### Pipeline run code and environment:
* Command: `/home/mjs5kd/.local/bin/refgenie build rn6/ensembl_gtf --files ensembl_gtf=/project/shefflab/www/refgenie_refgenomes.databio.org/rn6-ensembl_gtf-ensembl_gtf`
* Compute host: udc-aw29-24a
* Working dir: /sfs/qumulo/qproject/shefflab/deploy/rg.databio.org_full/rg.databio.org
* Outfolder: /project/shefflab/deploy/rg.databio.org_full/genomes/data/79168fd950d561cf5ce454dd27593c0af429b32cddce5ce9/ensembl_gtf/default/_refgenie_build/
* Pipeline started at: (04-07 15:41:09) 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`: `['rn6/ensembl_gtf']`
* `assets`: `None`
* `command`: `build`
* `config_file`: `refgenie.yaml`
* `docker`: `False`
* `files`: `[['ensembl_gtf=/project/shefflab/www/refgenie_refgenomes.databio.org/rn6-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/79168fd950d561cf5ce454dd27593c0af429b32cddce5ce9/ensembl_gtf/default/_refgenie_build/79168fd950d561cf5ce454dd27593c0af429b32cddce5ce9_ensembl_gtf__default.flag`
> `cp /project/shefflab/www/refgenie_refgenomes.databio.org/rn6-ensembl_gtf-ensembl_gtf /project/shefflab/deploy/rg.databio.org_full/genomes/data/79168fd950d561cf5ce454dd27593c0af429b32cddce5ce9/ensembl_gtf/default/79168fd950d561cf5ce454dd27593c0af429b32cddce5ce9.gtf.gz` (94715)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.001GB.
PID: 94715; Command: cp; Return code: 0; Memory used: 0.001GB
> `gzip -dcf /project/shefflab/deploy/rg.databio.org_full/genomes/data/79168fd950d561cf5ce454dd27593c0af429b32cddce5ce9/ensembl_gtf/default/79168fd950d561cf5ce454dd27593c0af429b32cddce5ce9.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/79168fd950d561cf5ce454dd27593c0af429b32cddce5ce9/ensembl_gtf/default/79168fd950d561cf5ce454dd27593c0af429b32cddce5ce9_ensembl_TSS.bed` (94716,94717,94718,94719,94720,94721,94722,94723)
Command completed. Elapsed time: 0:00:03. Running peak memory: 0.009GB.
PID: 94718; Command: sed; Return code: 0; Memory used: 0.001GB
PID: 94720; Command: sed; Return code: 0; Memory used: 0.001GB
PID: 94722; Command: awk; Return code: 0; Memory used: 0.001GB
PID: 94716; Command: gzip; Return code: 0; Memory used: 0.001GB
PID: 94719; Command: awk; Return code: 0; Memory used: 0.001GB
PID: 94723; Command: LC_COLLATE=C; Return code: 0; Memory used: 0.009GB
PID: 94717; Command: grep; Return code: 0; Memory used: 0.001GB
PID: 94721; Command: sed; Return code: 0; Memory used: 0.001GB
> `gzip -dcf /project/shefflab/deploy/rg.databio.org_full/genomes/data/79168fd950d561cf5ce454dd27593c0af429b32cddce5ce9/ensembl_gtf/default/79168fd950d561cf5ce454dd27593c0af429b32cddce5ce9.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/79168fd950d561cf5ce454dd27593c0af429b32cddce5ce9/ensembl_gtf/default/79168fd950d561cf5ce454dd27593c0af429b32cddce5ce9_ensembl_gene_body.bed` (94732,94733,94734,94735,94736,94737,94738,94739,94740,94741,94742,94743,94744)
Command completed. Elapsed time: 0:00:02. Running peak memory: 0.009GB.
PID: 94733; Command: awk; Return code: 0; Memory used: 0.001GB
PID: 94735; Command: awk; Return code: 0; Memory used: 0.001GB
PID: 94737; Command: sed; Return code: 0; Memory used: 0.001GB
PID: 94739; Command: awk; Return code: 0; Memory used: 0.001GB
PID: 94741; Command: awk; Return code: 0; Memory used: 0.001GB
PID: 94743; Command: awk; Return code: 0; Memory used: 0.001GB
PID: 94732; Command: gzip; Return code: 0; Memory used: 0.001GB
PID: 94736; Command: sed; Return code: 0; Memory used: 0.001GB
PID: 94740; Command: awk; Return code: 0; Memory used: 0.001GB
PID: 94744; Command: LC_COLLATE=C; Return code: 0; Memory used: 0.003GB
PID: 94734; Command: sed; Return code: 0; Memory used: 0.001GB
PID: 94742; Command: awk; Return code: 0; Memory used: 0.001GB
PID: 94738; Command: awk; Return code: 0; Memory used: 0.001GB
> `touch /project/shefflab/deploy/rg.databio.org_full/genomes/data/79168fd950d561cf5ce454dd27593c0af429b32cddce5ce9/ensembl_gtf/default/_refgenie_build/79168fd950d561cf5ce454dd27593c0af429b32cddce5ce9_ensembl_gtf__default.flag` (94752)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.009GB.
PID: 94752; Command: touch; Return code: 0; Memory used: 0.001GB
Asset digest: 813146b78037a00e15f4f119ddf0d6d2
Default tag for '79168fd950d561cf5ce454dd27593c0af429b32cddce5ce9/ensembl_gtf' set to: default
### Pipeline completed. Epilogue
* Elapsed time (this run): 0:00:06
* Total elapsed time (all runs): 0:00:48
* Peak memory (this run): 0.0089 GB
* Pipeline completed time: 2021-04-07 15:41:15
Finished building 'ensembl_gtf' asset
Created alias directories:
- /project/shefflab/deploy/rg.databio.org_full/genomes/alias/rn6/ensembl_gtf/default