### Pipeline run code and environment:
* Command: `/home/mjs5kd/.local/bin/refgenie build hg19/ensembl_gtf --files ensembl_gtf=/project/shefflab/www/refgenie_refgenomes.databio.org/hg19-ensembl_gtf-ensembl_gtf`
* 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/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c/ensembl_gtf/default/_refgenie_build/
* Pipeline started at: (04-07 15:40:39) 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/ensembl_gtf']`
* `assets`: `None`
* `command`: `build`
* `config_file`: `refgenie.yaml`
* `docker`: `False`
* `files`: `[['ensembl_gtf=/project/shefflab/www/refgenie_refgenomes.databio.org/hg19-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/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c/ensembl_gtf/default/_refgenie_build/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c_ensembl_gtf__default.flag`
> `cp /project/shefflab/www/refgenie_refgenomes.databio.org/hg19-ensembl_gtf-ensembl_gtf /project/shefflab/deploy/rg.databio.org_full/genomes/data/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c/ensembl_gtf/default/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c.gtf.gz` (193724)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.001GB.
PID: 193724; Command: cp; Return code: 0; Memory used: 0.001GB
> `gzip -dcf /project/shefflab/deploy/rg.databio.org_full/genomes/data/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c/ensembl_gtf/default/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c.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/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c/ensembl_gtf/default/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c_ensembl_TSS.bed` (193726,193727,193728,193729,193730,193731,193732,193733)
Command completed. Elapsed time: 0:00:10. Running peak memory: 0.009GB.
PID: 193726; Command: gzip; Return code: 0; Memory used: 0.001GB
PID: 193728; Command: sed; Return code: 0; Memory used: 0.001GB
PID: 193730; Command: sed; Return code: 0; Memory used: 0.001GB
PID: 193732; Command: awk; Return code: 0; Memory used: 0.001GB
PID: 193727; Command: grep; Return code: 0; Memory used: 0.001GB
PID: 193731; Command: sed; Return code: 0; Memory used: 0.001GB
PID: 193729; Command: awk; Return code: 0; Memory used: 0.001GB
PID: 193733; Command: LC_COLLATE=C; Return code: 0; Memory used: 0.009GB
> `gzip -dcf /project/shefflab/deploy/rg.databio.org_full/genomes/data/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c/ensembl_gtf/default/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c.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/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c/ensembl_gtf/default/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c_ensembl_gene_body.bed` (193742,193743,193744,193745,193746,193747,193748,193749,193750,193751,193752,193754,193755)
Command completed. Elapsed time: 0:00:06. Running peak memory: 0.009GB.
PID: 193748; Command: awk; Return code: 0; Memory used: 0.001GB
PID: 193750; Command: awk; Return code: 0; Memory used: 0.001GB
PID: 193752; Command: awk; Return code: 0; Memory used: 0.001GB
PID: 193755; Command: LC_COLLATE=C; Return code: 0; Memory used: 0.002GB
PID: 193742; Command: gzip; Return code: 0; Memory used: 0.001GB
PID: 193744; Command: sed; Return code: 0; Memory used: 0.001GB
PID: 193746; Command: sed; Return code: 0; Memory used: 0.001GB
PID: 193749; Command: awk; Return code: 0; Memory used: 0.001GB
PID: 193754; Command: awk; Return code: 0; Memory used: 0.001GB
PID: 193743; Command: awk; Return code: 0; Memory used: 0.001GB
PID: 193747; Command: sed; Return code: 0; Memory used: 0.001GB
PID: 193745; Command: awk; Return code: 0; Memory used: 0.001GB
PID: 193751; Command: awk; Return code: 0; Memory used: 0.001GB
> `touch /project/shefflab/deploy/rg.databio.org_full/genomes/data/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c/ensembl_gtf/default/_refgenie_build/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c_ensembl_gtf__default.flag` (193782)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.009GB.
PID: 193782; Command: touch; Return code: 0; Memory used: 0.001GB
Asset digest: 4091614d92520751bebf268dbdc74490
Waiting for file lock: /project/shefflab/deploy/rg.databio.org_full/rg.databio.org/config/lock.refgenie_config.yaml ......... File unlocked
Default tag for 'baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c/ensembl_gtf' set to: default
### Pipeline completed. Epilogue
* Elapsed time (this run): 0:00:28
* Total elapsed time (all runs): 0:02:30
* Peak memory (this run): 0.0089 GB
* Pipeline completed time: 2021-04-07 15:41:07
Finished building 'ensembl_gtf' asset
Created alias directories:
- /project/shefflab/deploy/rg.databio.org_full/genomes/alias/hg19/ensembl_gtf/default