smoothxg terminated by signal 6

[petersudmant]

I'm having an issue with smoothxg. wfmash and seqwish run no problem, but I get an unexpected signal 6 termination subsequently.

Any ideas?

[odgi::unchop] unchopped 542 nodes into 269 new nodes.
[smoothxg::main] smoothed graph length 374213302bp in 9248321 nodes
[smoothxg::main] writing smoothed graph to /data/out//input.fa.gz.c55a916.7bdde5a.2a74e36.smooth.gfa
[smoothxg::main] building xg index from smoothed graph
terminate called after throwing an instance of 'std::logic_error'
  what():  basic_string::_M_construct null not valid
Command terminated by signal 6
smoothxg -t 24 -T 24 -g /data/out//input.fa.gz.c55a916.7bdde5a.2a74e36.smooth.1.gfa -w 18028 -X 100 -I .8500 -R 0 -j 0 -e 0 -l 4507 -P 1,19,39,3,81,1 -O 0.03 -Y 400 -d 0 -D 0 -m /data/out//input.fa.gz.c55a916.7bdde5a.2a74e36.smooth.maf -Q Consensus_ -C /data/out//input.fa.gz.c55a916.7bdde5a.2a74e36.cons,cons,100,1000,10000 -o /data/out//input.fa.gz.c55a916.7bdde5a.2a74e36.smooth.gfa

[AndreaGuarracino]

I have a sad hypothesis, that you've got the same problem as #133, of which a full solution is still missing.

Before asking you for the input, would you please check if the input.fa.gz.c55a916.7bdde5a.2a74e36.smooth.1.gfa file has empty P lines?

[petersudmant]

actually... they are not... e.g.

P GRC38#CM000669.2 1+,2+,3+,5+,6+,8+,10+,11+,12+,14+,15+,17+,18+,19+,20+,22+,23+,25+,27+,29+,30+,32+,33+,35+,36+,37+,38+,40+,41+,43+,45+,46+,48+,49+...

[AndreaGuarracino]

@petersudmant thank you for sharing both input.fa.gz.c55a916.7bdde5a.2a74e36.smooth.1.gfa and input.fa.gz.c55a916.7bdde5a.2a74e36.smooth.gfa files.

Unfortunately, the sad prediction was right, in there are paths without any steps, but this is in the final graph, that you've also shared. The bug affects the consensus paths:

grep Consensus_36614 input.fa.gz.c55a916.7bdde5a.2a74e36.smooth.gfa

P       Consensus_36614         *

I have a possible solution, but it still needs some time. At the moment, the possible ways to get around the problem are

• do not generate consensus graphs (no -C/--consensus-spec option);
• disable padding (-O /--poa-padding set to 0 to disable it);
• run smoothxg again: it is not 100% deterministic, so there is a chance that the bug is not always triggered.

[petersudmant]

So, one issue it turns out, was that I had set my mash length wayyyy too long (100kb). I reduced it to 10kb and all was resolved.

[subwaystation]

Great, thanks for the feedback @petersudmant !