[0KRunning with gitlab-runner 12.9.0 (4c96e5ad) [0;m[0K on astrocyte-pipeline-tester qAESZL-b [0;msection_start:1617033648:prepare_executor [0K[0K[36;1mPreparing the "shell" executor[0;m [0;m[0KUsing Shell executor... [0;msection_end:1617033648:prepare_executor [0Ksection_start:1617033648:prepare_script [0K[0K[36;1mPreparing environment[0;m [0;mRunning on Nucleus009... section_end:1617033648:prepare_script [0Ksection_start:1617033648: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/9687/134263/.git/ [32;1mCreated fresh repository.[0;m From https://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis * [new ref] refs/pipelines/9687 -> refs/pipelines/9687 * [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_2.0.4 -> publish_2.0.4 [32;1mChecking out 64368529 as master...[0;m Removing .tmp/ [32;1mSkipping Git submodules setup[0;m section_end:1617033649:get_sources [0Ksection_start:1617033649:restore_cache [0K[0K[36;1mRestoring cache[0;m [0;msection_end:1617033649:restore_cache [0Ksection_start:1617033649:download_artifacts [0K[0K[36;1mDownloading artifacts[0;m [0;msection_end:1617033649:download_artifacts [0Ksection_start:1617033649: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 /home2/bicf_user/.local/lib/python3.6/site-packages (from pytest-pythonpath==0.7.1) (6.2.2) Requirement already satisfied: coverage>=3.7.1 in /home2/bicf_user/.local/lib/python3.6/site-packages (from pytest-cov==2.5.1) (5.4) Requirement already satisfied: attrs>=19.2.0 in /home2/bicf_user/.local/lib/python3.6/site-packages (from pytest>=2.5.2->pytest-pythonpath==0.7.1) (20.3.0) Requirement already satisfied: importlib-metadata>=0.12; python_version < "3.8" in /home2/bicf_user/.local/lib/python3.6/site-packages (from pytest>=2.5.2->pytest-pythonpath==0.7.1) (1.7.0) Requirement already satisfied: iniconfig in /home2/bicf_user/.local/lib/python3.6/site-packages (from pytest>=2.5.2->pytest-pythonpath==0.7.1) (1.1.1) Requirement already satisfied: packaging in /home2/bicf_user/.local/lib/python3.6/site-packages (from pytest>=2.5.2->pytest-pythonpath==0.7.1) (20.4) Requirement already satisfied: pluggy<1.0.0a1,>=0.12 in /home2/bicf_user/.local/lib/python3.6/site-packages (from pytest>=2.5.2->pytest-pythonpath==0.7.1) (0.13.1) Requirement already satisfied: toml in /home2/bicf_user/.local/lib/python3.6/site-packages (from pytest>=2.5.2->pytest-pythonpath==0.7.1) (0.10.2) Requirement already satisfied: py>=1.8.2 in /home2/bicf_user/.local/lib/python3.6/site-packages (from pytest>=2.5.2->pytest-pythonpath==0.7.1) (1.9.0) 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>=2.5.2->pytest-pythonpath==0.7.1) (3.1.0) Requirement already satisfied: pyparsing>=2.0.2 in /home2/bicf_user/.local/lib/python3.6/site-packages (from packaging->pytest>=2.5.2->pytest-pythonpath==0.7.1) (2.4.7) Requirement already satisfied: six in /home2/bicf_user/.local/lib/python3.6/site-packages (from packaging->pytest>=2.5.2->pytest-pythonpath==0.7.1) (1.15.0) You are using pip version 18.1, however version 21.0.1 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-6.2.2, py-1.9.0, pluggy-0.13.1 rootdir: /project/BICF/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/9687/134263, configfile: pytest.ini plugins: cov-2.5.1, pythonpath-0.7.1 collected 58 items / 40 deselected / 18 selected workflow/tests/test_check_design.py ......... [ 50%] workflow/tests/test_overlap_peaks.py . [ 55%] workflow/tests/test_pool_and_psuedoreplicate.py .. [ 66%] workflow/tests/test_utils.py ...... [100%] =============================== warnings summary =============================== ../../../../../../../../cm/shared/apps/python/3.6.1-2-anaconda/lib/python3.6/site-packages/pandas/util/testing.py:55 /cm/shared/apps/python/3.6.1-2-anaconda/lib/python3.6/site-packages/pandas/util/testing.py:55: PytestUnknownMarkWarning: Unknown pytest.mark.slow - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html slow = pytest.mark.slow workflow/tests/test_annotate_peaks.py:13 /project/BICF/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/9687/134263/workflow/tests/test_annotate_peaks.py:13: PytestUnknownMarkWarning: Unknown pytest.mark.singleend_human - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html @pytest.mark.singleend_human workflow/tests/test_annotate_peaks.py:24 /project/BICF/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/9687/134263/workflow/tests/test_annotate_peaks.py:24: PytestUnknownMarkWarning: Unknown pytest.mark.pairedend_mouse - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html @pytest.mark.pairedend_mouse workflow/tests/test_call_peaks_macs.py:11 /project/BICF/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/9687/134263/workflow/tests/test_call_peaks_macs.py:11: PytestUnknownMarkWarning: Unknown pytest.mark.singleend_human - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html @pytest.mark.singleend_human workflow/tests/test_call_peaks_macs.py:19 /project/BICF/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/9687/134263/workflow/tests/test_call_peaks_macs.py:19: PytestUnknownMarkWarning: Unknown pytest.mark.pairedend_mouse - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html @pytest.mark.pairedend_mouse workflow/tests/test_check_design.py:108 /project/BICF/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/9687/134263/workflow/tests/test_check_design.py:108: PytestUnknownMarkWarning: Unknown pytest.mark.unit - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html @pytest.mark.unit workflow/tests/test_check_design.py:117 /project/BICF/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/9687/134263/workflow/tests/test_check_design.py:117: PytestUnknownMarkWarning: Unknown pytest.mark.unit - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html @pytest.mark.unit workflow/tests/test_check_design.py:126 /project/BICF/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/9687/134263/workflow/tests/test_check_design.py:126: PytestUnknownMarkWarning: Unknown pytest.mark.unit - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html @pytest.mark.unit workflow/tests/test_check_design.py:134 /project/BICF/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/9687/134263/workflow/tests/test_check_design.py:134: PytestUnknownMarkWarning: Unknown pytest.mark.unit - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html @pytest.mark.unit workflow/tests/test_check_design.py:141 /project/BICF/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/9687/134263/workflow/tests/test_check_design.py:141: PytestUnknownMarkWarning: Unknown pytest.mark.unit - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html @pytest.mark.unit workflow/tests/test_check_design.py:148 /project/BICF/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/9687/134263/workflow/tests/test_check_design.py:148: PytestUnknownMarkWarning: Unknown pytest.mark.unit - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html @pytest.mark.unit workflow/tests/test_check_design.py:156 /project/BICF/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/9687/134263/workflow/tests/test_check_design.py:156: PytestUnknownMarkWarning: Unknown pytest.mark.unit - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html @pytest.mark.unit workflow/tests/test_check_design.py:164 /project/BICF/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/9687/134263/workflow/tests/test_check_design.py:164: PytestUnknownMarkWarning: Unknown pytest.mark.unit - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html @pytest.mark.unit workflow/tests/test_check_design.py:172 /project/BICF/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/9687/134263/workflow/tests/test_check_design.py:172: PytestUnknownMarkWarning: Unknown pytest.mark.unit - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html @pytest.mark.unit workflow/tests/test_check_design.py:179 /project/BICF/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/9687/134263/workflow/tests/test_check_design.py:179: PytestUnknownMarkWarning: Unknown pytest.mark.singleend_human - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html @pytest.mark.singleend_human workflow/tests/test_check_design.py:187 /project/BICF/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/9687/134263/workflow/tests/test_check_design.py:187: PytestUnknownMarkWarning: Unknown pytest.mark.pairedend_mouse - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html @pytest.mark.pairedend_mouse workflow/tests/test_convert_reads.py:10 /project/BICF/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/9687/134263/workflow/tests/test_convert_reads.py:10: PytestUnknownMarkWarning: Unknown pytest.mark.singleend_human - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html @pytest.mark.singleend_human workflow/tests/test_convert_reads.py:15 /project/BICF/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/9687/134263/workflow/tests/test_convert_reads.py:15: PytestUnknownMarkWarning: Unknown pytest.mark.pairedend_mouse - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html @pytest.mark.pairedend_mouse workflow/tests/test_experiment_design.py:28 /project/BICF/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/9687/134263/workflow/tests/test_experiment_design.py:28: PytestUnknownMarkWarning: Unknown pytest.mark.integration - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html @pytest.mark.integration workflow/tests/test_experiment_design.py:36 /project/BICF/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/9687/134263/workflow/tests/test_experiment_design.py:36: PytestUnknownMarkWarning: Unknown pytest.mark.integration - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html @pytest.mark.integration workflow/tests/test_experiment_qc.py:26 /project/BICF/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/9687/134263/workflow/tests/test_experiment_qc.py:26: PytestUnknownMarkWarning: Unknown pytest.mark.singleend_human - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html @pytest.mark.singleend_human workflow/tests/test_experiment_qc.py:33 /project/BICF/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/9687/134263/workflow/tests/test_experiment_qc.py:33: PytestUnknownMarkWarning: Unknown pytest.mark.singleend_human - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html @pytest.mark.singleend_human workflow/tests/test_experiment_qc.py:39 /project/BICF/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/9687/134263/workflow/tests/test_experiment_qc.py:39: PytestUnknownMarkWarning: Unknown pytest.mark.singleend_human - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html @pytest.mark.singleend_human workflow/tests/test_experiment_qc.py:45 /project/BICF/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/9687/134263/workflow/tests/test_experiment_qc.py:45: PytestUnknownMarkWarning: Unknown pytest.mark.pairedend_mouse - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html @pytest.mark.pairedend_mouse workflow/tests/test_experiment_qc.py:55 /project/BICF/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/9687/134263/workflow/tests/test_experiment_qc.py:55: PytestUnknownMarkWarning: Unknown pytest.mark.pairedend_mouse - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html @pytest.mark.pairedend_mouse workflow/tests/test_experiment_qc.py:61 /project/BICF/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/9687/134263/workflow/tests/test_experiment_qc.py:61: PytestUnknownMarkWarning: Unknown pytest.mark.pairedend_mouse - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html @pytest.mark.pairedend_mouse workflow/tests/test_generate_software_references.py:14 /project/BICF/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/9687/134263/workflow/tests/test_generate_software_references.py:14: PytestUnknownMarkWarning: Unknown pytest.mark.singleend_human - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html @pytest.mark.singleend_human workflow/tests/test_generate_software_references.py:32 /project/BICF/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/9687/134263/workflow/tests/test_generate_software_references.py:32: PytestUnknownMarkWarning: Unknown pytest.mark.pairedend_mouse - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html @pytest.mark.pairedend_mouse workflow/tests/test_generate_software_versions.py:12 /project/BICF/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/9687/134263/workflow/tests/test_generate_software_versions.py:12: PytestUnknownMarkWarning: Unknown pytest.mark.singleend_human - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html @pytest.mark.singleend_human workflow/tests/test_generate_software_versions.py:22 /project/BICF/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/9687/134263/workflow/tests/test_generate_software_versions.py:22: PytestUnknownMarkWarning: Unknown pytest.mark.pairedend_mouse - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html @pytest.mark.pairedend_mouse workflow/tests/test_map_qc.py:11 /project/BICF/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/9687/134263/workflow/tests/test_map_qc.py:11: PytestUnknownMarkWarning: Unknown pytest.mark.singleend_human - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html @pytest.mark.singleend_human workflow/tests/test_map_qc.py:17 /project/BICF/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/9687/134263/workflow/tests/test_map_qc.py:17: PytestUnknownMarkWarning: Unknown pytest.mark.singleend_human - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html @pytest.mark.singleend_human workflow/tests/test_map_qc.py:24 /project/BICF/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/9687/134263/workflow/tests/test_map_qc.py:24: PytestUnknownMarkWarning: Unknown pytest.mark.singleend_human - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html @pytest.mark.singleend_human workflow/tests/test_map_qc.py:32 /project/BICF/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/9687/134263/workflow/tests/test_map_qc.py:32: PytestUnknownMarkWarning: Unknown pytest.mark.singleend_human - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html @pytest.mark.singleend_human workflow/tests/test_map_qc.py:40 /project/BICF/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/9687/134263/workflow/tests/test_map_qc.py:40: PytestUnknownMarkWarning: Unknown pytest.mark.pairedend_mouse - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html @pytest.mark.pairedend_mouse workflow/tests/test_map_qc.py:46 /project/BICF/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/9687/134263/workflow/tests/test_map_qc.py:46: PytestUnknownMarkWarning: Unknown pytest.mark.pairedend_mouse - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html @pytest.mark.pairedend_mouse workflow/tests/test_map_qc.py:53 /project/BICF/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/9687/134263/workflow/tests/test_map_qc.py:53: PytestUnknownMarkWarning: Unknown pytest.mark.pairedend_mouse - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html @pytest.mark.pairedend_mouse workflow/tests/test_map_qc.py:61 /project/BICF/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/9687/134263/workflow/tests/test_map_qc.py:61: PytestUnknownMarkWarning: Unknown pytest.mark.pairedend_mouse - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html @pytest.mark.pairedend_mouse workflow/tests/test_map_reads.py:10 /project/BICF/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/9687/134263/workflow/tests/test_map_reads.py:10: PytestUnknownMarkWarning: Unknown pytest.mark.pairedend_mouse - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html @pytest.mark.pairedend_mouse workflow/tests/test_map_reads.py:20 /project/BICF/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/9687/134263/workflow/tests/test_map_reads.py:20: PytestUnknownMarkWarning: Unknown pytest.mark.singleend_human - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html @pytest.mark.singleend_human workflow/tests/test_overlap_peaks.py:28 /project/BICF/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/9687/134263/workflow/tests/test_overlap_peaks.py:28: PytestUnknownMarkWarning: Unknown pytest.mark.unit - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html @pytest.mark.unit workflow/tests/test_overlap_peaks.py:35 /project/BICF/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/9687/134263/workflow/tests/test_overlap_peaks.py:35: PytestUnknownMarkWarning: Unknown pytest.mark.singleend_human - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html @pytest.mark.singleend_human workflow/tests/test_overlap_peaks.py:45 /project/BICF/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/9687/134263/workflow/tests/test_overlap_peaks.py:45: PytestUnknownMarkWarning: Unknown pytest.mark.pairedend_mouse - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html @pytest.mark.pairedend_mouse workflow/tests/test_pool_and_psuedoreplicate.py:32 /project/BICF/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/9687/134263/workflow/tests/test_pool_and_psuedoreplicate.py:32: PytestUnknownMarkWarning: Unknown pytest.mark.unit - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html @pytest.mark.unit workflow/tests/test_pool_and_psuedoreplicate.py:38 /project/BICF/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/9687/134263/workflow/tests/test_pool_and_psuedoreplicate.py:38: PytestUnknownMarkWarning: Unknown pytest.mark.unit - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html @pytest.mark.unit workflow/tests/test_pool_and_psuedoreplicate.py:44 /project/BICF/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/9687/134263/workflow/tests/test_pool_and_psuedoreplicate.py:44: PytestUnknownMarkWarning: Unknown pytest.mark.singleend_human - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html @pytest.mark.singleend_human workflow/tests/test_pool_and_psuedoreplicate.py:51 /project/BICF/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/9687/134263/workflow/tests/test_pool_and_psuedoreplicate.py:51: PytestUnknownMarkWarning: Unknown pytest.mark.pairedend_mouse - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html @pytest.mark.pairedend_mouse workflow/tests/test_trim_reads.py:13 /project/BICF/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/9687/134263/workflow/tests/test_trim_reads.py:13: PytestUnknownMarkWarning: Unknown pytest.mark.pairedend_mouse - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html @pytest.mark.pairedend_mouse workflow/tests/test_trim_reads.py:36 /project/BICF/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/9687/134263/workflow/tests/test_trim_reads.py:36: PytestUnknownMarkWarning: Unknown pytest.mark.singleend_human - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html @pytest.mark.singleend_human workflow/tests/test_utils.py:32 /project/BICF/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/9687/134263/workflow/tests/test_utils.py:32: PytestUnknownMarkWarning: Unknown pytest.mark.unit - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html @pytest.mark.unit workflow/tests/test_utils.py:41 /project/BICF/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/9687/134263/workflow/tests/test_utils.py:41: PytestUnknownMarkWarning: Unknown pytest.mark.unit - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html @pytest.mark.unit workflow/tests/test_utils.py:50 /project/BICF/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/9687/134263/workflow/tests/test_utils.py:50: PytestUnknownMarkWarning: Unknown pytest.mark.unit - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html @pytest.mark.unit workflow/tests/test_utils.py:60 /project/BICF/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/9687/134263/workflow/tests/test_utils.py:60: PytestUnknownMarkWarning: Unknown pytest.mark.unit - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html @pytest.mark.unit workflow/tests/test_utils.py:66 /project/BICF/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/9687/134263/workflow/tests/test_utils.py:66: PytestUnknownMarkWarning: Unknown pytest.mark.unit - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html @pytest.mark.unit workflow/tests/test_utils.py:72 /project/BICF/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/9687/134263/workflow/tests/test_utils.py:72: PytestUnknownMarkWarning: Unknown pytest.mark.unit - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html @pytest.mark.unit workflow/tests/test_xcor.py:11 /project/BICF/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/9687/134263/workflow/tests/test_xcor.py:11: PytestUnknownMarkWarning: Unknown pytest.mark.singleend_human - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html @pytest.mark.singleend_human workflow/tests/test_xcor.py:16 /project/BICF/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/9687/134263/workflow/tests/test_xcor.py:16: PytestUnknownMarkWarning: Unknown pytest.mark.singleend_human - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html @pytest.mark.singleend_human workflow/tests/test_xcor.py:25 /project/BICF/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/9687/134263/workflow/tests/test_xcor.py:25: PytestUnknownMarkWarning: Unknown pytest.mark.pairedend_mouse - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html @pytest.mark.pairedend_mouse workflow/tests/test_xcor.py:30 /project/BICF/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/9687/134263/workflow/tests/test_xcor.py:30: PytestUnknownMarkWarning: Unknown pytest.mark.pairedend_mouse - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html @pytest.mark.pairedend_mouse -- Docs: https://docs.pytest.org/en/stable/warnings.html ----------- 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% ================ 18 passed, 40 deselected, 59 warnings in 2.42s ================ section_end:1617033654:build_script [0Ksection_start:1617033654:after_script [0K[0K[36;1mRunning after_script[0;m [0;msection_end:1617033654:after_script [0Ksection_start:1617033654:archive_cache [0K[0K[36;1mSaving cache[0;m [0;msection_end:1617033655:archive_cache [0Ksection_start:1617033655:upload_artifacts_on_success [0K[0K[36;1mUploading artifacts for successful job[0;m [0;msection_end:1617033655:upload_artifacts_on_success [0K[32;1mJob succeeded [0;m