### Pipeline run code and environment:

*              Command:  `/home/mjs5kd/.local/bin/refgenie build hg19/refgene_anno --files refgene=/project/shefflab/www/refgenie_refgenomes.databio.org/hg19-refgene_anno-refgene`
*         Compute host:  udc-aw34-6c0
*          Working dir:  /sfs/qumulo/qproject/shefflab/deploy/rg.databio.org_full/rg.databio.org
*            Outfolder:  /project/shefflab/deploy/rg.databio.org_full/genomes/data/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c/refgene_anno/default/_refgenie_build/
*  Pipeline started at:   (04-07 15:34:33) 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`:  `['hg19/refgene_anno']`
*             `assets`:  `None`
*            `command`:  `build`
*        `config_file`:  `refgenie.yaml`
*             `docker`:  `False`
*              `files`:  `[['refgene=/project/shefflab/www/refgenie_refgenomes.databio.org/hg19-refgene_anno-refgene']]`
*             `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/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c/refgene_anno/default/_refgenie_build/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c_refgene_anno__default.flag`  

> `cp /project/shefflab/www/refgenie_refgenomes.databio.org/hg19-refgene_anno-refgene /project/shefflab/deploy/rg.databio.org_full/genomes/data/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c/refgene_anno/default/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c_refGene.txt.gz` (252830)
<pre>
</pre>
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.001GB.  
  PID: 252830;	Command: cp;	Return code: 0;	Memory used: 0.001GB


> `gzip -dcf /project/shefflab/deploy/rg.databio.org_full/genomes/data/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c/refgene_anno/default/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c_refGene.txt.gz | awk '{if($4=="+"){print $3"	"$5"	"$5"	"$13"	.	"$4}else{print $3"	"$6"	"$6"	"$13"	.	"$4}}' | LC_COLLATE=C sort -k1,1 -k2,2n -u > /project/shefflab/deploy/rg.databio.org_full/genomes/data/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c/refgene_anno/default/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c_TSS.bed` (252851,252852,252853)
<pre>
</pre>
Command completed. Elapsed time: 0:00:02. Running peak memory: 0.009GB.  
  PID: 252851;	Command: gzip;	Return code: 0;	Memory used: 0.001GB  
  PID: 252852;	Command: awk;	Return code: 0;	Memory used: 0.001GB  
  PID: 252853;	Command: LC_COLLATE=C;	Return code: 0;	Memory used: 0.009GB


> `gzip -dcf /project/shefflab/deploy/rg.databio.org_full/genomes/data/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c/refgene_anno/default/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c_refGene.txt.gz | awk -v OFS='	' '$9>1' | awk -v OFS='	' '{ n = split($10, a, ","); split($11, b, ","); for(i=1; i<n; ++i) print $3, a[i], b[i], $13, i, $4 }' | awk -v OFS='	' '$6=="+" && $5!=1 {print $0} $6=="-" {print $0}' | awk '$4!=prev4 && prev6=="-" {prev4=$4; prev6=$6; delete line[NR-1]; idx-=1} {line[++idx]=$0; prev4=$4; prev6=$6} END {for (x=1; x<=idx; x++) print line[x]}' | LC_COLLATE=C sort -k1,1 -k2,2n -u > /project/shefflab/deploy/rg.databio.org_full/genomes/data/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c/refgene_anno/default/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c_exons.bed` (252857,252858,252859,252860,252861,252862)
<pre>
</pre>
Command completed. Elapsed time: 0:00:15. Running peak memory: 0.009GB.  
  PID: 252860;	Command: awk;	Return code: 0;	Memory used: 0.001GB  
  PID: 252857;	Command: gzip;	Return code: 0;	Memory used: 0.001GB  
  PID: 252859;	Command: awk;	Return code: 0;	Memory used: 0.001GB  
  PID: 252858;	Command: awk;	Return code: 0;	Memory used: 0.001GB  
  PID: 252862;	Command: LC_COLLATE=C;	Return code: 0;	Memory used: 0.009GB  
  PID: 252861;	Command: awk;	Return code: 0;	Memory used: 0.008GB


> `gzip -dcf /project/shefflab/deploy/rg.databio.org_full/genomes/data/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c/refgene_anno/default/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c_refGene.txt.gz | awk -v OFS='	' '$9>1' | awk -F'	' '{ exonCount=int($9);split($10,exonStarts,"[,]"); split($11,exonEnds,"[,]"); for(i=1;i<exonCount;i++) {printf("%s\t%s\t%s\t%s\t%d\t%s\n",$3,exonEnds[i],exonStarts[i+1],$13,($3=="+"?i:exonCount-i),$4);}}' | LC_COLLATE=C sort -k1,1 -k2,2n -u > /project/shefflab/deploy/rg.databio.org_full/genomes/data/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c/refgene_anno/default/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c_introns.bed` (252933,252934,252935,252936)
<pre>
</pre>
Command completed. Elapsed time: 0:00:14. Running peak memory: 0.009GB.  
  PID: 252935;	Command: awk;	Return code: 0;	Memory used: 0.001GB  
  PID: 252933;	Command: gzip;	Return code: 0;	Memory used: 0.001GB  
  PID: 252936;	Command: LC_COLLATE=C;	Return code: 0;	Memory used: 0.009GB  
  PID: 252934;	Command: awk;	Return code: 0;	Memory used: 0.001GB


> `gzip -dcf /project/shefflab/deploy/rg.databio.org_full/genomes/data/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c/refgene_anno/default/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c_refGene.txt.gz | grep 'cmpl' | awk  '{print $3"	"$5"	"$6"	"$13"	.	"$4}' | LC_COLLATE=C sort -k1,1 -k2,2n -u >  /project/shefflab/deploy/rg.databio.org_full/genomes/data/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c/refgene_anno/default/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c_pre-mRNA.bed` (253258,253259,253260,253261)
<pre>
</pre>
Command completed. Elapsed time: 0:00:01. Running peak memory: 0.009GB.  
  PID: 253258;	Command: gzip;	Return code: 0;	Memory used: 0.001GB  
  PID: 253260;	Command: awk;	Return code: 0;	Memory used: 0.001GB  
  PID: 253259;	Command: grep;	Return code: 0;	Memory used: 0.001GB  
  PID: 253261;	Command: LC_COLLATE=C;	Return code: 0;	Memory used: 0.006GB


> `touch /project/shefflab/deploy/rg.databio.org_full/genomes/data/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c/refgene_anno/default/_refgenie_build/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c_refgene_anno__default.flag` (253270)
<pre>
</pre>
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.009GB.  
  PID: 253270;	Command: touch;	Return code: 0;	Memory used: 0.001GB

Asset digest: f4e6d4a88c21af08d61443abcb5b7d4b
Default tag for 'baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c/refgene_anno' set to: default

### Pipeline completed. Epilogue
*        Elapsed time (this run):  0:00:32
*  Total elapsed time (all runs):  0:01:42
*         Peak memory (this run):  0.0089 GB
*        Pipeline completed time: 2021-04-07 15:35:06
Finished building 'refgene_anno' asset
Created alias directories: 
 - /project/shefflab/deploy/rg.databio.org_full/genomes/alias/hg19/refgene_anno/default