### Pipeline run code and environment:
* Command: `/home/mjs5kd/.local/bin/refgenie build hg18/star_index`
* Compute host: udc-ba25-18
* Working dir: /sfs/qumulo/qproject/shefflab/deploy/rg.databio.org_full/rg.databio.org
* Outfolder: /project/shefflab/deploy/rg.databio.org_full/genomes/data/9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01/star_index/default/_refgenie_build/
* Pipeline started at: (04-07 18:05:21) 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`: `['hg18/star_index']`
* `assets`: `None`
* `command`: `build`
* `config_file`: `refgenie.yaml`
* `docker`: `False`
* `files`: `None`
* `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/9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01/star_index/default/_refgenie_build/9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01_star_index__default.flag`
> `mkdir -p /project/shefflab/deploy/rg.databio.org_full/genomes/data/9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01/star_index/default` (20294)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.001GB.
PID: 20294; Command: mkdir; Return code: 0; Memory used: 0.001GB
> `STAR --runThreadN 8 --runMode genomeGenerate --genomeDir /project/shefflab/deploy/rg.databio.org_full/genomes/data/9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01/star_index/default --genomeFastaFiles /project/shefflab/deploy/rg.databio.org_full/genomes/data/9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01/fasta/default/9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01.fa` (20295)
[33mWARNING:[0m Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container
Apr 07 18:05:22 ..... started STAR run
Apr 07 18:05:22 ... starting to generate Genome files
Apr 07 18:06:44 ... starting to sort Suffix Array. This may take a long time...
Apr 07 18:07:03 ... sorting Suffix Array chunks and saving them to disk...
Apr 07 20:55:33 ... loading chunks from disk, packing SA...
Apr 07 20:58:12 ... finished generating suffix array
Apr 07 20:58:12 ... generating Suffix Array index
Apr 07 21:03:07 ... completed Suffix Array index
Apr 07 21:03:07 ... writing Genome to disk ...
Apr 07 21:03:22 ... writing Suffix Array to disk ...
Apr 07 21:06:00 ... writing SAindex to disk
Apr 07 21:06:14 ..... finished successfully
Command completed. Elapsed time: 3:00:54. Running peak memory: 31.577GB.
PID: 20295; Command: STAR; Return code: 0; Memory used: 31.577GB
> `touch /project/shefflab/deploy/rg.databio.org_full/genomes/data/9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01/star_index/default/_refgenie_build/9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01_star_index__default.flag` (24924)
Command completed. Elapsed time: 0:00:00. Running peak memory: 31.577GB.
PID: 24924; Command: touch; Return code: 0; Memory used: 0.001GB
Asset digest: 45331ae2a7b9df25955623eac07585d1
Default tag for '9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01/star_index' set to: default
### Pipeline completed. Epilogue
* Elapsed time (this run): 3:02:36
* Total elapsed time (all runs): 3:00:54
* Peak memory (this run): 31.5772 GB
* Pipeline completed time: 2021-04-07 21:07:57
Finished building 'star_index' asset
Created alias directories:
- /project/shefflab/deploy/rg.databio.org_full/genomes/alias/hg18/star_index/default