Running with gitlab-runner 12.9.0 (4c96e5ad)
  on astrocyte-pipeline-tester qAESZL-b
section_start:1596206042:prepare_executor
Preparing the "shell" executor
Using Shell executor...
section_end:1596206042:prepare_executor
section_start:1596206042:prepare_script
Preparing environment
Running on Nucleus009...
section_end:1596206042:prepare_script
section_start:1596206042:get_sources
Getting source from Git repository
Fetching changes...
Initialized empty Git repository in /project/BICF/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/7751/100345/.git/
Created fresh repository.
From https://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis
 * [new ref]         refs/pipelines/7751 -> refs/pipelines/7751
 * [new branch]      36-UpdateNextflow -> origin/36-UpdateNextflow
 * [new branch]      dev        -> origin/dev
 * [new branch]      master     -> origin/master
 * [new tag]         publish_1.0.0 -> publish_1.0.0
 * [new tag]         publish_2.0.3 -> publish_2.0.3
 * [new tag]         publish_2.0.4rc1 -> publish_2.0.4rc1
Checking out 66c9f064 as dev...
Removing .tmp/
Skipping Git submodules setup
section_end:1596206050:get_sources
section_start:1596206050:restore_cache
Restoring cache
section_end:1596206050:restore_cache
section_start:1596206050:download_artifacts
Downloading artifacts
section_end:1596206050:download_artifacts
section_start:1596206050:build_script
Running before_script and script
$ module add  python/3.6.1-2-anaconda
$ pip install --user pytest-pythonpath==0.7.1 pytest-cov==2.5.1
Requirement already satisfied: pytest-pythonpath==0.7.1 in /home2/bicf_user/.local/lib/python3.6/site-packages (0.7.1)
Requirement already satisfied: pytest-cov==2.5.1 in /home2/bicf_user/.local/lib/python3.6/site-packages (2.5.1)
Requirement already satisfied: pytest>=2.5.2 in /cm/shared/apps/python/3.6.1-2-anaconda/lib/python3.6/site-packages (from pytest-pythonpath==0.7.1) (3.0.7)
Requirement already satisfied: coverage>=3.7.1 in /home2/bicf_user/.local/lib/python3.6/site-packages (from pytest-cov==2.5.1) (4.5.2)
Requirement already satisfied: py>=1.4.29 in /cm/shared/apps/python/3.6.1-2-anaconda/lib/python3.6/site-packages (from pytest>=2.5.2->pytest-pythonpath==0.7.1) (1.4.33)
Requirement already satisfied: setuptools in /cm/shared/apps/python/3.6.1-2-anaconda/lib/python3.6/site-packages (from pytest>=2.5.2->pytest-pythonpath==0.7.1) (40.6.2)
You are using pip version 18.1, however version 20.2b1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
$ module load  nextflow/0.31.0
$ ln -s /project/shared/bicf_workflow_ref/workflow_testdata/atacseq/*fastq.gz test_data/
$ module load astrocyte/0.3.1
$ module unload nextflow
$ cd ..
$ astrocyte_cli validate atacseq_analysis
astrocyte_cli - version 0.3.1
-------------------------------
A command line interface for the Astrocyte Workflow System
D. C. Trudgian, UT Southwestern BioHPC
biohpc-help@utsouthwestern.edu

ERROR    [OSError] Workflow package directory atacseq_analysis not found.


section_end:1596206069:build_script
section_start:1596206069:after_script
Running after_script
section_end:1596206069:after_script
section_start:1596206069:archive_cache
Saving cache
section_end:1596206069:archive_cache
section_start:1596206069:upload_artifacts_on_success
Uploading artifacts for successful job
section_end:1596206070:upload_artifacts_on_success
Job succeeded