[0KRunning with gitlab-runner 12.9.0 (4c96e5ad)
[0;m[0K on Runner_GUDMAP.RBK zQsjNk-Q
[0;msection_start:1634270741:prepare_executor
[0K[0K[36;1mPreparing the "shell" executor[0;m
[0;m[0KUsing Shell executor...
[0;msection_end:1634270741:prepare_executor
[0Ksection_start:1634270741:prepare_script
[0K[0K[36;1mPreparing environment[0;m
[0;mRunning on Nucleus009...
section_end:1634270741:prepare_script
[0Ksection_start:1634270741:get_sources
[0K[0K[36;1mGetting source from Git repository[0;m
[0;m[32;1mFetching changes...[0;m
Initialized empty Git repository in /project/BICF/BICF_Core/shared/gudmap/runner/zQsjNk-Q/rna-seq/11217/148908/.git/
[32;1mCreated fresh repository.[0;m
From https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq
* [new ref] f9ecbb83c686046f1a688f74eb63dffec8b19527 -> refs/pipelines/11217
* [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
[32;1mChecking out f9ecbb83 as master...[0;m
Removing .tmp/
[32;1mSkipping Git submodules setup[0;m
section_end:1634270744:get_sources
[0Ksection_start:1634270744:restore_cache
[0K[0K[36;1mRestoring cache[0;m
[0;msection_end:1634270744:restore_cache
[0Ksection_start:1634270744:download_artifacts
[0K[0K[36;1mDownloading artifacts[0;m
[0;m[32;1mDownloading artifacts for build_badges (148907)...[0;m
Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=3514 revision[0;m=4c96e5ad version[0;m=12.9.0
Downloading artifacts from coordinator... ok [0;m id[0;m=148907 responseStatus[0;m=200 OK token[0;m=4v9bqWLw
section_end:1634270745:download_artifacts
[0Ksection_start:1634270745:build_script
[0K[0K[36;1mRunning before_script and script[0;m
[0;m[32;1m$ module load python/3.6.4-anaconda[0;m
[32;1m$ pip install --user attrs==20.3.0 pytest==6.2.2 pytest-pythonpath==0.7.3 pytest-cov==2.11.1[0;m
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: 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: 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: 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.
[32;1m$ module load singularity/3.5.3[0;m
[32;1m$ export SINGULARITY_CACHEDIR=${dir}cache/[0;m
[32;1m$ module load nextflow/20.01.0[0;m
[32;1m$ ln -sfn /project/BICF/BICF_Core/shared/gudmap/test_data/* ./test_data/[0;m
[32;1m$ mkdir -p ~/.deriva[0;m
[32;1m$ mkdir -p ~/.bdbag[0;m
[32;1m$ mkdir -p public[0;m
[32;1m$ mv badges/ public/badges/[0;m
section_end:1634270746:build_script
[0Ksection_start:1634270746:after_script
[0K[0K[36;1mRunning after_script[0;m
[0;m[32;1mRunning after script...[0;m
[32;1m$ unset SINGULARITY_CACHEDIR[0;m
section_end:1634270746:after_script
[0Ksection_start:1634270746:archive_cache
[0K[0K[36;1mSaving cache[0;m
[0;msection_end:1634270746:archive_cache
[0Ksection_start:1634270746:upload_artifacts_on_success
[0K[0K[36;1mUploading artifacts for successful job[0;m
[0;m[32;1mUploading artifacts...[0;m
Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=3746 revision[0;m=4c96e5ad version[0;m=12.9.0
public: found 40 matching files [0;m
Uploading artifacts to coordinator... ok [0;m id[0;m=148908 responseStatus[0;m=201 Created token[0;m=H7yR3Suu
section_end:1634270747:upload_artifacts_on_success
[0K[32;1mJob succeeded
[0;m