### Pipeline run code and environment: * Command: `/home/mjs5kd/.local/bin/refgenie build human_repeats/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/7319f9237651755047bc40d7f7a9770d42a537e840f4e105/suffixerator_index/default/_refgenie_build/ * Pipeline started at: (04-07 15:38:59) 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`: `['human_repeats/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/7319f9237651755047bc40d7f7a9770d42a537e840f4e105/suffixerator_index/default/_refgenie_build/7319f9237651755047bc40d7f7a9770d42a537e840f4e105_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/7319f9237651755047bc40d7f7a9770d42a537e840f4e105/fasta/default/7319f9237651755047bc40d7f7a9770d42a537e840f4e105.fa -indexname /project/shefflab/deploy/rg.databio.org_full/genomes/data/7319f9237651755047bc40d7f7a9770d42a537e840f4e105/suffixerator_index/default/7319f9237651755047bc40d7f7a9770d42a537e840f4e105.sft` (13984)
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/7319f9237651755047bc40d7f7a9770d42a537e840f4e105/suffixerator_index/default/7319f9237651755047bc40d7f7a9770d42a537e840f4e105.sft"
# prefixlength=automatic
# storespecialcodes=false
# inputfile[0]=/project/shefflab/deploy/rg.databio.org_full/genomes/data/7319f9237651755047bc40d7f7a9770d42a537e840f4e105/fasta/default/7319f9237651755047bc40d7f7a9770d42a537e840f4e105.fa
# indexname=/project/shefflab/deploy/rg.databio.org_full/genomes/data/7319f9237651755047bc40d7f7a9770d42a537e840f4e105/suffixerator_index/default/7319f9237651755047bc40d7f7a9770d42a537e840f4e105.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
# wildcardranges of length 1=8
# wildcardranges of length 2=1
# wildcardranges of length 3=1
# init character encoding (ushort, 35959 bytes, 2.03 bits/symbol)
# init ssptab encoding (ushort, 126 bytes, 0.01 bits/symbol)
# totallength=141829
# numofsequences=52
# specialcharacters=64
# specialranges=61
# realspecialranges=61
# wildcards=13
# wildcardranges=10
# realwildcardranges=10
# occurrences(a)=36240
# occurrences(c)=31834
# occurrences(g)=31214
# occurrences(t)=42477
# automatically determined prefixlength=6
# maxinsertionsort=3
# maxbltriesort=1000
# maxcountingsort=4000
# storespecialcodes=false
# cmpcharbychar=false
# totallength=141829
# sizeof (leftborder)=16388 bytes
# sizeof (countspecialcodes)=4096 bytes
# sizeof (distpfxidx)=1360 bytes
# sizeof (bcktab)=21844 bytes
# largest bucket size=1567
# derived parts=1
# widthofpart[0]=141765
# create suffix_sort_space: suftab uses 64bit values: maxvalue=141829,numofentries=141765
# used workspace for sorting: 0.11 MB
# countinsertionsort=0
# countbltriesort=2089
# countcountingsort=11
# countshortreadsort=2159
# countradixsort=0
# counttqsort=0
Command completed. Elapsed time: 0:00:02. Running peak memory: 0.021GB. PID: 13984; Command: gt; Return code: 0; Memory used: 0.021GB > `touch /project/shefflab/deploy/rg.databio.org_full/genomes/data/7319f9237651755047bc40d7f7a9770d42a537e840f4e105/suffixerator_index/default/_refgenie_build/7319f9237651755047bc40d7f7a9770d42a537e840f4e105_suffixerator_index__default.flag` (14070)

Command completed. Elapsed time: 0:00:00. Running peak memory: 0.021GB.  
  PID: 14070;	Command: touch;	Return code: 0;	Memory used: 0.0GB

Asset digest: 58d34093e5f2e22721161b8fb5525378
Default tag for '7319f9237651755047bc40d7f7a9770d42a537e840f4e105/suffixerator_index' set to: default

### Pipeline completed. Epilogue
*        Elapsed time (this run):  0:00:05
*  Total elapsed time (all runs):  0:00:02
*         Peak memory (this run):  0.0205 GB
*        Pipeline completed time: 2021-04-07 15:39:04
Finished building 'suffixerator_index' asset
Created alias directories: 
 - /project/shefflab/deploy/rg.databio.org_full/genomes/alias/human_repeats/suffixerator_index/default