### Pipeline run code and environment: * Command: `/home/mjs5kd/.local/bin/refgenie build hs38d1/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/45818b389d17308bb520512bb0d4f76764430c3eaaacc4a9/star_index/default/_refgenie_build/ * Pipeline started at: (04-07 18:14:49) 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`: `['hs38d1/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/45818b389d17308bb520512bb0d4f76764430c3eaaacc4a9/star_index/default/_refgenie_build/45818b389d17308bb520512bb0d4f76764430c3eaaacc4a9_star_index__default.flag` > `mkdir -p /project/shefflab/deploy/rg.databio.org_full/genomes/data/45818b389d17308bb520512bb0d4f76764430c3eaaacc4a9/star_index/default` (22268)

Command completed. Elapsed time: 0:00:00. Running peak memory: 0.0GB.  
  PID: 22268;	Command: mkdir;	Return code: 0;	Memory used: 0.0GB


> `STAR --runThreadN 8 --runMode genomeGenerate --genomeDir /project/shefflab/deploy/rg.databio.org_full/genomes/data/45818b389d17308bb520512bb0d4f76764430c3eaaacc4a9/star_index/default --genomeFastaFiles /project/shefflab/deploy/rg.databio.org_full/genomes/data/45818b389d17308bb520512bb0d4f76764430c3eaaacc4a9/fasta/default/45818b389d17308bb520512bb0d4f76764430c3eaaacc4a9.fa` (22269)
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 18:14:49 ..... started STAR run
Apr 07 18:14:49 ... starting to generate Genome files
WARNING: --genomeSAindexNbases 14 is too large for the genome size=625213440, which may cause seg-fault at the mapping step. Re-run genome generation with recommended --genomeSAindexNbases 13		 Apr 07 18:14:50
Apr 07 18:14:52 ... starting to sort Suffix Array. This may take a long time...
Apr 07 18:14:54 ... sorting Suffix Array chunks and saving them to disk...
Apr 07 18:15:08 ... loading chunks from disk, packing SA...
Apr 07 18:15:09 ... finished generating suffix array
Apr 07 18:15:09 ... generating Suffix Array index
Apr 07 18:15:14 ... completed Suffix Array index
Apr 07 18:15:14 ... writing Genome to disk ...
Apr 07 18:15:17 ... writing Suffix Array to disk ...
Apr 07 18:15:17 ... writing SAindex to disk
Apr 07 18:15:23 ..... finished successfully
Command completed. Elapsed time: 0:00:35. Running peak memory: 1.362GB. PID: 22269; Command: STAR; Return code: 0; Memory used: 1.362GB > `touch /project/shefflab/deploy/rg.databio.org_full/genomes/data/45818b389d17308bb520512bb0d4f76764430c3eaaacc4a9/star_index/default/_refgenie_build/45818b389d17308bb520512bb0d4f76764430c3eaaacc4a9_star_index__default.flag` (22646)

Command completed. Elapsed time: 0:00:00. Running peak memory: 1.362GB.  
  PID: 22646;	Command: touch;	Return code: 0;	Memory used: 0.0GB

Asset digest: c0e4985c6d8c02c6a53c6bffcde0535d
Default tag for '45818b389d17308bb520512bb0d4f76764430c3eaaacc4a9/star_index' set to: default

### Pipeline completed. Epilogue
*        Elapsed time (this run):  0:00:40
*  Total elapsed time (all runs):  0:00:35
*         Peak memory (this run):  1.3618 GB
*        Pipeline completed time: 2021-04-07 18:15:29
Finished building 'star_index' asset
Created alias directories: 
 - /project/shefflab/deploy/rg.databio.org_full/genomes/alias/hs38d1/star_index/default