### Pipeline run code and environment: * Command: `/home/mjs5kd/.local/bin/refgenie build mm10_primary/fasta --files fasta=/project/shefflab/www/refgenie_refgenomes.databio.org/mm10_primary-fasta-fasta` * Compute host: udc-aw34-18c0 * Working dir: /sfs/qumulo/qproject/shefflab/deploy/rg.databio.org_full/rg.databio.org * Outfolder: /project/shefflab/deploy/rg.databio.org_full/genomes/data/bfdbdd006617e34e64b298f48785022d9376acad57260aaf/fasta/default/_refgenie_build/ * Pipeline started at: (04-07 15:31:50) elapsed: 0.0 _TIME_ ### Version log: * Python version: 3.6.6 * Pypiper dir: `/sfs/qumulo/qhome/mjs5kd/.local/lib/python3.6/site-packages/pypiper` * Pypiper version: 0.12.1 * Pipeline dir: `/sfs/qumulo/qhome/mjs5kd/.local/bin` * Pipeline version: None ### Arguments passed to pipeline: * `asset_registry_paths`: `['mm10_primary/fasta']` * `assets`: `None` * `command`: `build` * `config_file`: `refgenie.yaml` * `docker`: `False` * `files`: `[['fasta=/project/shefflab/www/refgenie_refgenomes.databio.org/mm10_primary-fasta-fasta']]` * `genome`: `None` * `genome_config`: `None` * `genome_description`: `None` * `logdev`: `False` * `new_start`: `False` * `outfolder`: `/project/shefflab/deploy/rg.databio.org_full/genomes/data` * `params`: `None` * `recipe`: `None` * `recover`: `False` * `requirements`: `False` * `silent`: `False` * `skip_read_lock`: `False` * `tag_description`: `None` * `verbosity`: `None` * `volumes`: `None` ---------------------------------------- Target to produce: `/project/shefflab/deploy/rg.databio.org_full/genomes/data/bfdbdd006617e34e64b298f48785022d9376acad57260aaf/fasta/default/_refgenie_build/bfdbdd006617e34e64b298f48785022d9376acad57260aaf_fasta__default.flag` > `cp /project/shefflab/www/refgenie_refgenomes.databio.org/mm10_primary-fasta-fasta /project/shefflab/deploy/rg.databio.org_full/genomes/data/bfdbdd006617e34e64b298f48785022d9376acad57260aaf/fasta/default/bfdbdd006617e34e64b298f48785022d9376acad57260aaf.fa.gz` (47136)
Command completed. Elapsed time: 0:00:04. Running peak memory: 0.002GB. PID: 47136; Command: cp; Return code: 0; Memory used: 0.002GB > `gzip -df /project/shefflab/deploy/rg.databio.org_full/genomes/data/bfdbdd006617e34e64b298f48785022d9376acad57260aaf/fasta/default/bfdbdd006617e34e64b298f48785022d9376acad57260aaf.fa.gz` (47145)
Command completed. Elapsed time: 0:00:31. Running peak memory: 0.002GB. PID: 47145; Command: gzip; Return code: 0; Memory used: 0.001GB > `samtools faidx /project/shefflab/deploy/rg.databio.org_full/genomes/data/bfdbdd006617e34e64b298f48785022d9376acad57260aaf/fasta/default/bfdbdd006617e34e64b298f48785022d9376acad57260aaf.fa` (47207)
[33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in containerCommand completed. Elapsed time: 0:00:10. Running peak memory: 0.019GB. PID: 47207; Command: samtools; Return code: 0; Memory used: 0.019GB > `cut -f 1,2 /project/shefflab/deploy/rg.databio.org_full/genomes/data/bfdbdd006617e34e64b298f48785022d9376acad57260aaf/fasta/default/bfdbdd006617e34e64b298f48785022d9376acad57260aaf.fa.fai > /project/shefflab/deploy/rg.databio.org_full/genomes/data/bfdbdd006617e34e64b298f48785022d9376acad57260aaf/fasta/default/bfdbdd006617e34e64b298f48785022d9376acad57260aaf.chrom.sizes` (47268)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.019GB. PID: 47268; Command: cut; Return code: 0; Memory used: 0.001GB > `touch /project/shefflab/deploy/rg.databio.org_full/genomes/data/bfdbdd006617e34e64b298f48785022d9376acad57260aaf/fasta/default/_refgenie_build/bfdbdd006617e34e64b298f48785022d9376acad57260aaf_fasta__default.flag` (47271)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.019GB. PID: 47271; Command: touch; Return code: 0; Memory used: 0.001GB Asset digest: cbbc1680a4cea8e43f14bbdc39d37162 Default tag for 'bfdbdd006617e34e64b298f48785022d9376acad57260aaf/fasta' set to: default ### Pipeline completed. Epilogue * Elapsed time (this run): 0:00:51 * Total elapsed time (all runs): 0:00:45 * Peak memory (this run): 0.0189 GB * Pipeline completed time: 2021-04-07 15:32:40 Finished building 'fasta' asset Created alias directories: - /project/shefflab/deploy/rg.databio.org_full/genomes/alias/mm10_primary/fasta/default