### Pipeline run code and environment: * Command: `/home/mjs5kd/.local/bin/refgenie build hg18/fasta_txome --files fasta=/project/shefflab/www/refgenie_refgenomes.databio.org/hg18-fasta_txome-fasta` * Compute host: udc-aw34-1c1 * Working dir: /sfs/qumulo/qproject/shefflab/deploy/rg.databio.org_full/rg.databio.org * Outfolder: /project/shefflab/deploy/rg.databio.org_full/genomes/data/9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01/fasta_txome/default/_refgenie_build/ * Pipeline started at: (04-07 20:47:16) 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`: `['hg18/fasta_txome']` * `assets`: `None` * `command`: `build` * `config_file`: `refgenie.yaml` * `docker`: `False` * `files`: `[['fasta=/project/shefflab/www/refgenie_refgenomes.databio.org/hg18-fasta_txome-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/9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01/fasta_txome/default/_refgenie_build/9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01_fasta_txome__default.flag` > `cp /project/shefflab/www/refgenie_refgenomes.databio.org/hg18-fasta_txome-fasta /project/shefflab/deploy/rg.databio.org_full/genomes/data/9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01/fasta_txome/default/9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01.fa.gz` (25412)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.001GB. PID: 25412; Command: cp; Return code: 0; Memory used: 0.001GB > `gzip -df /project/shefflab/deploy/rg.databio.org_full/genomes/data/9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01/fasta_txome/default/9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01.fa.gz` (25442)
Command completed. Elapsed time: 0:00:01. Running peak memory: 0.001GB. PID: 25442; Command: gzip; Return code: 0; Memory used: 0.001GB > `samtools faidx /project/shefflab/deploy/rg.databio.org_full/genomes/data/9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01/fasta_txome/default/9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01.fa` (25445)
[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: 0.001GB. PID: 25445; Command: samtools; Return code: 0; Memory used: 0.001GB > `cut -f 1,2 /project/shefflab/deploy/rg.databio.org_full/genomes/data/9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01/fasta_txome/default/9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01.fa.fai > /project/shefflab/deploy/rg.databio.org_full/genomes/data/9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01/fasta_txome/default/9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01.chrom.sizes` (25486)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.001GB. PID: 25486; Command: cut; Return code: 0; Memory used: 0.001GB > `touch /project/shefflab/deploy/rg.databio.org_full/genomes/data/9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01/fasta_txome/default/_refgenie_build/9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01_fasta_txome__default.flag` (25488)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.001GB. PID: 25488; Command: touch; Return code: 0; Memory used: 0.001GB Asset digest: 456bf4dd716de36373539acf2595baf3 Default tag for '9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01/fasta_txome' set to: default ### Pipeline completed. Epilogue * Elapsed time (this run): 0:00:03 * Total elapsed time (all runs): 0:00:02 * Peak memory (this run): 0.0012 GB * Pipeline completed time: 2021-04-07 20:47:19 Finished building 'fasta_txome' asset Created alias directories: - /project/shefflab/deploy/rg.databio.org_full/genomes/alias/hg18/fasta_txome/default