Not completed in overlap_collect step

[kjyunm]

Hello,
I am trying to build a pangenome using pig data from multiple breeds. The input data is 4.5GB when compressed, and I am using the Docker image ghcr.io/pangenome/pggb:latest.

I ran the following command
docker run -it -v ${PWD}:/data -u $(id -u):$(id -g) ghcr.io/pangenome/pggb:latest pggb -i /data/pigs.assembly.fa.gz -o /data/out -t 20

However, during the execution, it gets stuck at the step
[seqwish::transclosure] 25082.955 81.34% 12280027975-12290027975 overlap_collect
and has not progressed for over a week.

Could you please advise if there are any additional options or preprocessing steps needed to resolve this issue? I would appreciate any suggestions on the cause of this hanging and how to resolve it.

Thank you!

[AndreaGuarracino]

@kjyunm maybe you caught a seqwish bug? You could try to increase -k/--min-match-len in pggb (23 by default) to make seqwish's life a bit easier

[kjyunm]

Thank you!
I adjusted the parameter k, and it progressed to the next step. However, after finishing the graph construction in the seqwish step, I encountered the following error and log message.

[seqwish::gfa] 31934.154 writing graph
Command terminated by signal 8
seqwish -s /data/pigs.assembly_only.fa.gz -p /data/out/pigs.assembly_only.fa.gz.bf3285f.alignments.wfmash.paf -k 50 -f 0 -g /data/out/pigs.assembly_only.fa.gz.bf3285f.e81ee67.seqwish.gfa -B 10M -t 20 --temp-dir /data/out -P
250262.86s user 18723.53s system 840% cpu 31984.70s total 43804008Kb max memory

I would like to know why I am getting Command terminated by signal 8 and if there is a solution to fix the problem.