### Pipeline run code and environment: * Command: `/home/mjs5kd/.local/bin/refgenie build human_alphasat/tallymer_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/tallymer_index/default/_refgenie_build/ * Pipeline started at: (02-26 15:47:26) 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/tallymer_index']` * `assets`: `None` * `command`: `build` * `config_file`: `/home/mjs5kd/.local/lib/python3.6/site-packages/refgenie/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/tallymer_index/default/_refgenie_build/3cd9f8c34e28a1e8823632449b6d8a6afe5a1032245e7475_tallymer_index__default.flag` > `gt tallymer mkindex -v -counts -pl -mersize 30 -minocc 2 -indexname /project/shefflab/deploy/rg.databio.org_full/genomes/data/3cd9f8c34e28a1e8823632449b6d8a6afe5a1032245e7475/tallymer_index/default/3cd9f8c34e28a1e8823632449b6d8a6afe5a1032245e7475.tal_30 -esa /project/shefflab/deploy/rg.databio.org_full/genomes/data/3cd9f8c34e28a1e8823632449b6d8a6afe5a1032245e7475/suffixerator_index/default/3cd9f8c34e28a1e8823632449b6d8a6afe5a1032245e7475.sft` (3166)
# mersize=30 # minocc=2 # maxocc=undefined # prefixlength=automatic # storeindex=/project/shefflab/deploy/rg.databio.org_full/genomes/data/3cd9f8c34e28a1e8823632449b6d8a6afe5a1032245e7475/tallymer_index/default/3cd9f8c34e28a1e8823632449b6d8a6afe5a1032245e7475.tal_30 # inputindex=/project/shefflab/deploy/rg.databio.org_full/genomes/data/3cd9f8c34e28a1e8823632449b6d8a6afe5a1032245e7475/suffixerator_index/default/3cd9f8c34e28a1e8823632449b6d8a6afe5a1032245e7475.sft # init character encoding (uchar, 24559 bytes, 2.04 bits/symbol) # init ssptab encoding (ushort, 100 bytes, 0.01 bits/symbol) # sat=uchar # totallength=96500 # specialcharacters=42 # specialranges=42 # realspecialranges=42 # lengthofspecialprefix=0 # lengthofspecialsuffix=0 # wildcards=0 # wildcardranges=0 # realwildcardranges=0 # lengthofwildcardprefix=0 # lengthofwildcardsuffix=0 # numofsequences=43 # numofdbsequences=43 # numofquerysequences=0 # numberofallsortedsuffixes=96501 # longest=8447 # prefixlength=6 # largelcpvalues=769 # averagelcp=33.46 # maxbranchdepth=445 # integersize=64 # littleendian=1 # readmode=0 # mirrored=0 # write 0 mercounts > 255 to file "/project/shefflab/deploy/rg.databio.org_full/genomes/data/3cd9f8c34e28a1e8823632449b6d8a6afe5a1032245e7475/tallymer_index/default/3cd9f8c34e28a1e8823632449b6d8a6afe5a1032245e7475.tal_30.mct" # number of 30-mers in index: 15845 # index size: 0.12 megabytes # construct mer buckets for prefixlength 4 # numofcodes = 256 # indexfilename = /project/shefflab/deploy/rg.databio.org_full/genomes/data/3cd9f8c34e28a1e8823632449b6d8a6afe5a1032245e7475/tallymer_index/default/3cd9f8c34e28a1e8823632449b6d8a6afe5a1032245e7475.tal_30 # alphasize = 4 # mersize = 30 # numofmers = 15845 # merbytes = 8Command completed. Elapsed time: 0:00:01. Running peak memory: 0.001GB. PID: 3166; Command: gt; Return code: 0; Memory used: 0.001GB > `gt tallymer search -output qseqnum qpos -strand fp -tyr /project/shefflab/deploy/rg.databio.org_full/genomes/data/3cd9f8c34e28a1e8823632449b6d8a6afe5a1032245e7475/tallymer_index/default/3cd9f8c34e28a1e8823632449b6d8a6afe5a1032245e7475.tal_30 -q /project/shefflab/deploy/rg.databio.org_full/genomes/data/3cd9f8c34e28a1e8823632449b6d8a6afe5a1032245e7475/fasta/default/3cd9f8c34e28a1e8823632449b6d8a6afe5a1032245e7475.fa > /project/shefflab/deploy/rg.databio.org_full/genomes/data/3cd9f8c34e28a1e8823632449b6d8a6afe5a1032245e7475/tallymer_index/default/3cd9f8c34e28a1e8823632449b6d8a6afe5a1032245e7475.tal_30.gtTxt` (3253)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.003GB. PID: 3253; Command: gt; Return code: 0; Memory used: 0.003GB > `touch /project/shefflab/deploy/rg.databio.org_full/genomes/data/3cd9f8c34e28a1e8823632449b6d8a6afe5a1032245e7475/tallymer_index/default/_refgenie_build/3cd9f8c34e28a1e8823632449b6d8a6afe5a1032245e7475_tallymer_index__default.flag` (3344)
Command completed. Elapsed time: 0:00:00. Running peak memory: 0.003GB. PID: 3344; Command: touch; Return code: 0; Memory used: 0.001GB Asset digest: 5d51d66872f7f74aeb1b4ebc4611251c The lock has been created in the split second since the last lock existence check. Waiting Waiting for file lock: /project/shefflab/deploy/rg.databio.org_full/rg.databio.org/config/lock.refgenie_config.yaml .. File unlocked Default tag for '3cd9f8c34e28a1e8823632449b6d8a6afe5a1032245e7475/tallymer_index' set to: default ### Pipeline completed. Epilogue * Elapsed time (this run): 0:00:02 * Total elapsed time (all runs): 0:00:01 * Peak memory (this run): 0.0029 GB * Pipeline completed time: 2021-02-26 15:47:28 Finished building 'tallymer_index' asset Waiting for file lock: /project/shefflab/deploy/rg.databio.org_full/rg.databio.org/config/lock.refgenie_config.yaml .. File unlocked Created alias directories: - /project/shefflab/deploy/rg.databio.org_full/genomes/alias/human_alphasat/tallymer_index/default