### Pipeline run code and environment: * Command: `/home/mjs5kd/.local/bin/refgenie build hg38_noalt_decoy/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/a735e331b2a8ae5cd4e7519575c4c09426a276175c57bd79/star_index/default/_refgenie_build/ * Pipeline started at: (04-07 18:15:50) 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`: `['hg38_noalt_decoy/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/a735e331b2a8ae5cd4e7519575c4c09426a276175c57bd79/star_index/default/_refgenie_build/a735e331b2a8ae5cd4e7519575c4c09426a276175c57bd79_star_index__default.flag` > `mkdir -p /project/shefflab/deploy/rg.databio.org_full/genomes/data/a735e331b2a8ae5cd4e7519575c4c09426a276175c57bd79/star_index/default` (22775)

Command completed. Elapsed time: 0:00:00. Running peak memory: 0.001GB.  
  PID: 22775;	Command: mkdir;	Return code: 0;	Memory used: 0.001GB


> `STAR --runThreadN 8 --runMode genomeGenerate --genomeDir /project/shefflab/deploy/rg.databio.org_full/genomes/data/a735e331b2a8ae5cd4e7519575c4c09426a276175c57bd79/star_index/default --genomeFastaFiles /project/shefflab/deploy/rg.databio.org_full/genomes/data/a735e331b2a8ae5cd4e7519575c4c09426a276175c57bd79/fasta/default/a735e331b2a8ae5cd4e7519575c4c09426a276175c57bd79.fa` (22776)
WARNING: 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 18:15:50 ..... started STAR run
Apr 07 18:15:50 ... starting to generate Genome files
Apr 07 18:17:08 ... starting to sort Suffix Array. This may take a long time...
Apr 07 18:17:29 ... sorting Suffix Array chunks and saving them to disk...
Apr 07 20:47:24 ... loading chunks from disk, packing SA...
Apr 07 20:49:04 ... finished generating suffix array
Apr 07 20:49:04 ... generating Suffix Array index
Apr 07 20:54:09 ... completed Suffix Array index
Apr 07 20:54:09 ... writing Genome to disk ...
Apr 07 20:54:24 ... writing Suffix Array to disk ...
Apr 07 20:56:31 ... writing SAindex to disk
Apr 07 20:56:40 ..... finished successfully
Command completed. Elapsed time: 2:40:51. Running peak memory: 33.369GB. PID: 22776; Command: STAR; Return code: 0; Memory used: 33.369GB > `touch /project/shefflab/deploy/rg.databio.org_full/genomes/data/a735e331b2a8ae5cd4e7519575c4c09426a276175c57bd79/star_index/default/_refgenie_build/a735e331b2a8ae5cd4e7519575c4c09426a276175c57bd79_star_index__default.flag` (22226)

Command completed. Elapsed time: 0:00:00. Running peak memory: 33.369GB.  
  PID: 22226;	Command: touch;	Return code: 0;	Memory used: 0.001GB

Asset digest: c7ff741217f4175af81bd133d6251247
Default tag for 'a735e331b2a8ae5cd4e7519575c4c09426a276175c57bd79/star_index' set to: default

### Pipeline completed. Epilogue
*        Elapsed time (this run):  2:41:54
*  Total elapsed time (all runs):  2:40:51
*         Peak memory (this run):  33.369 GB
*        Pipeline completed time: 2021-04-07 20:57:44
Finished building 'star_index' asset
Created alias directories: 
 - /project/shefflab/deploy/rg.databio.org_full/genomes/alias/hg38_noalt_decoy/star_index/default