### Pipeline run code and environment:
* Command: `/home/mjs5kd/.local/bin/refgenie build hg38_mm10/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/644d2b9de4adaccb31c8bde387f23edddc5834772dd51d33/bwa_index/default/_refgenie_build/
* Pipeline started at: (04-07 18:04:20) 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`: `['hg38_mm10/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/644d2b9de4adaccb31c8bde387f23edddc5834772dd51d33/bwa_index/default/_refgenie_build/644d2b9de4adaccb31c8bde387f23edddc5834772dd51d33_bwa_index__default.flag`
> `ln -sf /project/shefflab/deploy/rg.databio.org_full/genomes/data/644d2b9de4adaccb31c8bde387f23edddc5834772dd51d33/fasta/default/644d2b9de4adaccb31c8bde387f23edddc5834772dd51d33.fa /project/shefflab/deploy/rg.databio.org_full/genomes/data/644d2b9de4adaccb31c8bde387f23edddc5834772dd51d33/bwa_index/default` (19863)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.001GB.
PID: 19863; Command: ln; Return code: 0; Memory used: 0.001GB
> `bwa index /project/shefflab/deploy/rg.databio.org_full/genomes/data/644d2b9de4adaccb31c8bde387f23edddc5834772dd51d33/bwa_index/default/644d2b9de4adaccb31c8bde387f23edddc5834772dd51d33.fa` (19864)
[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... 50.34 sec
[bwa_index] Construct BWT for the packed sequence...
[BWTIncCreate] textLength=11627648140, availableWord=830163964
[BWTIncConstructFromPacked] 10 iterations done. 99999996 characters processed.
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[BWTIncConstructFromPacked] 1230 iterations done. 11627648140 characters processed.
[bwt_gen] Finished constructing BWT in 1230 iterations.
[bwa_index] 7940.30 seconds elapse.
[bwa_index] Update BWT... 38.03 sec
[bwa_index] Pack forward-only FASTA... 32.70 sec
[bwa_index] Construct SA from BWT and Occ... 2678.19 sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa index /project/shefflab/deploy/rg.databio.org_full/genomes/data/644d2b9de4adaccb31c8bde387f23edddc5834772dd51d33/bwa_index/default/644d2b9de4adaccb31c8bde387f23edddc5834772dd51d33.fa
[main] Real time: 10827.643 sec; CPU: 10739.597 sec
Command completed. Elapsed time: 3:00:28. Running peak memory: 8.736GB.
PID: 19864; Command: bwa; Return code: 0; Memory used: 8.736GB
> `touch /project/shefflab/deploy/rg.databio.org_full/genomes/data/644d2b9de4adaccb31c8bde387f23edddc5834772dd51d33/bwa_index/default/_refgenie_build/644d2b9de4adaccb31c8bde387f23edddc5834772dd51d33_bwa_index__default.flag` (24247)
Command completed. Elapsed time: 0:00:00. Running peak memory: 8.736GB.
PID: 24247; Command: touch; Return code: 0; Memory used: 0.001GB
Asset digest: 861b408e96cf1ca56c748dfc13a55396
Default tag for '644d2b9de4adaccb31c8bde387f23edddc5834772dd51d33/bwa_index' set to: default
### Pipeline completed. Epilogue
* Elapsed time (this run): 3:01:49
* Total elapsed time (all runs): 3:00:28
* Peak memory (this run): 8.7359 GB
* Pipeline completed time: 2021-04-07 21:06:09
Finished building 'bwa_index' asset
Created alias directories:
- /project/shefflab/deploy/rg.databio.org_full/genomes/alias/hg38_mm10/bwa_index/default