[0KRunning with gitlab-runner 12.9.0 (4c96e5ad) [0;m[0K on astrocyte-pipeline-tester qAESZL-b [0;msection_start:1621304943:prepare_executor [0K[0K[36;1mPreparing the "shell" executor[0;m [0;m[0KUsing Shell executor... [0;msection_end:1621304943:prepare_executor [0Ksection_start:1621304943:prepare_script [0K[0K[36;1mPreparing environment[0;m [0;mRunning on Nucleus009... section_end:1621304943:prepare_script [0Ksection_start:1621304943: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/9967/137495/.git/ [32;1mCreated fresh repository.[0;m From https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq * [new ref] e1839b0d0e43bb5b0d786de78ce7246e453b19df -> refs/pipelines/9967 * [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 e1839b0d as astrocyte_0.4.0...[0;m Removing .tmp/ [32;1mSkipping Git submodules setup[0;m section_end:1621304945:get_sources [0Ksection_start:1621304945:restore_cache [0K[0K[36;1mRestoring cache[0;m [0;msection_end:1621304945:restore_cache [0Ksection_start:1621304945:download_artifacts [0K[0K[36;1mDownloading artifacts[0;m [0;msection_end:1621304945:download_artifacts [0Ksection_start:1621304945: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) 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: 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: 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: 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: 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 21.1.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command. [32;1m$ module load nextflow/20.01.0[0;m [32;1m$ module load singularity/3.0.2[0;m [32;1m$ mkdir -p test_data/simple1[0;m [32;1m$ mkdir -p test_data/simple2[0;m [32;1m$ ln -sfn /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_mkfastq/simple1/* test_data/simple1/[0;m [32;1m$ ln -sfn /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_mkfastq/simple2/* test_data/simple2/[0;m [32;1m$ module unload nextflow[0;m [32;1m$ module load astrocyte/0.4.0[0;m [32;1m$ astrocyte_cli check .[0;m [32mINFO Running workflow validation[0m [32mINFO Validating workflow package /project/BICF/shared/astrocyte_test_ci/qAESZL-b/cellranger_mkfastq/9967/137495[0m [33mWARNING Missing vizapp server.r/ui.R - vizapp not enabled.[0m [32mINFO Linting Metadata File /project/BICF/shared/astrocyte_test_ci/qAESZL-b/cellranger_mkfastq/9967/137495/astrocyte_pkg.yml[0m [33mWARNING 19:81 warning line too long (88 > 80 characters) (line-length)[0m [33mWARNING 21:81 warning line too long (167 > 80 characters) (line-length)[0m [33mWARNING 26:81 warning line too long (119 > 80 characters) (line-length)[0m [33mWARNING 28:81 warning line too long (115 > 80 characters) (line-length)[0m [33mWARNING 29:81 warning line too long (120 > 80 characters) (line-length)[0m [33mWARNING 31:81 warning line too long (107 > 80 characters) (line-length)[0m [33mWARNING 32:81 warning line too long (120 > 80 characters) (line-length)[0m [33mWARNING 35:81 warning line too long (118 > 80 characters) (line-length)[0m [33mWARNING 37:81 warning line too long (110 > 80 characters) (line-length)[0m [33mWARNING 39:81 warning line too long (83 > 80 characters) (line-length)[0m [33mWARNING 103:81 warning line too long (140 > 80 characters) (line-length)[0m [33mWARNING 112:81 warning line too long (251 > 80 characters) (line-length)[0m [32mINFO Validating Metadata File /project/BICF/shared/astrocyte_test_ci/qAESZL-b/cellranger_mkfastq/9967/137495/astrocyte_pkg.yml against schema[0m [32mINFO Loading: /project/BICF/shared/astrocyte_test_ci/qAESZL-b/cellranger_mkfastq/9967/137495/astrocyte_pkg.yml[0m [32mINFO Loading: /cm/shared/apps/astrocyte/0.4.0/lib/python3.6/site-packages/astrocyte-0.4.0-py3.6.egg/astrocyte/schema/astrocyte_pkg.jsonschema.yml[0m [32mINFO Metadata is valid[0m [32mINFO Loading: /project/BICF/shared/astrocyte_test_ci/qAESZL-b/cellranger_mkfastq/9967/137495/astrocyte_pkg.yml[0m [32mINFO Found documentation file: index.md at /project/BICF/shared/astrocyte_test_ci/qAESZL-b/cellranger_mkfastq/9967/137495/docs/index.md[0m [32mINFO Validated documentation file: index.md[0m [32mINFO Workflow package /project/BICF/shared/astrocyte_test_ci/qAESZL-b/cellranger_mkfastq/9967/137495 is valid[0m [32mINFO Validation Successful[0m astrocyte_cli - version 0.4.0 ------------------------------- A command line interface for the Astrocyte Workflow System UT Southwestern BioHPC biohpc-help@utsouthwestern.edu section_end:1621304951:build_script [0Ksection_start:1621304951:after_script [0K[0K[36;1mRunning after_script[0;m [0;msection_end:1621304951:after_script [0Ksection_start:1621304951:archive_cache [0K[0K[36;1mSaving cache[0;m [0;msection_end:1621304951:archive_cache [0Ksection_start:1621304951:upload_artifacts_on_success [0K[0K[36;1mUploading artifacts for successful job[0;m [0;msection_end:1621304951:upload_artifacts_on_success [0K[32;1mJob succeeded [0;m