[0KRunning with gitlab-runner 12.9.0 (4c96e5ad) [0;m[0K on astrocyte-pipeline-tester qAESZL-b [0;msection_start:1617033673:prepare_executor [0K[0K[36;1mPreparing the "shell" executor[0;m [0;m[0KUsing Shell executor... [0;msection_end:1617033673:prepare_executor [0Ksection_start:1617033673:prepare_script [0K[0K[36;1mPreparing environment[0;m [0;mRunning on Nucleus009... section_end:1617033673:prepare_script [0Ksection_start:1617033673: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/9687/134265/.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:1617033674:get_sources [0Ksection_start:1617033674:restore_cache [0K[0K[36;1mRestoring cache[0;m [0;msection_end:1617033674:restore_cache [0Ksection_start:1617033674:download_artifacts [0K[0K[36;1mDownloading artifacts[0;m [0;msection_end:1617033674:download_artifacts [0Ksection_start:1617033674: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: 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: 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: 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: 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: 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: 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: 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: 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) 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) 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$ NXF_OPTS="-Dleveldb.mmap=false" nextflow run workflow/main.nf --ci true --dev true[0;m Picked up _JAVA_OPTIONS: -Dhttp.proxyHost=proxy.swmed.edu -Dhttp.proxyPort=3128 -Dhttps.proxyHost=proxy.swmed.edu -Dhttps.proxyPort=3128 [33mWarning: Couldn't create cached classpath folder: /cm/shared/apps/nextflow/0.31.0/tmp/launcher/nextflow-one_0.31.0/Nucleus009 -- Maybe NXF_HOME is not writable?(B[m Picked up _JAVA_OPTIONS: -Dhttp.proxyHost=proxy.swmed.edu -Dhttp.proxyPort=3128 -Dhttps.proxyHost=proxy.swmed.edu -Dhttps.proxyPort=3128 N E X T F L O W ~ version 0.31.0 Launching `workflow/main.nf` [goofy_goldberg] - revision: 912160bc01 [warm up] executor > slurm [warm up] executor > local WARN: The `into` operator should be used to connect two or more target channels -- consider to replace it with `.set { preDiffDesign }` [c3/1c6a77] Submitted process > checkDesignFile (1) [fd/c1fb66] Submitted process > trackStart [3f/7330f5] Submitted process > trimReads (ENCLB170KFO-1) [c9/15682a] Submitted process > trimReads (ENCLB969KTX-3) [00/b959d4] Submitted process > trimReads (ENCLB622FZX-2) [f4/5ea051] Submitted process > alignReads (ENCLB969KTX-3) [43/bfd0e3] Submitted process > alignReads (ENCLB170KFO-1) [d5/f9c02f] Submitted process > alignReads (ENCLB622FZX-2) [42/1bbdb9] Submitted process > filterReads (ENCLB969KTX-3) [cd/4900bc] Submitted process > filterReads (ENCLB170KFO-1) [b8/10f450] Submitted process > filterReads (ENCLB622FZX-2) [65/c2ca3b] Submitted process > convertReads (ENCLB969KTX-3) [3a/337276] Submitted process > convertReads (ENCLB170KFO-1) [77/68b364] Submitted process > crossReads (ENCLB969KTX-3) [82/dddb2e] Submitted process > crossReads (ENCLB170KFO-1) [df/4b705c] Submitted process > convertReads (ENCLB622FZX-2) [e0/8efd6c] Submitted process > crossReads (ENCLB622FZX-2) [c4/cfaa6a] Submitted process > defineExpDesignFiles (1) [6f/00de27] Submitted process > poolAndPsuedoReads (ENCSR265ZXX) [56/e4081c] Submitted process > callPeaksMACS (ENCSR265ZXX_pr2-2_pr) [02/66b6d0] Submitted process > callPeaksMACS (ENCSR265ZXX_pooled-pooled) [11/c604a7] Submitted process > callPeaksMACS (ENCLB170KFO-1) [4a/64db0c] Submitted process > callPeaksMACS (ENCSR265ZXX_pr1-1_pr) [04/a3f39a] Submitted process > callPeaksMACS (ENCLB622FZX-2) [06/8944e6] Submitted process > callPeaksMACS (ENCLB969KTX-3) [1d/7e91f1] Submitted process > consensusPeaks (1) [f2/d26215] Submitted process > peakAnnotation (1) [5f/691f26] Submitted process > experimentQC (1) [a1/d78648] Submitted process > multiqcReport [32;1m$ pytest -m singleend_human[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/9687/134265, configfile: pytest.ini plugins: cov-2.5.1, pythonpath-0.7.1 collected 58 items / 39 deselected / 19 selected workflow/tests/test_annotate_peaks.py . [ 5%] workflow/tests/test_call_peaks_macs.py . [ 10%] workflow/tests/test_check_design.py . [ 15%] workflow/tests/test_convert_reads.py . [ 21%] workflow/tests/test_experiment_qc.py ... [ 36%] workflow/tests/test_generate_software_references.py . [ 42%] workflow/tests/test_generate_software_versions.py . [ 47%] workflow/tests/test_map_qc.py .... [ 68%] workflow/tests/test_map_reads.py . [ 73%] workflow/tests/test_overlap_peaks.py . [ 78%] workflow/tests/test_pool_and_psuedoreplicate.py . [ 84%] workflow/tests/test_trim_reads.py . [ 89%] workflow/tests/test_xcor.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/9687/134265/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/9687/134265/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/9687/134265/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/9687/134265/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/9687/134265/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/9687/134265/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/9687/134265/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/9687/134265/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/9687/134265/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/9687/134265/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/9687/134265/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/9687/134265/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/9687/134265/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/9687/134265/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/9687/134265/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/9687/134265/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/9687/134265/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/9687/134265/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/9687/134265/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/9687/134265/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/9687/134265/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/9687/134265/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/9687/134265/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/9687/134265/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/9687/134265/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/9687/134265/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/9687/134265/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/9687/134265/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/9687/134265/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/9687/134265/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/9687/134265/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/9687/134265/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/9687/134265/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/9687/134265/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/9687/134265/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/9687/134265/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/9687/134265/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/9687/134265/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/9687/134265/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/9687/134265/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/9687/134265/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/9687/134265/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/9687/134265/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/9687/134265/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/9687/134265/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/9687/134265/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/9687/134265/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/9687/134265/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/9687/134265/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/9687/134265/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/9687/134265/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/9687/134265/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/9687/134265/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/9687/134265/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/9687/134265/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/9687/134265/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/9687/134265/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/9687/134265/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 ========== 19 passed, 39 deselected, 59 warnings in 535.50s (0:08:55) ========== section_end:1617047923:build_script [0Ksection_start:1617047923:after_script [0K[0K[36;1mRunning after_script[0;m [0;msection_end:1617047923:after_script [0Ksection_start:1617047923:archive_cache [0K[0K[36;1mSaving cache[0;m [0;msection_end:1617047923:archive_cache [0Ksection_start:1617047923:upload_artifacts_on_success [0K[0K[36;1mUploading artifacts for successful job[0;m [0;msection_end:1617047924:upload_artifacts_on_success [0K[32;1mJob succeeded [0;m