### Pipeline run code and environment: * Command: `/home/mjs5kd/.local/bin/refgenie build hg38_chr22/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/fec6bcce9821b57f98ffc5d46ebec4f2f756c2e9db800ab7/suffixerator_index/default/_refgenie_build/ * Pipeline started at: (04-07 15:37:07) 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_chr22/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/fec6bcce9821b57f98ffc5d46ebec4f2f756c2e9db800ab7/suffixerator_index/default/_refgenie_build/fec6bcce9821b57f98ffc5d46ebec4f2f756c2e9db800ab7_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/fec6bcce9821b57f98ffc5d46ebec4f2f756c2e9db800ab7/fasta/default/fec6bcce9821b57f98ffc5d46ebec4f2f756c2e9db800ab7.fa -indexname /project/shefflab/deploy/rg.databio.org_full/genomes/data/fec6bcce9821b57f98ffc5d46ebec4f2f756c2e9db800ab7/suffixerator_index/default/fec6bcce9821b57f98ffc5d46ebec4f2f756c2e9db800ab7.sft` (11545)
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/fec6bcce9821b57f98ffc5d46ebec4f2f756c2e9db800ab7/suffixerator_index/default/fec6bcce9821b57f98ffc5d46ebec4f2f756c2e9db800ab7.sft"
# prefixlength=automatic
# storespecialcodes=false
# inputfile[0]=/project/shefflab/deploy/rg.databio.org_full/genomes/data/fec6bcce9821b57f98ffc5d46ebec4f2f756c2e9db800ab7/fasta/default/fec6bcce9821b57f98ffc5d46ebec4f2f756c2e9db800ab7.fa
# indexname=/project/shefflab/deploy/rg.databio.org_full/genomes/data/fec6bcce9821b57f98ffc5d46ebec4f2f756c2e9db800ab7/suffixerator_index/default/fec6bcce9821b57f98ffc5d46ebec4f2f756c2e9db800ab7.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=5
# wildcardranges of length 25=5
# wildcardranges of length 76=1
# wildcardranges of length 100=1
# wildcardranges of length 113=1
# wildcardranges of length 189=1
# wildcardranges of length 320=1
# wildcardranges of length 411=1
# wildcardranges of length 493=1
# wildcardranges of length 494=1
# wildcardranges of length 557=1
# wildcardranges of length 879=1
# wildcardranges of length 1131=1
# wildcardranges of length 1217=1
# wildcardranges of length 2175=1
# wildcardranges of length 2248=1
# wildcardranges of length 2477=1
# wildcardranges of length 2829=1
# wildcardranges of length 3201=1
# wildcardranges of length 3535=1
# wildcardranges of length 7856=1
# wildcardranges of length 23171=1
# init character encoding (uint32, 10687255 bytes, 2.00 bits/symbol)
# init ssptab encoding (uint32, 244 bytes, 0.00 bits/symbol)
# totallength=42746301
# numofsequences=60
# specialcharacters=53661
# specialranges=89
# realspecialranges=89
# wildcards=53602
# wildcardranges=30
# realwildcardranges=30
# occurrences(a)=11345849
# occurrences(c)=9963208
# occurrences(g)=10083370
# occurrences(t)=11300213
# automatically determined prefixlength=10
# maxinsertionsort=3
# maxbltriesort=1000
# maxcountingsort=4000
# storespecialcodes=false
# cmpcharbychar=false
# totallength=42746301
# sizeof (leftborder)=4194308 bytes
# sizeof (countspecialcodes)=1048576 bytes
# sizeof (distpfxidx)=349520 bytes
# sizeof (bcktab)=5592404 bytes
# largest bucket size=56488
# derived parts=1
# widthofpart[0]=42692640
# create suffix_sort_space: suftab uses 64bit values: maxvalue=42746301,numofentries=42692640
# used workspace for sorting: 0.11 MB
# countinsertionsort=95245
# countbltriesort=946047
# countcountingsort=2759
# countshortreadsort=0
# countradixsort=0
# counttqsort=342
Command completed. Elapsed time: 0:01:20. Running peak memory: 0.381GB. PID: 11545; Command: gt; Return code: 0; Memory used: 0.381GB > `touch /project/shefflab/deploy/rg.databio.org_full/genomes/data/fec6bcce9821b57f98ffc5d46ebec4f2f756c2e9db800ab7/suffixerator_index/default/_refgenie_build/fec6bcce9821b57f98ffc5d46ebec4f2f756c2e9db800ab7_suffixerator_index__default.flag` (13375)

Command completed. Elapsed time: 0:00:00. Running peak memory: 0.381GB.  
  PID: 13375;	Command: touch;	Return code: 0;	Memory used: 0.001GB

Asset digest: b109666768e027c5b333aa09c372da6a
Default tag for 'fec6bcce9821b57f98ffc5d46ebec4f2f756c2e9db800ab7/suffixerator_index' set to: default

### Pipeline completed. Epilogue
*        Elapsed time (this run):  0:01:25
*  Total elapsed time (all runs):  0:01:20
*         Peak memory (this run):  0.3812 GB
*        Pipeline completed time: 2021-04-07 15:38:32
Finished building 'suffixerator_index' asset
Created alias directories: 
 - /project/shefflab/deploy/rg.databio.org_full/genomes/alias/hg38_chr22/suffixerator_index/default