### Pipeline run code and environment:
* Command: `/home/mjs5kd/.local/bin/refgenie build hg19/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/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c/star_index/default/_refgenie_build/
* Pipeline started at: (04-07 18:09:09) 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`: `['hg19/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/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c/star_index/default/_refgenie_build/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c_star_index__default.flag`
> `mkdir -p /project/shefflab/deploy/rg.databio.org_full/genomes/data/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c/star_index/default` (20903)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.001GB.
PID: 20903; Command: mkdir; Return code: 0; Memory used: 0.001GB
> `STAR --runThreadN 8 --runMode genomeGenerate --genomeDir /project/shefflab/deploy/rg.databio.org_full/genomes/data/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c/star_index/default --genomeFastaFiles /project/shefflab/deploy/rg.databio.org_full/genomes/data/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c/fasta/default/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c.fa` (20904)
[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 18:09:09 ..... started STAR run
Apr 07 18:09:09 ... starting to generate Genome files
Apr 07 18:10:33 ... starting to sort Suffix Array. This may take a long time...
Apr 07 18:10:52 ... sorting Suffix Array chunks and saving them to disk...
Apr 07 20:57:38 ... loading chunks from disk, packing SA...
Apr 07 20:59:11 ... finished generating suffix array
Apr 07 20:59:11 ... generating Suffix Array index
Apr 07 21:04:08 ... completed Suffix Array index
Apr 07 21:04:09 ... writing Genome to disk ...
Apr 07 21:04:37 ... writing Suffix Array to disk ...
Apr 07 21:06:54 ... writing SAindex to disk
Apr 07 21:07:05 ..... finished successfully
Command completed. Elapsed time: 2:57:56. Running peak memory: 31.785GB.
PID: 20904; Command: STAR; Return code: 0; Memory used: 31.785GB
> `touch /project/shefflab/deploy/rg.databio.org_full/genomes/data/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c/star_index/default/_refgenie_build/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c_star_index__default.flag` (25423)
Command completed. Elapsed time: 0:00:00. Running peak memory: 31.785GB.
PID: 25423; Command: touch; Return code: 0; Memory used: 0.001GB
Asset digest: 3db00cbcdd1c60b924910bbe14d76dcd
Default tag for 'baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c/star_index' set to: default
### Pipeline completed. Epilogue
* Elapsed time (this run): 2:59:00
* Total elapsed time (all runs): 2:57:56
* Peak memory (this run): 31.7846 GB
* Pipeline completed time: 2021-04-07 21:08:09
Finished building 'star_index' asset
Created alias directories:
- /project/shefflab/deploy/rg.databio.org_full/genomes/alias/hg19/star_index/default