### Pipeline run code and environment:
* Command: `/home/mjs5kd/.local/bin/refgenie build mouse_chrM2x/fasta --genome-description test description mouse chrM2x --files fasta=/project/shefflab/www/refgenie_rg.databio.org/mouse_chrM2x-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/43f14ba8beed34d52edb244e26f193df6edbb467bd55d37a/fasta/default/_refgenie_build/
* Pipeline started at: (04-07 15:22:22) 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`: `['mouse_chrM2x/fasta']`
* `assets`: `None`
* `command`: `build`
* `config_file`: `refgenie.yaml`
* `docker`: `False`
* `files`: `[['fasta=/project/shefflab/www/refgenie_rg.databio.org/mouse_chrM2x-fasta-fasta']]`
* `genome`: `None`
* `genome_config`: `None`
* `genome_description`: `test description mouse chrM2x`
* `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/43f14ba8beed34d52edb244e26f193df6edbb467bd55d37a/fasta/default/_refgenie_build/43f14ba8beed34d52edb244e26f193df6edbb467bd55d37a_fasta__default.flag`
> `cp /project/shefflab/www/refgenie_rg.databio.org/mouse_chrM2x-fasta-fasta /project/shefflab/deploy/rg.databio.org_full/genomes/data/43f14ba8beed34d52edb244e26f193df6edbb467bd55d37a/fasta/default/43f14ba8beed34d52edb244e26f193df6edbb467bd55d37a.fa.gz` (85592)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.001GB.
PID: 85592; Command: cp; Return code: 0; Memory used: 0.001GB
> `gzip -df /project/shefflab/deploy/rg.databio.org_full/genomes/data/43f14ba8beed34d52edb244e26f193df6edbb467bd55d37a/fasta/default/43f14ba8beed34d52edb244e26f193df6edbb467bd55d37a.fa.gz` (85593)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.001GB.
PID: 85593; Command: gzip; Return code: 0; Memory used: 0.001GB
> `samtools faidx /project/shefflab/deploy/rg.databio.org_full/genomes/data/43f14ba8beed34d52edb244e26f193df6edbb467bd55d37a/fasta/default/43f14ba8beed34d52edb244e26f193df6edbb467bd55d37a.fa` (85594)
[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
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.001GB.
PID: 85594; Command: samtools; Return code: 0; Memory used: 0.001GB
> `cut -f 1,2 /project/shefflab/deploy/rg.databio.org_full/genomes/data/43f14ba8beed34d52edb244e26f193df6edbb467bd55d37a/fasta/default/43f14ba8beed34d52edb244e26f193df6edbb467bd55d37a.fa.fai > /project/shefflab/deploy/rg.databio.org_full/genomes/data/43f14ba8beed34d52edb244e26f193df6edbb467bd55d37a/fasta/default/43f14ba8beed34d52edb244e26f193df6edbb467bd55d37a.chrom.sizes` (85633)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.001GB.
PID: 85633; Command: cut; Return code: 0; Memory used: 0.001GB
> `touch /project/shefflab/deploy/rg.databio.org_full/genomes/data/43f14ba8beed34d52edb244e26f193df6edbb467bd55d37a/fasta/default/_refgenie_build/43f14ba8beed34d52edb244e26f193df6edbb467bd55d37a_fasta__default.flag` (85635)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.001GB.
PID: 85635; Command: touch; Return code: 0; Memory used: 0.001GB
Asset digest: 8dfe402f7d29d5b036dd8937119e4404
Default tag for '43f14ba8beed34d52edb244e26f193df6edbb467bd55d37a/fasta' set to: default
### Pipeline completed. Epilogue
* Elapsed time (this run): 0:00:01
* Total elapsed time (all runs): 0:00:01
* Peak memory (this run): 0.0015 GB
* Pipeline completed time: 2021-04-07 15:22:23
Finished building 'fasta' asset
Created alias directories:
- /project/shefflab/deploy/rg.databio.org_full/genomes/alias/mouse_chrM2x/fasta/default
### Pipeline run code and environment:
* Command: `/home/mjs5kd/.local/bin/refgenie build mouse_chrM2x/fasta --genome-description test description mouse chrM2x --files fasta=/project/shefflab/www/refgenie_refgenomes.databio.org/mouse_chrM2x-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/43f14ba8beed34d52edb244e26f193df6edbb467bd55d37a/fasta/default/_refgenie_build/
* Pipeline started at: (04-07 15:26:55) 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`: `['mouse_chrM2x/fasta']`
* `assets`: `None`
* `command`: `build`
* `config_file`: `refgenie.yaml`
* `docker`: `False`
* `files`: `[['fasta=/project/shefflab/www/refgenie_refgenomes.databio.org/mouse_chrM2x-fasta-fasta']]`
* `genome`: `None`
* `genome_config`: `None`
* `genome_description`: `test description mouse chrM2x`
* `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 exists: `/project/shefflab/deploy/rg.databio.org_full/genomes/data/43f14ba8beed34d52edb244e26f193df6edbb467bd55d37a/fasta/default/_refgenie_build/43f14ba8beed34d52edb244e26f193df6edbb467bd55d37a_fasta__default.flag`
Asset digest: 8dfe402f7d29d5b036dd8937119e4404
### Pipeline completed. Epilogue
* Elapsed time (this run): 0:00:00
* Total elapsed time (all runs): 0:00:01
* Peak memory (this run): 0 GB
* Pipeline completed time: 2021-04-07 15:26:55
Finished building 'fasta' asset
Removed existing flag: '/project/shefflab/deploy/rg.databio.org_full/genomes/data/43f14ba8beed34d52edb244e26f193df6edbb467bd55d37a/fasta/default/_refgenie_build/refgenie_completed.flag'
### Pipeline run code and environment:
* Command: `/home/mjs5kd/.local/bin/refgenie build mouse_chrM2x/fasta --genome-description test description mouse chrM2x --files fasta=/project/shefflab/www/refgenie_refgenomes.databio.org/mouse_chrM2x-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/43f14ba8beed34d52edb244e26f193df6edbb467bd55d37a/fasta/default/_refgenie_build/
* Pipeline started at: (04-07 15:30:59) 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`: `['mouse_chrM2x/fasta']`
* `assets`: `None`
* `command`: `build`
* `config_file`: `refgenie.yaml`
* `docker`: `False`
* `files`: `[['fasta=/project/shefflab/www/refgenie_refgenomes.databio.org/mouse_chrM2x-fasta-fasta']]`
* `genome`: `None`
* `genome_config`: `None`
* `genome_description`: `test description mouse chrM2x`
* `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 exists: `/project/shefflab/deploy/rg.databio.org_full/genomes/data/43f14ba8beed34d52edb244e26f193df6edbb467bd55d37a/fasta/default/_refgenie_build/43f14ba8beed34d52edb244e26f193df6edbb467bd55d37a_fasta__default.flag`
Asset digest: 8dfe402f7d29d5b036dd8937119e4404
### Pipeline completed. Epilogue
* Elapsed time (this run): 0:00:00
* Total elapsed time (all runs): 0:00:01
* Peak memory (this run): 0 GB
* Pipeline completed time: 2021-04-07 15:30:59
Finished building 'fasta' asset
Removed existing flag: '/project/shefflab/deploy/rg.databio.org_full/genomes/data/43f14ba8beed34d52edb244e26f193df6edbb467bd55d37a/fasta/default/_refgenie_build/refgenie_completed.flag'