### Pipeline run code and environment: * Command: `/home/mjs5kd/.local/bin/refgenie build human_alphasat/suffixerator_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/3cd9f8c34e28a1e8823632449b6d8a6afe5a1032245e7475/suffixerator_index/default/_refgenie_build/ * Pipeline started at: (04-07 15:39:20) 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`: `['human_alphasat/suffixerator_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/3cd9f8c34e28a1e8823632449b6d8a6afe5a1032245e7475/suffixerator_index/default/_refgenie_build/3cd9f8c34e28a1e8823632449b6d8a6afe5a1032245e7475_suffixerator_index__default.flag` > `gt suffixerator -dna -pl -tis -suf -lcp -v -showprogress -memlimit 8GB -db /project/shefflab/deploy/rg.databio.org_full/genomes/data/3cd9f8c34e28a1e8823632449b6d8a6afe5a1032245e7475/fasta/default/3cd9f8c34e28a1e8823632449b6d8a6afe5a1032245e7475.fa -indexname /project/shefflab/deploy/rg.databio.org_full/genomes/data/3cd9f8c34e28a1e8823632449b6d8a6afe5a1032245e7475/suffixerator_index/default/3cd9f8c34e28a1e8823632449b6d8a6afe5a1032245e7475.sft` (14317)
WARNING: Skipping mount /opt/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container
# dna=yes
# indexname="/project/shefflab/deploy/rg.databio.org_full/genomes/data/3cd9f8c34e28a1e8823632449b6d8a6afe5a1032245e7475/suffixerator_index/default/3cd9f8c34e28a1e8823632449b6d8a6afe5a1032245e7475.sft"
# prefixlength=automatic
# storespecialcodes=false
# inputfile[0]=/project/shefflab/deploy/rg.databio.org_full/genomes/data/3cd9f8c34e28a1e8823632449b6d8a6afe5a1032245e7475/fasta/default/3cd9f8c34e28a1e8823632449b6d8a6afe5a1032245e7475.fa
# indexname=/project/shefflab/deploy/rg.databio.org_full/genomes/data/3cd9f8c34e28a1e8823632449b6d8a6afe5a1032245e7475/suffixerator_index/default/3cd9f8c34e28a1e8823632449b6d8a6afe5a1032245e7475.sft
# outtistab=true,outsuftab=true,outlcptab=true,outbwttab=false,outbcktab=false,outdestab=true,outsdstab=true,outssptab=true,outkystab=false
# maximumspace=8192 MB
# maxinsertionsort=3
# maxbltriesort=1000
# maxcountingsort=4000
# lcpdist=false
# sizeof (GtUword)=64
# init character encoding (uchar, 24559 bytes, 2.04 bits/symbol)
# init ssptab encoding (ushort, 100 bytes, 0.01 bits/symbol)
# totallength=96500
# numofsequences=43
# specialcharacters=42
# specialranges=42
# realspecialranges=42
# wildcards=0
# wildcardranges=0
# realwildcardranges=0
# occurrences(a)=29271
# occurrences(c)=17589
# occurrences(g)=18951
# occurrences(t)=30647
# automatically determined prefixlength=6
# maxinsertionsort=3
# maxbltriesort=1000
# maxcountingsort=4000
# storespecialcodes=false
# cmpcharbychar=false
# totallength=96500
# sizeof (leftborder)=16388 bytes
# sizeof (countspecialcodes)=4096 bytes
# sizeof (distpfxidx)=1360 bytes
# sizeof (bcktab)=21844 bytes
# largest bucket size=1560
# derived parts=1
# widthofpart[0]=96458
# create suffix_sort_space: suftab uses 64bit values: maxvalue=96500,numofentries=96458
# used workspace for sorting: 0.11 MB
# countinsertionsort=0
# countbltriesort=1102
# countcountingsort=11
# countshortreadsort=2257
# countradixsort=0
# counttqsort=0
Command completed. Elapsed time: 0:00:03. Running peak memory: 0.02GB. PID: 14317; Command: gt; Return code: 0; Memory used: 0.02GB > `touch /project/shefflab/deploy/rg.databio.org_full/genomes/data/3cd9f8c34e28a1e8823632449b6d8a6afe5a1032245e7475/suffixerator_index/default/_refgenie_build/3cd9f8c34e28a1e8823632449b6d8a6afe5a1032245e7475_suffixerator_index__default.flag` (14399)

Command completed. Elapsed time: 0:00:00. Running peak memory: 0.02GB.  
  PID: 14399;	Command: touch;	Return code: 0;	Memory used: 0.0GB

Asset digest: 878a08f12e8106c43fd8a4f5aff91288
Default tag for '3cd9f8c34e28a1e8823632449b6d8a6afe5a1032245e7475/suffixerator_index' set to: default

### Pipeline completed. Epilogue
*        Elapsed time (this run):  0:00:07
*  Total elapsed time (all runs):  0:00:03
*         Peak memory (this run):  0.0196 GB
*        Pipeline completed time: 2021-04-07 15:39:28
Finished building 'suffixerator_index' asset
Created alias directories: 
 - /project/shefflab/deploy/rg.databio.org_full/genomes/alias/human_alphasat/suffixerator_index/default