### Pipeline run code and environment: * Command: `/home/mjs5kd/.local/bin/refgenie build hs38d1/bwa_index` * Compute host: udc-ba25-18 * Working dir: /sfs/qumulo/qproject/shefflab/deploy/rg.databio.org_full/rg.databio.org * Outfolder: /project/shefflab/deploy/rg.databio.org_full/genomes/data/45818b389d17308bb520512bb0d4f76764430c3eaaacc4a9/bwa_index/default/_refgenie_build/ * Pipeline started at: (04-07 16:44:04) 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`: `['hs38d1/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/45818b389d17308bb520512bb0d4f76764430c3eaaacc4a9/bwa_index/default/_refgenie_build/45818b389d17308bb520512bb0d4f76764430c3eaaacc4a9_bwa_index__default.flag` > `ln -sf /project/shefflab/deploy/rg.databio.org_full/genomes/data/45818b389d17308bb520512bb0d4f76764430c3eaaacc4a9/fasta/default/45818b389d17308bb520512bb0d4f76764430c3eaaacc4a9.fa /project/shefflab/deploy/rg.databio.org_full/genomes/data/45818b389d17308bb520512bb0d4f76764430c3eaaacc4a9/bwa_index/default` (4879)

Command completed. Elapsed time: 0:00:00. Running peak memory: 0.0GB.  
  PID: 4879;	Command: ln;	Return code: 0;	Memory used: 0.0GB


> `bwa index /project/shefflab/deploy/rg.databio.org_full/genomes/data/45818b389d17308bb520512bb0d4f76764430c3eaaacc4a9/bwa_index/default/45818b389d17308bb520512bb0d4f76764430c3eaaacc4a9.fa` (4880)
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... 0.05 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 2.48 seconds elapse.
[bwa_index] Update BWT... 0.04 sec
[bwa_index] Pack forward-only FASTA... 0.03 sec
[bwa_index] Construct SA from BWT and Occ... 0.82 sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa index /project/shefflab/deploy/rg.databio.org_full/genomes/data/45818b389d17308bb520512bb0d4f76764430c3eaaacc4a9/bwa_index/default/45818b389d17308bb520512bb0d4f76764430c3eaaacc4a9.fa
[main] Real time: 3.732 sec; CPU: 3.471 sec
Command completed. Elapsed time: 0:00:04. Running peak memory: 0.072GB. PID: 4880; Command: bwa; Return code: 0; Memory used: 0.072GB > `touch /project/shefflab/deploy/rg.databio.org_full/genomes/data/45818b389d17308bb520512bb0d4f76764430c3eaaacc4a9/bwa_index/default/_refgenie_build/45818b389d17308bb520512bb0d4f76764430c3eaaacc4a9_bwa_index__default.flag` (4978)

Command completed. Elapsed time: 0:00:00. Running peak memory: 0.072GB.  
  PID: 4978;	Command: touch;	Return code: 0;	Memory used: 0.001GB

Asset digest: 0e960702cf0cc29e3aba6d7868e988db
Default tag for '45818b389d17308bb520512bb0d4f76764430c3eaaacc4a9/bwa_index' set to: default

### Pipeline completed. Epilogue
*        Elapsed time (this run):  0:00:05
*  Total elapsed time (all runs):  0:00:04
*         Peak memory (this run):  0.0722 GB
*        Pipeline completed time: 2021-04-07 16:44:09
Finished building 'bwa_index' asset
Created alias directories: 
 - /project/shefflab/deploy/rg.databio.org_full/genomes/alias/hs38d1/bwa_index/default