### Pipeline run code and environment: * Command: `/home/mjs5kd/.local/bin/refgenie build dm6/refgene_anno --files refgene=/project/shefflab/www/refgenie_refgenomes.databio.org/dm6-refgene_anno-refgene` * Compute host: udc-aw29-20b * Working dir: /sfs/qumulo/qproject/shefflab/deploy/rg.databio.org_full/rg.databio.org * Outfolder: /project/shefflab/deploy/rg.databio.org_full/genomes/data/8baf9d24ad8f5678f0fe1f5b21a812d410755d49e3123158/refgene_anno/default/_refgenie_build/ * Pipeline started at: (04-07 15:40:08) 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`: `['dm6/refgene_anno']` * `assets`: `None` * `command`: `build` * `config_file`: `refgenie.yaml` * `docker`: `False` * `files`: `[['refgene=/project/shefflab/www/refgenie_refgenomes.databio.org/dm6-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/8baf9d24ad8f5678f0fe1f5b21a812d410755d49e3123158/refgene_anno/default/_refgenie_build/8baf9d24ad8f5678f0fe1f5b21a812d410755d49e3123158_refgene_anno__default.flag` > `cp /project/shefflab/www/refgenie_refgenomes.databio.org/dm6-refgene_anno-refgene /project/shefflab/deploy/rg.databio.org_full/genomes/data/8baf9d24ad8f5678f0fe1f5b21a812d410755d49e3123158/refgene_anno/default/8baf9d24ad8f5678f0fe1f5b21a812d410755d49e3123158_refGene.txt.gz` (193525)

Command completed. Elapsed time: 0:00:00. Running peak memory: 0.001GB.  
  PID: 193525;	Command: cp;	Return code: 0;	Memory used: 0.001GB


> `gzip -dcf /project/shefflab/deploy/rg.databio.org_full/genomes/data/8baf9d24ad8f5678f0fe1f5b21a812d410755d49e3123158/refgene_anno/default/8baf9d24ad8f5678f0fe1f5b21a812d410755d49e3123158_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/8baf9d24ad8f5678f0fe1f5b21a812d410755d49e3123158/refgene_anno/default/8baf9d24ad8f5678f0fe1f5b21a812d410755d49e3123158_TSS.bed` (193526,193527,193528)

Command completed. Elapsed time: 0:00:01. Running peak memory: 0.009GB.  
  PID: 193526;	Command: gzip;	Return code: 0;	Memory used: 0.001GB  
  PID: 193528;	Command: LC_COLLATE=C;	Return code: 0;	Memory used: 0.009GB  
  PID: 193527;	Command: awk;	Return code: 0;	Memory used: 0.001GB


> `gzip -dcf /project/shefflab/deploy/rg.databio.org_full/genomes/data/8baf9d24ad8f5678f0fe1f5b21a812d410755d49e3123158/refgene_anno/default/8baf9d24ad8f5678f0fe1f5b21a812d410755d49e3123158_refGene.txt.gz | awk -v OFS='	' '$9>1' | awk -v OFS='	' '{ n = split($10, a, ","); split($11, b, ","); for(i=1; i /project/shefflab/deploy/rg.databio.org_full/genomes/data/8baf9d24ad8f5678f0fe1f5b21a812d410755d49e3123158/refgene_anno/default/8baf9d24ad8f5678f0fe1f5b21a812d410755d49e3123158_exons.bed` (193530,193531,193532,193533,193534,193536)

Command completed. Elapsed time: 0:00:03. Running peak memory: 0.034GB.  
  PID: 193530;	Command: gzip;	Return code: 0;	Memory used: 0.001GB  
  PID: 193532;	Command: awk;	Return code: 0;	Memory used: 0.001GB  
  PID: 193531;	Command: awk;	Return code: 0;	Memory used: 0.001GB  
  PID: 193534;	Command: awk;	Return code: 0;	Memory used: 0.034GB  
  PID: 193533;	Command: awk;	Return code: 0;	Memory used: 0.001GB  
  PID: 193536;	Command: LC_COLLATE=C;	Return code: 0;	Memory used: 0.009GB


> `gzip -dcf /project/shefflab/deploy/rg.databio.org_full/genomes/data/8baf9d24ad8f5678f0fe1f5b21a812d410755d49e3123158/refgene_anno/default/8baf9d24ad8f5678f0fe1f5b21a812d410755d49e3123158_refGene.txt.gz | awk -v OFS='	' '$9>1' | awk -F'	' '{ exonCount=int($9);split($10,exonStarts,"[,]"); split($11,exonEnds,"[,]"); for(i=1;i /project/shefflab/deploy/rg.databio.org_full/genomes/data/8baf9d24ad8f5678f0fe1f5b21a812d410755d49e3123158/refgene_anno/default/8baf9d24ad8f5678f0fe1f5b21a812d410755d49e3123158_introns.bed` (193544,193545,193546,193547)

Command completed. Elapsed time: 0:00:03. Running peak memory: 0.034GB.  
  PID: 193545;	Command: awk;	Return code: 0;	Memory used: 0.001GB  
  PID: 193544;	Command: gzip;	Return code: 0;	Memory used: 0.001GB  
  PID: 193547;	Command: LC_COLLATE=C;	Return code: 0;	Memory used: 0.009GB  
  PID: 193546;	Command: awk;	Return code: 0;	Memory used: 0.001GB


> `gzip -dcf /project/shefflab/deploy/rg.databio.org_full/genomes/data/8baf9d24ad8f5678f0fe1f5b21a812d410755d49e3123158/refgene_anno/default/8baf9d24ad8f5678f0fe1f5b21a812d410755d49e3123158_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/8baf9d24ad8f5678f0fe1f5b21a812d410755d49e3123158/refgene_anno/default/8baf9d24ad8f5678f0fe1f5b21a812d410755d49e3123158_pre-mRNA.bed` (193551,193552,193553,193554)

Command completed. Elapsed time: 0:00:01. Running peak memory: 0.034GB.  
  PID: 193551;	Command: gzip;	Return code: 0;	Memory used: 0.001GB  
  PID: 193553;	Command: awk;	Return code: 0;	Memory used: 0.001GB  
  PID: 193552;	Command: grep;	Return code: 0;	Memory used: 0.001GB  
  PID: 193554;	Command: LC_COLLATE=C;	Return code: 0;	Memory used: 0.006GB


> `touch /project/shefflab/deploy/rg.databio.org_full/genomes/data/8baf9d24ad8f5678f0fe1f5b21a812d410755d49e3123158/refgene_anno/default/_refgenie_build/8baf9d24ad8f5678f0fe1f5b21a812d410755d49e3123158_refgene_anno__default.flag` (193557)

Command completed. Elapsed time: 0:00:00. Running peak memory: 0.034GB.  
  PID: 193557;	Command: touch;	Return code: 0;	Memory used: 0.001GB

Asset digest: ce9f8496894eace73fe972025fa338e0
Default tag for '8baf9d24ad8f5678f0fe1f5b21a812d410755d49e3123158/refgene_anno' set to: default

### Pipeline completed. Epilogue
*        Elapsed time (this run):  0:00:08
*  Total elapsed time (all runs):  0:00:25
*         Peak memory (this run):  0.0341 GB
*        Pipeline completed time: 2021-04-07 15:40:16
Finished building 'refgene_anno' asset
Created alias directories: 
 - /project/shefflab/deploy/rg.databio.org_full/genomes/alias/dm6/refgene_anno/default