### 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)
WARNING: 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 sec
Command 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