Output of a CWL workflow run from a GNU Guix container

gistfile1.txt

/gnu/store/ik2j18y8gd370ndinna725c2ikldyh0r-cwltool-1.0.20181012180214/bin/.cwltool-real 1.0
Resolved 'Workflows/test-workflow.cwl' to 'file:///gnu/export/local/home/wrk/izip/git/opensource/cwl/hacchy1983-CWL-workflows/Workflows/test-workflow.cwl'
[workflow ] start
[workflow ] starting step trimPE
[step trimPE] start
[job trimPE] /tmp/ypu930v1$ java \
    -jar \
    /gnu/store/f09s746mp061ric48gdb1xaav9ki0b7q-trimmomatic-jar-0.38/lib/share/jar/trimmomatic-0.38.jar \
    PE \
    /tmp/tmpt5_80dad/stg2b137de8-6a7f-4ff7-882b-69a5f0ab4d61/small.ERR034597_1.fastq \
    /tmp/tmpt5_80dad/stgfaf198c2-7896-40a0-9788-fa2a554cfc72/small.ERR034597_2.fastq \
    small.ERR034597_1.fastq.trim.1P.fastq \
    small.ERR034597_1.fastq.trim.1U.fastq \
    small.ERR034597_2.fastq.trim.2P.fastq \
    small.ERR034597_2.fastq.trim.2U.fastq \
    ILLUMINACLIP:/lib/share/jar/trimmomatic-0.38.jar/lib/share/jar/adapters/TruSeq2-PE.fa:2:40:15
TrimmomaticPE: Started with arguments:
 /tmp/tmpt5_80dad/stg2b137de8-6a7f-4ff7-882b-69a5f0ab4d61/small.ERR034597_1.fastq /tmp/tmpt5_80dad/stgfaf198c2-7896-40a0-9788-fa2a554cfc72/small.ERR034597_2.fastq small.ERR034597_1.fastq.trim.1P.fastq small.ERR034597_1.fastq.trim.1U.fastq small.ERR034597_2.fastq.trim.2P.fastq small.ERR034597_2.fastq.trim.2U.fastq ILLUMINACLIP:/lib/share/jar/trimmomatic-0.38.jar/lib/share/jar/adapters/TruSeq2-PE.fa:2:40:15
Multiple cores found: Using 4 threads
java.io.FileNotFoundException: /lib/share/jar/trimmomatic-0.38.jar/lib/share/jar/adapters/TruSeq2-PE.fa (No such file or directory)
	at java.io.FileInputStream.open0(Native Method)
	at java.io.FileInputStream.open(FileInputStream.java:195)
	at java.io.FileInputStream.<init>(FileInputStream.java:138)
	at org.usadellab.trimmomatic.fasta.FastaParser.parse(FastaParser.java:54)
	at org.usadellab.trimmomatic.trim.IlluminaClippingTrimmer.loadSequences(IlluminaClippingTrimmer.java:110)
	at org.usadellab.trimmomatic.trim.IlluminaClippingTrimmer.makeIlluminaClippingTrimmer(IlluminaClippingTrimmer.java:71)
	at org.usadellab.trimmomatic.trim.TrimmerFactory.makeTrimmer(TrimmerFactory.java:32)
	at org.usadellab.trimmomatic.Trimmomatic.createTrimmers(Trimmomatic.java:59)
	at org.usadellab.trimmomatic.TrimmomaticPE.run(TrimmomaticPE.java:552)
	at org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:80)
Quality encoding detected as phred33
Input Read Pairs: 25000 Both Surviving: 25000 (100.00%) Forward Only Surviving: 0 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%)
TrimmomaticPE: Completed successfully
Could not collect memory usage, job ended before monitoring began.
[job trimPE] completed success
[step trimPE] completed success
[workflow ] starting step qc2
[step qc2] start
[job qc2] /tmp/0dcgjdjv$ fastqc \
    -o \
    . \
    /tmp/tmp63aq_dlf/stg050cc461-0a24-49cd-b02f-03868008cbb5/small.ERR034597_2.fastq
Started analysis of small.ERR034597_2.fastq
Approx 5% complete for small.ERR034597_2.fastq
Approx 10% complete for small.ERR034597_2.fastq
Approx 15% complete for small.ERR034597_2.fastq
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Approx 80% complete for small.ERR034597_2.fastq
Approx 85% complete for small.ERR034597_2.fastq
Approx 90% complete for small.ERR034597_2.fastq
Approx 95% complete for small.ERR034597_2.fastq
Approx 100% complete for small.ERR034597_2.fastq
Analysis complete for small.ERR034597_2.fastq
[job qc2] Max memory used: 148MiB
[job qc2] completed success
[step qc2] completed success
[workflow ] starting step map
[step map] start
[job map] /tmp/gcuf5995$ /bin/sh \
    -c \
    'bwa' 'mem' '-t' '4' '/tmp/tmp76qmpmin/stg18b83a9b-54bd-416f-b928-08e7a2ce4f5a/small.chr22.fa' '/tmp/tmp76qmpmin/stg763c6049-ab8d-49b5-8e3e-0bc757f07fd5/small.ERR034597_1.fastq.trim.1P.fastq' '/tmp/tmp76qmpmin/stg0d3cf07c-5d90-45ae-b210-7adfe976c43c/small.ERR034597_2.fastq.trim.2P.fastq' > /tmp/gcuf5995/output.sam
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 50000 sequences (4500000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 43, 0, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (188, 220, 285)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 479)
[M::mem_pestat] mean and std.dev: (233.23, 76.21)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 576)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 50000 reads in 2.776 CPU sec, 0.707 real sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa mem -t 4 /tmp/tmp76qmpmin/stg18b83a9b-54bd-416f-b928-08e7a2ce4f5a/small.chr22.fa /tmp/tmp76qmpmin/stg763c6049-ab8d-49b5-8e3e-0bc757f07fd5/small.ERR034597_1.fastq.trim.1P.fastq /tmp/tmp76qmpmin/stg0d3cf07c-5d90-45ae-b210-7adfe976c43c/small.ERR034597_2.fastq.trim.2P.fastq
[main] Real time: 0.746 sec; CPU: 2.816 sec
Could not collect memory usage, job ended before monitoring began.
[job map] completed success
[step map] completed success
[workflow ] starting step qc1
[step qc1] start
[job qc1] /tmp/098rskrv$ fastqc \
    -o \
    . \
    /tmp/tmp9vvzwo3r/stg8b902b52-a40b-4ce6-941f-a6be9b613e23/small.ERR034597_1.fastq
Started analysis of small.ERR034597_1.fastq
Approx 5% complete for small.ERR034597_1.fastq
Approx 10% complete for small.ERR034597_1.fastq
Approx 15% complete for small.ERR034597_1.fastq
Approx 20% complete for small.ERR034597_1.fastq
Approx 25% complete for small.ERR034597_1.fastq
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Approx 95% complete for small.ERR034597_1.fastq
Approx 100% complete for small.ERR034597_1.fastq
Analysis complete for small.ERR034597_1.fastq
[job qc1] Max memory used: 140MiB
[job qc1] completed success
[step qc1] completed success
[workflow ] starting step qc2P
[step qc2P] start
[job qc2P] /tmp/y7fap1ym$ fastqc \
    -o \
    . \
    /tmp/tmpdmnw8vu0/stg732a95da-3bde-4631-a939-aad809927179/small.ERR034597_2.fastq.trim.2P.fastq
Started analysis of small.ERR034597_2.fastq.trim.2P.fastq
Approx 5% complete for small.ERR034597_2.fastq.trim.2P.fastq
Approx 10% complete for small.ERR034597_2.fastq.trim.2P.fastq
Approx 15% complete for small.ERR034597_2.fastq.trim.2P.fastq
Approx 20% complete for small.ERR034597_2.fastq.trim.2P.fastq
Approx 25% complete for small.ERR034597_2.fastq.trim.2P.fastq
Approx 30% complete for small.ERR034597_2.fastq.trim.2P.fastq
Approx 35% complete for small.ERR034597_2.fastq.trim.2P.fastq
Approx 40% complete for small.ERR034597_2.fastq.trim.2P.fastq
Approx 45% complete for small.ERR034597_2.fastq.trim.2P.fastq
Approx 50% complete for small.ERR034597_2.fastq.trim.2P.fastq
Approx 55% complete for small.ERR034597_2.fastq.trim.2P.fastq
Approx 60% complete for small.ERR034597_2.fastq.trim.2P.fastq
Approx 65% complete for small.ERR034597_2.fastq.trim.2P.fastq
Approx 70% complete for small.ERR034597_2.fastq.trim.2P.fastq
Approx 75% complete for small.ERR034597_2.fastq.trim.2P.fastq
Approx 80% complete for small.ERR034597_2.fastq.trim.2P.fastq
Approx 85% complete for small.ERR034597_2.fastq.trim.2P.fastq
Approx 90% complete for small.ERR034597_2.fastq.trim.2P.fastq
Approx 95% complete for small.ERR034597_2.fastq.trim.2P.fastq
Approx 100% complete for small.ERR034597_2.fastq.trim.2P.fastq
Analysis complete for small.ERR034597_2.fastq.trim.2P.fastq
[job qc2P] Max memory used: 147MiB
[job qc2P] completed success
[step qc2P] completed success
[workflow ] starting step qc1P
[step qc1P] start
[job qc1P] /tmp/isc5zrxx$ fastqc \
    -o \
    . \
    /tmp/tmp2kws4_gr/stgffbcdcf4-db24-4887-b230-2919df5576e0/small.ERR034597_1.fastq.trim.1P.fastq
Started analysis of small.ERR034597_1.fastq.trim.1P.fastq
Approx 5% complete for small.ERR034597_1.fastq.trim.1P.fastq
Approx 10% complete for small.ERR034597_1.fastq.trim.1P.fastq
Approx 15% complete for small.ERR034597_1.fastq.trim.1P.fastq
Approx 20% complete for small.ERR034597_1.fastq.trim.1P.fastq
Approx 25% complete for small.ERR034597_1.fastq.trim.1P.fastq
Approx 30% complete for small.ERR034597_1.fastq.trim.1P.fastq
Approx 35% complete for small.ERR034597_1.fastq.trim.1P.fastq
Approx 40% complete for small.ERR034597_1.fastq.trim.1P.fastq
Approx 45% complete for small.ERR034597_1.fastq.trim.1P.fastq
Approx 50% complete for small.ERR034597_1.fastq.trim.1P.fastq
Approx 55% complete for small.ERR034597_1.fastq.trim.1P.fastq
Approx 60% complete for small.ERR034597_1.fastq.trim.1P.fastq
Approx 65% complete for small.ERR034597_1.fastq.trim.1P.fastq
Approx 70% complete for small.ERR034597_1.fastq.trim.1P.fastq
Approx 75% complete for small.ERR034597_1.fastq.trim.1P.fastq
Approx 80% complete for small.ERR034597_1.fastq.trim.1P.fastq
Approx 85% complete for small.ERR034597_1.fastq.trim.1P.fastq
Approx 90% complete for small.ERR034597_1.fastq.trim.1P.fastq
Approx 95% complete for small.ERR034597_1.fastq.trim.1P.fastq
Approx 100% complete for small.ERR034597_1.fastq.trim.1P.fastq
Analysis complete for small.ERR034597_1.fastq.trim.1P.fastq
[job qc1P] Max memory used: 137MiB
[job qc1P] completed success
[step qc1P] completed success
[workflow ] completed success
{
    "oqc1": {
        "location": "file:///gnu/export/local/home/wrk/izip/git/opensource/cwl/hacchy1983-CWL-workflows/small.ERR034597_1_fastqc.html",
        "basename": "small.ERR034597_1_fastqc.html",
        "class": "File",
        "checksum": "sha1$b7a06f10a759019036d9aa8da4cc08c7b29625b2",
        "size": 231270,
        "path": "/gnu/export/local/home/wrk/izip/git/opensource/cwl/hacchy1983-CWL-workflows/small.ERR034597_1_fastqc.html"
    },
    "oqc1P": {
        "location": "file:///gnu/export/local/home/wrk/izip/git/opensource/cwl/hacchy1983-CWL-workflows/small.ERR034597_1.fastq.trim.1P_fastqc.html",
        "basename": "small.ERR034597_1.fastq.trim.1P_fastqc.html",
        "class": "File",
        "checksum": "sha1$c864cfb5164ec960f845d02e1cae5d89d2ddc60c",
        "size": 231312,
        "path": "/gnu/export/local/home/wrk/izip/git/opensource/cwl/hacchy1983-CWL-workflows/small.ERR034597_1.fastq.trim.1P_fastqc.html"
    },
    "oqc2": {
        "location": "file:///gnu/export/local/home/wrk/izip/git/opensource/cwl/hacchy1983-CWL-workflows/small.ERR034597_2_fastqc.html",
        "basename": "small.ERR034597_2_fastqc.html",
        "class": "File",
        "checksum": "sha1$e42d37813ebb7266cdba4b598adf4fc27c6c181c",
        "size": 260623,
        "path": "/gnu/export/local/home/wrk/izip/git/opensource/cwl/hacchy1983-CWL-workflows/small.ERR034597_2_fastqc.html"
    },
    "oqc2P": {
        "location": "file:///gnu/export/local/home/wrk/izip/git/opensource/cwl/hacchy1983-CWL-workflows/small.ERR034597_2.fastq.trim.2P_fastqc.html",
        "basename": "small.ERR034597_2.fastq.trim.2P_fastqc.html",
        "class": "File",
        "checksum": "sha1$8dfb94c60c348a93c4d7b96b3f7780c18773d625",
        "size": 260665,
        "path": "/gnu/export/local/home/wrk/izip/git/opensource/cwl/hacchy1983-CWL-workflows/small.ERR034597_2.fastq.trim.2P_fastqc.html"
    },
    "sam": {
        "location": "file:///gnu/export/local/home/wrk/izip/git/opensource/cwl/hacchy1983-CWL-workflows/output.sam",
        "basename": "output.sam",
        "class": "File",
        "checksum": "sha1$bc6477fb017cb527c420d1af3df24e0d97eae991",
        "size": 11615554,
        "format": "http://edamontology.org/format_2573",
        "path": "/gnu/export/local/home/wrk/izip/git/opensource/cwl/hacchy1983-CWL-workflows/output.sam"
    }
}
Final process status is success