simple_2FC
Venkat Malladi
1Running with gitlab-runner 12.9.0 (4c96e5ad)2 on astrocyte-pipeline-tester qAESZL-b4Using Shell executor...6Running on Nucleus009...8Fetching changes...9Initialized empty Git repository in /project/BICF/shared/astrocyte_test_ci/qAESZL-b/cellranger_mkfastq/10212/139116/.git/10Created fresh repository.12 * [new ref] 52c52f084b9e16c83a685e60e7646cd2f1782fd7 -> refs/pipelines/1021213 * [new branch] Vizapp -> origin/Vizapp14 * [new branch] astrocyte_0.4.0 -> origin/astrocyte_0.4.015 * [new branch] cellranger-4.0.0_ref-2020A -> origin/cellranger-4.0.0_ref-2020A16 * [new branch] containerize -> origin/containerize17 * [new branch] develop -> origin/develop18 * [new branch] master -> origin/master19 * [new tag] containerized -> containerized20 * [new tag] publish_1.0.0 -> publish_1.0.021 * [new tag] publish_1.1.4 -> publish_1.1.422 * [new tag] publish_1.2.0 -> publish_1.2.023 * [new tag] publish_1.3.1 -> publish_1.3.124 * [new tag] publish_2.1.5 -> publish_2.1.525 * [new tag] publish_2.2.0 -> publish_2.2.026 * [new tag] test_2.2.0 -> test_2.2.027 * [new tag] test_2.2.0rc2 -> test_2.2.0rc228 * [new tag] test_2.2.0rc3 -> test_2.2.0rc329 * [new tag] test_2.2.0rc4 -> test_2.2.0rc430 * [new tag] test_2.2.0rc5 -> test_2.2.0rc531Checking out 52c52f08 as astrocyte_0.4.0...32Removing .tmp/33Skipping Git submodules setup37$ module load python/3.6.1-2-anaconda38$ pip install --user pytest-pythonpath==0.7.1 pytest-cov==2.5.139Requirement already satisfied: pytest-pythonpath==0.7.1 in /home2/bicf_user/.local/lib/python3.6/site-packages (0.7.1)40Requirement already satisfied: pytest-cov==2.5.1 in /home2/bicf_user/.local/lib/python3.6/site-packages (2.5.1)41Requirement 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)42Requirement already satisfied: coverage>=3.7.1 in /home2/bicf_user/.local/lib/python3.6/site-packages (from pytest-cov==2.5.1) (5.4)43Requirement 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)44Requirement 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)45Requirement 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)46Requirement 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)47Requirement 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)48Requirement 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)49Requirement 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)50Requirement 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)51Requirement 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)52Requirement 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)53You are using pip version 18.1, however version 21.1.2 is available.54You should consider upgrading via the 'pip install --upgrade pip' command.55$ module load nextflow/20.01.056$ module load singularity/3.5.357$ mkdir -p test_data/simple158$ mkdir -p test_data/simple259$ ln -sfn /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_mkfastq/simple1/* test_data/simple1/60$ ln -sfn /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_mkfastq/simple2/* test_data/simple2/61$ 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 true62Picked up _JAVA_OPTIONS: -Dhttp.proxyHost=proxy.swmed.edu -Dhttp.proxyPort=3128 -Dhttps.proxyHost=proxy.swmed.edu -Dhttps.proxyPort=312863N E X T F L O W ~ version 20.01.064Launching `workflow/main.nf` [focused_shannon] - revision: ea5a388fe965WARN: There's no process matching config selector: trackStart66================================67BICF cellranger_mkfastq Pipeline68================================69Run name : run70bcl : test_data/simple2/*.tar.gz71Design File : test_data/simple2/cellranger-tiny-bcl-simple-1_2_0.csv72Output Directory: /project/BICF/shared/astrocyte_test_ci/qAESZL-b/cellranger_mkfastq/10212/139116/workflow/output73--------------------------------74Nextflow Version: 20.01.075Pipeline Version: 2.2.0-indev.cont76Session ID : 3027ec8f-9d93-4506-9270-a167c9b171c077--------------------------------78Astrocyte : false79CI : true80Development : false81--------------------------------82[- ] process > checkDesignFile -83[- ] process > checkDesignFile [ 0%] 0 of 184[- ] process > untarBCL [ 0%] 0 of 185[- ] process > mkfastq -86[- ] process > fastqc -87[- ] process > versions -88[- ] process > multiqc -89Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/36UzkDKOKNSx3990[b1/cfb3b8] process > checkDesignFile [ 0%] 0 of 191[- ] process > untarBCL [ 0%] 0 of 292[- ] process > mkfastq -93[- ] process > fastqc -94[- ] process > versions -95[- ] process > multiqc -96Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/36UzkDKOKNSx3997executor > local (1), slurm (2)98[b1/cfb3b8] process > checkDesignFile [ 0%] 0 of 199[c2/652727] process > untarBCL [ 0%] 0 of 2100[- ] process > mkfastq -101[- ] process > fastqc -102[- ] process > versions -103[- ] process > multiqc -104Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/36UzkDKOKNSx39105executor > local (1), slurm (2)106[b1/cfb3b8] process > checkDesignFile [100%] 1 of 1 ✔107[c2/652727] process > untarBCL [ 0%] 0 of 2108[- ] process > mkfastq -109[- ] process > fastqc -110[- ] process > versions -111[- ] process > multiqc -112Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/36UzkDKOKNSx39113executor > local (1), slurm (2)114[b1/cfb3b8] process > checkDesignFile [100%] 1 of 1 ✔115[c2/652727] process > untarBCL [ 50%] 1 of 2116[- ] process > mkfastq -117[- ] process > fastqc -118[- ] process > versions -119[- ] process > multiqc -120Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/36UzkDKOKNSx39121executor > local (1), slurm (4)122[b1/cfb3b8] process > checkDesignFile [100%] 1 of 1 ✔123[79/595c11] process > untarBCL [100%] 2 of 2 ✔124[3c/0a6aab] process > mkfastq [ 0%] 0 of 2125[- ] process > fastqc -126[- ] process > versions -127[- ] process > multiqc -128Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/36UzkDKOKNSx39129executor > local (1), slurm (4)130[b1/cfb3b8] process > checkDesignFile [100%] 1 of 1 ✔131[79/595c11] process > untarBCL [100%] 2 of 2 ✔132[3c/0a6aab] process > mkfastq [ 0%] 0 of 2133[- ] process > fastqc -134[- ] process > versions -135[- ] process > multiqc -136Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/36UzkDKOKNSx39137executor > local (1), slurm (4)138[b1/cfb3b8] process > checkDesignFile [100%] 1 of 1 ✔139[79/595c11] process > untarBCL [100%] 2 of 2 ✔140[0d/fab7cd] process > mkfastq [ 50%] 1 of 2141[- ] process > fastqc -142[- ] process > versions -143[- ] process > multiqc -144Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/36UzkDKOKNSx39145executor > local (1), slurm (4)146[b1/cfb3b8] process > checkDesignFile [100%] 1 of 1 ✔147[79/595c11] process > untarBCL [100%] 2 of 2 ✔148[3c/0a6aab] process > mkfastq [100%] 2 of 2 ✔149[- ] process > fastqc -150[- ] process > versions -151[- ] process > multiqc -152Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/36UzkDKOKNSx39153executor > local (1), slurm (4)154[b1/cfb3b8] process > checkDesignFile [100%] 1 of 1 ✔155[79/595c11] process > untarBCL [100%] 2 of 2 ✔156[3c/0a6aab] process > mkfastq [100%] 2 of 2 ✔157[- ] process > fastqc [ 0%] 0 of 1158[- ] process > versions -159[- ] process > multiqc -160Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/36UzkDKOKNSx39161executor > local (1), slurm (4)162[b1/cfb3b8] process > checkDesignFile [100%] 1 of 1 ✔163[79/595c11] process > untarBCL [100%] 2 of 2 ✔164[3c/0a6aab] process > mkfastq [100%] 2 of 2 ✔165[- ] process > fastqc [ 0%] 0 of 2166[- ] process > versions -167[- ] process > multiqc -168Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/36UzkDKOKNSx39169executor > local (1), slurm (5)170[b1/cfb3b8] process > checkDesignFile [100%] 1 of 1 ✔171[79/595c11] process > untarBCL [100%] 2 of 2 ✔172[3c/0a6aab] process > mkfastq [100%] 2 of 2 ✔173[a6/f4a21f] process > fastqc [ 0%] 0 of 2174[- ] process > versions -175[- ] process > multiqc -176Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/36UzkDKOKNSx39177executor > local (1), slurm (6)178[b1/cfb3b8] process > checkDesignFile [100%] 1 of 1 ✔179[79/595c11] process > untarBCL [100%] 2 of 2 ✔180[3c/0a6aab] process > mkfastq [100%] 2 of 2 ✔181[ce/60ee8e] process > fastqc [ 0%] 0 of 2182[- ] process > versions -183[- ] process > multiqc -184Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/36UzkDKOKNSx39185executor > local (1), slurm (6)186[b1/cfb3b8] process > checkDesignFile [100%] 1 of 1 ✔187[79/595c11] process > untarBCL [100%] 2 of 2 ✔188[3c/0a6aab] process > mkfastq [100%] 2 of 2 ✔189[ce/60ee8e] process > fastqc [ 0%] 0 of 2190[- ] process > versions -191[- ] process > multiqc -192Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/36UzkDKOKNSx39193executor > local (2), slurm (6)194[b1/cfb3b8] process > checkDesignFile [100%] 1 of 1 ✔195[79/595c11] process > untarBCL [100%] 2 of 2 ✔196[3c/0a6aab] process > mkfastq [100%] 2 of 2 ✔197[ce/60ee8e] process > fastqc [100%] 2 of 2 ✔198[1d/8c4d24] process > versions [ 0%] 0 of 1199[- ] process > multiqc -200Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/36UzkDKOKNSx39201executor > local (2), slurm (6)202[b1/cfb3b8] process > checkDesignFile [100%] 1 of 1 ✔203[79/595c11] process > untarBCL [100%] 2 of 2 ✔204[3c/0a6aab] process > mkfastq [100%] 2 of 2 ✔205[ce/60ee8e] process > fastqc [100%] 2 of 2 ✔206[1d/8c4d24] process > versions [100%] 1 of 1 ✔207[- ] process > multiqc -208Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/36UzkDKOKNSx39209executor > local (3), slurm (6)210[b1/cfb3b8] process > checkDesignFile [100%] 1 of 1 ✔211[79/595c11] process > untarBCL [100%] 2 of 2 ✔212[3c/0a6aab] process > mkfastq [100%] 2 of 2 ✔213[ce/60ee8e] process > fastqc [100%] 2 of 2 ✔214[1d/8c4d24] process > versions [100%] 1 of 1 ✔215[a4/642caa] process > multiqc [ 0%] 0 of 1216Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/36UzkDKOKNSx39217executor > local (3), slurm (6)218[b1/cfb3b8] process > checkDesignFile [100%] 1 of 1 ✔219[79/595c11] process > untarBCL [100%] 2 of 2 ✔220[3c/0a6aab] process > mkfastq [100%] 2 of 2 ✔221[ce/60ee8e] process > fastqc [100%] 2 of 2 ✔222[1d/8c4d24] process > versions [100%] 1 of 1 ✔223[a4/642caa] process > multiqc [ 0%] 0 of 1224Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/36UzkDKOKNSx39225executor > local (3), slurm (6)226[b1/cfb3b8] process > checkDesignFile [100%] 1 of 1 ✔227[79/595c11] process > untarBCL [100%] 2 of 2 ✔228[3c/0a6aab] process > mkfastq [100%] 2 of 2 ✔229[ce/60ee8e] process > fastqc [100%] 2 of 2 ✔230[1d/8c4d24] process > versions [100%] 1 of 1 ✔231[a4/642caa] process > multiqc [100%] 1 of 1 ✔232Monitor the execution with Nextflow Tower using this url https://tower.nf/watch/36UzkDKOKNSx39233executor > local (3), slurm (6)234[b1/cfb3b8] process > checkDesignFile [100%] 1 of 1 ✔235[79/595c11] process > untarBCL [100%] 2 of 2 ✔236[3c/0a6aab] process > mkfastq [100%] 2 of 2 ✔237[ce/60ee8e] process > fastqc [100%] 2 of 2 ✔238[1d/8c4d24] process > versions [100%] 1 of 1 ✔239[a4/642caa] process > multiqc [100%] 1 of 1 ✔240Completed at: 14-Jun-2021 09:08:37241Duration : 5m 35s242CPU hours : (a few seconds)243Succeeded : 9247Uploading artifacts...252Job succeeded