[0KRunning with gitlab-runner 12.9.0 (4c96e5ad) [0;m[0K on astrocyte-pipeline-tester qAESZL-b [0;msection_start:1596205985:prepare_executor [0K[0K[36;1mPreparing the "shell" executor[0;m [0;m[0KUsing Shell executor... [0;msection_end:1596205985:prepare_executor [0Ksection_start:1596205985:prepare_script [0K[0K[36;1mPreparing environment[0;m [0;mRunning on Nucleus009... section_end:1596205985:prepare_script [0Ksection_start:1596205985: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/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/7751/100344/.git/ [32;1mCreated fresh repository.[0;m 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 [32;1mChecking out 66c9f064 as dev...[0;m Removing .tmp/ [32;1mSkipping Git submodules setup[0;m section_end:1596205997:get_sources [0Ksection_start:1596205997:restore_cache [0K[0K[36;1mRestoring cache[0;m [0;msection_end:1596205997:restore_cache [0Ksection_start:1596205997:download_artifacts [0K[0K[36;1mDownloading artifacts[0;m [0;msection_end:1596205997:download_artifacts [0Ksection_start:1596205997:build_script [0K[0K[36;1mRunning before_script and script[0;m [0;m[32;1m$ module add python/3.6.1-2-anaconda[0;m [32;1m$ pip install --user pytest-pythonpath==0.7.1 pytest-cov==2.5.1[0;m 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. [32;1m$ module load nextflow/0.31.0[0;m [32;1m$ ln -s /project/shared/bicf_workflow_ref/workflow_testdata/atacseq/*fastq.gz test_data/[0;m [32;1m$ pytest -m unit --cov=./workflow/scripts[0;m ============================= test session starts ============================== platform linux -- Python 3.6.1, pytest-3.0.7, py-1.4.33, pluggy-0.4.0 rootdir: /project/BICF/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/7751/100344, inifile: pytest.ini plugins: pythonpath-0.7.1, cov-2.5.1 collected 58 items workflow/tests/test_check_design.py ......... workflow/tests/test_overlap_peaks.py . workflow/tests/test_pool_and_psuedoreplicate.py .. workflow/tests/test_utils.py ...... ----------- coverage: platform linux, python 3.6.1-final-0 ----------- Name Stmts Miss Cover ------------------------------------------------------------------ workflow/scripts/atac_qc.py 86 86 0% workflow/scripts/call_peaks_macs.py 123 123 0% workflow/scripts/check_design.py 117 37 68% workflow/scripts/convert_reads.py 68 68 0% workflow/scripts/experiment_design.py 28 15 46% workflow/scripts/experiment_qc.py 141 114 19% workflow/scripts/frip.py 39 39 0% workflow/scripts/generate_references.py 27 27 0% workflow/scripts/generate_versions.py 63 63 0% workflow/scripts/map_qc.py 151 151 0% workflow/scripts/map_reads.py 150 150 0% workflow/scripts/overlap_peaks.py 111 85 23% workflow/scripts/pool_and_psuedoreplicate.py 137 113 18% workflow/scripts/trim_reads.py 72 72 0% workflow/scripts/utils.py 77 36 53% workflow/scripts/xcor.py 68 68 0% ------------------------------------------------------------------ TOTAL 1458 1247 14% ============================= 40 tests deselected ============================== ================== 18 passed, 40 deselected in 15.03 seconds =================== section_end:1596206039:build_script [0Ksection_start:1596206039:after_script [0K[0K[36;1mRunning after_script[0;m [0;msection_end:1596206039:after_script [0Ksection_start:1596206039:archive_cache [0K[0K[36;1mSaving cache[0;m [0;msection_end:1596206039:archive_cache [0Ksection_start:1596206039:upload_artifacts_on_success [0K[0K[36;1mUploading artifacts for successful job[0;m [0;msection_end:1596206039:upload_artifacts_on_success [0K[32;1mJob succeeded [0;m