### Pipeline run code and environment: * Command: `/home/mjs5kd/.local/bin/refgenie build hg19/fasta --files fasta=/project/shefflab/www/refgenie_refgenomes.databio.org/hg19-fasta-fasta` * Compute host: udc-aw34-2c1 * 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/fasta/default/_refgenie_build/ * Pipeline started at: (04-07 15:29:19) 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/fasta']` * `assets`: `None` * `command`: `build` * `config_file`: `refgenie.yaml` * `docker`: `False` * `files`: `[['fasta=/project/shefflab/www/refgenie_refgenomes.databio.org/hg19-fasta-fasta']]` * `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/fasta/default/_refgenie_build/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c_fasta__default.flag` > `cp /project/shefflab/www/refgenie_refgenomes.databio.org/hg19-fasta-fasta /project/shefflab/deploy/rg.databio.org_full/genomes/data/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c/fasta/default/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c.fa.gz` (88011)

Command completed. Elapsed time: 0:00:04. Running peak memory: 0.002GB.  
  PID: 88011;	Command: cp;	Return code: 0;	Memory used: 0.002GB


> `gzip -df /project/shefflab/deploy/rg.databio.org_full/genomes/data/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c/fasta/default/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c.fa.gz` (88031)

Command completed. Elapsed time: 0:00:33. Running peak memory: 0.002GB.  
  PID: 88031;	Command: gzip;	Return code: 0;	Memory used: 0.001GB


> `samtools faidx /project/shefflab/deploy/rg.databio.org_full/genomes/data/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c/fasta/default/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c.fa` (88145)
WARNING: Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container
Command completed. Elapsed time: 0:00:11. Running peak memory: 0.017GB. PID: 88145; Command: samtools; Return code: 0; Memory used: 0.017GB > `cut -f 1,2 /project/shefflab/deploy/rg.databio.org_full/genomes/data/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c/fasta/default/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c.fa.fai > /project/shefflab/deploy/rg.databio.org_full/genomes/data/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c/fasta/default/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c.chrom.sizes` (88561)

Command completed. Elapsed time: 0:00:00. Running peak memory: 0.017GB.  
  PID: 88561;	Command: cut;	Return code: 0;	Memory used: 0.001GB


> `touch /project/shefflab/deploy/rg.databio.org_full/genomes/data/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c/fasta/default/_refgenie_build/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c_fasta__default.flag` (88563)

Command completed. Elapsed time: 0:00:00. Running peak memory: 0.017GB.  
  PID: 88563;	Command: touch;	Return code: 0;	Memory used: 0.001GB

Asset digest: 7ce3b03e30d6ef76af8c3ad09a141dfc
Default tag for 'baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c/fasta' set to: default

### Pipeline completed. Epilogue
*        Elapsed time (this run):  0:00:55
*  Total elapsed time (all runs):  0:00:49
*         Peak memory (this run):  0.0167 GB
*        Pipeline completed time: 2021-04-07 15:30:14
Finished building 'fasta' asset
Created alias directories: 
 - /project/shefflab/deploy/rg.databio.org_full/genomes/alias/hg19/fasta/default