 2555, 6002)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 17252)\n", "[M::mem_pestat] mean and std.dev: (3481.92, 3042.22)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 22877)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3665, 4909, 5417)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (161, 8921)\n", "[M::mem_pestat] mean and std.dev: (4273.04, 1793.79)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 11448)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 47.512 CPU sec, 5.896 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 6\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (55, 218331, 40, 45)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3312, 4214, 5902)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 11082)\n", "[M::mem_pestat] mean and std.dev: (4581.84, 2634.48)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 15120)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (309, 355, 401)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (125, 585)\n", "[M::mem_pestat] mean and std.dev: (355.10, 69.17)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (33, 677)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (214, 1013, 1656)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 4540)\n", "[M::mem_pestat] mean and std.dev: (790.71, 585.27)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 5982)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3439, 4237, 5235)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 8827)\n", "[M::mem_pestat] mean and std.dev: (4094.26, 1736.27)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 11039)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 48.192 CPU sec, 5.975 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 7\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (33, 218039, 32, 45)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (1972, 3884, 8486)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 21514)\n", "[M::mem_pestat] mean and std.dev: (4468.33, 3270.77)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 28028)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (310, 356, 401)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (128, 583)\n", "[M::mem_pestat] mean and std.dev: (355.80, 69.19)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (37, 674)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (95, 1031, 1704)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 4922)\n", "[M::mem_pestat] mean and std.dev: (852.81, 946.29)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 6531)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3509, 4178, 5227)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (73, 8663)\n", "[M::mem_pestat] mean and std.dev: (3988.12, 1850.28)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 11389)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 48.341 CPU sec, 5.989 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 8\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (39, 218723, 25, 73)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3999, 4405, 6235)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 10707)\n", "[M::mem_pestat] mean and std.dev: (5250.69, 2605.81)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 15674)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (311, 356, 402)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (129, 584)\n", "[M::mem_pestat] mean and std.dev: (356.35, 68.87)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (38, 675)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (73, 1582, 7478)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 22288)\n", "[M::mem_pestat] mean and std.dev: (3101.80, 3198.04)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 29693)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3231, 4195, 5471)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 9951)\n", "[M::mem_pestat] mean and std.dev: (4179.58, 2358.50)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 13614)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 47.218 CPU sec, 5.865 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 9\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (56, 218162, 39, 61)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2826, 3975, 4793)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 8727)\n", "[M::mem_pestat] mean and std.dev: (3471.70, 1710.33)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 10694)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (310, 356, 402)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (126, 586)\n", "[M::mem_pestat] mean and std.dev: (356.20, 69.34)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (34, 678)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (250, 1592, 5715)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 16645)\n", "[M::mem_pestat] mean and std.dev: (2537.31, 2614.20)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 22110)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3657, 4611, 5420)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (131, 8946)\n", "[M::mem_pestat] mean and std.dev: (4435.52, 2305.18)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 13656)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 48.647 CPU sec, 6.031 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 10\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (57, 218052, 31, 52)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3335, 4337, 5837)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 10841)\n", "[M::mem_pestat] mean and std.dev: (4580.32, 2656.82)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 15208)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (310, 356, 402)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (126, 586)\n", "[M::mem_pestat] mean and std.dev: (356.16, 69.37)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (34, 678)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (141, 539, 5799)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 17115)\n", "[M::mem_pestat] mean and std.dev: (2543.29, 3157.06)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 22773)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3545, 3901, 5159)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (317, 8387)\n", "[M::mem_pestat] mean and std.dev: (3939.62, 1529.08)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 10056)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 48.180 CPU sec, 5.958 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 11\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 25517700, nseq: 170118\n", "\t[0000][ M::kt_pipeline] read 170118 sequences (25517700 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (51, 217793, 35, 54)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2822, 4211, 5998)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 12350)\n", "[M::mem_pestat] mean and std.dev: (4312.75, 2566.23)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 15526)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (310, 355, 401)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (128, 583)\n", "[M::mem_pestat] mean and std.dev: (355.65, 69.26)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (37, 674)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (117, 1137, 5741)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 16989)\n", "[M::mem_pestat] mean and std.dev: (2359.71, 2713.05)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 22613)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3267, 3938, 5472)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 9882)\n", "[M::mem_pestat] mean and std.dev: (4224.40, 2446.24)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 14009)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 47.470 CPU sec, 5.986 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 12\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 0, nseq: 0\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 170118\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (21, 69272, 16, 13)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3493, 4018, 4425)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1629, 6289)\n", "[M::mem_pestat] mean and std.dev: (4207.00, 804.08)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (697, 7423)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (308, 354, 400)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (124, 584)\n", "[M::mem_pestat] mean and std.dev: (354.48, 69.42)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (32, 676)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (184, 904, 3147)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 9073)\n", "[M::mem_pestat] mean and std.dev: (1554.94, 1986.62)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 12036)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3935, 4506, 6206)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 10748)\n", "[M::mem_pestat] mean and std.dev: (5033.92, 1588.65)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 13019)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 170118 reads in 15.752 CPU sec, 1.988 real sec\n", "[0000] read_chunk: 80000000, work_chunk_size: 0, nseq: 0\n", "[0000] Computation ends..\n", "No. of OMP threads: 8\n", "Processor is runnig @2294.792480 MHz\n", "Runtime profile:\n", "\n", "\t Time taken for main_mem function: 75.29 Sec\n", "\n", "\tIO times (sec) :\n", "\tReading IO time (reads) avg: 12.65, (12.65, 12.65)\n", "\tWriting IO time (SAM) avg: 7.21, (7.21, 7.21)\n", "\tReading IO time (Reference Genome) avg: 0.02, (0.02, 0.02)\n", "\tIndex read time avg: 0.21, (0.21, 0.21)\n", "\n", "\tOverall time (sec) (Excluding Index reading time):\n", "\tPROCESS() (Total compute time + (read + SAM) IO time) : 75.06\n", "\tMEM_PROCESS_SEQ() (Total compute time (Kernel + SAM)), avg: 73.68, (73.68, 73.68)\n", "\n", "\t SAM Processing time (sec):\n", "\t--WORKER_SAM avg: 16.82, (16.82, 16.82)\n", "\n", "\tKernels' compute time (sec):\n", "\tTotal kernel (smem+sal+bsw) time avg: 55.37, (55.37, 55.37)\n", "\t\tSMEM compute avg: 24.84, (24.92, 24.78)\n", "\t\tSAL compute avg: 2.44, (2.51, 2.38)\n", "\t\tBSW time, avg: 26.91, (26.94, 26.86)\n", "\n", "\tTotal allocs: 7141941 = 7141941 out total requests: 11495283, Rate: 0.62\n", "\n", "Important parameter settings: \n", "\tBATCH_SIZE: 512\n", "\tMAX_SEQ_LEN_REF: 256\n", "\tMAX_SEQ_LEN_QER: 128\n", "\tMAX_SEQ_LEN8: 128\n", "\tSEEDS_PER_READ: 500\n", "\tSIMD_WIDTH8 X: 32\n", "\tSIMD_WIDTH16 X: 16\n", "\tAVG_SEEDS_PER_READ: 64\n", "[bam_sort_core] merging from 0 files and 4 in-memory blocks...\n", "######################\n", "Flagstat D119 \n", "######################\n", " Filtering D119 \n", "######################\n", " Mapping E2 \n", "-----------------------------\n", "Executing in AVX2 mode!!\n", "-----------------------------\n", "Ref file: /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna\n", "Entering FMI_search\n", "reference seq len = 30148641\n", "count\n", "0,\t1\n", "1,\t7834026\n", "2,\t15074321\n", "3,\t22314616\n", "4,\t30148641\n", "\n", "Reading other elements of the index from files /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna\n", "prefix: /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna\n", "[M::bwa_idx_load_ele] read 0 ALT contigs\n", "Done reading Index!!\n", "Reading reference genome..\n", "Binary seq file = /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna.0123\n", "Reference genome size: 30148640 bp\n", "Done readng reference genome !!\n", "\n", "[0000] 1: Calling process()\n", "\n", "Threads used (compute): 8\n", "Info: projected #read in a task: 529811\n", "------------------------------------------\n", "Memory pre-allocation for chaining: 1114.7223 MB\n", "Memory pre-allocation for BSW: 1916.9362 MB\n", "Memory pre-allocation for BWT: 618.5134 MB\n", "------------------------------------------\n", "No. of pipeline threads: 2\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000462, nseq: 320480\n", "\t[0000][ M::kt_pipeline] read 320480 sequences (80000462 bp)...\n", "[0000] 2. Calling mem_process_seqs.., task: 0\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000177, nseq: 320476\n", "\t[0000][ M::kt_pipeline] read 320476 sequences (80000177 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 320480\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (17, 145437, 13, 5)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3596, 4898, 8358)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 17882)\n", "[M::mem_pestat] mean and std.dev: (5449.00, 2859.18)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 22644)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (252, 318, 407)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 717)\n", "[M::mem_pestat] mean and std.dev: (336.23, 113.85)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 872)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (142, 219, 2450)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 7066)\n", "[M::mem_pestat] mean and std.dev: (915.18, 1040.69)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 9374)\n", "[M::mem_pestat] skip orientation RR as there are not enough pairs\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 320480 reads in 40.185 CPU sec, 5.071 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 1\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000371, nseq: 320476\n", "\t[0000][ M::kt_pipeline] read 320476 sequences (80000371 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 320476\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (9, 145469, 12, 11)\n", "[M::mem_pestat] skip orientation FF as there are not enough pairs\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (253, 317, 408)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 718)\n", "[M::mem_pestat] mean and std.dev: (336.58, 113.75)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 873)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (175, 2239, 2376)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 6778)\n", "[M::mem_pestat] mean and std.dev: (1337.55, 1095.89)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 8979)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (4733, 5094, 6998)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (203, 11528)\n", "[M::mem_pestat] mean and std.dev: (5217.45, 1908.95)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 13793)\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 320476 reads in 39.199 CPU sec, 4.830 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 2\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000439, nseq: 320478\n", "\t[0000][ M::kt_pipeline] read 320478 sequences (80000439 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 320476\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (10, 145483, 18, 18)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3784, 5089, 8238)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 17146)\n", "[M::mem_pestat] mean and std.dev: (5310.30, 2687.63)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 21600)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (252, 316, 405)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 711)\n", "[M::mem_pestat] mean and std.dev: (334.63, 112.80)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 864)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (161, 2254, 2319)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 6635)\n", "[M::mem_pestat] mean and std.dev: (1695.41, 1360.93)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 8793)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2201, 4811, 7389)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 17765)\n", "[M::mem_pestat] mean and std.dev: (4720.83, 2608.70)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 22953)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 320476 reads in 38.470 CPU sec, 4.766 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 3\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 69968066, nseq: 280288\n", "\t[0000][ M::kt_pipeline] read 280288 sequences (69968066 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 320478\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (8, 145465, 12, 13)\n", "[M::mem_pestat] skip orientation FF as there are not enough pairs\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (251, 316, 404)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 710)\n", "[M::mem_pestat] mean and std.dev: (334.35, 112.31)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 863)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (201, 2104, 2332)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 6594)\n", "[M::mem_pestat] mean and std.dev: (1135.18, 1036.58)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 8725)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3777, 5094, 7096)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 13734)\n", "[M::mem_pestat] mean and std.dev: (5143.08, 2450.38)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 17053)\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 320478 reads in 37.995 CPU sec, 4.718 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 4\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 0, nseq: 0\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 280288\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (6, 127374, 9, 13)\n", "[M::mem_pestat] skip orientation FF as there are not enough pairs\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (251, 315, 404)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 710)\n", "[M::mem_pestat] mean and std.dev: (334.07, 112.81)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 863)\n", "[M::mem_pestat] skip orientation RF as there are not enough pairs\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2110, 3921, 8350)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 20830)\n", "[M::mem_pestat] mean and std.dev: (5250.46, 2871.69)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 27070)\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 280288 reads in 32.699 CPU sec, 4.137 real sec\n", "[0000] read_chunk: 80000000, work_chunk_size: 0, nseq: 0\n", "[0000] Computation ends..\n", "No. of OMP threads: 8\n", "Processor is runnig @2294.917480 MHz\n", "Runtime profile:\n", "\n", "\t Time taken for main_mem function: 25.26 Sec\n", "\n", "\tIO times (sec) :\n", "\tReading IO time (reads) avg: 5.40, (5.40, 5.40)\n", "\tWriting IO time (SAM) avg: 2.15, (2.15, 2.15)\n", "\tReading IO time (Reference Genome) avg: 0.02, (0.02, 0.02)\n", "\tIndex read time avg: 0.20, (0.20, 0.20)\n", "\n", "\tOverall time (sec) (Excluding Index reading time):\n", "\tPROCESS() (Total compute time + (read + SAM) IO time) : 25.04\n", "\tMEM_PROCESS_SEQ() (Total compute time (Kernel + SAM)), avg: 23.52, (23.52, 23.52)\n", "\n", "\t SAM Processing time (sec):\n", "\t--WORKER_SAM avg: 3.32, (3.32, 3.32)\n", "\n", "\tKernels' compute time (sec):\n", "\tTotal kernel (smem+sal+bsw) time avg: 19.83, (19.83, 19.83)\n", "\t\tSMEM compute avg: 7.95, (7.99, 7.90)\n", "\t\tSAL compute avg: 0.89, (0.94, 0.85)\n", "\t\tBSW time, avg: 10.49, (10.56, 10.41)\n", "\n", "\tTotal allocs: 1924136 = 1924136 out total requests: 2288551, Rate: 0.84\n", "\n", "Important parameter settings: \n", "\tBATCH_SIZE: 512\n", "\tMAX_SEQ_LEN_REF: 256\n", "\tMAX_SEQ_LEN_QER: 128\n", "\tMAX_SEQ_LEN8: 128\n", "\tSEEDS_PER_READ: 500\n", "\tSIMD_WIDTH8 X: 32\n", "\tSIMD_WIDTH16 X: 16\n", "\tAVG_SEEDS_PER_READ: 64\n", "[bam_sort_core] merging from 0 files and 4 in-memory blocks...\n", "######################\n", "Flagstat E2 \n", "######################\n", " Filtering E2 \n", "######################\n", " Mapping E318 \n", "-----------------------------\n", "Executing in AVX2 mode!!\n", "-----------------------------\n", "Ref file: /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna\n", "Entering FMI_search\n", "reference seq len = 30148641\n", "count\n", "0,\t1\n", "1,\t7834026\n", "2,\t15074321\n", "3,\t22314616\n", "4,\t30148641\n", "\n", "Reading other elements of the index from files /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna\n", "prefix: /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna\n", "[M::bwa_idx_load_ele] read 0 ALT contigs\n", "Done reading Index!!\n", "Reading reference genome..\n", "Binary seq file = /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna.0123\n", "Reference genome size: 30148640 bp\n", "Done readng reference genome !!\n", "\n", "[0000] 1: Calling process()\n", "\n", "Threads used (compute): 8\n", "Info: projected #read in a task: 529811\n", "------------------------------------------\n", "Memory pre-allocation for chaining: 1114.7223 MB\n", "Memory pre-allocation for BSW: 1916.9362 MB\n", "Memory pre-allocation for BWT: 618.5134 MB\n", "------------------------------------------\n", "No. of pipeline threads: 2\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "Reallocating initial memory allocations!!\n", "[0000] 2. Calling mem_process_seqs.., task: 0\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (39, 198890, 34, 47)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3625, 4020, 5647)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 9691)\n", "[M::mem_pestat] mean and std.dev: (4191.84, 2287.08)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 13340)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (328, 373, 419)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (146, 601)\n", "[M::mem_pestat] mean and std.dev: (373.99, 69.44)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (55, 692)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (175, 2647, 6257)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 18421)\n", "[M::mem_pestat] mean and std.dev: (3664.38, 3620.38)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 24503)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3439, 4085, 4667)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (983, 7123)\n", "[M::mem_pestat] mean and std.dev: (4119.12, 950.24)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 8351)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 46.480 CPU sec, 5.938 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 1\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (53, 199041, 64, 52)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3558, 4172, 5799)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 10281)\n", "[M::mem_pestat] mean and std.dev: (4729.85, 2562.09)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 14978)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (328, 373, 418)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (148, 598)\n", "[M::mem_pestat] mean and std.dev: (373.64, 69.04)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (58, 688)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (116, 445, 2697)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 7859)\n", "[M::mem_pestat] mean and std.dev: (1644.29, 2396.87)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 11232)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3605, 4685, 5650)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 9740)\n", "[M::mem_pestat] mean and std.dev: (4690.96, 1908.88)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 12326)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 44.630 CPU sec, 5.538 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 2\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (45, 198487, 59, 34)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3769, 4521, 5274)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (759, 8284)\n", "[M::mem_pestat] mean and std.dev: (4511.72, 780.38)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 9789)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (328, 373, 419)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (146, 601)\n", "[M::mem_pestat] mean and std.dev: (373.87, 69.34)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (55, 692)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (125, 603, 3277)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 9581)\n", "[M::mem_pestat] mean and std.dev: (1720.35, 2444.21)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 12733)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3541, 3931, 4624)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1375, 6790)\n", "[M::mem_pestat] mean and std.dev: (4090.11, 687.60)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (292, 7873)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 45.575 CPU sec, 5.646 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 3\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (44, 199298, 43, 38)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3160, 4250, 5500)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 10180)\n", "[M::mem_pestat] mean and std.dev: (4276.55, 2375.72)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 13779)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (328, 373, 419)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (146, 601)\n", "[M::mem_pestat] mean and std.dev: (374.25, 69.62)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (55, 692)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (102, 311, 2580)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 7536)\n", "[M::mem_pestat] mean and std.dev: (1121.79, 1679.04)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 10014)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3232, 4545, 5480)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 9976)\n", "[M::mem_pestat] mean and std.dev: (4193.32, 2214.35)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 13051)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 44.796 CPU sec, 5.579 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 4\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (45, 199209, 43, 50)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3020, 3609, 4653)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 7919)\n", "[M::mem_pestat] mean and std.dev: (3495.73, 1455.37)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 9552)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (329, 373, 419)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (149, 599)\n", "[M::mem_pestat] mean and std.dev: (374.44, 69.35)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (59, 689)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (81, 655, 2576)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 7566)\n", "[M::mem_pestat] mean and std.dev: (1412.64, 2035.19)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 10061)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3262, 4107, 5740)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 10696)\n", "[M::mem_pestat] mean and std.dev: (4774.26, 2523.31)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 14868)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 44.894 CPU sec, 5.561 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 5\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (44, 198884, 43, 48)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3197, 4201, 5500)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 10106)\n", "[M::mem_pestat] mean and std.dev: (4434.00, 2433.79)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 14169)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (328, 373, 419)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (146, 601)\n", "[M::mem_pestat] mean and std.dev: (374.19, 69.24)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (55, 692)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (99, 386, 3369)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 9909)\n", "[M::mem_pestat] mean and std.dev: (2229.91, 2788.93)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 13386)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2260, 3674, 5471)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 11893)\n", "[M::mem_pestat] mean and std.dev: (3997.08, 2549.96)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 15104)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 45.326 CPU sec, 5.624 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 6\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (28, 199673, 49, 36)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3834, 4725, 6024)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 10404)\n", "[M::mem_pestat] mean and std.dev: (4925.54, 2268.14)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 13998)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (329, 374, 420)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (147, 602)\n", "[M::mem_pestat] mean and std.dev: (374.97, 69.38)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (56, 693)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (65, 230, 1212)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3506)\n", "[M::mem_pestat] mean and std.dev: (566.43, 944.15)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 4653)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2406, 4205, 7266)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 16986)\n", "[M::mem_pestat] mean and std.dev: (4716.94, 2877.20)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 21846)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 45.077 CPU sec, 5.595 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 7\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (39, 199250, 49, 54)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3109, 4357, 5500)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 10282)\n", "[M::mem_pestat] mean and std.dev: (4534.10, 2599.44)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 14932)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (329, 374, 419)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (149, 599)\n", "[M::mem_pestat] mean and std.dev: (374.60, 69.06)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (59, 689)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (91, 892, 5730)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 17008)\n", "[M::mem_pestat] mean and std.dev: (2797.47, 3392.71)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 22647)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2900, 4204, 5358)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 10274)\n", "[M::mem_pestat] mean and std.dev: (4427.39, 2356.07)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 13852)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 44.937 CPU sec, 5.583 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 8\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (39, 198421, 43, 48)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3609, 4412, 5500)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 9282)\n", "[M::mem_pestat] mean and std.dev: (4198.47, 1803.22)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 11411)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (328, 373, 419)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (146, 601)\n", "[M::mem_pestat] mean and std.dev: (374.15, 69.23)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (55, 692)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (77, 194, 2628)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 7730)\n", "[M::mem_pestat] mean and std.dev: (1487.55, 2028.85)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 10281)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3369, 3908, 5430)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 9552)\n", "[M::mem_pestat] mean and std.dev: (3914.49, 2318.64)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 13189)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 45.318 CPU sec, 5.628 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 9\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (43, 198323, 63, 44)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3103, 4332, 5231)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 9487)\n", "[M::mem_pestat] mean and std.dev: (3724.80, 1957.16)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 11615)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (328, 373, 419)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (146, 601)\n", "[M::mem_pestat] mean and std.dev: (374.10, 69.18)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (55, 692)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (89, 163, 1190)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 3392)\n", "[M::mem_pestat] mean and std.dev: (603.11, 878.20)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 4493)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3474, 3838, 5487)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 9513)\n", "[M::mem_pestat] mean and std.dev: (3841.34, 2067.15)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 12110)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 45.722 CPU sec, 5.672 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 10\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (33, 198502, 46, 62)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3020, 3841, 4940)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 8780)\n", "[M::mem_pestat] mean and std.dev: (3700.81, 1826.61)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 11007)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (329, 374, 420)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (147, 602)\n", "[M::mem_pestat] mean and std.dev: (375.14, 69.56)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (56, 693)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (167, 916, 3197)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 9257)\n", "[M::mem_pestat] mean and std.dev: (1774.09, 2237.92)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 12287)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3529, 4048, 5114)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (359, 8284)\n", "[M::mem_pestat] mean and std.dev: (4062.45, 1240.62)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 9869)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 45.804 CPU sec, 5.669 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 11\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (50, 199173, 56, 42)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2983, 3964, 5018)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 9088)\n", "[M::mem_pestat] mean and std.dev: (3838.64, 2300.11)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 13039)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (329, 375, 420)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (147, 602)\n", "[M::mem_pestat] mean and std.dev: (375.48, 69.57)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (56, 693)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (95, 398, 5876)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 17438)\n", "[M::mem_pestat] mean and std.dev: (2647.93, 3330.52)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 23219)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3433, 4201, 5301)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 9037)\n", "[M::mem_pestat] mean and std.dev: (4186.66, 2088.26)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 12540)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 45.278 CPU sec, 5.602 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 12\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (52, 198778, 28, 43)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3786, 4798, 5490)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (378, 8898)\n", "[M::mem_pestat] mean and std.dev: (4969.52, 1847.68)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 12360)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (329, 374, 420)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (147, 602)\n", "[M::mem_pestat] mean and std.dev: (375.33, 69.40)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (56, 693)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (117, 569, 6204)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 18378)\n", "[M::mem_pestat] mean and std.dev: (2746.75, 3551.84)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 24465)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3497, 3783, 4863)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (765, 7595)\n", "[M::mem_pestat] mean and std.dev: (4048.10, 891.49)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 8961)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 45.384 CPU sec, 5.639 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 13\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (37, 199181, 50, 34)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2199, 3956, 5292)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 11478)\n", "[M::mem_pestat] mean and std.dev: (3623.76, 2230.44)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 14571)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (330, 375, 420)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (150, 600)\n", "[M::mem_pestat] mean and std.dev: (375.55, 69.32)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (60, 690)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (127, 732, 6207)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 18367)\n", "[M::mem_pestat] mean and std.dev: (3177.20, 3551.03)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 24447)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2830, 3980, 5770)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 11650)\n", "[M::mem_pestat] mean and std.dev: (4295.62, 2118.21)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 14590)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 45.011 CPU sec, 5.568 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 14\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (42, 198759, 47, 57)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3497, 4791, 7301)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 14909)\n", "[M::mem_pestat] mean and std.dev: (5026.00, 2756.55)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 18713)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (329, 374, 420)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (147, 602)\n", "[M::mem_pestat] mean and std.dev: (375.04, 69.00)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (56, 693)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (103, 551, 3197)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 9385)\n", "[M::mem_pestat] mean and std.dev: (1708.70, 2325.07)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 12479)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3564, 4399, 5583)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 9621)\n", "[M::mem_pestat] mean and std.dev: (4150.04, 1928.79)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 11865)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 45.596 CPU sec, 5.659 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 15\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 2164800, nseq: 14432\n", "\t[0000][ M::kt_pipeline] read 14432 sequences (2164800 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (48, 198777, 49, 53)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3950, 4443, 5375)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1100, 8225)\n", "[M::mem_pestat] mean and std.dev: (4562.50, 1070.04)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 9650)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (329, 374, 419)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (149, 599)\n", "[M::mem_pestat] mean and std.dev: (374.48, 69.00)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (59, 689)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (63, 515, 5600)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 16674)\n", "[M::mem_pestat] mean and std.dev: (2215.51, 2886.90)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 22211)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3009, 3822, 5480)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 10422)\n", "[M::mem_pestat] mean and std.dev: (3907.55, 1887.02)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 12893)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 44.620 CPU sec, 5.646 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 16\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 14432\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (1, 5409, 1, 0)\n", "[M::mem_pestat] skip orientation FF as there are not enough pairs\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (324, 370, 417)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (138, 603)\n", "[M::mem_pestat] mean and std.dev: (370.49, 69.23)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (45, 696)\n", "[M::mem_pestat] skip orientation RF as there are not enough pairs\n", "[M::mem_pestat] skip orientation RR as there are not enough pairs\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 14432 reads in 1.726 CPU sec, 0.230 real sec\n", "[0000] read_chunk: 80000000, work_chunk_size: 0, nseq: 0\n", "[0000] read_chunk: 80000000, work_chunk_size: 0, nseq: 0\n", "[0000] Computation ends..\n", "No. of OMP threads: 8\n", "Processor is runnig @2295.079572 MHz\n", "Runtime profile:\n", "\n", "\t Time taken for main_mem function: 96.70 Sec\n", "\n", "\tIO times (sec) :\n", "\tReading IO time (reads) avg: 15.93, (15.93, 15.93)\n", "\tWriting IO time (SAM) avg: 13.84, (13.84, 13.84)\n", "\tReading IO time (Reference Genome) avg: 0.02, (0.02, 0.02)\n", "\tIndex read time avg: 0.19, (0.19, 0.19)\n", "\n", "\tOverall time (sec) (Excluding Index reading time):\n", "\tPROCESS() (Total compute time + (read + SAM) IO time) : 96.48\n", "\tMEM_PROCESS_SEQ() (Total compute time (Kernel + SAM)), avg: 90.36, (90.36, 90.36)\n", "\n", "\t SAM Processing time (sec):\n", "\t--WORKER_SAM avg: 20.15, (20.15, 20.15)\n", "\n", "\tKernels' compute time (sec):\n", "\tTotal kernel (smem+sal+bsw) time avg: 68.37, (68.37, 68.37)\n", "\t\tSMEM compute avg: 32.14, (32.18, 32.11)\n", "\t\tSAL compute avg: 2.81, (2.85, 2.76)\n", "\t\tBSW time, avg: 32.00, (32.03, 31.97)\n", "\n", "\tTotal allocs: 8421808 = 8421808 out total requests: 13554190, Rate: 0.62\n", "\n", "Important parameter settings: \n", "\tBATCH_SIZE: 512\n", "\tMAX_SEQ_LEN_REF: 256\n", "\tMAX_SEQ_LEN_QER: 128\n", "\tMAX_SEQ_LEN8: 128\n", "\tSEEDS_PER_READ: 500\n", "\tSIMD_WIDTH8 X: 32\n", "\tSIMD_WIDTH16 X: 16\n", "\tAVG_SEEDS_PER_READ: 64\n", "[bam_sort_core] merging from 4 files and 4 in-memory blocks...\n", "######################\n", "Flagstat E318 \n", "######################\n", " Filtering E318 \n", "######################\n", " Mapping G11 \n", "-----------------------------\n", "Executing in AVX2 mode!!\n", "-----------------------------\n", "Ref file: /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna\n", "Entering FMI_search\n", "reference seq len = 30148641\n", "count\n", "0,\t1\n", "1,\t7834026\n", "2,\t15074321\n", "3,\t22314616\n", "4,\t30148641\n", "\n", "Reading other elements of the index from files /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna\n", "prefix: /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna\n", "[M::bwa_idx_load_ele] read 0 ALT contigs\n", "Done reading Index!!\n", "Reading reference genome..\n", "Binary seq file = /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna.0123\n", "Reference genome size: 30148640 bp\n", "Done readng reference genome !!\n", "\n", "[0000] 1: Calling process()\n", "\n", "Threads used (compute): 8\n", "Info: projected #read in a task: 529811\n", "------------------------------------------\n", "Memory pre-allocation for chaining: 1114.7223 MB\n", "Memory pre-allocation for BSW: 1916.9362 MB\n", "Memory pre-allocation for BWT: 618.5134 MB\n", "------------------------------------------\n", "No. of pipeline threads: 2\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000094, nseq: 320480\n", "\t[0000][ M::kt_pipeline] read 320480 sequences (80000094 bp)...\n", "[0000] 2. Calling mem_process_seqs.., task: 0\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000412, nseq: 320484\n", "\t[0000][ M::kt_pipeline] read 320484 sequences (80000412 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 320480\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 132860, 15, 2)\n", "[M::mem_pestat] skip orientation FF as there are not enough pairs\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (235, 289, 364)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 622)\n", "[M::mem_pestat] mean and std.dev: (304.07, 96.50)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 751)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2233, 2401, 5698)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 12628)\n", "[M::mem_pestat] mean and std.dev: (3460.67, 2773.89)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 16093)\n", "[M::mem_pestat] skip orientation RR as there are not enough pairs\n", "[M::mem_pestat] skip orientation RF\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 320480 reads in 36.851 CPU sec, 4.645 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 1\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000316, nseq: 320480\n", "\t[0000][ M::kt_pipeline] read 320480 sequences (80000316 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 320484\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (3, 132873, 17, 3)\n", "[M::mem_pestat] skip orientation FF as there are not enough pairs\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (235, 289, 362)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 616)\n", "[M::mem_pestat] mean and std.dev: (303.43, 95.96)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 743)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2199, 2269, 2388)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1821, 2766)\n", "[M::mem_pestat] mean and std.dev: (2306.64, 98.43)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1632, 2955)\n", "[M::mem_pestat] skip orientation RR as there are not enough pairs\n", "[M::mem_pestat] skip orientation RF\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 320484 reads in 37.091 CPU sec, 4.578 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 2\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000129, nseq: 320480\n", "\t[0000][ M::kt_pipeline] read 320480 sequences (80000129 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 320480\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (4, 133179, 18, 3)\n", "[M::mem_pestat] skip orientation FF as there are not enough pairs\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (235, 289, 363)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 619)\n", "[M::mem_pestat] mean and std.dev: (303.65, 96.02)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 747)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2164, 2350, 2487)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1518, 3133)\n", "[M::mem_pestat] mean and std.dev: (2313.70, 100.94)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1195, 3456)\n", "[M::mem_pestat] skip orientation RR as there are not enough pairs\n", "[M::mem_pestat] skip orientation RF\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 320480 reads in 36.073 CPU sec, 4.444 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 3\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 68729350, nseq: 275328\n", "\t[0000][ M::kt_pipeline] read 275328 sequences (68729350 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 320480\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 133281, 16, 7)\n", "[M::mem_pestat] skip orientation FF as there are not enough pairs\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (235, 288, 363)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 619)\n", "[M::mem_pestat] mean and std.dev: (303.42, 95.94)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 747)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2260, 2346, 2410)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1960, 2710)\n", "[M::mem_pestat] mean and std.dev: (2346.75, 74.21)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1810, 2860)\n", "[M::mem_pestat] skip orientation RR as there are not enough pairs\n", "[M::mem_pestat] skip orientation RF\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 320480 reads in 35.901 CPU sec, 4.495 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 4\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 0, nseq: 0\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 275328\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 114433, 9, 4)\n", "[M::mem_pestat] skip orientation FF as there are not enough pairs\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (235, 288, 362)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 616)\n", "[M::mem_pestat] mean and std.dev: (302.86, 95.50)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 743)\n", "[M::mem_pestat] skip orientation RF as there are not enough pairs\n", "[M::mem_pestat] skip orientation RR as there are not enough pairs\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 275328 reads in 30.166 CPU sec, 3.804 real sec\n", "[0000] read_chunk: 80000000, work_chunk_size: 0, nseq: 0\n", "[0000] Computation ends..\n", "No. of OMP threads: 8\n", "Processor is runnig @2295.112570 MHz\n", "Runtime profile:\n", "\n", "\t Time taken for main_mem function: 23.62 Sec\n", "\n", "\tIO times (sec) :\n", "\tReading IO time (reads) avg: 5.25, (5.25, 5.25)\n", "\tWriting IO time (SAM) avg: 2.15, (2.15, 2.15)\n", "\tReading IO time (Reference Genome) avg: 0.03, (0.03, 0.03)\n", "\tIndex read time avg: 0.22, (0.22, 0.22)\n", "\n", "\tOverall time (sec) (Excluding Index reading time):\n", "\tPROCESS() (Total compute time + (read + SAM) IO time) : 23.37\n", "\tMEM_PROCESS_SEQ() (Total compute time (Kernel + SAM)), avg: 21.96, (21.96, 21.96)\n", "\n", "\t SAM Processing time (sec):\n", "\t--WORKER_SAM avg: 2.84, (2.84, 2.84)\n", "\n", "\tKernels' compute time (sec):\n", "\tTotal kernel (smem+sal+bsw) time avg: 18.76, (18.76, 18.76)\n", "\t\tSMEM compute avg: 7.98, (8.01, 7.95)\n", "\t\tSAL compute avg: 0.77, (0.81, 0.75)\n", "\t\tBSW time, avg: 9.51, (9.55, 9.44)\n", "\n", "\tTotal allocs: 1732220 = 1732220 out total requests: 2073330, Rate: 0.84\n", "\n", "Important parameter settings: \n", "\tBATCH_SIZE: 512\n", "\tMAX_SEQ_LEN_REF: 256\n", "\tMAX_SEQ_LEN_QER: 128\n", "\tMAX_SEQ_LEN8: 128\n", "\tSEEDS_PER_READ: 500\n", "\tSIMD_WIDTH8 X: 32\n", "\tSIMD_WIDTH16 X: 16\n", "\tAVG_SEEDS_PER_READ: 64\n", "[bam_sort_core] merging from 0 files and 4 in-memory blocks...\n", "######################\n", "Flagstat G11 \n", "######################\n", " Filtering G11 \n", "######################\n", " Mapping H44 \n", "-----------------------------\n", "Executing in AVX2 mode!!\n", "-----------------------------\n", "Ref file: /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna\n", "Entering FMI_search\n", "reference seq len = 30148641\n", "count\n", "0,\t1\n", "1,\t7834026\n", "2,\t15074321\n", "3,\t22314616\n", "4,\t30148641\n", "\n", "Reading other elements of the index from files /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna\n", "prefix: /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna\n", "[M::bwa_idx_load_ele] read 0 ALT contigs\n", "Done reading Index!!\n", "Reading reference genome..\n", "Binary seq file = /home/jovyan/SV_DATA/REF/GCA_002220235.1_ASM222023v1_genomic.fna.0123\n", "Reference genome size: 30148640 bp\n", "Done readng reference genome !!\n", "\n", "[0000] 1: Calling process()\n", "\n", "Threads used (compute): 8\n", "Info: projected #read in a task: 529811\n", "------------------------------------------\n", "Memory pre-allocation for chaining: 1114.7223 MB\n", "Memory pre-allocation for BSW: 1916.9362 MB\n", "Memory pre-allocation for BWT: 618.5134 MB\n", "------------------------------------------\n", "No. of pipeline threads: 2\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "Reallocating initial memory allocations!!\n", "[0000] 2. Calling mem_process_seqs.., task: 0\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (47, 222632, 32, 56)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3357, 4150, 4766)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (539, 7584)\n", "[M::mem_pestat] mean and std.dev: (4058.85, 1243.57)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 9033)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (295, 340, 383)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (119, 559)\n", "[M::mem_pestat] mean and std.dev: (339.24, 66.79)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (31, 647)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (84, 205, 5820)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 17292)\n", "[M::mem_pestat] mean and std.dev: (2523.91, 3325.23)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 23028)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3453, 4145, 5826)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 10572)\n", "[M::mem_pestat] mean and std.dev: (4384.18, 2341.91)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 13752)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 48.890 CPU sec, 6.248 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 1\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (41, 222705, 37, 50)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3710, 4289, 5216)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (698, 8228)\n", "[M::mem_pestat] mean and std.dev: (4177.80, 1032.06)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 9734)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (295, 339, 383)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (119, 559)\n", "[M::mem_pestat] mean and std.dev: (338.87, 66.74)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (31, 647)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (90, 2413, 7428)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 22104)\n", "[M::mem_pestat] mean and std.dev: (3202.00, 3513.95)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 29442)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (1670, 3976, 5354)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 12722)\n", "[M::mem_pestat] mean and std.dev: (3759.58, 2305.47)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 16406)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 47.686 CPU sec, 5.934 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 2\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (37, 222310, 30, 45)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3425, 4138, 7406)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 15368)\n", "[M::mem_pestat] mean and std.dev: (4939.30, 2747.71)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 19349)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (294, 339, 383)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (116, 561)\n", "[M::mem_pestat] mean and std.dev: (338.99, 66.86)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (27, 650)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (131, 5870, 7578)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 22472)\n", "[M::mem_pestat] mean and std.dev: (4497.20, 3973.19)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 29919)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3575, 4093, 6227)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 11531)\n", "[M::mem_pestat] mean and std.dev: (4530.49, 2362.06)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 14183)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 48.433 CPU sec, 6.021 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 3\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (36, 222651, 37, 39)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2787, 3883, 5297)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 10317)\n", "[M::mem_pestat] mean and std.dev: (4138.69, 2441.85)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 13906)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (295, 339, 383)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (119, 559)\n", "[M::mem_pestat] mean and std.dev: (339.21, 66.69)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (31, 647)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (124, 373, 7479)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 22189)\n", "[M::mem_pestat] mean and std.dev: (3416.43, 3665.96)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 29544)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2184, 3441, 4433)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 8931)\n", "[M::mem_pestat] mean and std.dev: (3314.89, 2232.01)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 12243)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 48.076 CPU sec, 5.963 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 4\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (46, 222795, 24, 46)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3468, 4335, 6051)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 11217)\n", "[M::mem_pestat] mean and std.dev: (4643.78, 2406.52)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 14270)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (295, 339, 383)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (119, 559)\n", "[M::mem_pestat] mean and std.dev: (339.32, 66.78)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (31, 647)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (143, 192, 5796)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 17102)\n", "[M::mem_pestat] mean and std.dev: (2638.08, 3705.94)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 22755)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3270, 4196, 5853)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 11019)\n", "[M::mem_pestat] mean and std.dev: (4612.59, 2633.46)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 15146)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 47.808 CPU sec, 5.912 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 5\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (38, 222629, 29, 58)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (1949, 4099, 5463)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 12491)\n", "[M::mem_pestat] mean and std.dev: (4001.29, 2289.70)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 16005)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (296, 340, 384)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (120, 560)\n", "[M::mem_pestat] mean and std.dev: (339.81, 66.49)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (32, 648)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (138, 2413, 7611)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 22557)\n", "[M::mem_pestat] mean and std.dev: (3249.34, 3636.05)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 30030)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2976, 4216, 5354)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 10110)\n", "[M::mem_pestat] mean and std.dev: (4201.21, 2509.83)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 14241)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 48.268 CPU sec, 6.004 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 6\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (42, 222768, 33, 44)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3025, 4128, 5653)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 10909)\n", "[M::mem_pestat] mean and std.dev: (4241.88, 2346.53)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 13628)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (295, 340, 383)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (119, 559)\n", "[M::mem_pestat] mean and std.dev: (339.50, 66.74)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (31, 647)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (125, 225, 7500)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 22250)\n", "[M::mem_pestat] mean and std.dev: (2997.79, 3674.45)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 29625)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3597, 4041, 5089)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (613, 8073)\n", "[M::mem_pestat] mean and std.dev: (4120.97, 1113.52)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 9565)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 47.676 CPU sec, 5.916 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 7\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (42, 223147, 38, 40)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3181, 3908, 5255)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 9403)\n", "[M::mem_pestat] mean and std.dev: (3911.65, 1571.74)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 11477)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (295, 339, 383)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (119, 559)\n", "[M::mem_pestat] mean and std.dev: (339.08, 66.46)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (31, 647)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (112, 397, 5786)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 17134)\n", "[M::mem_pestat] mean and std.dev: (2462.34, 3138.81)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 22808)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (1619, 3969, 4869)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 11369)\n", "[M::mem_pestat] mean and std.dev: (3674.25, 2460.17)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 14619)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 48.189 CPU sec, 5.989 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 8\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (42, 222395, 30, 55)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2049, 3809, 4577)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 9633)\n", "[M::mem_pestat] mean and std.dev: (3398.93, 1720.10)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 12161)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (295, 340, 383)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (119, 559)\n", "[M::mem_pestat] mean and std.dev: (339.69, 66.54)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (31, 647)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (115, 2446, 6320)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 18730)\n", "[M::mem_pestat] mean and std.dev: (3495.23, 3631.40)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 24935)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3525, 4061, 5472)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 9366)\n", "[M::mem_pestat] mean and std.dev: (4105.57, 2242.62)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 13076)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 48.930 CPU sec, 6.071 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 9\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (53, 222316, 33, 44)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2640, 4432, 6254)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 13482)\n", "[M::mem_pestat] mean and std.dev: (4679.34, 2952.54)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 17096)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (295, 339, 384)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (117, 562)\n", "[M::mem_pestat] mean and std.dev: (339.83, 66.88)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (28, 651)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (85, 133, 3366)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 9928)\n", "[M::mem_pestat] mean and std.dev: (2071.00, 3297.85)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 15262)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (1949, 3805, 5268)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 11906)\n", "[M::mem_pestat] mean and std.dev: (3797.70, 2283.75)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 15225)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 48.722 CPU sec, 6.045 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 10\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (36, 222188, 37, 46)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3704, 4463, 5596)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 9380)\n", "[M::mem_pestat] mean and std.dev: (4106.85, 2051.46)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 12313)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (296, 340, 384)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (120, 560)\n", "[M::mem_pestat] mean and std.dev: (340.24, 66.78)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (32, 648)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (138, 208, 5897)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 17415)\n", "[M::mem_pestat] mean and std.dev: (2693.57, 3404.57)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 23174)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2525, 4435, 5476)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 11378)\n", "[M::mem_pestat] mean and std.dev: (4313.54, 2560.22)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 14554)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 48.087 CPU sec, 5.947 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 11\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (37, 222453, 40, 31)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3519, 4265, 5543)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 9591)\n", "[M::mem_pestat] mean and std.dev: (4249.17, 2289.93)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 13409)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (296, 340, 384)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (120, 560)\n", "[M::mem_pestat] mean and std.dev: (340.32, 66.77)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (32, 648)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (151, 2402, 7544)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 22330)\n", "[M::mem_pestat] mean and std.dev: (3870.85, 4012.73)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 29723)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (1546, 4111, 4515)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 10453)\n", "[M::mem_pestat] mean and std.dev: (3574.58, 2270.01)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 13422)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 48.629 CPU sec, 6.039 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 12\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 80000100, nseq: 533334\n", "\t[0000][ M::kt_pipeline] read 533334 sequences (80000100 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (45, 222952, 38, 52)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3740, 4435, 5500)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (220, 9020)\n", "[M::mem_pestat] mean and std.dev: (4486.67, 1749.81)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 11486)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (296, 341, 385)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (118, 563)\n", "[M::mem_pestat] mean and std.dev: (340.86, 66.80)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (29, 652)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (96, 312, 7475)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 22233)\n", "[M::mem_pestat] mean and std.dev: (3140.58, 3794.07)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 29612)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3450, 3892, 4725)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (900, 7275)\n", "[M::mem_pestat] mean and std.dev: (3800.20, 1004.93)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 8550)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 48.450 CPU sec, 6.003 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 13\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 68160000, nseq: 454400\n", "\t[0000][ M::kt_pipeline] read 454400 sequences (68160000 bp)...\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 533334\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (35, 222324, 31, 45)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3538, 4098, 5336)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 8932)\n", "[M::mem_pestat] mean and std.dev: (4008.79, 1851.77)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 11416)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (296, 340, 384)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (120, 560)\n", "[M::mem_pestat] mean and std.dev: (340.24, 66.58)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (32, 648)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (137, 4089, 7644)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 22658)\n", "[M::mem_pestat] mean and std.dev: (4103.58, 3676.10)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 30165)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2954, 4119, 5917)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 11843)\n", "[M::mem_pestat] mean and std.dev: (4106.89, 2555.03)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 14806)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 533334 reads in 48.723 CPU sec, 6.064 real sec\n", "[0000] 2. Calling mem_process_seqs.., task: 14\n", "[0000] 3. Calling kt_for - worker_bwt\n", "[0000] read_chunk: 80000000, work_chunk_size: 0, nseq: 0\n", "[0000] 3. Calling kt_for - worker_aln\n", "Inferring insert size distribution from data, l_pac: 15074320, n: 454400\n", "[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (40, 189362, 32, 41)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (2322, 3769, 4564)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 9048)\n", "[M::mem_pestat] mean and std.dev: (3424.08, 2217.94)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 12296)\n", "[M::mem_pestat] analyzing insert size distribution for orientation FR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (296, 340, 384)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (120, 560)\n", "[M::mem_pestat] mean and std.dev: (340.11, 66.66)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (32, 648)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RF...\n", "[M::mem_pestat] (25, 50, 75) percentile: (104, 3264, 6229)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 18479)\n", "[M::mem_pestat] mean and std.dev: (3125.16, 3222.64)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 24604)\n", "[M::mem_pestat] analyzing insert size distribution for orientation RR...\n", "[M::mem_pestat] (25, 50, 75) percentile: (3096, 3682, 4529)\n", "[M::mem_pestat] low and high boundaries for computing mean and std.dev: (230, 7395)\n", "[M::mem_pestat] mean and std.dev: (3798.86, 1438.33)\n", "[M::mem_pestat] low and high boundaries for proper pairs: (1, 9552)\n", "[M::mem_pestat] skip orientation FF\n", "[M::mem_pestat] skip orientation RF\n", "[M::mem_pestat] skip orientation RR\n", "[0000] 10. Calling kt_for - worker_sam\n", "\t[0000][ M::mem_process_seqs] Processed 454400 reads in 40.567 CPU sec, 5.146 real sec\n", "[0000] read_chunk: 80000000, work_chunk_size: 0, nseq: 0\n", "[0000] Computation ends..\n", "No. of OMP threads: 8\n", "Processor is runnig @2295.175940 MHz\n", "Runtime profile:\n", "\n", "\t Time taken for main_mem function: 91.10 Sec\n", "\n", "\tIO times (sec) :\n", "\tReading IO time (reads) avg: 15.11, (15.11, 15.11)\n", "\tWriting IO time (SAM) avg: 9.62, (9.62, 9.62)\n", "\tReading IO time (Reference Genome) avg: 0.02, (0.02, 0.02)\n", "\tIndex read time avg: 0.18, (0.18, 0.18)\n", "\n", "\tOverall time (sec) (Excluding Index reading time):\n", "\tPROCESS() (Total compute time + (read + SAM) IO time) : 90.90\n", "\tMEM_PROCESS_SEQ() (Total compute time (Kernel + SAM)), avg: 89.28, (89.28, 89.28)\n", "\n", "\t SAM Processing time (sec):\n", "\t--WORKER_SAM avg: 20.54, (20.54, 20.54)\n", "\n", "\tKernels' compute time (sec):\n", "\tTotal kernel (smem+sal+bsw) time avg: 66.89, (66.89, 66.89)\n", "\t\tSMEM compute avg: 29.55, (29.62, 29.49)\n", "\t\tSAL compute avg: 2.95, (3.02, 2.88)\n", "\t\tBSW time, avg: 32.93, (32.95, 32.91)\n", "\n", "\tTotal allocs: 8796650 = 8796650 out total requests: 14109061, Rate: 0.62\n", "\n", "Important parameter settings: \n", "\tBATCH_SIZE: 512\n", "\tMAX_SEQ_LEN_REF: 256\n", "\tMAX_SEQ_LEN_QER: 128\n", "\tMAX_SEQ_LEN8: 128\n", "\tSEEDS_PER_READ: 500\n", "\tSIMD_WIDTH8 X: 32\n", "\tSIMD_WIDTH16 X: 16\n", "\tAVG_SEEDS_PER_READ: 64\n", "[bam_sort_core] merging from 0 files and 4 in-memory blocks...\n", "######################\n", "Flagstat H44 \n", "######################\n", " Filtering H44 \n" ] } ], "source": [ "res_dir=\"/home/jovyan/SV_DATA/RESULTS\"\n", "bam_raw_dir=\"${res_dir}/1_bam_raw\"\n", "bam_stat_dir=\"${res_dir}/2_bam_flagstat\"\n", "bam_filtered_dir=\"${res_dir}/3_bam_filtered\"\n", "\n", "data_dir=\"/home/jovyan/SV_DATA\"\n", "ref=\"${data_dir}/REF/GCA_002220235.1_ASM222023v1_genomic.fna\"\n", "\n", "cd $res_dir\n", "mkdir -p $bam_raw_dir\n", "mkdir -p $bam_stat_dir\n", "mkdir -p $bam_filtered_dir\n", "\n", "for sample in 1613 1868 4752 5417 685 716 A1 A8 B1 B218 B8 C218 C2 D119 E2 E318 G11 H44\n", " do\n", " \n", " fq1=\"${data_dir}/SHORT_READS/${sample}_R1.fastq.gz\"\n", " fq2=\"${data_dir}/SHORT_READS/${sample}_R2.fastq.gz\"\n", " \n", " echo -e \"######################\\n Mapping ${sample} \"\n", " # PUT BWA MEM CDE ADAPTED\n", " bwa-mem2 mem -R \"@RG\\tID:${sample}\\tSM:${sample}\" -t 8 ${ref} ${fq1} ${fq2} | samtools sort -@ 4 -o ${bam_raw_dir}/${sample}.sorted.bam\n", " \n", " echo -e \"######################\\nFlagstat ${sample} \"\n", " # PUT FLAGSTAT\n", " samtools flagstat ${bam_raw_dir}/${sample}.sorted.bam > ${bam_stat_dir}/${sample}.flagstat \n", " \n", " # PUT FILTER\n", " echo -e \"######################\\n Filtering ${sample} \"\n", " samtools view -bh -@4 -f 0x02 -o ${bam_filtered_dir}/${sample}.mappedpaired.bam ${bam_raw_dir}/${sample}.sorted.bam\n", " \n", " # PUT INDEX\n", " samtools index ${bam_filtered_dir}/${sample}.mappedpaired.bam\n", " \n", " done;" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### List recursively the content of the `RESULTS` directory - `ls -R`" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "# PUT COMMAND" ] }, { "cell_type": "code", "execution_count": 51, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ ".:\n", "1613.flagstat 1616_1868.vcf 1_bam_raw\n", "1613.mappedpaired.bam 1868.flagstat 2_bam_flagstat\n", "1613.mappedpaired.bam.bai 1868.mappedpaired.bam 3_bam_filtered\n", "1613.sorted.bam 1868.mappedpaired.bam.bai\n", "1616_1868.bcf 1868.sorted.bam\n", "\n", "./1_bam_raw:\n", "1613.sorted.bam 716.sorted.bam B8.sorted.bam E318.sorted.bam\n", "1868.sorted.bam A1.sorted.bam C218.sorted.bam G11.sorted.bam\n", "4752.sorted.bam A8.sorted.bam C2.sorted.bam H44.sorted.bam\n", "5417.sorted.bam B1.sorted.bam D119.sorted.bam\n", "685.sorted.bam B218.sorted.bam E2.sorted.bam\n", "\n", "./2_bam_flagstat:\n", "1613.flagstat 5417.flagstat A8.flagstat C218.flagstat E318.flagstat\n", "1615.flagstat 685.flagstat B1.flagstat C2.flagstat G11.flagstat\n", "1868.flagstat 716.flagstat B218.flagstat D119.flagstat H44.flagstat\n", "4752.flagstat A1.flagstat B8.flagstat E2.flagstat\n", "\n", "./3_bam_filtered:\n", "1613.mappedpaired.bam A1.mappedpaired.bam C2.mappedpaired.bam\n", "1613.mappedpaired.bam.bai A1.mappedpaired.bam.bai C2.mappedpaired.bam.bai\n", "1868.mappedpaired.bam A8.mappedpaired.bam D119.mappedpaired.bam\n", "1868.mappedpaired.bam.bai A8.mappedpaired.bam.bai D119.mappedpaired.bam.bai\n", "4752.mappedpaired.bam B1.mappedpaired.bam E2.mappedpaired.bam\n", "4752.mappedpaired.bam.bai B1.mappedpaired.bam.bai E2.mappedpaired.bam.bai\n", "5417.mappedpaired.bam B218.mappedpaired.bam E318.mappedpaired.bam\n", "5417.mappedpaired.bam.bai B218.mappedpaired.bam.bai E318.mappedpaired.bam.bai\n", "685.mappedpaired.bam B8.mappedpaired.bam G11.mappedpaired.bam\n", "685.mappedpaired.bam.bai B8.mappedpaired.bam.bai G11.mappedpaired.bam.bai\n", "716.mappedpaired.bam C218.mappedpaired.bam H44.mappedpaired.bam\n", "716.mappedpaired.bam.bai C218.mappedpaired.bam.bai H44.mappedpaired.bam.bai\n" ] } ], "source": [ "ls -R" ] }, { "cell_type": "code", "execution_count": 50, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/home/jovyan/SV_DATA/RESULTS\n" ] } ], "source": [ "pwd" ] }, { "cell_type": "markdown", "metadata": { "tags": [] }, "source": [ "## SNPs calling using all bams just generated" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "# PUT COMMAND" ] }, { "cell_type": "code", "execution_count": 52, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid\n", "[mpileup] 18 samples in 18 input files\n", "[mpileup] maximum number of reads per input file set to -d 250\n" ] } ], "source": [ "bcftools mpileup --threads 8 -f ../REF/GCA_002220235.1_ASM222023v1_genomic.fna 3_bam_filtered/*.bam | bcftools call --threads 8 -cv -Oz -o all_samples.bcf" ] }, { "cell_type": "code", "execution_count": 54, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "total 76\n", "-rw-r--r-- 1 jovyan users 0 Oct 3 19:35 1615.flagstat\n", "-rw-r--r-- 1 jovyan users 521 Oct 3 19:44 1613.flagstat\n", "-rw-r--r-- 1 jovyan users 519 Oct 3 19:45 1868.flagstat\n", "-rw-r--r-- 1 jovyan users 517 Oct 3 19:45 4752.flagstat\n", "-rw-r--r-- 1 jovyan users 521 Oct 3 19:46 5417.flagstat\n", "-rw-r--r-- 1 jovyan users 520 Oct 3 19:47 685.flagstat\n", "-rw-r--r-- 1 jovyan users 515 Oct 3 19:47 716.flagstat\n", "-rw-r--r-- 1 jovyan users 527 Oct 3 19:49 A1.flagstat\n", "-rw-r--r-- 1 jovyan users 520 Oct 3 19:50 A8.flagstat\n", "-rw-r--r-- 1 jovyan users 521 Oct 3 19:50 B1.flagstat\n", "-rw-r--r-- 1 jovyan users 443 Oct 3 19:50 B218.flagstat\n", "-rw-r--r-- 1 jovyan users 521 Oct 3 19:51 B8.flagstat\n", "-rw-r--r-- 1 jovyan users 524 Oct 3 19:53 C218.flagstat\n", "-rw-r--r-- 1 jovyan users 521 Oct 3 19:54 C2.flagstat\n", "-rw-r--r-- 1 jovyan users 524 Oct 3 19:55 D119.flagstat\n", "-rw-r--r-- 1 jovyan users 521 Oct 3 19:56 E2.flagstat\n", "-rw-r--r-- 1 jovyan users 525 Oct 3 19:58 E318.flagstat\n", "-rw-r--r-- 1 jovyan users 519 Oct 3 19:58 G11.flagstat\n", "-rw-r--r-- 1 jovyan users 525 Oct 3 20:00 H44.flagstat\n", "-rw-r--r-- 1 jovyan users 490 Oct 3 20:18 all_stat.csv\n" ] } ], "source": [ "ls -lrt 2_bam_flagstat" ] } ], "metadata": { "kernelspec": { "display_name": "Bash", "language": "bash", "name": "bash" }, "language_info": { "codemirror_mode": "shell", "file_extension": ".sh", "mimetype": "text/x-sh", "name": "bash" } }, "nbformat": 4, "nbformat_minor": 4 }