### Pipeline run code and environment: * Command: `/home/mjs5kd/.local/bin/refgenie build mouse_chrM2x/suffixerator_index` * Compute host: udc-ba25-17 * Working dir: /sfs/qumulo/qproject/shefflab/deploy/rg.databio.org_full/rg.databio.org * Outfolder: /project/shefflab/deploy/rg.databio.org_full/genomes/data/43f14ba8beed34d52edb244e26f193df6edbb467bd55d37a/suffixerator_index/default/_refgenie_build/ * Pipeline started at: (04-07 15:40:24) elapsed: 1.0 _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`: `['mouse_chrM2x/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/43f14ba8beed34d52edb244e26f193df6edbb467bd55d37a/suffixerator_index/default/_refgenie_build/43f14ba8beed34d52edb244e26f193df6edbb467bd55d37a_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/43f14ba8beed34d52edb244e26f193df6edbb467bd55d37a/fasta/default/43f14ba8beed34d52edb244e26f193df6edbb467bd55d37a.fa -indexname /project/shefflab/deploy/rg.databio.org_full/genomes/data/43f14ba8beed34d52edb244e26f193df6edbb467bd55d37a/suffixerator_index/default/43f14ba8beed34d52edb244e26f193df6edbb467bd55d37a.sft` (3682)
[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/43f14ba8beed34d52edb244e26f193df6edbb467bd55d37a/suffixerator_index/default/43f14ba8beed34d52edb244e26f193df6edbb467bd55d37a.sft" # prefixlength=automatic # storespecialcodes=false # inputfile[0]=/project/shefflab/deploy/rg.databio.org_full/genomes/data/43f14ba8beed34d52edb244e26f193df6edbb467bd55d37a/fasta/default/43f14ba8beed34d52edb244e26f193df6edbb467bd55d37a.fa # indexname=/project/shefflab/deploy/rg.databio.org_full/genomes/data/43f14ba8beed34d52edb244e26f193df6edbb467bd55d37a/suffixerator_index/default/43f14ba8beed34d52edb244e26f193df6edbb467bd55d37a.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 (eqlen 32598, 8583 bytes, 2.11 bits/symbol) # totallength=32598 # numofsequences=1 # specialcharacters=0 # specialranges=0 # realspecialranges=0 # wildcards=0 # wildcardranges=0 # realwildcardranges=0 # occurrences(a)=11258 # occurrences(c)=7952 # occurrences(g)=4026 # occurrences(t)=9362 # automatically determined prefixlength=5 # maxinsertionsort=3 # maxbltriesort=1000 # maxcountingsort=4000 # storespecialcodes=false # cmpcharbychar=false # totallength=32598 # sizeof (leftborder)=4100 bytes # sizeof (countspecialcodes)=1024 bytes # sizeof (distpfxidx)=336 bytes # sizeof (bcktab)=5460 bytes # largest bucket size=190 # derived parts=1 # widthofpart[0]=32598 # create suffix_sort_space: suftab uses 64bit values: maxvalue=32598,numofentries=32598 # used workspace for sorting: 0.11 MB # countinsertionsort=0 # countbltriesort=423 # countcountingsort=0 # countshortreadsort=578 # countradixsort=0 # counttqsort=0Command completed. Elapsed time: 0:00:01. Running peak memory: 0.001GB. PID: 3682; Command: gt; Return code: 0; Memory used: 0.001GB > `touch /project/shefflab/deploy/rg.databio.org_full/genomes/data/43f14ba8beed34d52edb244e26f193df6edbb467bd55d37a/suffixerator_index/default/_refgenie_build/43f14ba8beed34d52edb244e26f193df6edbb467bd55d37a_suffixerator_index__default.flag` (3722)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.001GB. PID: 3722; Command: touch; Return code: 0; Memory used: 0.001GB Asset digest: 052309ba88ab260c846fb649cfd0243e Default tag for '43f14ba8beed34d52edb244e26f193df6edbb467bd55d37a/suffixerator_index' set to: default ### Pipeline completed. Epilogue * Elapsed time (this run): 0:00:03 * Total elapsed time (all runs): 0:00:01 * Peak memory (this run): 0.0015 GB * Pipeline completed time: 2021-04-07 15:40:27 Finished building 'suffixerator_index' asset Created alias directories: - /project/shefflab/deploy/rg.databio.org_full/genomes/alias/mouse_chrM2x/suffixerator_index/default