pggb: Latest version - Command terminated by signal 4

Hello, I have been using pggb for a while now and over a couple of different builds. I have been able to run it previously and can still run a previous version (pulled February 8) without seeing this error. Yesterday I used Singularity and pulled the newest version to try the --poa-params variable but have so far been unable to run this version. I have tried running this version both using wfmash and edyeet, but both terminate at the same place. I do seem to produce alignments as I can see a readable “wfmash-us6ZOJ”-file in the directory where I ran pggb. Any help that allows me to continue is greatly appreciated!

This is the log with the error I am seeing:

Starting pggb on Mon Feb 22 17:15:29 CET 2021

Command: /usr/local/bin/pggb -i /proj/uppstore2017270/Emilio/pggb/indata/Erik_test_data/complete_reference_genomes.fa -s 500 -w 25000 -p 85 -a 85 -n 14 -W -t 10 --poa-params 1,4,6,2,26,1 -v -o /proj/uppstore2017270/Emilio/pggb/new_version_out/Erik_suggested/All_wfmash

PARAMETERS

general: input-fasta: /proj/uppstore2017270/Emilio/pggb/indata/Erik_test_data/complete_reference_genomes.fa output-dir: /proj/uppstore2017270/Emilio/pggb/new_version_out/Erik_suggested/All_wfmash resume: false threads: 10 alignment: mapping-tool: wfmash no-splits: false segment-length: 500 block-length: 1500 no-merge-segments: false map-pct-id: 85 align-pct-id: 85 n-secondary: 14 mash-kmer: 16 wfmash: true exclude-delim: false seqwish: min-match-len: 19 transclose-batch: 1000000 smoothxg: block-weight-max: 25000 path-jump-max: 5000 edge-jump-max: 5000 poa-length-max: 10000 poa-params: 1,4,6,2,26,1 consensus-spec: 10,100,1000,10000 block-id-min: 0 ratio-contain: 0 odgi: viz: true layout: false stats: false reporting: multiqc: false

Running pggb

[wfmash::map] Reference = [/proj/uppstore2017270/Emilio/pggb/indata/Erik_test_data/complete_reference_genomes.fa] [wfmash::map] Query = [/proj/uppstore2017270/Emilio/pggb/indata/Erik_test_data/complete_reference_genomes.fa] [wfmash::map] Kmer size = 16 [wfmash::map] Window size = 20 [wfmash::map] Segment length = 500 (read split allowed) [wfmash::map] Block length min = 1500 [wfmash::map] Alphabet = DNA [wfmash::map] Percentage identity threshold = 0.85% [wfmash::map] Mapping output file = /crex/proj/uppstore2017270/Emilio/pggb/wfmash-us6ZOJ [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 = 2330611 [wfmash::skch::Sketch::index] unique minimizers = 761163 [wfmash::skch::Sketch::computeFreqHist] Frequency histogram of minimizers = (1, 371539) … (282, 1) [wfmash::skch::Sketch::computeFreqHist] With threshold 0.001%, ignore minimizers occurring >= 67 times during lookup. [wfmash::map] time spent computing the reference index: 1.84586 sec [wfmash::skch::Map::mapQuery] WARNING, no .fai index found for /proj/uppstore2017270/Emilio/pggb/indata/Erik_test_data/complete_reference_genomes.fa, reading file to sum sequence length (slow) [wfmash::skch::Map::mapQuery] mapped 100.00% @ 3.15e+06 bp/s elapsed: 00:00:00:07 remain: 00:00:00:00 [wfmash::skch::Map::mapQuery] count of mapped reads = 14, reads qualified for mapping = 15, total input reads = 15, total input bp = 24465645 [wfmash::map] time spent mapping the query: 7.81e+00 sec [wfmash::map] mapping results saved in: /crex/proj/uppstore2017270/Emilio/pggb/wfmash-us6ZOJ [wfmash::align] Reference = [/proj/uppstore2017270/Emilio/pggb/indata/Erik_test_data/complete_reference_genomes.fa] [wfmash::align] Query = [/proj/uppstore2017270/Emilio/pggb/indata/Erik_test_data/complete_reference_genomes.fa] [wfmash::align] Mapping file = /crex/proj/uppstore2017270/Emilio/pggb/wfmash-us6ZOJ [wfmash::align] Alignment identity cutoff = 8.50e-01% [wfmash::align] Alignment output file = /dev/stdout [wfmash::align] time spent read the reference sequences: 4.60e-02 sec Command terminated by signal 4 wfmash -X -s 500 -l 1500 -p 85 -n 14 -k 16 -t 10 /proj/uppstore2017270/Emilio/pggb/indata/Erik_test_data/complete_reference_genomes.fa /proj/uppstore2017270/Emilio/pggb/indata/Erik_test_data/complete_reference_genomes.fa 56.16s user 1.49s system 557% cpu 10.33s total 254096Kb max memory