### Pipeline run code and environment:
* Command: `/home/mjs5kd/.local/bin/refgenie build dm6/ensembl_gtf --files ensembl_gtf=/project/shefflab/www/refgenie_refgenomes.databio.org/dm6-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/8baf9d24ad8f5678f0fe1f5b21a812d410755d49e3123158/ensembl_gtf/default/_refgenie_build/
* Pipeline started at: (04-07 15:41:12) 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/ensembl_gtf']`
* `assets`: `None`
* `command`: `build`
* `config_file`: `refgenie.yaml`
* `docker`: `False`
* `files`: `[['ensembl_gtf=/project/shefflab/www/refgenie_refgenomes.databio.org/dm6-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/8baf9d24ad8f5678f0fe1f5b21a812d410755d49e3123158/ensembl_gtf/default/_refgenie_build/8baf9d24ad8f5678f0fe1f5b21a812d410755d49e3123158_ensembl_gtf__default.flag`
> `cp /project/shefflab/www/refgenie_refgenomes.databio.org/dm6-ensembl_gtf-ensembl_gtf /project/shefflab/deploy/rg.databio.org_full/genomes/data/8baf9d24ad8f5678f0fe1f5b21a812d410755d49e3123158/ensembl_gtf/default/8baf9d24ad8f5678f0fe1f5b21a812d410755d49e3123158.gtf.gz` (256119)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.001GB.
PID: 256119; Command: cp; Return code: 0; Memory used: 0.001GB
> `gzip -dcf /project/shefflab/deploy/rg.databio.org_full/genomes/data/8baf9d24ad8f5678f0fe1f5b21a812d410755d49e3123158/ensembl_gtf/default/8baf9d24ad8f5678f0fe1f5b21a812d410755d49e3123158.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/8baf9d24ad8f5678f0fe1f5b21a812d410755d49e3123158/ensembl_gtf/default/8baf9d24ad8f5678f0fe1f5b21a812d410755d49e3123158_ensembl_TSS.bed` (256120,256121,256122,256123,256124,256126,256127,256134)
Command completed. Elapsed time: 0:00:02. Running peak memory: 0.008GB.
PID: 256121; Command: grep; Return code: 0; Memory used: 0.001GB
PID: 256123; Command: awk; Return code: 0; Memory used: 0.001GB
PID: 256126; Command: sed; Return code: 0; Memory used: 0.001GB
PID: 256134; Command: LC_COLLATE=C; Return code: 0; Memory used: 0.008GB
PID: 256120; Command: gzip; Return code: 0; Memory used: 0.001GB
PID: 256124; Command: sed; Return code: 0; Memory used: 0.001GB
PID: 256122; Command: sed; Return code: 0; Memory used: 0.001GB
PID: 256127; Command: awk; Return code: 0; Memory used: 0.001GB
> `gzip -dcf /project/shefflab/deploy/rg.databio.org_full/genomes/data/8baf9d24ad8f5678f0fe1f5b21a812d410755d49e3123158/ensembl_gtf/default/8baf9d24ad8f5678f0fe1f5b21a812d410755d49e3123158.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/8baf9d24ad8f5678f0fe1f5b21a812d410755d49e3123158/ensembl_gtf/default/8baf9d24ad8f5678f0fe1f5b21a812d410755d49e3123158_ensembl_gene_body.bed` (256146,256147,256148,256149,256150,256151,256152,256153,256154,256155,256156,256157,256158)
Command completed. Elapsed time: 0:00:01. Running peak memory: 0.008GB.
PID: 256146; Command: gzip; Return code: 0; Memory used: 0.001GB
PID: 256148; Command: sed; Return code: 0; Memory used: 0.001GB
PID: 256150; Command: sed; Return code: 0; Memory used: 0.001GB
PID: 256152; Command: awk; Return code: 0; Memory used: 0.001GB
PID: 256154; Command: awk; Return code: 0; Memory used: 0.001GB
PID: 256156; Command: awk; Return code: 0; Memory used: 0.001GB
PID: 256158; Command: LC_COLLATE=C; Return code: 0; Memory used: 0.003GB
PID: 256147; Command: awk; Return code: 0; Memory used: 0.001GB
PID: 256151; Command: sed; Return code: 0; Memory used: 0.001GB
PID: 256155; Command: awk; Return code: 0; Memory used: 0.001GB
PID: 256149; Command: awk; Return code: 0; Memory used: 0.001GB
PID: 256157; Command: awk; Return code: 0; Memory used: 0.001GB
PID: 256153; Command: awk; Return code: 0; Memory used: 0.001GB
> `touch /project/shefflab/deploy/rg.databio.org_full/genomes/data/8baf9d24ad8f5678f0fe1f5b21a812d410755d49e3123158/ensembl_gtf/default/_refgenie_build/8baf9d24ad8f5678f0fe1f5b21a812d410755d49e3123158_ensembl_gtf__default.flag` (256161)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.008GB.
PID: 256161; Command: touch; Return code: 0; Memory used: 0.0GB
Asset digest: 39649956004eb926fde3c23d9db73e7f
Default tag for '8baf9d24ad8f5678f0fe1f5b21a812d410755d49e3123158/ensembl_gtf' set to: default
### Pipeline completed. Epilogue
* Elapsed time (this run): 0:00:04
* Total elapsed time (all runs): 0:00:29
* Peak memory (this run): 0.0078 GB
* Pipeline completed time: 2021-04-07 15:41:16
Finished building 'ensembl_gtf' asset
Created alias directories:
- /project/shefflab/deploy/rg.databio.org_full/genomes/alias/dm6/ensembl_gtf/default