### Pipeline run code and environment:

*              Command:  `/home/mjs5kd/.local/bin/refgenie build hg38_chr22/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/fec6bcce9821b57f98ffc5d46ebec4f2f756c2e9db800ab7/bwa_index/default/_refgenie_build/
*  Pipeline started at:   (04-07 17:09:14) 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_chr22/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/fec6bcce9821b57f98ffc5d46ebec4f2f756c2e9db800ab7/bwa_index/default/_refgenie_build/fec6bcce9821b57f98ffc5d46ebec4f2f756c2e9db800ab7_bwa_index__default.flag`  

> `ln -sf /project/shefflab/deploy/rg.databio.org_full/genomes/data/fec6bcce9821b57f98ffc5d46ebec4f2f756c2e9db800ab7/fasta/default/fec6bcce9821b57f98ffc5d46ebec4f2f756c2e9db800ab7.fa /project/shefflab/deploy/rg.databio.org_full/genomes/data/fec6bcce9821b57f98ffc5d46ebec4f2f756c2e9db800ab7/bwa_index/default` (9456)
<pre>
</pre>
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.001GB.  
  PID: 9456;	Command: ln;	Return code: 0;	Memory used: 0.001GB


> `bwa index /project/shefflab/deploy/rg.databio.org_full/genomes/data/fec6bcce9821b57f98ffc5d46ebec4f2f756c2e9db800ab7/bwa_index/default/fec6bcce9821b57f98ffc5d46ebec4f2f756c2e9db800ab7.fa` (9457)
<pre>
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... 0.37 sec
[bwa_index] Construct BWT for the packed sequence...
[BWTIncCreate] textLength=85492484, availableWord=18015308
[BWTIncConstructFromPacked] 10 iterations done. 29716420 characters processed.
[BWTIncConstructFromPacked] 20 iterations done. 54897060 characters processed.
[BWTIncConstructFromPacked] 30 iterations done. 77273652 characters processed.
[bwt_gen] Finished constructing BWT in 34 iterations.
[bwa_index] 30.87 seconds elapse.
[bwa_index] Update BWT... 0.28 sec
[bwa_index] Pack forward-only FASTA... 0.24 sec
[bwa_index] Construct SA from BWT and Occ... 10.88 sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa index /project/shefflab/deploy/rg.databio.org_full/genomes/data/fec6bcce9821b57f98ffc5d46ebec4f2f756c2e9db800ab7/bwa_index/default/fec6bcce9821b57f98ffc5d46ebec4f2f756c2e9db800ab7.fa
[main] Real time: 44.214 sec; CPU: 42.687 sec
</pre>
Command completed. Elapsed time: 0:00:45. Running peak memory: 0.085GB.  
  PID: 9457;	Command: bwa;	Return code: 0;	Memory used: 0.085GB


> `touch /project/shefflab/deploy/rg.databio.org_full/genomes/data/fec6bcce9821b57f98ffc5d46ebec4f2f756c2e9db800ab7/bwa_index/default/_refgenie_build/fec6bcce9821b57f98ffc5d46ebec4f2f756c2e9db800ab7_bwa_index__default.flag` (9585)
<pre>
</pre>
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.085GB.  
  PID: 9585;	Command: touch;	Return code: 0;	Memory used: 0.001GB

Asset digest: 30166540072e3a4a927e548909ab4b7e
Default tag for 'fec6bcce9821b57f98ffc5d46ebec4f2f756c2e9db800ab7/bwa_index' set to: default

### Pipeline completed. Epilogue
*        Elapsed time (this run):  0:00:47
*  Total elapsed time (all runs):  0:00:45
*         Peak memory (this run):  0.0849 GB
*        Pipeline completed time: 2021-04-07 17:10:01
Finished building 'bwa_index' asset
Created alias directories: 
 - /project/shefflab/deploy/rg.databio.org_full/genomes/alias/hg38_chr22/bwa_index/default