Running with gitlab-runner 12.9.0 (4c96e5ad)
  on astrocyte-pipeline-tester qAESZL-b
section_start:1617033648:prepare_executor
Preparing the "shell" executor
Using Shell executor...
section_end:1617033648:prepare_executor
section_start:1617033648:prepare_script
Preparing environment
Running on Nucleus009...
section_end:1617033648:prepare_script
section_start:1617033648:get_sources
Getting source from Git repository
Fetching changes...
Initialized empty Git repository in /project/BICF/shared/astrocyte_test_ci/qAESZL-b/atacseq_analysis/9687/134263/.git/
Created fresh repository.
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
Checking out 64368529 as master...
Removing .tmp/
Skipping Git submodules setup
section_end:1617033649:get_sources
section_start:1617033649:restore_cache
Restoring cache
section_end:1617033649:restore_cache
section_start:1617033649:download_artifacts
Downloading artifacts
section_end:1617033649:download_artifacts
section_start:1617033649: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 /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.
$ module load  nextflow/0.31.0
$ ln -s /project/shared/bicf_workflow_ref/workflow_testdata/atacseq/*fastq.gz test_data/
$ pytest -m unit --cov=./workflow/scripts
============================= 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
section_start:1617033654:after_script
Running after_script
section_end:1617033654:after_script
section_start:1617033654:archive_cache
Saving cache
section_end:1617033655:archive_cache
section_start:1617033655:upload_artifacts_on_success
Uploading artifacts for successful job
section_end:1617033655:upload_artifacts_on_success
Job succeeded