### Pipeline run code and environment: * Command: `/home/mjs5kd/.local/bin/refgenie build human_alphasat/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/3cd9f8c34e28a1e8823632449b6d8a6afe5a1032245e7475/suffixerator_index/default/_refgenie_build/ * Pipeline started at: (04-07 15:39:20) 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_alphasat/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/3cd9f8c34e28a1e8823632449b6d8a6afe5a1032245e7475/suffixerator_index/default/_refgenie_build/3cd9f8c34e28a1e8823632449b6d8a6afe5a1032245e7475_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/3cd9f8c34e28a1e8823632449b6d8a6afe5a1032245e7475/fasta/default/3cd9f8c34e28a1e8823632449b6d8a6afe5a1032245e7475.fa -indexname /project/shefflab/deploy/rg.databio.org_full/genomes/data/3cd9f8c34e28a1e8823632449b6d8a6afe5a1032245e7475/suffixerator_index/default/3cd9f8c34e28a1e8823632449b6d8a6afe5a1032245e7475.sft` (14317)
[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/3cd9f8c34e28a1e8823632449b6d8a6afe5a1032245e7475/suffixerator_index/default/3cd9f8c34e28a1e8823632449b6d8a6afe5a1032245e7475.sft" # prefixlength=automatic # storespecialcodes=false # inputfile[0]=/project/shefflab/deploy/rg.databio.org_full/genomes/data/3cd9f8c34e28a1e8823632449b6d8a6afe5a1032245e7475/fasta/default/3cd9f8c34e28a1e8823632449b6d8a6afe5a1032245e7475.fa # indexname=/project/shefflab/deploy/rg.databio.org_full/genomes/data/3cd9f8c34e28a1e8823632449b6d8a6afe5a1032245e7475/suffixerator_index/default/3cd9f8c34e28a1e8823632449b6d8a6afe5a1032245e7475.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 (uchar, 24559 bytes, 2.04 bits/symbol) # init ssptab encoding (ushort, 100 bytes, 0.01 bits/symbol) # totallength=96500 # numofsequences=43 # specialcharacters=42 # specialranges=42 # realspecialranges=42 # wildcards=0 # wildcardranges=0 # realwildcardranges=0 # occurrences(a)=29271 # occurrences(c)=17589 # occurrences(g)=18951 # occurrences(t)=30647 # automatically determined prefixlength=6 # maxinsertionsort=3 # maxbltriesort=1000 # maxcountingsort=4000 # storespecialcodes=false # cmpcharbychar=false # totallength=96500 # sizeof (leftborder)=16388 bytes # sizeof (countspecialcodes)=4096 bytes # sizeof (distpfxidx)=1360 bytes # sizeof (bcktab)=21844 bytes # largest bucket size=1560 # derived parts=1 # widthofpart[0]=96458 # create suffix_sort_space: suftab uses 64bit values: maxvalue=96500,numofentries=96458 # used workspace for sorting: 0.11 MB # countinsertionsort=0 # countbltriesort=1102 # countcountingsort=11 # countshortreadsort=2257 # countradixsort=0 # counttqsort=0Command completed. Elapsed time: 0:00:03. Running peak memory: 0.02GB. PID: 14317; Command: gt; Return code: 0; Memory used: 0.02GB > `touch /project/shefflab/deploy/rg.databio.org_full/genomes/data/3cd9f8c34e28a1e8823632449b6d8a6afe5a1032245e7475/suffixerator_index/default/_refgenie_build/3cd9f8c34e28a1e8823632449b6d8a6afe5a1032245e7475_suffixerator_index__default.flag` (14399)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.02GB. PID: 14399; Command: touch; Return code: 0; Memory used: 0.0GB Asset digest: 878a08f12e8106c43fd8a4f5aff91288 Default tag for '3cd9f8c34e28a1e8823632449b6d8a6afe5a1032245e7475/suffixerator_index' set to: default ### Pipeline completed. Epilogue * Elapsed time (this run): 0:00:07 * Total elapsed time (all runs): 0:00:03 * Peak memory (this run): 0.0196 GB * Pipeline completed time: 2021-04-07 15:39:28 Finished building 'suffixerator_index' asset Created alias directories: - /project/shefflab/deploy/rg.databio.org_full/genomes/alias/human_alphasat/suffixerator_index/default