### 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)
WARNING: 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
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# wildcardranges of length 100=462
# wildcardranges of length 101=1
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# wildcardranges of length 104=1
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# wildcardranges of length 127=1
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# wildcardranges of length 200=2
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# wildcardranges of length 500=1
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# wildcardranges of length 1000=3
# wildcardranges of length 1006=1
# wildcardranges of length 1199=1
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# wildcardranges of length 1343=2
# wildcardranges of length 1359=1
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# wildcardranges of length 1600=1
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# 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
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# wildcardranges of length 16576=1
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# 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
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# wildcardranges of length 27000=1
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# wildcardranges of length 28000=1
# wildcardranges of length 30000=7
# wildcardranges of length 33000=1
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# wildcardranges of length 35000=1
# wildcardranges of length 40000=5
# wildcardranges of length 44000=1
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# wildcardranges of length 100000=25
# wildcardranges of length 101000=1
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# wildcardranges of length 200000=3
# wildcardranges of length 207000=1
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# wildcardranges of length 260000=1
# wildcardranges of length 400000=2
# wildcardranges of length 500000=1
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# wildcardranges of length 1000000=2
# wildcardranges of length 1363998=1
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# 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=72985
Command 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