Command terminated by signal 9

[Zoeyoungxy]

Hi all, I got the error message while using the command pggb -i /home/zoey/wd_20230411/wd_all/chr5/chr5_combined.fa -o /home/zoey/wd_20230412/chr5 -n 210 -t 128 -p 98 -s 5000 -V 'CHM13v2:#:1000' The log is:

Starting pggb on 04-13-2023_15:59:49

Command: /home/zoey/anaconda3/envs/pggb/bin/pggb -i /home/zoey/wd_20230411/wd_all/chr5/chr5_combined.fa -o /home/zoey/wd_20230412/chr5 -n 210 -t 128 -p 98 -s 5000 -V CHM13v2:#:1000

PARAMETERS

general: input-fasta: /home/zoey/wd_20230411/wd_all/chr5/chr5_combined.fa output-dir: /home/zoey/wd_20230412/chr5 temp-dir: /home/zoey/wd_20230412/chr5 resume: false compress: false threads: 128 poa_threads: 128 wfmash: version: v0.10.2-0-g2aaba27 segment-length: 5000 block-length: 25000 map-pct-id: 98 n-mappings: 210 no-splits: false sparse-map: false mash-kmer: 19 mash-kmer-thres: 0.001 exclude-delim: false no-merge-segments: false seqwish: version: v0.7.8-0-gf362f6f min-match-len: 19 sparse-factor: 0 transclose-batch: 10000000 smoothxg: version: v0.6.8-0-ga8a0e9e skip-normalization: false n-haps: 210 path-jump-max: 0 edge-jump-max: 0 poa-length-target: 700,900,1100 poa-params: 1,19,39,3,81,1 poa_padding: 0.001 run_abpoa: false run_globalpoa: false pad-max-depth: 100 write-maf: false consensus-spec: false consensus-prefix: Consensus block-id-min: .9800 block-ratio-min: 0 odgi: version: v0.8.2-0-g8715c55 viz: true layout: true stats: false gfaffix: version: v0.1.4 reduce-redundancy: true vg: version: v1.46.0 deconstruct: CHM13v2:#:1000 reporting: version: v1.14 multiqc: false

Running pggb

[wfmash::map] Reference = [/home/zoey/wd_20230411/wd_all/chr5/chr5_combined.fa] [wfmash::map] Query = [/home/zoey/wd_20230411/wd_all/chr5/chr5_combined.fa] [wfmash::map] Kmer size = 19 [wfmash::map] Window size = 226 [wfmash::map] Segment length = 5000 (read split allowed) [wfmash::map] Block length min = 25000 [wfmash::map] Chaining gap max = 100000 [wfmash::map] Percentage identity threshold = 98% [wfmash::map] Skip self mappings [wfmash::map] Mapping output file = /dev/stdout [wfmash::map] Filter mode = 1 (1 = map, 2 = one-to-one, 3 = none) [wfmash::map] Execution threads = 128 [wfmash::skch::Sketch::build] minimizers picked from reference = 675103571 [wfmash::skch::Sketch::index] unique minimizers = 1498281 [wfmash::skch::Sketch::computeFreqHist] Frequency histogram of minimizers = (1, 19) ... (2011447, 1) [wfmash::skch::Sketch::computeFreqHist] With threshold 0.001%, ignore minimizers occurring >= 599723 times during lookup. [wfmash::map] time spent computing the reference index: 764.234 sec

[wfmash::skch::Map::mapQuery] mapped 0.00% @ 0.00e+00 bp/s elapsed: 00:00:00:00 remain: 00:00:00:00 ... [wfmash::skch::Map::mapQuery] mapped 6.52% @ 9.70e+05 bp/s elapsed: 00:00:54:33 remain: 00:13:02:09Command terminated by signal 9 wfmash -s 5000 -l 25000 -p 98 -n 209 -k 19 -H 0.001 -X -t 128 --tmp-base /home/zoey/wd_20230412/chr5 /home/zoey/wd_20230411/wd_all/chr5/chr5_combined.fa --approx-map 15954.21s user 5672.44s system 532% cpu 4063.87s total 39730540Kb max memory

I would like to know the reason that Command terminated by signal 9 occuerred and there any solutions to solve the problem? Any suggestions will be highly appreciated.

Thank You, Zoey

[AndreaGuarracino]

@Zoeyoungxy, how many Gb of RAM do you have? It seems an out of memory problem.

[Zoeyoungxy]

@Zoeyoungxy, how many Gb of RAM do you have? It seems an out of memory problem.

$ free -h total used free shared buff/cache available Mem: 1.0T 777G 1.2G 21M 229G 229G Swap: 4.0G 3.3G 701M

[AndreaGuarracino]

Can you share the data?

[Zoeyoungxy]

Sure, I am willing to share. But the data is quite large, with an uncompressed fasta of 73Gb. Can I send the gzipped fasta file to your email?

[AndreaGuarracino]

Thank you! Please compress the file with bgzip -@ 32 -l 9 chr5_combined.fa and upload it on GoogleDrive or similar. You can then send the link to my email aguarra1@uthsc.edu

[Zoeyoungxy]

Thank you! Please compress the file with bgzip -@ 32 -l 9 chr5_combined.fa and upload it on GoogleDrive or similar. You can then send the link to my email aguarra1@uthsc.edu

Sure! Thank you!

[AndreaGuarracino]

@Zoeyoungxy, did you avoid such a problem with newer versions of PGGB?