### Pipeline run code and environment: * Command: `/home/mjs5kd/.local/bin/refgenie build rCRSd/bwa_index` * Compute host: udc-ba25-17 * 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/bwa_index/default/_refgenie_build/ * Pipeline started at: (04-07 17:39:30) 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/bwa_index']` * `assets`: `None` * `command`: `build` * `config_file`: `refgenie.yaml` * `docker`: `False` * `files`: `None` * `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/94e0d21feb576e6af61cd2a798ad30682ef2428bb7eabbb4/bwa_index/default/_refgenie_build/94e0d21feb576e6af61cd2a798ad30682ef2428bb7eabbb4_bwa_index__default.flag` > `ln -sf /project/shefflab/deploy/rg.databio.org_full/genomes/data/94e0d21feb576e6af61cd2a798ad30682ef2428bb7eabbb4/fasta/default/94e0d21feb576e6af61cd2a798ad30682ef2428bb7eabbb4.fa /project/shefflab/deploy/rg.databio.org_full/genomes/data/94e0d21feb576e6af61cd2a798ad30682ef2428bb7eabbb4/bwa_index/default` (28495)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.001GB. PID: 28495; Command: ln; Return code: 0; Memory used: 0.001GB > `bwa index /project/shefflab/deploy/rg.databio.org_full/genomes/data/94e0d21feb576e6af61cd2a798ad30682ef2428bb7eabbb4/bwa_index/default/94e0d21feb576e6af61cd2a798ad30682ef2428bb7eabbb4.fa` (28496)
[33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container [bwa_index] Pack FASTA... 0.00 sec [bwa_index] Construct BWT for the packed sequence... [bwa_index] 0.01 seconds elapse. [bwa_index] Update BWT... 0.00 sec [bwa_index] Pack forward-only FASTA... 0.00 sec [bwa_index] Construct SA from BWT and Occ... 0.00 sec [main] Version: 0.7.17-r1188 [main] CMD: bwa index /project/shefflab/deploy/rg.databio.org_full/genomes/data/94e0d21feb576e6af61cd2a798ad30682ef2428bb7eabbb4/bwa_index/default/94e0d21feb576e6af61cd2a798ad30682ef2428bb7eabbb4.fa [main] Real time: 0.048 sec; CPU: 0.053 secCommand completed. Elapsed time: 0:00:00. Running peak memory: 0.001GB. PID: 28496; Command: bwa; Return code: 0; Memory used: 0.001GB > `touch /project/shefflab/deploy/rg.databio.org_full/genomes/data/94e0d21feb576e6af61cd2a798ad30682ef2428bb7eabbb4/bwa_index/default/_refgenie_build/94e0d21feb576e6af61cd2a798ad30682ef2428bb7eabbb4_bwa_index__default.flag` (28535)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.001GB. PID: 28535; Command: touch; Return code: 0; Memory used: 0.001GB Asset digest: de383551ccf544bd9bbee7d4c529f39b Default tag for '94e0d21feb576e6af61cd2a798ad30682ef2428bb7eabbb4/bwa_index' set to: default ### Pipeline completed. Epilogue * Elapsed time (this run): 0:00:01 * Total elapsed time (all runs): 0:00:00 * Peak memory (this run): 0.0012 GB * Pipeline completed time: 2021-04-07 17:39:30 Finished building 'bwa_index' asset Created alias directories: - /project/shefflab/deploy/rg.databio.org_full/genomes/alias/rCRSd/bwa_index/default