### 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)
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: 0:00:00. 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'