### Pipeline run code and environment: * Command: `/home/mjs5kd/.local/bin/refgenie build rCRSd/fasta --genome-description test description rCRSd --files fasta=/project/shefflab/www/refgenie_rg.databio.org/rCRSd-fasta-fasta` * Compute host: udc-aw29-20b * Working dir: /sfs/qumulo/qproject/shefflab/deploy/rg.databio.org_full/rg.databio.org * Outfolder: /project/shefflab/deploy/rg.databio.org_full/genomes/data/94e0d21feb576e6af61cd2a798ad30682ef2428bb7eabbb4/fasta/default/_refgenie_build/ * Pipeline started at: (04-07 15:19:10) 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`: `['rCRSd/fasta']` * `assets`: `None` * `command`: `build` * `config_file`: `refgenie.yaml` * `docker`: `False` * `files`: `[['fasta=/project/shefflab/www/refgenie_rg.databio.org/rCRSd-fasta-fasta']]` * `genome`: `None` * `genome_config`: `None` * `genome_description`: `test description rCRSd` * `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/94e0d21feb576e6af61cd2a798ad30682ef2428bb7eabbb4/fasta/default/_refgenie_build/94e0d21feb576e6af61cd2a798ad30682ef2428bb7eabbb4_fasta__default.flag` > `cp /project/shefflab/www/refgenie_rg.databio.org/rCRSd-fasta-fasta /project/shefflab/deploy/rg.databio.org_full/genomes/data/94e0d21feb576e6af61cd2a798ad30682ef2428bb7eabbb4/fasta/default/94e0d21feb576e6af61cd2a798ad30682ef2428bb7eabbb4.fa.gz` (187944)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.001GB. PID: 187944; Command: cp; Return code: 0; Memory used: 0.001GB > `gzip -df /project/shefflab/deploy/rg.databio.org_full/genomes/data/94e0d21feb576e6af61cd2a798ad30682ef2428bb7eabbb4/fasta/default/94e0d21feb576e6af61cd2a798ad30682ef2428bb7eabbb4.fa.gz` (187945)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.001GB. PID: 187945; Command: gzip; Return code: 0; Memory used: 0.001GB > `samtools faidx /project/shefflab/deploy/rg.databio.org_full/genomes/data/94e0d21feb576e6af61cd2a798ad30682ef2428bb7eabbb4/fasta/default/94e0d21feb576e6af61cd2a798ad30682ef2428bb7eabbb4.fa` (187946)
[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: 0:00:01. Running peak memory: 0.019GB. PID: 187946; Command: samtools; Return code: 0; Memory used: 0.019GB > `cut -f 1,2 /project/shefflab/deploy/rg.databio.org_full/genomes/data/94e0d21feb576e6af61cd2a798ad30682ef2428bb7eabbb4/fasta/default/94e0d21feb576e6af61cd2a798ad30682ef2428bb7eabbb4.fa.fai > /project/shefflab/deploy/rg.databio.org_full/genomes/data/94e0d21feb576e6af61cd2a798ad30682ef2428bb7eabbb4/fasta/default/94e0d21feb576e6af61cd2a798ad30682ef2428bb7eabbb4.chrom.sizes` (187986)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.019GB. PID: 187986; Command: cut; Return code: 0; Memory used: 0.001GB > `touch /project/shefflab/deploy/rg.databio.org_full/genomes/data/94e0d21feb576e6af61cd2a798ad30682ef2428bb7eabbb4/fasta/default/_refgenie_build/94e0d21feb576e6af61cd2a798ad30682ef2428bb7eabbb4_fasta__default.flag` (187988)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.019GB. PID: 187988; Command: touch; Return code: 0; Memory used: 0.001GB Asset digest: 4eb430296bc02ed7e4006624f1d5ac53 Default tag for '94e0d21feb576e6af61cd2a798ad30682ef2428bb7eabbb4/fasta' set to: default ### Pipeline completed. Epilogue * Elapsed time (this run): 0:00:01 * Total elapsed time (all runs): 0:00:01 * Peak memory (this run): 0.019 GB * Pipeline completed time: 2021-04-07 15:19:11 Finished building 'fasta' asset Created alias directories: - /project/shefflab/deploy/rg.databio.org_full/genomes/alias/rCRSd/fasta/default ### Pipeline run code and environment: * Command: `/home/mjs5kd/.local/bin/refgenie build rCRSd/fasta --genome-description test description rCRSd --files fasta=/project/shefflab/www/refgenie_refgenomes.databio.org/rCRSd-fasta-fasta` * Compute host: udc-aw29-20b * Working dir: /sfs/qumulo/qproject/shefflab/deploy/rg.databio.org_full/rg.databio.org * Outfolder: /project/shefflab/deploy/rg.databio.org_full/genomes/data/94e0d21feb576e6af61cd2a798ad30682ef2428bb7eabbb4/fasta/default/_refgenie_build/ * Pipeline started at: (04-07 15:23:51) 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`: `['rCRSd/fasta']` * `assets`: `None` * `command`: `build` * `config_file`: `refgenie.yaml` * `docker`: `False` * `files`: `[['fasta=/project/shefflab/www/refgenie_refgenomes.databio.org/rCRSd-fasta-fasta']]` * `genome`: `None` * `genome_config`: `None` * `genome_description`: `test description rCRSd` * `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 exists: `/project/shefflab/deploy/rg.databio.org_full/genomes/data/94e0d21feb576e6af61cd2a798ad30682ef2428bb7eabbb4/fasta/default/_refgenie_build/94e0d21feb576e6af61cd2a798ad30682ef2428bb7eabbb4_fasta__default.flag` Asset digest: 4eb430296bc02ed7e4006624f1d5ac53 ### Pipeline completed. Epilogue * Elapsed time (this run): 0:00:00 * Total elapsed time (all runs): 0:00:01 * Peak memory (this run): 0 GB * Pipeline completed time: 2021-04-07 15:23:51 Finished building 'fasta' asset Removed existing flag: '/project/shefflab/deploy/rg.databio.org_full/genomes/data/94e0d21feb576e6af61cd2a798ad30682ef2428bb7eabbb4/fasta/default/_refgenie_build/refgenie_completed.flag' ### Pipeline run code and environment: * Command: `/home/mjs5kd/.local/bin/refgenie build rCRSd/fasta --genome-description test description rCRSd --files fasta=/project/shefflab/www/refgenie_refgenomes.databio.org/rCRSd-fasta-fasta` * Compute host: udc-aw34-2c1 * Working dir: /sfs/qumulo/qproject/shefflab/deploy/rg.databio.org_full/rg.databio.org * Outfolder: /project/shefflab/deploy/rg.databio.org_full/genomes/data/94e0d21feb576e6af61cd2a798ad30682ef2428bb7eabbb4/fasta/default/_refgenie_build/ * Pipeline started at: (04-07 15:27:55) 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`: `['rCRSd/fasta']` * `assets`: `None` * `command`: `build` * `config_file`: `refgenie.yaml` * `docker`: `False` * `files`: `[['fasta=/project/shefflab/www/refgenie_refgenomes.databio.org/rCRSd-fasta-fasta']]` * `genome`: `None` * `genome_config`: `None` * `genome_description`: `test description rCRSd` * `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 exists: `/project/shefflab/deploy/rg.databio.org_full/genomes/data/94e0d21feb576e6af61cd2a798ad30682ef2428bb7eabbb4/fasta/default/_refgenie_build/94e0d21feb576e6af61cd2a798ad30682ef2428bb7eabbb4_fasta__default.flag` Asset digest: 4eb430296bc02ed7e4006624f1d5ac53 ### Pipeline completed. Epilogue * Elapsed time (this run): 0:00:00 * Total elapsed time (all runs): 0:00:01 * Peak memory (this run): 0 GB * Pipeline completed time: 2021-04-07 15:27:55 Finished building 'fasta' asset Removed existing flag: '/project/shefflab/deploy/rg.databio.org_full/genomes/data/94e0d21feb576e6af61cd2a798ad30682ef2428bb7eabbb4/fasta/default/_refgenie_build/refgenie_completed.flag'