### Pipeline run code and environment:
* Command: `/home/mjs5kd/.local/bin/refgenie build hg38/suffixerator_index --params memlimit=32GB`
* 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/2230c535660fb4774114bfa966a62f823fdb6d21acf138d4/suffixerator_index/default/_refgenie_build/
* Pipeline started at: (04-07 15:40:10) 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/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`: `[['memlimit=32GB']]`
* `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/2230c535660fb4774114bfa966a62f823fdb6d21acf138d4/suffixerator_index/default/_refgenie_build/2230c535660fb4774114bfa966a62f823fdb6d21acf138d4_suffixerator_index__default.flag`
> `gt suffixerator -dna -pl -tis -suf -lcp -v -showprogress -memlimit 32GB -db /project/shefflab/deploy/rg.databio.org_full/genomes/data/2230c535660fb4774114bfa966a62f823fdb6d21acf138d4/fasta/default/2230c535660fb4774114bfa966a62f823fdb6d21acf138d4.fa -indexname /project/shefflab/deploy/rg.databio.org_full/genomes/data/2230c535660fb4774114bfa966a62f823fdb6d21acf138d4/suffixerator_index/default/2230c535660fb4774114bfa966a62f823fdb6d21acf138d4.sft` (15320)
[33mWARNING:[0m 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/2230c535660fb4774114bfa966a62f823fdb6d21acf138d4/suffixerator_index/default/2230c535660fb4774114bfa966a62f823fdb6d21acf138d4.sft"
# prefixlength=automatic
# storespecialcodes=false
# inputfile[0]=/project/shefflab/deploy/rg.databio.org_full/genomes/data/2230c535660fb4774114bfa966a62f823fdb6d21acf138d4/fasta/default/2230c535660fb4774114bfa966a62f823fdb6d21acf138d4.fa
# indexname=/project/shefflab/deploy/rg.databio.org_full/genomes/data/2230c535660fb4774114bfa966a62f823fdb6d21acf138d4/suffixerator_index/default/2230c535660fb4774114bfa966a62f823fdb6d21acf138d4.sft
# outtistab=true,outsuftab=true,outlcptab=true,outbwttab=false,outbcktab=false,outdestab=true,outsdstab=true,outssptab=true,outkystab=false
# maximumspace=32768 MB
# maxinsertionsort=3
# maxbltriesort=1000
# maxcountingsort=4000
# lcpdist=false
# sizeof (GtUword)=64
# wildcardranges of length 1=211
# wildcardranges of length 2=19
# wildcardranges of length 3=3
# wildcardranges of length 4=1
# wildcardranges of length 5=1
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# wildcardranges of length 30000000=1
# init character encoding (uint32, 774989423 bytes, 2.00 bits/symbol)
# init ssptab encoding (uint32, 784 bytes, 0.00 bits/symbol)
# totallength=3099922735
# numofsequences=195
# specialcharacters=165046284
# specialranges=1184
# realspecialranges=1184
# wildcards=165046090
# wildcardranges=1037
# realwildcardranges=1037
# occurrences(a)=866420001
# occurrences(c)=598683433
# occurrences(g)=600854940
# occurrences(t)=868918077
# automatically determined prefixlength=13
# maxinsertionsort=3
# maxbltriesort=1000
# maxcountingsort=4000
# storespecialcodes=false
# cmpcharbychar=false
# totallength=3099922735
# sizeof (leftborder)=268435460 bytes
# sizeof (countspecialcodes)=67108864 bytes
# sizeof (distpfxidx)=22369616 bytes
# sizeof (bcktab)=357913940 bytes
# largest bucket size=1739494
# derived parts=1
# widthofpart[0]=2934876451
# create suffix_sort_space: suftab uses 64bit values: maxvalue=3099922735,numofentries=2934876451
# used workspace for sorting: 0.11 MB
# countinsertionsort=8522740
# countbltriesort=54957977
# countcountingsort=293720
# countshortreadsort=0
# countradixsort=0
# counttqsort=79367
Command completed. Elapsed time: 0:49:31. Running peak memory: 24.604GB.
PID: 15320; Command: gt; Return code: 0; Memory used: 24.604GB
> `touch /project/shefflab/deploy/rg.databio.org_full/genomes/data/2230c535660fb4774114bfa966a62f823fdb6d21acf138d4/suffixerator_index/default/_refgenie_build/2230c535660fb4774114bfa966a62f823fdb6d21acf138d4_suffixerator_index__default.flag` (954)
Command completed. Elapsed time: 0:00:00. Running peak memory: 24.604GB.
PID: 954; Command: touch; Return code: 0; Memory used: 0.0GB
Asset digest: a90e2301049a1af60443c1ef03f4f9da
Waiting for file lock: /project/shefflab/deploy/rg.databio.org_full/rg.databio.org/config/lock.refgenie_config.yaml . File unlocked
Default tag for '2230c535660fb4774114bfa966a62f823fdb6d21acf138d4/suffixerator_index' set to: default
### Pipeline completed. Epilogue
* Elapsed time (this run): 0:55:49
* Total elapsed time (all runs): 0:49:31
* Peak memory (this run): 24.604 GB
* Pipeline completed time: 2021-04-07 16:35:59
Finished building 'suffixerator_index' asset
Created alias directories:
- /project/shefflab/deploy/rg.databio.org_full/genomes/alias/hg38/suffixerator_index/default