### 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)
[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/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=0Command 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