summaryrefslogtreecommitdiff
path: root/opendc-trace/opendc-trace-wfformat/src/test/resources/trace.json
diff options
context:
space:
mode:
authorDante Niewenhuis <d.niewenhuis@hotmail.com>2024-04-16 09:29:53 +0200
committerGitHub <noreply@github.com>2024-04-16 09:29:53 +0200
commitfff89d25bd3c7b874e68261d21695c473c30ed7d (patch)
treebe368dd745e8119dbdefd9cd0b012c7ff9080a7a /opendc-trace/opendc-trace-wfformat/src/test/resources/trace.json
parenta7b0afbb5b7059274962ade234a50240677008fd (diff)
Revamped the trace system. All TraceFormat files are now in the api m… (#216)
* Revamped the trace system. All TraceFormat files are now in the api module. This fixes some problems with not being able to use types of traces * applied spotless
Diffstat (limited to 'opendc-trace/opendc-trace-wfformat/src/test/resources/trace.json')
-rw-r--r--opendc-trace/opendc-trace-wfformat/src/test/resources/trace.json1342
1 files changed, 0 insertions, 1342 deletions
diff --git a/opendc-trace/opendc-trace-wfformat/src/test/resources/trace.json b/opendc-trace/opendc-trace-wfformat/src/test/resources/trace.json
deleted file mode 100644
index d21f024d..00000000
--- a/opendc-trace/opendc-trace-wfformat/src/test/resources/trace.json
+++ /dev/null
@@ -1,1342 +0,0 @@
-{
- "name": "eager-nextflow-chameleon",
- "description": "Instance generated with WfCommons - https://wfcommons.org",
- "createdAt": "2021-09-06T03:43:31.762479",
- "schemaVersion": "1.2",
- "author": {
- "name": "cc",
- "email": "support@wfcommons.org"
- },
- "wms": {
- "name": "Nextflow",
- "version": "21.04.3",
- "url": "https://www.nextflow.io"
- },
- "workflow": {
- "executedAt": "20210906T034331+0000",
- "makespan": 275,
- "jobs": [
- {
- "name": "makebwaindex_mammoth_mt_krause.fasta",
- "type": "compute",
- "runtime": 172.182,
- "command": {
- "program": "makebwaindex",
- "arguments": [
- "bwa",
- "index",
- "Mammoth_MT_Krause.fasta",
- "mkdir",
- "BWAIndex",
- "&&",
- "mv",
- "Mammoth_MT_Krause.fasta*",
- "BWAIndex"
- ]
- },
- "parents": [],
- "children": [
- "makeseqdict_mammoth_mt_krause.fasta"
- ],
- "files": [],
- "cores": 1.0,
- "id": "ID000001",
- "category": "makebwaindex",
- "avgCPU": 5.8,
- "bytesRead": 124,
- "bytesWritten": 126,
- "memory": 4248
- },
- {
- "name": "makeseqdict_mammoth_mt_krause.fasta",
- "type": "compute",
- "runtime": 175.427,
- "command": {
- "program": "makeseqdict",
- "arguments": [
- "picard",
- "-Xmx6144M",
- "CreateSequenceDictionary",
- "R=Mammoth_MT_Krause.fasta",
- "O=\"Mammoth_MT_Krause.dict\""
- ]
- },
- "parents": [
- "makebwaindex_mammoth_mt_krause.fasta"
- ],
- "children": [
- "makefastaindex_mammoth_mt_krause.fasta"
- ],
- "files": [],
- "cores": 1.0,
- "id": "ID000003",
- "category": "makeseqdict",
- "avgCPU": 83.5,
- "bytesRead": 22728,
- "bytesWritten": 1300,
- "memory": 104416
- },
- {
- "name": "makefastaindex_mammoth_mt_krause.fasta",
- "type": "compute",
- "runtime": 170.797,
- "command": {
- "program": "makefastaindex",
- "arguments": [
- "samtools",
- "faidx",
- "Mammoth_MT_Krause.fasta"
- ]
- },
- "parents": [
- "makeseqdict_mammoth_mt_krause.fasta"
- ],
- "children": [
- "output_documentation"
- ],
- "files": [],
- "cores": 1.0,
- "id": "ID000002",
- "category": "makefastaindex",
- "avgCPU": 23.8,
- "bytesRead": 66,
- "bytesWritten": 4,
- "memory": 6096
- },
- {
- "name": "output_documentation",
- "type": "compute",
- "runtime": 173.479,
- "command": {
- "program": "output_documentation",
- "arguments": [
- "markdown_to_html.py",
- "output.md",
- "-o",
- "results_description.html"
- ]
- },
- "parents": [
- "makefastaindex_mammoth_mt_krause.fasta"
- ],
- "children": [
- "get_software_versions"
- ],
- "files": [],
- "cores": 1.0,
- "id": "ID000005",
- "category": "output_documentation",
- "avgCPU": 84.0,
- "bytesRead": 8222,
- "bytesWritten": 15165,
- "memory": 11488
- },
- {
- "name": "get_software_versions",
- "type": "compute",
- "runtime": 183.445,
- "command": {
- "program": "get_software_versions",
- "arguments": [
- "echo",
- "2.3.5",
- "&>",
- "v_pipeline.txt",
- "echo",
- "21.04.3",
- "&>",
- "v_nextflow.txt",
- "fastqc",
- "--version",
- "&>",
- "v_fastqc.txt",
- "2>&1",
- "||",
- "true",
- "AdapterRemoval",
- "--version",
- "&>",
- "v_adapterremoval.txt",
- "2>&1",
- "||",
- "true",
- "fastp",
- "--version",
- "&>",
- "v_fastp.txt",
- "2>&1",
- "||",
- "true",
- "bwa",
- "&>",
- "v_bwa.txt",
- "2>&1",
- "||",
- "true",
- "circulargenerator",
- "--help",
- "|",
- "head",
- "-n",
- "1",
- "&>",
- "v_circulargenerator.txt",
- "2>&1",
- "||",
- "true",
- "samtools",
- "--version",
- "&>",
- "v_samtools.txt",
- "2>&1",
- "||",
- "true",
- "dedup",
- "-v",
- "&>",
- "v_dedup.txt",
- "2>&1",
- "||",
- "true",
- "##",
- "bioconda",
- "recipe",
- "of",
- "picard",
- "is",
- "incorrectly",
- "set",
- "up",
- "and",
- "extra",
- "warning",
- "made",
- "with",
- "stderr,",
- "this",
- "ugly",
- "command",
- "ensures",
- "only",
- "version",
- "exported",
- "(",
- "exec",
- "7>&1",
- "picard",
- "MarkDuplicates",
- "--version",
- "2>&1",
- ">&7",
- "|",
- "grep",
- "-v",
- "/",
- ">&2",
- ")",
- "2>",
- "v_markduplicates.txt",
- "||",
- "true",
- "qualimap",
- "--version",
- "&>",
- "v_qualimap.txt",
- "2>&1",
- "||",
- "true",
- "preseq",
- "&>",
- "v_preseq.txt",
- "2>&1",
- "||",
- "true",
- "gatk",
- "--version",
- "2>&1",
- "|",
- "head",
- "-n",
- "1",
- ">",
- "v_gatk.txt",
- "2>&1",
- "||",
- "true",
- "gatk3",
- "--version",
- "2>&1",
- ">",
- "v_gatk3.txt",
- "2>&1",
- "||",
- "true",
- "freebayes",
- "--version",
- "&>",
- "v_freebayes.txt",
- "2>&1",
- "||",
- "true",
- "bedtools",
- "--version",
- "&>",
- "v_bedtools.txt",
- "2>&1",
- "||",
- "true",
- "damageprofiler",
- "--version",
- "&>",
- "v_damageprofiler.txt",
- "2>&1",
- "||",
- "true",
- "bam",
- "--version",
- "&>",
- "v_bamutil.txt",
- "2>&1",
- "||",
- "true",
- "pmdtools",
- "--version",
- "&>",
- "v_pmdtools.txt",
- "2>&1",
- "||",
- "true",
- "angsd",
- "-h",
- "|&",
- "head",
- "-n",
- "1",
- "|",
- "cut",
- "-d",
- "-f3-4",
- "&>",
- "v_angsd.txt",
- "2>&1",
- "||",
- "true",
- "multivcfanalyzer",
- "--help",
- "|",
- "head",
- "-n",
- "1",
- "&>",
- "v_multivcfanalyzer.txt",
- "2>&1",
- "||",
- "true",
- "malt-run",
- "--help",
- "|&",
- "tail",
- "-n",
- "3",
- "|",
- "head",
- "-n",
- "1",
- "|",
- "cut",
- "-f",
- "2",
- "-d(",
- "|",
- "cut",
- "-f",
- "1",
- "-d",
- ",",
- "&>",
- "v_malt.txt",
- "2>&1",
- "||",
- "true",
- "MaltExtract",
- "--help",
- "|",
- "head",
- "-n",
- "2",
- "|",
- "tail",
- "-n",
- "1",
- "&>",
- "v_maltextract.txt",
- "2>&1",
- "||",
- "true",
- "multiqc",
- "--version",
- "&>",
- "v_multiqc.txt",
- "2>&1",
- "||",
- "true",
- "vcf2genome",
- "-h",
- "|&",
- "head",
- "-n",
- "1",
- "&>",
- "v_vcf2genome.txt",
- "||",
- "true",
- "mtnucratio",
- "--help",
- "&>",
- "v_mtnucratiocalculator.txt",
- "||",
- "true",
- "sexdeterrmine",
- "--version",
- "&>",
- "v_sexdeterrmine.txt",
- "||",
- "true",
- "kraken2",
- "--version",
- "|",
- "head",
- "-n",
- "1",
- "&>",
- "v_kraken.txt",
- "||",
- "true",
- "endorS.py",
- "--version",
- "&>",
- "v_endorSpy.txt",
- "||",
- "true",
- "pileupCaller",
- "--version",
- "&>",
- "v_sequencetools.txt",
- "2>&1",
- "||",
- "true",
- "bowtie2",
- "--version",
- "|",
- "grep",
- "-a",
- "bowtie2-.*",
- "-fdebug",
- ">",
- "v_bowtie2.txt",
- "||",
- "true",
- "eigenstrat_snp_coverage",
- "--version",
- "|",
- "cut",
- "-d",
- "-f2",
- ">v_eigenstrat_snp_coverage.txt",
- "||",
- "true",
- "mapDamage",
- "--version",
- ">",
- "v_mapdamage.txt",
- "||",
- "true",
- "bbduk.sh",
- "|",
- "grep",
- "Last",
- "modified",
- "|",
- "cut",
- "-d",
- "-f",
- "3-99",
- ">",
- "v_bbduk.txt",
- "||",
- "true",
- "scrape_software_versions.py",
- "&>",
- "software_versions_mqc.yaml"
- ]
- },
- "parents": [
- "output_documentation"
- ],
- "children": [
- "fastqc_jk2782_l1",
- "fastqc_jk2802_l2"
- ],
- "files": [],
- "cores": 2.0,
- "id": "ID000006",
- "category": "get_software_versions",
- "avgCPU": 147.8,
- "bytesRead": 172760,
- "bytesWritten": 1048,
- "memory": 387324
- },
- {
- "name": "fastqc_jk2782_l1",
- "type": "compute",
- "runtime": 175.205,
- "command": {
- "program": "fastqc",
- "arguments": [
- "fastqc",
- "-t",
- "2",
- "-q",
- "JK2782_TGGCCGATCAACGA_L008_R1_001.fastq.gz.tengrand.fq.gz",
- "JK2782_TGGCCGATCAACGA_L008_R2_001.fastq.gz.tengrand.fq.gz",
- "rename",
- "s/_fastqc.zip$/_raw_fastqc.zip/",
- "*_fastqc.zip",
- "rename",
- "s/_fastqc.html$/_raw_fastqc.html/",
- "*_fastqc.html"
- ]
- },
- "parents": [
- "get_software_versions"
- ],
- "children": [
- "adapter_removal_jk2782_l1",
- "adapter_removal_jk2802_l2"
- ],
- "files": [],
- "cores": 2.0,
- "id": "ID000007",
- "category": "fastqc",
- "avgCPU": 161.8,
- "bytesRead": 35981,
- "bytesWritten": 3967,
- "memory": 270124
- },
- {
- "name": "adapter_removal_jk2782_l1",
- "type": "compute",
- "runtime": 172.643,
- "command": {
- "program": "adapter_removal",
- "arguments": [
- "mkdir",
- "-p",
- "output",
- "AdapterRemoval",
- "--file1",
- "JK2782_TGGCCGATCAACGA_L008_R1_001.fastq.gz.tengrand.fq.gz",
- "--file2",
- "JK2782_TGGCCGATCAACGA_L008_R2_001.fastq.gz.tengrand.fq.gz",
- "--basename",
- "JK2782_TGGCCGATCAACGA_L008_R1_001.fastq.gz.tengrand.fq_L1.pe",
- "--gzip",
- "--threads",
- "2",
- "--qualitymax",
- "41",
- "--collapse",
- "--trimns",
- "--trimqualities",
- "--adapter1",
- "AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC",
- "--adapter2",
- "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA",
- "--minlength",
- "30",
- "--minquality",
- "20",
- "--minadapteroverlap",
- "1",
- "cat",
- "*.collapsed.gz",
- "*.collapsed.truncated.gz",
- "*.singleton.truncated.gz",
- "*.pair1.truncated.gz",
- "*.pair2.truncated.gz",
- ">",
- "output/JK2782_TGGCCGATCAACGA_L008_R1_001.fastq.gz.tengrand.fq_L1.pe.combined.tmp.fq.gz",
- "mv",
- "*.settings",
- "output/",
- "##",
- "Add",
- "R_",
- "and",
- "L_",
- "for",
- "unmerged",
- "reads",
- "for",
- "DeDup",
- "compatibility",
- "AdapterRemovalFixPrefix",
- "-Xmx4g",
- "output/JK2782_TGGCCGATCAACGA_L008_R1_001.fastq.gz.tengrand.fq_L1.pe.combined.tmp.fq.gz",
- "|",
- "pigz",
- "-p",
- "1",
- ">",
- "output/JK2782_TGGCCGATCAACGA_L008_R1_001.fastq.gz.tengrand.fq_L1.pe.combined.fq.gz"
- ]
- },
- "parents": [
- "fastqc_jk2782_l1",
- "fastqc_jk2802_l2"
- ],
- "children": [
- "fastqc_after_clipping_jk2782_l1",
- "fastqc_after_clipping_jk2802_l2"
- ],
- "files": [],
- "cores": 2.0,
- "id": "ID000008",
- "category": "adapter_removal",
- "avgCPU": 160.9,
- "bytesRead": 17357,
- "bytesWritten": 4405,
- "memory": 79308
- },
- {
- "name": "fastqc_jk2802_l2",
- "type": "compute",
- "runtime": 177.338,
- "command": {
- "program": "fastqc",
- "arguments": [
- "fastqc",
- "-q",
- "JK2802_AGAATAACCTACCA_L008_R1_001.fastq.gz.tengrand.fq.gz",
- "rename",
- "s/_fastqc.zip$/_raw_fastqc.zip/",
- "*_fastqc.zip",
- "rename",
- "s/_fastqc.html$/_raw_fastqc.html/",
- "*_fastqc.html"
- ]
- },
- "parents": [
- "get_software_versions"
- ],
- "children": [
- "adapter_removal_jk2782_l1",
- "adapter_removal_jk2802_l2"
- ],
- "files": [],
- "cores": 2.0,
- "id": "ID000009",
- "category": "fastqc",
- "avgCPU": 120.1,
- "bytesRead": 24457,
- "bytesWritten": 2181,
- "memory": 181060
- },
- {
- "name": "adapter_removal_jk2802_l2",
- "type": "compute",
- "runtime": 174.313,
- "command": {
- "program": "adapter_removal",
- "arguments": [
- "mkdir",
- "-p",
- "output",
- "AdapterRemoval",
- "--file1",
- "JK2802_AGAATAACCTACCA_L008_R1_001.fastq.gz.tengrand.fq.gz",
- "--basename",
- "JK2802_AGAATAACCTACCA_L008_R1_001.fastq.gz.tengrand.fq_L2.se",
- "--gzip",
- "--threads",
- "2",
- "--qualitymax",
- "41",
- "--trimns",
- "--trimqualities",
- "--adapter1",
- "AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC",
- "--adapter2",
- "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA",
- "--minlength",
- "30",
- "--minquality",
- "20",
- "--minadapteroverlap",
- "1",
- "mv",
- "*.settings",
- "*.se.truncated.gz",
- "output/"
- ]
- },
- "parents": [
- "fastqc_jk2782_l1",
- "fastqc_jk2802_l2"
- ],
- "children": [
- "fastqc_after_clipping_jk2782_l1",
- "fastqc_after_clipping_jk2802_l2"
- ],
- "files": [],
- "cores": 2.0,
- "id": "ID000010",
- "category": "adapter_removal",
- "avgCPU": 106.5,
- "bytesRead": 683,
- "bytesWritten": 897,
- "memory": 12136
- },
- {
- "name": "fastqc_after_clipping_jk2782_l1",
- "type": "compute",
- "runtime": 15.371,
- "command": {
- "program": "fastqc_after_clipping",
- "arguments": [
- "fastqc",
- "-t",
- "2",
- "-q",
- "JK2782_TGGCCGATCAACGA_L008_R1_001.fastq.gz.tengrand.fq_L1.pe.combined.fq.gz"
- ]
- },
- "parents": [
- "adapter_removal_jk2782_l1",
- "adapter_removal_jk2802_l2"
- ],
- "children": [
- "bwa_jk2802",
- "bwa_jk2782"
- ],
- "files": [],
- "cores": 2.0,
- "id": "ID000013",
- "category": "fastqc_after_clipping",
- "avgCPU": 133.3,
- "bytesRead": 23788,
- "bytesWritten": 1998,
- "memory": 215020
- },
- {
- "name": "fastqc_after_clipping_jk2802_l2",
- "type": "compute",
- "runtime": 15.272,
- "command": {
- "program": "fastqc_after_clipping",
- "arguments": [
- "fastqc",
- "-t",
- "2",
- "-q",
- "JK2802_AGAATAACCTACCA_L008_R1_001.fastq.gz.tengrand.fq_L2.se.truncated.gz"
- ]
- },
- "parents": [
- "adapter_removal_jk2782_l1",
- "adapter_removal_jk2802_l2"
- ],
- "children": [
- "bwa_jk2802",
- "bwa_jk2782"
- ],
- "files": [],
- "cores": 2.0,
- "id": "ID000014",
- "category": "fastqc_after_clipping",
- "avgCPU": 124.1,
- "bytesRead": 23882,
- "bytesWritten": 2143,
- "memory": 213064
- },
- {
- "name": "bwa_jk2802",
- "type": "compute",
- "runtime": 9.566,
- "command": {
- "program": "bwa",
- "arguments": [
- "bwa",
- "aln",
- "-t",
- "2",
- "BWAIndex/Mammoth_MT_Krause.fasta",
- "JK2802_AGAATAACCTACCA_L008_R1_001.fastq.gz.tengrand.fq_L2.se.truncated.gz",
- "-n",
- "0.04",
- "-l",
- "1024",
- "-k",
- "2",
- "-o",
- "1",
- "-f",
- "JK2802.sai",
- "bwa",
- "samse",
- "-r",
- "\"@RGtID:ILLUMINA-JK2802tSM:JK2802tPL:illuminatPU:ILLUMINA-JK2802-SE\"",
- "BWAIndex/Mammoth_MT_Krause.fasta",
- "JK2802.sai",
- "JK2802_AGAATAACCTACCA_L008_R1_001.fastq.gz.tengrand.fq_L2.se.truncated.gz",
- "|",
- "samtools",
- "sort",
- "-@",
- "1",
- "-O",
- "bam",
- "-",
- ">",
- "\"JK2802\"_\"SE\".mapped.bam",
- "samtools",
- "index",
- "\"JK2802\"_\"SE\".mapped.bam"
- ]
- },
- "parents": [
- "fastqc_after_clipping_jk2782_l1",
- "fastqc_after_clipping_jk2802_l2"
- ],
- "children": [
- "samtools_flagstat_jk2782",
- "samtools_flagstat_jk2802"
- ],
- "files": [],
- "cores": 2.0,
- "id": "ID000016",
- "category": "bwa",
- "avgCPU": 15.7,
- "bytesRead": 3774,
- "bytesWritten": 3367,
- "memory": 10628
- },
- {
- "name": "bwa_jk2782",
- "type": "compute",
- "runtime": 9.652,
- "command": {
- "program": "bwa",
- "arguments": [
- "bwa",
- "aln",
- "-t",
- "2",
- "BWAIndex/Mammoth_MT_Krause.fasta",
- "JK2782_TGGCCGATCAACGA_L008_R1_001.fastq.gz.tengrand.fq_L1.pe.combined.fq.gz",
- "-n",
- "0.04",
- "-l",
- "1024",
- "-k",
- "2",
- "-o",
- "1",
- "-f",
- "JK2782.sai",
- "bwa",
- "samse",
- "-r",
- "\"@RGtID:ILLUMINA-JK2782tSM:JK2782tPL:illuminatPU:ILLUMINA-JK2782-PE\"",
- "BWAIndex/Mammoth_MT_Krause.fasta",
- "JK2782.sai",
- "JK2782_TGGCCGATCAACGA_L008_R1_001.fastq.gz.tengrand.fq_L1.pe.combined.fq.gz",
- "|",
- "samtools",
- "sort",
- "-@",
- "1",
- "-O",
- "bam",
- "-",
- ">",
- "\"JK2782\"_\"PE\".mapped.bam",
- "samtools",
- "index",
- "\"JK2782\"_\"PE\".mapped.bam"
- ]
- },
- "parents": [
- "fastqc_after_clipping_jk2782_l1",
- "fastqc_after_clipping_jk2802_l2"
- ],
- "children": [
- "samtools_flagstat_jk2782",
- "samtools_flagstat_jk2802"
- ],
- "files": [],
- "cores": 2.0,
- "id": "ID000015",
- "category": "bwa",
- "avgCPU": 69.8,
- "bytesRead": 3705,
- "bytesWritten": 3355,
- "memory": 12876
- },
- {
- "name": "samtools_flagstat_jk2782",
- "type": "compute",
- "runtime": 13.011,
- "command": {
- "program": "samtools_flagstat",
- "arguments": [
- "samtools",
- "flagstat",
- "JK2782_PE.mapped.bam",
- ">",
- "JK2782_flagstat.stats"
- ]
- },
- "parents": [
- "bwa_jk2802",
- "bwa_jk2782"
- ],
- "children": [
- "markduplicates_jk2782",
- "markduplicates_jk2802"
- ],
- "files": [],
- "cores": 1.0,
- "id": "ID000026",
- "category": "samtools_flagstat",
- "avgCPU": 30.1,
- "bytesRead": 478,
- "bytesWritten": 5,
- "memory": 6468
- },
- {
- "name": "samtools_flagstat_jk2802",
- "type": "compute",
- "runtime": 13.129,
- "command": {
- "program": "samtools_flagstat",
- "arguments": [
- "samtools",
- "flagstat",
- "JK2802_SE.mapped.bam",
- ">",
- "JK2802_flagstat.stats"
- ]
- },
- "parents": [
- "bwa_jk2802",
- "bwa_jk2782"
- ],
- "children": [
- "markduplicates_jk2782",
- "markduplicates_jk2802"
- ],
- "files": [],
- "cores": 1.0,
- "id": "ID000024",
- "category": "samtools_flagstat",
- "avgCPU": 118.5,
- "bytesRead": 551,
- "bytesWritten": 5
- },
- {
- "name": "markduplicates_jk2782",
- "type": "compute",
- "runtime": 22.655,
- "command": {
- "program": "markduplicates",
- "arguments": [
- "mv",
- "JK2782_PE.mapped.bam",
- "JK2782.bam",
- "picard",
- "-Xmx4096M",
- "MarkDuplicates",
- "INPUT=JK2782.bam",
- "OUTPUT=JK2782_rmdup.bam",
- "REMOVE_DUPLICATES=TRUE",
- "AS=TRUE",
- "METRICS_FILE=\"JK2782_rmdup.metrics\"",
- "VALIDATION_STRINGENCY=SILENT",
- "samtools",
- "index",
- "JK2782_rmdup.bam"
- ]
- },
- "parents": [
- "samtools_flagstat_jk2782",
- "samtools_flagstat_jk2802"
- ],
- "children": [
- "preseq_jk2782",
- "preseq_jk2802"
- ],
- "files": [],
- "cores": 2.0,
- "id": "ID000021",
- "category": "markduplicates",
- "avgCPU": 173.6,
- "bytesRead": 24055,
- "bytesWritten": 2319,
- "memory": 1400048
- },
- {
- "name": "markduplicates_jk2802",
- "type": "compute",
- "runtime": 21.545,
- "command": {
- "program": "markduplicates",
- "arguments": [
- "mv",
- "JK2802_SE.mapped.bam",
- "JK2802.bam",
- "picard",
- "-Xmx4096M",
- "MarkDuplicates",
- "INPUT=JK2802.bam",
- "OUTPUT=JK2802_rmdup.bam",
- "REMOVE_DUPLICATES=TRUE",
- "AS=TRUE",
- "METRICS_FILE=\"JK2802_rmdup.metrics\"",
- "VALIDATION_STRINGENCY=SILENT",
- "samtools",
- "index",
- "JK2802_rmdup.bam"
- ]
- },
- "parents": [
- "samtools_flagstat_jk2782",
- "samtools_flagstat_jk2802"
- ],
- "children": [
- "preseq_jk2782",
- "preseq_jk2802"
- ],
- "files": [],
- "cores": 2.0,
- "id": "ID000020",
- "category": "markduplicates",
- "avgCPU": 182.6,
- "bytesRead": 24242,
- "bytesWritten": 2466,
- "memory": 1404624
- },
- {
- "name": "preseq_jk2782",
- "type": "compute",
- "runtime": 12.299,
- "command": {
- "program": "preseq",
- "arguments": [
- "preseq",
- "c_curve",
- "-s",
- "1000",
- "-o",
- "JK2782_PE.mapped.ccurve",
- "-B",
- "JK2782_PE.mapped.bam"
- ]
- },
- "parents": [
- "markduplicates_jk2782",
- "markduplicates_jk2802"
- ],
- "children": [
- "endorspy_jk2782",
- "endorspy_jk2802"
- ],
- "files": [],
- "cores": 1.0,
- "id": "ID000030",
- "category": "preseq",
- "avgCPU": 81.9,
- "bytesRead": 473,
- "bytesWritten": 4,
- "memory": 12032
- },
- {
- "name": "preseq_jk2802",
- "type": "compute",
- "runtime": 10.188,
- "command": {
- "program": "preseq",
- "arguments": [
- "preseq",
- "c_curve",
- "-s",
- "1000",
- "-o",
- "JK2802_SE.mapped.ccurve",
- "-B",
- "JK2802_SE.mapped.bam"
- ]
- },
- "parents": [
- "markduplicates_jk2782",
- "markduplicates_jk2802"
- ],
- "children": [
- "endorspy_jk2782",
- "endorspy_jk2802"
- ],
- "files": [],
- "cores": 1.0,
- "id": "ID000027",
- "category": "preseq",
- "avgCPU": 77.6,
- "bytesRead": 548,
- "bytesWritten": 4,
- "memory": 11972
- },
- {
- "name": "endorspy_jk2782",
- "type": "compute",
- "runtime": 7.537,
- "command": {
- "program": "endorspy",
- "arguments": [
- "endorS.py",
- "-o",
- "json",
- "-n",
- "JK2782",
- "JK2782_flagstat.stats"
- ]
- },
- "parents": [
- "preseq_jk2782",
- "preseq_jk2802"
- ],
- "children": [
- "damageprofiler_jk2802",
- "damageprofiler_jk2782"
- ],
- "files": [],
- "cores": 1.0,
- "id": "ID000031",
- "category": "endorspy",
- "avgCPU": 44.7,
- "bytesRead": 623,
- "bytesWritten": 4,
- "memory": 12264
- },
- {
- "name": "endorspy_jk2802",
- "type": "compute",
- "runtime": 8.0,
- "command": {
- "program": "endorspy",
- "arguments": [
- "endorS.py",
- "-o",
- "json",
- "-n",
- "JK2802",
- "JK2802_flagstat.stats"
- ]
- },
- "parents": [
- "preseq_jk2782",
- "preseq_jk2802"
- ],
- "children": [
- "damageprofiler_jk2802",
- "damageprofiler_jk2782"
- ],
- "files": [],
- "cores": 1.0,
- "id": "ID000032",
- "category": "endorspy",
- "avgCPU": 54.0,
- "bytesRead": 623,
- "bytesWritten": 4,
- "memory": 12224
- },
- {
- "name": "damageprofiler_jk2802",
- "type": "compute",
- "runtime": 18.596,
- "command": {
- "program": "damageprofiler",
- "arguments": [
- "damageprofiler",
- "-Xmx4g",
- "-i",
- "JK2802_rmdup.bam",
- "-r",
- "Mammoth_MT_Krause.fasta",
- "-l",
- "100",
- "-t",
- "15",
- "-o",
- ".",
- "-yaxis_damageplot",
- "0.30"
- ]
- },
- "parents": [
- "endorspy_jk2782",
- "endorspy_jk2802"
- ],
- "children": [
- "qualimap_jk2802",
- "qualimap_jk2782"
- ],
- "files": [],
- "cores": 1.0,
- "id": "ID000033",
- "category": "damageprofiler",
- "avgCPU": 88.6,
- "bytesRead": 25744,
- "bytesWritten": 391,
- "memory": 242940
- },
- {
- "name": "damageprofiler_jk2782",
- "type": "compute",
- "runtime": 16.736,
- "command": {
- "program": "damageprofiler",
- "arguments": [
- "damageprofiler",
- "-Xmx4g",
- "-i",
- "JK2782_rmdup.bam",
- "-r",
- "Mammoth_MT_Krause.fasta",
- "-l",
- "100",
- "-t",
- "15",
- "-o",
- ".",
- "-yaxis_damageplot",
- "0.30"
- ]
- },
- "parents": [
- "endorspy_jk2782",
- "endorspy_jk2802"
- ],
- "children": [
- "qualimap_jk2802",
- "qualimap_jk2782"
- ],
- "files": [],
- "cores": 1.0,
- "id": "ID000036",
- "category": "damageprofiler",
- "avgCPU": 88.3,
- "bytesRead": 25661,
- "bytesWritten": 327,
- "memory": 198276
- },
- {
- "name": "qualimap_jk2802",
- "type": "compute",
- "runtime": 15.368,
- "command": {
- "program": "qualimap",
- "arguments": [
- "qualimap",
- "bamqc",
- "-bam",
- "JK2802_rmdup.bam",
- "-nt",
- "2",
- "-outdir",
- ".",
- "-outformat",
- "\"HTML\"",
- "--java-mem-size=4G"
- ]
- },
- "parents": [
- "damageprofiler_jk2802",
- "damageprofiler_jk2782"
- ],
- "children": [
- "multiqc_1"
- ],
- "files": [],
- "cores": 2.0,
- "id": "ID000053",
- "category": "qualimap",
- "avgCPU": 177.7,
- "bytesRead": 35038,
- "bytesWritten": 1712,
- "memory": 209440
- },
- {
- "name": "qualimap_jk2782",
- "type": "compute",
- "runtime": 14.223,
- "command": {
- "program": "qualimap",
- "arguments": [
- "qualimap",
- "bamqc",
- "-bam",
- "JK2782_rmdup.bam",
- "-nt",
- "2",
- "-outdir",
- ".",
- "-outformat",
- "\"HTML\"",
- "--java-mem-size=4G"
- ]
- },
- "parents": [
- "damageprofiler_jk2802",
- "damageprofiler_jk2782"
- ],
- "children": [
- "multiqc_1"
- ],
- "files": [],
- "cores": 2.0,
- "id": "ID000054",
- "category": "qualimap",
- "avgCPU": 181.9,
- "bytesRead": 34954,
- "bytesWritten": 1937,
- "memory": 232196
- },
- {
- "name": "multiqc_1",
- "type": "compute",
- "runtime": 46.376,
- "command": {
- "program": "multiqc",
- "arguments": [
- "multiqc",
- "-f",
- "multiqc_config.yaml",
- "."
- ]
- },
- "parents": [
- "qualimap_jk2802",
- "qualimap_jk2782"
- ],
- "children": [],
- "files": [],
- "cores": 1.0,
- "id": "ID000056",
- "category": "multiqc",
- "avgCPU": 93.0,
- "bytesRead": 1215169,
- "bytesWritten": 22599,
- "memory": 139496
- }
- ]
- }
-}