Running with gitlab-runner 12.9.0 (4c96e5ad)
  on Runner_GUDMAP.RBK zQsjNk-Q
section_start:1634189816:prepare_executor
Preparing the "shell" executor
Using Shell executor...
section_end:1634189816:prepare_executor
section_start:1634189816:prepare_script
Preparing environment
Running on Nucleus009...
section_end:1634189816:prepare_script
section_start:1634189816:get_sources
Getting source from Git repository
Fetching changes...
Initialized empty Git repository in /project/BICF/BICF_Core/shared/gudmap/runner/zQsjNk-Q/rna-seq/11216/148901/.git/
Created fresh repository.
From https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq
 * [new ref]         f9ecbb83c686046f1a688f74eb63dffec8b19527 -> refs/pipelines/11216
 * [new branch]      develop    -> origin/develop
 * [new branch]      master     -> origin/master
 * [new tag]         0.0.2      -> 0.0.2
 * [new tag]         0.0.3      -> 0.0.3
 * [new tag]         0.0.4_indev -> 0.0.4_indev
 * [new tag]         0.1.0      -> 0.1.0
 * [new tag]         aws        -> aws
 * [new tag]         v0.0.1     -> v0.0.1
 * [new tag]         v1.0.0     -> v1.0.0
 * [new tag]         v1.0.1     -> v1.0.1
 * [new tag]         v1.0.2     -> v1.0.2
 * [new tag]         v2.0.0     -> v2.0.0
 * [new tag]         v2.0.0rc01 -> v2.0.0rc01
 * [new tag]         v2.0.0rc02 -> v2.0.0rc02
 * [new tag]         v2.0.1     -> v2.0.1
Checking out f9ecbb83 as master...
Removing .tmp/
Skipping Git submodules setup
section_end:1634189820:get_sources
section_start:1634189820:restore_cache
Restoring cache
section_end:1634189820:restore_cache
section_start:1634189820:download_artifacts
Downloading artifacts
Downloading artifacts for aws (148899)...
Runtime platform                                    arch=amd64 os=linux pid=23553 revision=4c96e5ad version=12.9.0
Downloading artifacts from coordinator... ok        id=148899 responseStatus=200 OK token=NbgYffdW
section_end:1634189820:download_artifacts
section_start:1634189820:build_script
Running before_script and script
$ module load python/3.6.4-anaconda
$ pip install --user attrs==20.3.0 pytest==6.2.2 pytest-pythonpath==0.7.3 pytest-cov==2.11.1
Requirement already satisfied: attrs==20.3.0 in /home2/bicf_user/.local/lib/python3.6/site-packages
Requirement already satisfied: pytest==6.2.2 in /home2/bicf_user/.local/lib/python3.6/site-packages
Requirement already satisfied: pytest-pythonpath==0.7.3 in /home2/bicf_user/.local/lib/python3.6/site-packages
Requirement already satisfied: pytest-cov==2.11.1 in /home2/bicf_user/.local/lib/python3.6/site-packages
Requirement already satisfied: pluggy<1.0.0a1,>=0.12 in /home2/bicf_user/.local/lib/python3.6/site-packages (from pytest==6.2.2)
Requirement already satisfied: toml in /home2/bicf_user/.local/lib/python3.6/site-packages (from pytest==6.2.2)
Requirement already satisfied: py>=1.8.2 in /home2/bicf_user/.local/lib/python3.6/site-packages (from pytest==6.2.2)
Requirement already satisfied: importlib-metadata>=0.12; python_version < "3.8" in /home2/bicf_user/.local/lib/python3.6/site-packages (from pytest==6.2.2)
Requirement already satisfied: packaging in /home2/bicf_user/.local/lib/python3.6/site-packages (from pytest==6.2.2)
Requirement already satisfied: iniconfig in /home2/bicf_user/.local/lib/python3.6/site-packages (from pytest==6.2.2)
Requirement already satisfied: coverage>=5.2.1 in /home2/bicf_user/.local/lib/python3.6/site-packages (from pytest-cov==2.11.1)
Requirement already satisfied: zipp>=0.5 in /home2/bicf_user/.local/lib/python3.6/site-packages (from importlib-metadata>=0.12; python_version < "3.8"->pytest==6.2.2)
Requirement already satisfied: pyparsing>=2.0.2 in /home2/bicf_user/.local/lib/python3.6/site-packages (from packaging->pytest==6.2.2)
Requirement already satisfied: six in /home2/bicf_user/.local/lib/python3.6/site-packages (from packaging->pytest==6.2.2)
You are using pip version 9.0.1, however version 21.3 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
$ module load singularity/3.5.3
$ export SINGULARITY_CACHEDIR=${dir}cache/
$ module load nextflow/20.01.0
$ ln -sfn /project/BICF/BICF_Core/shared/gudmap/test_data/* ./test_data/
$ mkdir -p ~/.deriva
$ mkdir -p ~/.bdbag
$ derivaImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep deriva | cut -d"/" -f2 | cut -d":" -f1)
$ derivaVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep deriva | cut -d"/" -f2 | cut -d":" -f2)
$ echo ${dir}${derivaImg}_${derivaVar}.sif
/project/BICF/BICF_Core/shared/gudmap/singularity_cache/deriva1.4_1.0.1.sif
$ singularity run ${dir}${derivaImg}_${derivaVar}.sif deriva-download-cli --version > version_deriva.txt
$ singularity run ${dir}${derivaImg}_${derivaVar}.sif bdbag --version > version_bdbag.txt
$ pythonImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep python | cut -d"/" -f2 | cut -d":" -f1)
$ pythonVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep python | cut -d"/" -f2 | cut -d":" -f2)
$ echo ${dir}${pythonImg}_${pythonVar}.sif
/project/BICF/BICF_Core/shared/gudmap/singularity_cache/python3_1.0.1.sif
$ singularity run ${dir}${pythonImg}_${pythonVar}.sif python3 --version > version_python.txt
$ fastqcImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep fastqc | cut -d"/" -f2 | cut -d":" -f1)
$ fastqcVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep fastqc | cut -d"/" -f2 | cut -d":" -f2)
$ echo ${dir}${fastqcImg}_${fastqcVar}.sif
/project/BICF/BICF_Core/shared/gudmap/singularity_cache/fastqc0.11.9_1.0.1.sif
$ singularity run ${dir}${fastqcImg}_${fastqcVar}.sif fastqc --version > version_fastqc.txt
Picked up _JAVA_OPTIONS: -Dhttp.proxyHost=proxy.swmed.edu -Dhttp.proxyPort=3128 -Dhttps.proxyHost=proxy.swmed.edu -Dhttps.proxyPort=3128
$ seqwhoImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep seqwho | cut -d"/" -f2 | cut -d":" -f1)
$ seqwhoVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep seqwho | cut -d"/" -f2 | cut -d":" -f2)
$ echo ${dir}${seqwhoImg}_${seqwhoVar}.sif
/project/BICF/BICF_Core/shared/gudmap/singularity_cache/seqwho1.0.0_1.0.0.sif
$ singularity run ${dir}${seqwhoImg}_${seqwhoVar}.sif seqwho.py -h | grep -o Version.* > version_seqwho.txt &
$ trimgaloreImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep trimgalore | cut -d"/" -f2 | cut -d":" -f1)
$ trimgaloreVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep trimgalore | cut -d"/" -f2 | cut -d":" -f2)
$ echo ${dir}${trimgaloreImg}_${trimgaloreVar}.sif
/project/BICF/BICF_Core/shared/gudmap/singularity_cache/trimgalore0.6.6_1.0.0.sif
$ singularity run ${dir}${trimgaloreImg}_${trimgaloreVar}.sif trim_galore --version > version_trimgalore.txt
$ seqtkImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep seqtk | cut -d"/" -f2 | cut -d":" -f1)
$ seqtkVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep seqtk | cut -d"/" -f2 | cut -d":" -f2)
$ echo ${dir}${seqtkImg}_${seqtkVar}.sif
/project/BICF/BICF_Core/shared/gudmap/singularity_cache/seqtk1.3_1.0.1.sif
$ singularity run ${dir}${seqtkImg}_${seqtkVar}.sif seqtk 2>&1 | grep -o Version.* > version_seqtk.txt &
$ rseqcImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep rseqc | cut -d"/" -f2 | cut -d":" -f1)
$ rseqcVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep rseqc | cut -d"/" -f2 | cut -d":" -f2)
$ echo ${dir}${rseqcImg}_${rseqcVar}.sif
/project/BICF/BICF_Core/shared/gudmap/singularity_cache/rseqc4.0.0_1.0.1.sif
$ singularity run ${dir}${rseqcImg}_${rseqcVar}.sif infer_experiment.py --version > version_rseqc.txt
$ hisatImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep hisat | cut -d"/" -f2 | cut -d":" -f1)
$ hisatVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep hisat | cut -d"/" -f2 | cut -d":" -f2)
$ echo ${dir}${hisatImg}_${hisatVar}.sif
/project/BICF/BICF_Core/shared/gudmap/singularity_cache/hisat2.2.1_1.0.1.sif
$ singularity run ${dir}${hisatImg}_${hisatVar}.sif hisat2 --version > version_hisat2.txt
$ singularity run ${dir}${hisatImg}_${hisatVar}.sif samtools --version > version_samtools.txt
$ picardImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep picard | cut -d"/" -f2 | cut -d":" -f1)
$ picardVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep picard | cut -d"/" -f2 | cut -d":" -f2)
$ echo ${dir}${picardImg}_${picardVar}.sif
/project/BICF/BICF_Core/shared/gudmap/singularity_cache/picard2.25.0_1.0.0.sif
$ singularity run ${dir}${picardImg}_${picardVar}.sif java -jar /picard/build/libs/picard.jar MarkDuplicates --version 2> version_markdups.txt &
$ subreadImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep subread | cut -d"/" -f2 | cut -d":" -f1)
$ subreadVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep subread | cut -d"/" -f2 | cut -d":" -f2)
$ echo ${dir}${subreadImg}_${subreadVar}.sif
/project/BICF/BICF_Core/shared/gudmap/singularity_cache/subread2.0.1_1.0.1.sif
$ singularity run ${dir}${subreadImg}_${subreadVar}.sif featureCounts -v &> version_featurecounts.txt
$ singularity run ${dir}${subreadImg}_${subreadVar}.sif R --version > version_r.txt
$ deeptoolsImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep deeptools | cut -d"/" -f2 | cut -d":" -f1)
$ deeptoolsVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep deeptools | cut -d"/" -f2 | cut -d":" -f2)
$ echo ${dir}${deeptoolsImg}_${deeptoolsVar}.sif
/project/BICF/BICF_Core/shared/gudmap/singularity_cache/deeptools3.5.0_1.0.1.sif
$ singularity run ${dir}${deeptoolsImg}_${deeptoolsVar}.sif deeptools --version > version_deeptools.txt
$ multiqcImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep multiqc | cut -d"/" -f2 | cut -d":" -f1)
$ multiqcVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep multiqc | cut -d"/" -f2 | cut -d":" -f2)
$ echo ${dir}${multiqcImg}_${multiqcVar}.sif
/project/BICF/BICF_Core/shared/gudmap/singularity_cache/multiqc1.10_1.0.0.sif
$ singularity run ${dir}${multiqcImg}_${multiqcVar}.sif multiqc --version > version_multiqc.txt
section_end:1634189846:build_script
section_start:1634189846:after_script
Running after_script
Running after script...
$ unset SINGULARITY_CACHEDIR
section_end:1634189846:after_script
section_start:1634189846:archive_cache
Saving cache
section_end:1634189846:archive_cache
section_start:1634189846:upload_artifacts_on_success
Uploading artifacts for successful job
Uploading artifacts...
Runtime platform                                    arch=amd64 os=linux pid=25734 revision=4c96e5ad version=12.9.0
version_deriva.txt: found 1 matching files         
version_bdbag.txt: found 1 matching files          
version_python.txt: found 1 matching files         
version_fastqc.txt: found 1 matching files         
version_seqwho.txt: found 1 matching files         
version_trimgalore.txt: found 1 matching files     
version_seqtk.txt: found 1 matching files          
version_rseqc.txt: found 1 matching files          
version_hisat2.txt: found 1 matching files         
version_samtools.txt: found 1 matching files       
version_markdups.txt: found 1 matching files       
version_featurecounts.txt: found 1 matching files  
version_r.txt: found 1 matching files              
version_deeptools.txt: found 1 matching files      
version_multiqc.txt: found 1 matching files        
Uploading artifacts to coordinator... ok            id=148901 responseStatus=201 Created token=53aBSuzr
section_end:1634189847:upload_artifacts_on_success
Job succeeded