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hic-dirt02-001.json
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{
"name": "hic",
"description": "Trace generated from Nextflow (via https://github.com/wfcommons/nextflow_workflow_tracer)",
"createdAt": "2023-03-29T04:01:35.898087+00:00",
"schemaVersion": "1.4",
"wms": {
"name": "Nextflow",
"url": "https://www.nextflow.io/",
"version": "23.04.1"
},
"workflow": {
"repo": "https://github.com/nf-core/hic",
"runName": "focused_newton",
"executedAt": "2023-03-28T18:01:31-10:00",
"tasks": [
{
"name": "NFCORE_HIC.HIC.INPUT_CHECK.SAMPLESHEET_CHECK",
"id": "4",
"type": "compute",
"command": {
"program": "check_samplesheet.py \\\n samplesheet.csv \\\n samplesheet.valid.csv\n\n cat <<-END_VERSIONS > versions.yml\n \"NFCORE_HIC:HIC:INPUT_CHECK:SAMPLESHEET_CHECK\":\n python: $(python --version | sed 's/Python //g')\n END_VERSIONS",
"arguments": []
},
"parents": [],
"children": [],
"files": [
{
"link": "input",
"name": "samplesheet.csv",
"path": "/hic/assets/",
"sizeInBytes": 194
},
{
"link": "output",
"name": "samplesheet.valid.csv",
"path": "/85/87f3aa798384909507c3133e8e4b53/",
"sizeInBytes": 213
},
{
"link": "output",
"name": "versions.yml",
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"sizeInBytes": 66
}
],
"avgCPU": 28.2,
"inputFilesBytes": 194,
"outputFilesBytes": 279,
"memoryInBytes": 2822144,
"writtenBytes": 580,
"readBytes": 919661,
"runtimeInSeconds": 1.0
},
{
"name": "NFCORE_HIC.HIC.PREPARE_GENOME.CUSTOM_GETCHROMSIZES",
"id": "1",
"type": "compute",
"command": {
"program": "samtools faidx W303_SGD_2015_JRIU00000000.fsa\n cut -f 1,2 W303_SGD_2015_JRIU00000000.fsa.fai > W303_SGD_2015_JRIU00000000.fsa.sizes\n\n cat <<-END_VERSIONS > versions.yml\n \"NFCORE_HIC:HIC:PREPARE_GENOME:CUSTOM_GETCHROMSIZES\":\n getchromsizes: $(echo $(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*$//')\n END_VERSIONS",
"arguments": []
},
"parents": [],
"children": [],
"files": [
{
"link": "input",
"name": "W303_SGD_2015_JRIU00000000.fsa",
"path": "/nf-core/test-datasets/raw/hic/reference/",
"sizeInBytes": 11542637
},
{
"link": "output",
"name": "W303_SGD_2015_JRIU00000000.fsa.sizes",
"path": "/97/a908a7b50657bf930ebe0f9ab3c820/",
"sizeInBytes": 8889
},
{
"link": "output",
"name": "W303_SGD_2015_JRIU00000000.fsa.fai",
"path": "/97/a908a7b50657bf930ebe0f9ab3c820/",
"sizeInBytes": 12249
},
{
"link": "output",
"name": "versions.yml",
"path": "/97/a908a7b50657bf930ebe0f9ab3c820/",
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}
],
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"readBytes": 11666952,
"runtimeInSeconds": 0.0
},
{
"name": "NFCORE_HIC.HIC.PREPARE_GENOME.GET_RESTRICTION_FRAGMENTS",
"id": "3",
"type": "compute",
"command": {
"program": "digest_genome.py -r A^AGCTT -o restriction_fragments.bed W303_SGD_2015_JRIU00000000.fsa\n\n cat <<-END_VERSIONS > versions.yml\n \"NFCORE_HIC:HIC:PREPARE_GENOME:GET_RESTRICTION_FRAGMENTS\":\n python: $(echo $(python --version 2>&1) | sed 's/Python //')\n END_VERSIONS",
"arguments": []
},
"parents": [],
"children": [],
"files": [
{
"link": "input",
"name": "W303_SGD_2015_JRIU00000000.fsa",
"path": "/nf-core/test-datasets/raw/hic/reference/",
"sizeInBytes": 11542637
},
{
"link": "output",
"name": "restriction_fragments.bed",
"path": "/0b/313dd189c0ce9ff0b943b5fa234f56/",
"sizeInBytes": 390905
},
{
"link": "output",
"name": "versions.yml",
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}
],
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"readBytes": 26991963,
"runtimeInSeconds": 1.0
},
{
"name": "NFCORE_HIC.HIC.PREPARE_GENOME.BOWTIE2_BUILD",
"id": "2",
"type": "compute",
"command": {
"program": "mkdir bowtie2\n bowtie2-build --threads 1 W303_SGD_2015_JRIU00000000.fsa bowtie2/W303_SGD_2015_JRIU00000000\n cat <<-END_VERSIONS > versions.yml\n \"NFCORE_HIC:HIC:PREPARE_GENOME:BOWTIE2_BUILD\":\n bowtie2: $(echo $(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*$//')\n END_VERSIONS",
"arguments": []
},
"parents": [],
"children": [],
"files": [
{
"link": "input",
"name": "W303_SGD_2015_JRIU00000000.fsa",
"path": "/nf-core/test-datasets/raw/hic/reference/",
"sizeInBytes": 11542637
},
{
"link": "output",
"name": "bowtie2",
"path": "/91/fe0694b427ce8596a46dedbb80ef45/",
"sizeInBytes": 24532794
},
{
"link": "output",
"name": "versions.yml",
"path": "/91/fe0694b427ce8596a46dedbb80ef45/",
"sizeInBytes": 66
}
],
"avgCPU": 88.9,
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"memoryInBytes": 59977728,
"writtenBytes": 24549507,
"readBytes": 47699597,
"runtimeInSeconds": 20.0
},
{
"name": "NFCORE_HIC.HIC.COOLER.COOLER_MAKEBINS",
"id": "6",
"type": "compute",
"command": {
"program": "cooler makebins \\\n \\\n W303_SGD_2015_JRIU00000000.fsa.sizes \\\n 1000 > cooler_bins_1000.bed\n\n cat <<-END_VERSIONS > versions.yml\n \"NFCORE_HIC:HIC:COOLER:COOLER_MAKEBINS\":\n cooler: $(cooler --version 2>&1 | sed 's/cooler, version //')\n END_VERSIONS",
"arguments": []
},
"parents": [],
"children": [],
"files": [
{
"link": "input",
"name": "W303_SGD_2015_JRIU00000000.fsa.sizes",
"path": "/97/a908a7b50657bf930ebe0f9ab3c820/",
"sizeInBytes": 8889
},
{
"link": "output",
"name": "cooler_bins_1000.bed",
"path": "/c3/9d13c2126693b8724af96451d360fb/",
"sizeInBytes": 505925
},
{
"link": "output",
"name": "versions.yml",
"path": "/c3/9d13c2126693b8724af96451d360fb/",
"sizeInBytes": 60
}
],
"avgCPU": 81.9,
"inputFilesBytes": 8889,
"outputFilesBytes": 505985,
"memoryInBytes": 84967424,
"writtenBytes": 506357,
"readBytes": 19638526,
"runtimeInSeconds": 3.9
},
{
"name": "NFCORE_HIC.HIC.COOLER.COOLER_MAKEBINS",
"id": "5",
"type": "compute",
"command": {
"program": "cooler makebins \\\n \\\n W303_SGD_2015_JRIU00000000.fsa.sizes \\\n 2000 > cooler_bins_2000.bed\n\n cat <<-END_VERSIONS > versions.yml\n \"NFCORE_HIC:HIC:COOLER:COOLER_MAKEBINS\":\n cooler: $(cooler --version 2>&1 | sed 's/cooler, version //')\n END_VERSIONS",
"arguments": []
},
"parents": [],
"children": [],
"files": [
{
"link": "input",
"name": "W303_SGD_2015_JRIU00000000.fsa.sizes",
"path": "/97/a908a7b50657bf930ebe0f9ab3c820/",
"sizeInBytes": 8889
},
{
"link": "output",
"name": "cooler_bins_2000.bed",
"path": "/da/cbe6b4cd9cc556da46f763d7a630f1/",
"sizeInBytes": 255773
},
{
"link": "output",
"name": "versions.yml",
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"sizeInBytes": 60
}
],
"avgCPU": 86.5,
"inputFilesBytes": 8889,
"outputFilesBytes": 255833,
"memoryInBytes": 82583552,
"writtenBytes": 256204,
"readBytes": 19638526,
"runtimeInSeconds": 3.914
},
{
"name": "NFCORE_HIC.HIC.FASTQC",
"id": "7",
"type": "compute",
"command": {
"program": "printf \"%s %s\\n\" SRR4292758_00_R1.fastq.gz SRR4292758_1.gz SRR4292758_00_R2.fastq.gz SRR4292758_2.gz | while read old_name new_name; do\n [ -f \"${new_name}\" ] || ln -s $old_name $new_name\n done\n fastqc --threads 1 SRR4292758_1.gz SRR4292758_2.gz\n\n cat <<-END_VERSIONS > versions.yml\n \"NFCORE_HIC:HIC:FASTQC\":\n fastqc: $( fastqc --version | sed -e \"s/FastQC v//g\" )\n END_VERSIONS",
"arguments": []
},
"parents": [],
"children": [],
"files": [
{
"link": "input",
"name": "SRR4292758_00_R1.fastq.gz",
"path": "/nf-core/test-datasets/raw/hic/data/",
"sizeInBytes": 26066317
},
{
"link": "input",
"name": "SRR4292758_00_R2.fastq.gz",
"path": "/nf-core/test-datasets/raw/hic/data/",
"sizeInBytes": 26201604
},
{
"link": "output",
"name": "SRR4292758_1_fastqc.html",
"path": "/48/cca69448ab94d6e6086249c75aee81/",
"sizeInBytes": 584447
},
{
"link": "output",
"name": "SRR4292758_2_fastqc.html",
"path": "/48/cca69448ab94d6e6086249c75aee81/",
"sizeInBytes": 583231
},
{
"link": "output",
"name": "SRR4292758_1_fastqc.zip",
"path": "/48/cca69448ab94d6e6086249c75aee81/",
"sizeInBytes": 306974
},
{
"link": "output",
"name": "SRR4292758_2_fastqc.zip",
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"sizeInBytes": 308165
},
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"link": "output",
"name": "versions.yml",
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}
],
"avgCPU": 91.5,
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"memoryInBytes": 305795072,
"writtenBytes": 3525144,
"readBytes": 73983920,
"runtimeInSeconds": 25.0
},
{
"name": "NFCORE_HIC.HIC.HICPRO.HICPRO_MAPPING.BOWTIE2_ALIGN",
"id": "9",
"type": "compute",
"command": {
"program": "INDEX=`find -L ./ -name \"*.rev.1.bt2\" | sed \"s/\\.rev.1.bt2$//\"`\n [ -z \"$INDEX\" ] && INDEX=`find -L ./ -name \"*.rev.1.bt2l\" | sed \"s/\\.rev.1.bt2l$//\"`\n [ -z \"$INDEX\" ] && echo \"Bowtie2 index files not found\" 1>&2 && exit 1\n\n bowtie2 \\\n -x $INDEX \\\n -U SRR4292758_00_R2.fastq.gz \\\n --threads 1 \\\n --un-gz SRR4292758_0_R2.unmapped.fastq.gz \\\n --very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder \\\n 2> SRR4292758_0_R2.bowtie2.log \\\n | samtools view -F 4 --threads 1 -o SRR4292758_0_R2.bam -\n\n if [ -f SRR4292758_0_R2.unmapped.fastq.1.gz ]; then\n mv SRR4292758_0_R2.unmapped.fastq.1.gz SRR4292758_0_R2.unmapped_1.fastq.gz\n fi\n\n if [ -f SRR4292758_0_R2.unmapped.fastq.2.gz ]; then\n mv SRR4292758_0_R2.unmapped.fastq.2.gz SRR4292758_0_R2.unmapped_2.fastq.gz\n fi\n\n cat <<-END_VERSIONS > versions.yml\n \"NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:BOWTIE2_ALIGN\":\n bowtie2: $(echo $(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*$//')\n samtools: $(echo $(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*$//')\n pigz: $( pigz --version 2>&1 | sed 's/pigz //g' )\n END_VERSIONS",
"arguments": []
},
"parents": [],
"children": [],
"files": [
{
"link": "input",
"name": "SRR4292758_00_R2.fastq.gz",
"path": "/nf-core/test-datasets/raw/hic/data/",
"sizeInBytes": 26201604
},
{
"link": "input",
"name": "bowtie2",
"path": "/91/fe0694b427ce8596a46dedbb80ef45/",
"sizeInBytes": 24532794
},
{
"link": "output",
"name": "SRR4292758_0_R2.bam",
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"sizeInBytes": 19374983
},
{
"link": "output",
"name": "SRR4292758_0_R2.bowtie2.log",
"path": "/96/c0dee37e55a15a86730695f61755b9/",
"sizeInBytes": 211
},
{
"link": "output",
"name": "SRR4292758_0_R2.unmapped.fastq.gz",
"path": "/96/c0dee37e55a15a86730695f61755b9/",
"sizeInBytes": 6031893
},
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