[0KRunning with gitlab-runner 12.9.0 (4c96e5ad) [0;m[0K on astrocyte-pipeline-tester qAESZL-b [0;msection_start:1623702060:prepare_executor [0K[0K[36;1mPreparing the "shell" executor[0;m [0;m[0KUsing Shell executor... [0;msection_end:1623702060:prepare_executor [0Ksection_start:1623702060:prepare_script [0K[0K[36;1mPreparing environment[0;m [0;mRunning on Nucleus009... section_end:1623702060:prepare_script [0Ksection_start:1623702060: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/cellranger_mkfastq/10215/139137/.git/ [32;1mCreated fresh repository.[0;m From https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq * [new ref] 5326d1be74437f3f736f6a9bc4aaf5c5092ced0f -> refs/pipelines/10215 * [new branch] Vizapp -> origin/Vizapp * [new branch] astrocyte_0.4.0 -> origin/astrocyte_0.4.0 * [new branch] cellranger-4.0.0_ref-2020A -> origin/cellranger-4.0.0_ref-2020A * [new branch] containerize -> origin/containerize * [new branch] develop -> origin/develop * [new branch] master -> origin/master * [new tag] containerized -> containerized * [new tag] publish_1.0.0 -> publish_1.0.0 * [new tag] publish_1.1.4 -> publish_1.1.4 * [new tag] publish_1.2.0 -> publish_1.2.0 * [new tag] publish_1.3.1 -> publish_1.3.1 * [new tag] publish_2.1.5 -> publish_2.1.5 * [new tag] publish_2.2.0 -> publish_2.2.0 * [new tag] test_2.2.0 -> test_2.2.0 * [new tag] test_2.2.0rc2 -> test_2.2.0rc2 * [new tag] test_2.2.0rc3 -> test_2.2.0rc3 * [new tag] test_2.2.0rc4 -> test_2.2.0rc4 * [new tag] test_2.2.0rc5 -> test_2.2.0rc5 [32;1mChecking out 5326d1be as astrocyte_0.4.0...[0;m Removing .tmp/ [32;1mSkipping Git submodules setup[0;m section_end:1623702061:get_sources [0Ksection_start:1623702061:restore_cache [0K[0K[36;1mRestoring cache[0;m [0;msection_end:1623702061:restore_cache [0Ksection_start:1623702061:download_artifacts [0K[0K[36;1mDownloading artifacts[0;m [0;msection_end:1623702061:download_artifacts [0Ksection_start:1623702061:build_script [0K[0K[36;1mRunning before_script and script[0;m [0;m[32;1m$ module load 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) Collecting pytest-cov==2.5.1 Using cached https://files.pythonhosted.org/packages/30/7d/7f6a78ae44a1248ee28cc777586c18b28a1df903470e5d34a6e25712b8aa/pytest_cov-2.5.1-py2.py3-none-any.whl 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: 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: 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: 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: 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: 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: 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) Could not install packages due to an EnvironmentError: [Errno 2] No such file or directory: '/home2/bicf_user/.local/lib/python3.6/site-packages/pytest_cov-2.11.1.dist-info/METADATA' You are using pip version 18.1, however version 21.1.2 is available. You should consider upgrading via the 'pip install --upgrade pip' command. section_end:1623702063:build_script [0Ksection_start:1623702063:after_script [0K[0K[36;1mRunning after_script[0;m [0;msection_end:1623702063:after_script [0Ksection_start:1623702063:upload_artifacts_on_failure [0K[0K[36;1mUploading artifacts for failed job[0;m [0;msection_end:1623702063:upload_artifacts_on_failure [0K[31;1mERROR: Job failed: exit status 1 [0;m