### Pipeline run code and environment:
* Command: `/home/mjs5kd/.local/bin/refgenie build mm10/ensembl_gtf --files ensembl_gtf=/project/shefflab/www/refgenie_refgenomes.databio.org/mm10-ensembl_gtf-ensembl_gtf`
* 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/0f10d83b1050c08dd53189986f60970b92a315aa7a16a6f1/ensembl_gtf/default/_refgenie_build/
* Pipeline started at: (04-07 15:40:43) 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`: `['mm10/ensembl_gtf']`
* `assets`: `None`
* `command`: `build`
* `config_file`: `refgenie.yaml`
* `docker`: `False`
* `files`: `[['ensembl_gtf=/project/shefflab/www/refgenie_refgenomes.databio.org/mm10-ensembl_gtf-ensembl_gtf']]`
* `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/0f10d83b1050c08dd53189986f60970b92a315aa7a16a6f1/ensembl_gtf/default/_refgenie_build/0f10d83b1050c08dd53189986f60970b92a315aa7a16a6f1_ensembl_gtf__default.flag`
> `cp /project/shefflab/www/refgenie_refgenomes.databio.org/mm10-ensembl_gtf-ensembl_gtf /project/shefflab/deploy/rg.databio.org_full/genomes/data/0f10d83b1050c08dd53189986f60970b92a315aa7a16a6f1/ensembl_gtf/default/0f10d83b1050c08dd53189986f60970b92a315aa7a16a6f1.gtf.gz` (255842)
Command completed. Elapsed time: 0:00:01. Running peak memory: 0.0GB.
PID: 255842; Command: cp; Return code: 0; Memory used: 0.0GB
> `gzip -dcf /project/shefflab/deploy/rg.databio.org_full/genomes/data/0f10d83b1050c08dd53189986f60970b92a315aa7a16a6f1/ensembl_gtf/default/0f10d83b1050c08dd53189986f60970b92a315aa7a16a6f1.gtf.gz | grep 'exon_number "1";' | sed 's/^/chr/' | awk -v OFS=' ' '{print $1, $4, $5, $20, $14, $7}' | sed 's/";//g' | sed 's/"//g' | awk '{if($6=="+"){print $1" "$2+20" "$2+120" "$4" "$5" "$6}else{print $1" "$3-120" "$3-20" "$4" "$5" "$6}}' | LC_COLLATE=C sort -k1,1 -k2,2n -u > /project/shefflab/deploy/rg.databio.org_full/genomes/data/0f10d83b1050c08dd53189986f60970b92a315aa7a16a6f1/ensembl_gtf/default/0f10d83b1050c08dd53189986f60970b92a315aa7a16a6f1_ensembl_TSS.bed` (255845,255846,255847,255848,255849,255850,255851,255852)
Command completed. Elapsed time: 0:00:07. Running peak memory: 0.009GB.
PID: 255845; Command: gzip; Return code: 0; Memory used: 0.001GB
PID: 255847; Command: sed; Return code: 0; Memory used: 0.001GB
PID: 255849; Command: sed; Return code: 0; Memory used: 0.001GB
PID: 255851; Command: awk; Return code: 0; Memory used: 0.001GB
PID: 255846; Command: grep; Return code: 0; Memory used: 0.001GB
PID: 255850; Command: sed; Return code: 0; Memory used: 0.001GB
PID: 255848; Command: awk; Return code: 0; Memory used: 0.001GB
PID: 255852; Command: LC_COLLATE=C; Return code: 0; Memory used: 0.009GB
> `gzip -dcf /project/shefflab/deploy/rg.databio.org_full/genomes/data/0f10d83b1050c08dd53189986f60970b92a315aa7a16a6f1/ensembl_gtf/default/0f10d83b1050c08dd53189986f60970b92a315aa7a16a6f1.gtf.gz | awk '$3 == "gene"' | sed 's/^/chr/' | awk -v OFS=' ' '{print $1,$4,$5,$14,$6,$7}' | sed 's/";//g' | sed 's/"//g' | awk '$4!="Metazoa_SRP"' | awk '$4!="U3"' | awk '$4!="7SK"' | awk '($3-$2)>200' | awk '{if($6=="+"){print $1" "$2+500" "$3" "$4" "$5" "$6}else{print $1" "$2" "$3-500" "$4" "$5" "$6}}' | awk '$3>$2' | LC_COLLATE=C sort -k4 -u > /project/shefflab/deploy/rg.databio.org_full/genomes/data/0f10d83b1050c08dd53189986f60970b92a315aa7a16a6f1/ensembl_gtf/default/0f10d83b1050c08dd53189986f60970b92a315aa7a16a6f1_ensembl_gene_body.bed` (255859,255860,255861,255862,255863,255864,255865,255866,255867,255868,255869,255870,255871)
Command completed. Elapsed time: 0:00:04. Running peak memory: 0.009GB.
PID: 255863; Command: sed; Return code: 0; Memory used: 0.001GB
PID: 255865; Command: awk; Return code: 0; Memory used: 0.001GB
PID: 255867; Command: awk; Return code: 0; Memory used: 0.001GB
PID: 255869; Command: awk; Return code: 0; Memory used: 0.001GB
PID: 255871; Command: LC_COLLATE=C; Return code: 0; Memory used: 0.002GB
PID: 255859; Command: gzip; Return code: 0; Memory used: 0.001GB
PID: 255861; Command: sed; Return code: 0; Memory used: 0.001GB
PID: 255864; Command: sed; Return code: 0; Memory used: 0.001GB
PID: 255868; Command: awk; Return code: 0; Memory used: 0.001GB
PID: 255860; Command: awk; Return code: 0; Memory used: 0.001GB
PID: 255866; Command: awk; Return code: 0; Memory used: 0.001GB
PID: 255862; Command: awk; Return code: 0; Memory used: 0.001GB
PID: 255870; Command: awk; Return code: 0; Memory used: 0.001GB
> `touch /project/shefflab/deploy/rg.databio.org_full/genomes/data/0f10d83b1050c08dd53189986f60970b92a315aa7a16a6f1/ensembl_gtf/default/_refgenie_build/0f10d83b1050c08dd53189986f60970b92a315aa7a16a6f1_ensembl_gtf__default.flag` (255899)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.009GB.
PID: 255899; Command: touch; Return code: 0; Memory used: 0.0GB
Asset digest: 1f79aef492221ed46fb75cfd7fe345ba
Default tag for '0f10d83b1050c08dd53189986f60970b92a315aa7a16a6f1/ensembl_gtf' set to: default
### Pipeline completed. Epilogue
* Elapsed time (this run): 0:00:13
* Total elapsed time (all runs): 0:01:51
* Peak memory (this run): 0.0089 GB
* Pipeline completed time: 2021-04-07 15:40:55
Finished building 'ensembl_gtf' asset
Created alias directories:
- /project/shefflab/deploy/rg.databio.org_full/genomes/alias/mm10/ensembl_gtf/default