### Pipeline run code and environment:

*              Command:  `/home/mjs5kd/.local/bin/refgenie build rCRSd/star_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/94e0d21feb576e6af61cd2a798ad30682ef2428bb7eabbb4/star_index/default/_refgenie_build/
*  Pipeline started at:   (04-07 18:43:52) 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/star_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/star_index/default/_refgenie_build/94e0d21feb576e6af61cd2a798ad30682ef2428bb7eabbb4_star_index__default.flag`  

> `mkdir -p /project/shefflab/deploy/rg.databio.org_full/genomes/data/94e0d21feb576e6af61cd2a798ad30682ef2428bb7eabbb4/star_index/default` (28255)
<pre>
</pre>
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.001GB.  
  PID: 28255;	Command: mkdir;	Return code: 0;	Memory used: 0.001GB


> `STAR --runThreadN 8 --runMode genomeGenerate --genomeDir /project/shefflab/deploy/rg.databio.org_full/genomes/data/94e0d21feb576e6af61cd2a798ad30682ef2428bb7eabbb4/star_index/default --genomeFastaFiles /project/shefflab/deploy/rg.databio.org_full/genomes/data/94e0d21feb576e6af61cd2a798ad30682ef2428bb7eabbb4/fasta/default/94e0d21feb576e6af61cd2a798ad30682ef2428bb7eabbb4.fa` (28256)
<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
Apr 07 18:43:52 ..... started STAR run
Apr 07 18:43:52 ... starting to generate Genome files
WARNING: --genomeSAindexNbases 14 is too large for the genome size=262144, which may cause seg-fault at the mapping step. Re-run genome generation with recommended --genomeSAindexNbases 8		 Apr 07 18:43:52
Apr 07 18:43:52 ... starting to sort Suffix Array. This may take a long time...
Apr 07 18:43:52 ... sorting Suffix Array chunks and saving them to disk...
Apr 07 18:43:53 ... loading chunks from disk, packing SA...
Apr 07 18:43:53 ... finished generating suffix array
Apr 07 18:43:53 ... generating Suffix Array index
Apr 07 18:43:56 ... completed Suffix Array index
Apr 07 18:43:56 ... writing Genome to disk ...
Apr 07 18:43:56 ... writing Suffix Array to disk ...
Apr 07 18:43:56 ... writing SAindex to disk
Apr 07 18:44:03 ..... finished successfully
</pre>
Command completed. Elapsed time: 0:00:11. Running peak memory: 1.579GB.  
  PID: 28256;	Command: STAR;	Return code: 0;	Memory used: 1.579GB


> `touch /project/shefflab/deploy/rg.databio.org_full/genomes/data/94e0d21feb576e6af61cd2a798ad30682ef2428bb7eabbb4/star_index/default/_refgenie_build/94e0d21feb576e6af61cd2a798ad30682ef2428bb7eabbb4_star_index__default.flag` (28323)
<pre>
</pre>
Command completed. Elapsed time: 0:00:00. Running peak memory: 1.579GB.  
  PID: 28323;	Command: touch;	Return code: 0;	Memory used: 0.001GB

Asset digest: e4e0e12736f8ec4db297174f2d506bc0
Default tag for '94e0d21feb576e6af61cd2a798ad30682ef2428bb7eabbb4/star_index' set to: default

### Pipeline completed. Epilogue
*        Elapsed time (this run):  0:00:15
*  Total elapsed time (all runs):  0:00:11
*         Peak memory (this run):  1.5787 GB
*        Pipeline completed time: 2021-04-07 18:44:07
Finished building 'star_index' asset
Created alias directories: 
 - /project/shefflab/deploy/rg.databio.org_full/genomes/alias/rCRSd/star_index/default