Running with gitlab-runner 12.9.0 (4c96e5ad)
  on Runner_GUDMAP.RBK zQsjNk-Q
section_start:1634184206:prepare_executor
Preparing the "shell" executor
Using Shell executor...
section_end:1634184206:prepare_executor
section_start:1634184206:prepare_script
Preparing environment
Running on Nucleus009...
section_end:1634184206:prepare_script
section_start:1634184206: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/11214/148888/.git/
Created fresh repository.
From https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq
 * [new ref]         f9ecbb83c686046f1a688f74eb63dffec8b19527 -> refs/pipelines/11214
 * [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:1634184209:get_sources
section_start:1634184209:restore_cache
Restoring cache
section_end:1634184209:restore_cache
section_start:1634184209:download_artifacts
Downloading artifacts
section_end:1634184210:download_artifacts
section_start:1634184210: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: py>=1.8.2 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: iniconfig in /home2/bicf_user/.local/lib/python3.6/site-packages (from pytest==6.2.2)
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: 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: 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: six in /home2/bicf_user/.local/lib/python3.6/site-packages (from packaging->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)
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
$ mkdir -p ${dir}cache/
$ cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | xargs -P 1 -I {} bash -c "singularity pull --dir ${dir} 'docker://'{} || true"
FATAL:   Image file already exists: "/project/BICF/BICF_Core/shared/gudmap/singularity_cache/deeptools3.5.0_1.0.1.sif" - will not overwrite
FATAL:   Image file already exists: "/project/BICF/BICF_Core/shared/gudmap/singularity_cache/deriva1.4_1.0.1.sif" - will not overwrite
FATAL:   Image file already exists: "/project/BICF/BICF_Core/shared/gudmap/singularity_cache/fastqc0.11.9_1.0.1.sif" - will not overwrite
FATAL:   Image file already exists: "/project/BICF/BICF_Core/shared/gudmap/singularity_cache/gudmap-rbk_base_1.0.1.sif" - will not overwrite
FATAL:   Image file already exists: "/project/BICF/BICF_Core/shared/gudmap/singularity_cache/hisat2.2.1_1.0.1.sif" - will not overwrite
FATAL:   Image file already exists: "/project/BICF/BICF_Core/shared/gudmap/singularity_cache/multiqc1.10_1.0.0.sif" - will not overwrite
FATAL:   Image file already exists: "/project/BICF/BICF_Core/shared/gudmap/singularity_cache/picard2.25.0_1.0.0.sif" - will not overwrite
FATAL:   Image file already exists: "/project/BICF/BICF_Core/shared/gudmap/singularity_cache/python3_1.0.1.sif" - will not overwrite
FATAL:   Image file already exists: "/project/BICF/BICF_Core/shared/gudmap/singularity_cache/rseqc4.0.0_1.0.1.sif" - will not overwrite
FATAL:   Image file already exists: "/project/BICF/BICF_Core/shared/gudmap/singularity_cache/seqtk1.3_1.0.1.sif" - will not overwrite
FATAL:   Image file already exists: "/project/BICF/BICF_Core/shared/gudmap/singularity_cache/seqwho1.0.0_1.0.0.sif" - will not overwrite
FATAL:   Image file already exists: "/project/BICF/BICF_Core/shared/gudmap/singularity_cache/subread2.0.1_1.0.1.sif" - will not overwrite
FATAL:   Image file already exists: "/project/BICF/BICF_Core/shared/gudmap/singularity_cache/trimgalore0.6.6_1.0.0.sif" - will not overwrite
$ wait
$ echo images cached
images cached
section_end:1634184211:build_script
section_start:1634184211:after_script
Running after_script
Running after script...
$ unset SINGULARITY_CACHEDIR
section_end:1634184211:after_script
section_start:1634184211:archive_cache
Saving cache
section_end:1634184211:archive_cache
section_start:1634184211:upload_artifacts_on_success
Uploading artifacts for successful job
section_end:1634184212:upload_artifacts_on_success
Job succeeded