Latest version - Command terminated by signal 11

[emilio-r]

Hi!

This morning I pulled PGGB as I did in #62 and tried running with the same two samples as mentioned in that issue. Both which are samples that I have previously been bale to run without any issues. While the other sample work, this sample (and other ones) fail with this error:

Starting pggb on Tue Jun 15 08:37:30 CEST 2021

Command: /usr/local/bin/pggb -i ./New_indata/messy_genomes_concatenated.fa -s 500 -w 25000 -p 85 -n 9 -P 1,9,16,2,41,1 -t 10 -v -C 1000 -L -o ./runtest_3

PARAMETERS

general:
  input-fasta:        ./New_indata/messy_genomes_concatenated.fa
  output-dir:         ./runtest_3
  resume:             false
  pigz-compress:      false
  threads:            10
alignment:
  mapping-tool:       wfmash
  no-splits:          false
  segment-length:     500
  block-length:       1500
  no-merge-segments:  false
  map-pct-id:         85
  n-secondary:        9
  mash-kmer:          16
  exclude-delim:      false
seqwish:
  min-match-len:      19
  transclose-batch:   10000000
smoothxg:
  block-weight-max:   25000
  path-jump-max:      100
  edge-jump-max:      0
  poa-length-target:  5000
  poa-params:         1,9,16,2,41,1
  write-maf:          false
  consensus-prefix:   Consensus_
  consensus-spec:     1000
  split-min-depth:    2000
  block-id-min:       0
  block-ratio-min:    0
odgi:
  viz:                true
  layout:             true
  stats:              false
reporting:
  multiqc:            false

Running pggb

[wfmash::map] Reference = [./New_indata/messy_genomes_concatenated.fa]
[wfmash::map] Query = [./New_indata/messy_genomes_concatenated.fa]
[wfmash::map] Kmer size = 16
[wfmash::map] Window size = 1
[wfmash::map] Segment length = 500 (read split allowed)
[wfmash::map] Block length min = 1500
[wfmash::map] Alphabet = DNA
[wfmash::map] Percentage identity threshold = 85%
[wfmash::map] Mapping output file = /crex/proj/uppstore2017270/Emilio/pggb/wfmash-E66Pry
[wfmash::map] Filter mode = 1 (1 = map, 2 = one-to-one, 3 = none)
[wfmash::map] Execution threads  = 10
[wfmash::skch::Sketch::build] minimizers picked from reference = 16424393
[wfmash::skch::Sketch::index] unique minimizers = 5451643
[wfmash::skch::Sketch::computeFreqHist] Frequency histogram of minimizers = (1, 2430033) ... (364, 1)
[wfmash::skch::Sketch::computeFreqHist] With threshold 0.001%, ignore minimizers occurring >= 65 times during lookup.
[wfmash::map] time spent computing the reference index: 4.96914 sec
[wfmash::skch::Map::mapQuery] WARNING, no .fai index found for ./New_indata/messy_genomes_concatenated.fa, reading file to sum sequence length (slow)
[wfmash::skch::Map::mapQuery] mapped 100.00% @ 3.73e+05 bp/s elapsed: 00:00:00:44 remain: 00:00:00:00
[wfmash::skch::Map::mapQuery] count of mapped reads = 172, reads qualified for mapping = 174, total input reads = 174, total input bp = 16427933
[wfmash::map] time spent mapping the query: 4.41e+01 sec
[wfmash::map] mapping results saved in: /crex/proj/uppstore2017270/Emilio/pggb/wfmash-E66Pry
[wfmash::align] Reference = [./New_indata/messy_genomes_concatenated.fa]
[wfmash::align] Query = [./New_indata/messy_genomes_concatenated.fa]
[wfmash::align] Mapping file = /crex/proj/uppstore2017270/Emilio/pggb/wfmash-E66Pry
[wfmash::align] Alignment identity cutoff = 8.50e-01%
[wfmash::align] Alignment output file = /dev/stdout
[wfmash::align] time spent read the reference sequences: 5.63e-02 sec
[wfmash::align::computeAlignments] aligned 21.53% @ 6.75e+05 bp/s elapsed: 00:00:00:19 remain: 00:00:01:12Command terminated by signal 11
wfmash -X -s 500 -l 1500 -p 85 -n 9 -k 16 -t 10 ./New_indata/messy_genomes_concatenated.fa ./New_indata/messy_genomes_concatenated.fa
478.35s user 10.79s system 698% cpu 70.05s total 1223272Kb max memory

Running either with, or without, the -Y "_" flag both fails with this error. Any help is greatly appreciated!

[AndreaGuarracino]

Hi @emilio-r , long time no bug! I can reproduce the problem, I am working on it.

[AndreaGuarracino]

@emilio-r , I've fixed the bug, and updated PGGB. Would you please check if the last version (docker pull ghcr.io/pangenome/pggb:20210615131929694b48) works for you too?

[emilio-r]

@AndreaGuarracino I can once more say that your changes solved my issue. As always, thanks for the quick help, and I'll be sure to return with something new in the future!