### Pipeline run code and environment: * Command: `/home/mjs5kd/.local/bin/refgenie build hg18/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/9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01/suffixerator_index/default/_refgenie_build/ * Pipeline started at: (04-07 15:35:20) 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`: `['hg18/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/9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01/suffixerator_index/default/_refgenie_build/9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01_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/9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01/fasta/default/9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01.fa -indexname /project/shefflab/deploy/rg.databio.org_full/genomes/data/9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01/suffixerator_index/default/9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01.sft` (8843)
[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/9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01/suffixerator_index/default/9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01.sft" # prefixlength=automatic # storespecialcodes=false # inputfile[0]=/project/shefflab/deploy/rg.databio.org_full/genomes/data/9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01/fasta/default/9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01.fa # indexname=/project/shefflab/deploy/rg.databio.org_full/genomes/data/9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01/suffixerator_index/default/9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01.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=6011 # wildcardranges of length 2=658 # wildcardranges of length 3=269 # wildcardranges of length 4=205 # wildcardranges of length 5=134 # wildcardranges of length 6=95 # wildcardranges of length 7=74 # wildcardranges of length 8=53 # wildcardranges of length 9=35 # wildcardranges of length 10=35 # wildcardranges of length 11=21 # wildcardranges of length 12=21 # wildcardranges of length 13=15 # wildcardranges of length 14=10 # wildcardranges of length 15=9 # wildcardranges of length 16=8 # wildcardranges of length 17=5 # wildcardranges of length 18=4 # wildcardranges of length 19=3 # wildcardranges of length 20=3 # wildcardranges of length 21=1 # wildcardranges of length 24=1 # wildcardranges of length 25=2 # wildcardranges of length 26=1 # wildcardranges of length 28=1 # wildcardranges of length 29=1 # wildcardranges of length 34=1 # wildcardranges of length 36=1 # wildcardranges of length 41=1 # wildcardranges of length 50=1 # wildcardranges of length 73=1 # wildcardranges of length 84=2 # wildcardranges of length 100=462 # wildcardranges of length 101=1 # wildcardranges of length 102=4 # wildcardranges of length 104=1 # wildcardranges of length 107=1 # wildcardranges of length 122=1 # wildcardranges of length 125=1 # wildcardranges of length 127=1 # wildcardranges of length 180=1 # wildcardranges of length 181=1 # wildcardranges of length 200=2 # wildcardranges of length 217=1 # wildcardranges of length 221=1 # wildcardranges of length 323=1 # wildcardranges of length 418=1 # wildcardranges of length 420=1 # wildcardranges of length 491=1 # wildcardranges of length 493=2 # wildcardranges of length 500=1 # wildcardranges of length 525=1 # wildcardranges of length 544=1 # wildcardranges of length 559=1 # wildcardranges of length 625=1 # wildcardranges of length 656=1 # wildcardranges of length 704=1 # wildcardranges of length 746=1 # wildcardranges of length 847=1 # wildcardranges of length 851=1 # wildcardranges of length 933=2 # wildcardranges of length 1000=3 # wildcardranges of length 1006=1 # wildcardranges of length 1199=1 # wildcardranges of length 1201=1 # wildcardranges of length 1332=1 # wildcardranges of length 1336=1 # wildcardranges of length 1343=2 # wildcardranges of length 1359=1 # wildcardranges of length 1372=1 # wildcardranges of length 1397=1 # wildcardranges of length 1468=1 # wildcardranges of length 1600=1 # wildcardranges of length 2199=1 # wildcardranges of length 2313=1 # wildcardranges of length 2555=1 # wildcardranges of length 2605=1 # wildcardranges of length 2717=1 # wildcardranges of length 3000=1 # wildcardranges of length 4100=1 # wildcardranges of length 5000=6 # wildcardranges of length 7100=1 # wildcardranges of length 8000=2 # wildcardranges of length 10000=3 # wildcardranges of length 10100=1 # wildcardranges of length 11000=1 # wildcardranges of length 12000=2 # wildcardranges of length 12500=1 # wildcardranges of length 15000=1 # wildcardranges of length 15562=1 # wildcardranges of length 16000=1 # wildcardranges of length 16576=1 # wildcardranges of length 16700=1 # wildcardranges of length 17400=1 # wildcardranges of length 17500=1 # wildcardranges of length 17788=1 # wildcardranges of length 18000=1 # wildcardranges of length 19700=1 # wildcardranges of length 20000=8 # wildcardranges of length 22000=2 # wildcardranges of length 23000=1 # wildcardranges of length 25000=4 # wildcardranges of length 26431=1 # wildcardranges of length 26975=1 # wildcardranges of length 27000=1 # wildcardranges of length 27050=1 # wildcardranges of length 28000=1 # wildcardranges of length 30000=7 # wildcardranges of length 33000=1 # wildcardranges of length 34000=1 # wildcardranges of length 35000=1 # wildcardranges of length 40000=5 # wildcardranges of length 44000=1 # wildcardranges of length 45000=1 # wildcardranges of length 46522=1 # wildcardranges of length 47000=1 # wildcardranges of length 50000=171 # wildcardranges of length 50006=1 # wildcardranges of length 50107=1 # wildcardranges of length 50646=1 # wildcardranges of length 51000=1 # wildcardranges of length 51150=1 # wildcardranges of length 52793=1 # wildcardranges of length 55000=1 # wildcardranges of length 57000=1 # wildcardranges of length 59000=1 # wildcardranges of length 60000=5 # wildcardranges of length 63000=1 # wildcardranges of length 65000=1 # wildcardranges of length 66100=1 # wildcardranges of length 70000=1 # wildcardranges of length 71000=1 # wildcardranges of length 73000=1 # wildcardranges of length 80000=2 # wildcardranges of length 87300=1 # wildcardranges of length 90000=3 # wildcardranges of length 100000=25 # wildcardranges of length 101000=1 # wildcardranges of length 110000=1 # wildcardranges of length 120000=1 # wildcardranges of length 124100=1 # wildcardranges of length 142000=1 # wildcardranges of length 150000=14 # wildcardranges of length 153000=1 # wildcardranges of length 159310=1 # wildcardranges of length 175000=1 # wildcardranges of length 180000=1 # wildcardranges of length 200000=3 # wildcardranges of length 207000=1 # wildcardranges of length 250000=2 # wildcardranges of length 260000=1 # wildcardranges of length 400000=2 # wildcardranges of length 500000=1 # wildcardranges of length 600000=1 # wildcardranges of length 1000000=2 # wildcardranges of length 1363998=1 # wildcardranges of length 1395000=1 # wildcardranges of length 1765661=1 # wildcardranges of length 2480000=1 # wildcardranges of length 3000000=7 # wildcardranges of length 3050000=2 # wildcardranges of length 4400000=1 # wildcardranges of length 8000000=1 # wildcardranges of length 9719767=1 # wildcardranges of length 9800000=1 # wildcardranges of length 14430000=1 # wildcardranges of length 17918000=1 # wildcardranges of length 18070000=1 # wildcardranges of length 18100000=1 # wildcardranges of length 18260000=1 # wildcardranges of length 20290000=1 # wildcardranges of length 30000000=1 # init character encoding (uint32, 776988159 bytes, 2.00 bits/symbol) # init ssptab encoding (uint32, 200 bytes, 0.00 bits/symbol) # totallength=3107677321 # numofsequences=49 # specialcharacters=226255625 # specialranges=8569 # realspecialranges=8569 # wildcards=226255577 # wildcardranges=8548 # realwildcardranges=8548 # occurrences(a)=850568906 # occurrences(c)=589382566 # occurrences(g)=589735358 # occurrences(t)=851734866 # automatically determined prefixlength=13 # maxinsertionsort=3 # maxbltriesort=1000 # maxcountingsort=4000 # storespecialcodes=false # cmpcharbychar=false # totallength=3107677321 # sizeof (leftborder)=268435460 bytes # sizeof (countspecialcodes)=67108864 bytes # sizeof (distpfxidx)=22369616 bytes # sizeof (bcktab)=357913940 bytes # largest bucket size=1750537 # derived parts=1 # widthofpart[0]=2881421696 # create suffix_sort_space: suftab uses 64bit values: maxvalue=3107677321,numofentries=2881421696 # used workspace for sorting: 0.11 MB # countinsertionsort=8246095 # countbltriesort=54333604 # countcountingsort=252637 # countshortreadsort=0 # countradixsort=0 # counttqsort=72985Command completed. Elapsed time: 1:00:25. Running peak memory: 24.161GB. PID: 8843; Command: gt; Return code: 0; Memory used: 24.161GB > `touch /project/shefflab/deploy/rg.databio.org_full/genomes/data/9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01/suffixerator_index/default/_refgenie_build/9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01_suffixerator_index__default.flag` (2730)
Command completed. Elapsed time: 0:00:00. Running peak memory: 24.161GB. PID: 2730; Command: touch; Return code: 0; Memory used: 0.0GB Asset digest: 709146b0d3bfce3a5e4b19873cd763c6 Default tag for '9b7fd88cae1bd01bf53760fb426e2aeb299150cc64af2b01/suffixerator_index' set to: default ### Pipeline completed. Epilogue * Elapsed time (this run): 1:03:38 * Total elapsed time (all runs): 1:00:25 * Peak memory (this run): 24.1615 GB * Pipeline completed time: 2021-04-07 16:38:58 Finished building 'suffixerator_index' asset Created alias directories: - /project/shefflab/deploy/rg.databio.org_full/genomes/alias/hg18/suffixerator_index/default