### 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 = 8
Command 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