[0KRunning with gitlab-runner 12.9.0 (4c96e5ad) [0;m[0K on astrocyte-pipeline-tester qAESZL-b [0;msection_start:1621305284:prepare_executor [0K[0K[36;1mPreparing the "shell" executor[0;m [0;m[0KUsing Shell executor... [0;msection_end:1621305284:prepare_executor [0Ksection_start:1621305284:prepare_script [0K[0K[36;1mPreparing environment[0;m [0;mRunning on Nucleus009... section_end:1621305284:prepare_script [0Ksection_start:1621305284: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/9967/137498/.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:1621305285:get_sources [0Ksection_start:1621305285:restore_cache [0K[0K[36;1mRestoring cache[0;m [0;msection_end:1621305285:restore_cache [0Ksection_start:1621305285:download_artifacts [0K[0K[36;1mDownloading artifacts[0;m [0;msection_end:1621305285:download_artifacts [0Ksection_start:1621305285: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: 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: 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: 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: 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: 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) 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) 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$ nextflow run -c workflow/configs/nextflow.config workflow/main.nf -profile biohpc,cluster --bcl "test_data/simple2/*.tar.gz" --designFile "test_data/simple2/cellranger-tiny-bcl-simple-1_2_0.csv" --ci true[0;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 20.01.0 Launching `workflow/main.nf` [dreamy_bassi] - revision: ea5a388fe9 WARN: There's no process matching config selector: trackStart ================================ BICF cellranger_mkfastq Pipeline ================================ Run name : run bcl : test_data/simple2/*.tar.gz Design File : test_data/simple2/cellranger-tiny-bcl-simple-1_2_0.csv Output Directory: /project/BICF/shared/astrocyte_test_ci/qAESZL-b/cellranger_mkfastq/9967/137498/workflow/output -------------------------------- Nextflow Version: 20.01.0 Pipeline Version: 2.2.0-indev.cont Session ID : e256d592-2ad1-43b5-8ea1-bf03f0725328 -------------------------------- Astrocyte : false CI : true Development : false -------------------------------- [- ] process > checkDesignFile - [- ] process > untarBCL - [- ] process > mkfastq - [- ] process > fastqc - [- ] process > versions - [- ] process > multiqc - Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/7wj8TZr1bH6pa executor > local (1), slurm (1) [6b/8869f7] process > checkDesignFile [ 0%] 0 of 1 [ab/e4f03b] process > untarBCL [ 0%] 0 of 2 [- ] process > mkfastq - [- ] process > fastqc - [- ] process > versions - [- ] process > multiqc - Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/7wj8TZr1bH6pa executor > local (1), slurm (2) [6b/8869f7] process > checkDesignFile [ 0%] 0 of 1 [35/731415] process > untarBCL [ 0%] 0 of 2 [- ] process > mkfastq - [- ] process > fastqc - [- ] process > versions - [- ] process > multiqc - Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/7wj8TZr1bH6pa executor > local (1), slurm (2) [6b/8869f7] process > checkDesignFile [100%] 1 of 1 ✔ [35/731415] process > untarBCL [ 0%] 0 of 2 [- ] process > mkfastq - [- ] process > fastqc - [- ] process > versions - [- ] process > multiqc - Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/7wj8TZr1bH6pa executor > local (1), slurm (2) [6b/8869f7] process > checkDesignFile [100%] 1 of 1 ✔ [ab/e4f03b] process > untarBCL [ 50%] 1 of 2 [- ] process > mkfastq - [- ] process > fastqc - [- ] process > versions - [- ] process > multiqc - Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/7wj8TZr1bH6pa executor > local (1), slurm (2) [6b/8869f7] process > checkDesignFile [100%] 1 of 1 ✔ [35/731415] process > untarBCL [100%] 2 of 2 ✔ [- ] process > mkfastq - [- ] process > fastqc - [- ] process > versions - [- ] process > multiqc - Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/7wj8TZr1bH6pa executor > local (1), slurm (4) [6b/8869f7] process > checkDesignFile [100%] 1 of 1 ✔ [35/731415] process > untarBCL [100%] 2 of 2 ✔ [11/b20717] process > mkfastq [ 0%] 0 of 2 [- ] process > fastqc - [- ] process > versions - [- ] process > multiqc - Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/7wj8TZr1bH6pa executor > local (1), slurm (4) [6b/8869f7] process > checkDesignFile [100%] 1 of 1 ✔ [35/731415] process > untarBCL [100%] 2 of 2 ✔ [11/b20717] process > mkfastq [ 0%] 0 of 2 [- ] process > fastqc - [- ] process > versions - [- ] process > multiqc - Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/7wj8TZr1bH6pa executor > local (1), slurm (4) [6b/8869f7] process > checkDesignFile [100%] 1 of 1 ✔ [35/731415] process > untarBCL [100%] 2 of 2 ✔ [ef/ed1ad8] process > mkfastq [ 50%] 1 of 2 [- ] process > fastqc - [- ] process > versions - [- ] process > multiqc - Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/7wj8TZr1bH6pa executor > local (1), slurm (6) [6b/8869f7] process > checkDesignFile [100%] 1 of 1 ✔ [35/731415] process > untarBCL [100%] 2 of 2 ✔ [11/b20717] process > mkfastq [100%] 2 of 2 ✔ [fd/a06062] process > fastqc [ 0%] 0 of 2 [- ] process > versions - [- ] process > multiqc - Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/7wj8TZr1bH6pa executor > local (1), slurm (6) [6b/8869f7] process > checkDesignFile [100%] 1 of 1 ✔ [35/731415] process > untarBCL [100%] 2 of 2 ✔ [11/b20717] process > mkfastq [100%] 2 of 2 ✔ [fd/a06062] process > fastqc [ 0%] 0 of 2 [- ] process > versions - [- ] process > multiqc - Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/7wj8TZr1bH6pa executor > local (2), slurm (6) [6b/8869f7] process > checkDesignFile [100%] 1 of 1 ✔ [35/731415] process > untarBCL [100%] 2 of 2 ✔ [11/b20717] process > mkfastq [100%] 2 of 2 ✔ [fd/a06062] process > fastqc [100%] 2 of 2 ✔ [3f/0a0d02] process > versions [ 0%] 0 of 1 [- ] process > multiqc - Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/7wj8TZr1bH6pa executor > local (3), slurm (6) [6b/8869f7] process > checkDesignFile [100%] 1 of 1 ✔ [35/731415] process > untarBCL [100%] 2 of 2 ✔ [11/b20717] process > mkfastq [100%] 2 of 2 ✔ [fd/a06062] process > fastqc [100%] 2 of 2 ✔ [3f/0a0d02] process > versions [100%] 1 of 1 ✔ [4b/25c11a] process > multiqc [ 0%] 0 of 1 Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/7wj8TZr1bH6pa executor > local (3), slurm (6) [6b/8869f7] process > checkDesignFile [100%] 1 of 1 ✔ [35/731415] process > untarBCL [100%] 2 of 2 ✔ [11/b20717] process > mkfastq [100%] 2 of 2 ✔ [fd/a06062] process > fastqc [100%] 2 of 2 ✔ [3f/0a0d02] process > versions [100%] 1 of 1 ✔ [4b/25c11a] process > multiqc [100%] 1 of 1 ✔ Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/7wj8TZr1bH6pa executor > local (3), slurm (6) [6b/8869f7] process > checkDesignFile [100%] 1 of 1 ✔ [35/731415] process > untarBCL [100%] 2 of 2 ✔ [11/b20717] process > mkfastq [100%] 2 of 2 ✔ [fd/a06062] process > fastqc [100%] 2 of 2 ✔ [3f/0a0d02] process > versions [100%] 1 of 1 ✔ [4b/25c11a] process > multiqc [100%] 1 of 1 ✔ Completed at: 17-May-2021 21:40:38 Duration : 5m 47s CPU hours : (a few seconds) Succeeded : 9 section_end:1621305638:build_script [0Ksection_start:1621305638:after_script [0K[0K[36;1mRunning after_script[0;m [0;msection_end:1621305638:after_script [0Ksection_start:1621305638:archive_cache [0K[0K[36;1mSaving cache[0;m [0;msection_end:1621305639:archive_cache [0Ksection_start:1621305639:upload_artifacts_on_success [0K[0K[36;1mUploading artifacts for successful job[0;m [0;m[32;1mUploading artifacts...[0;m Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=143541 revision[0;m=4c96e5ad version[0;m=12.9.0 .nextflow.log: found 1 matching files [0;m workflow/output/multiqc/run/multiqc_report.html: found 1 matching files[0;m Uploading artifacts to coordinator... ok [0;m id[0;m=137498 responseStatus[0;m=201 Created token[0;m=SEAKfNvV section_end:1621305640:upload_artifacts_on_success [0K[32;1mJob succeeded [0;m