Error (core dumped)

[Seajull]

Hello,

I'm trying to use HG-CoLoR to correct minion reads with illumina reads but i end up with a error at the Blasr step :

[INFO] 2019-04-30T10:47:00 [blasr] started. Warning: resetting nCandidates to nBest 50 terminate called after throwing an instance of std::invalid_argument what(): stoi /datas/Save/Clement/soft/HG-CoLoR/HG-CoLoR : ligne 237 : 31495 Abandon (core dumped) $hgf/bin/HG-CoLoR -t "$tmpdir" -K "$K" -d "$seedsdistance" -o "$seedsoverlap" -k "$k" -b "$branches" -s "$seedskips" -m "$mismatches" -j "$nproc" -r $tmpdir/"$formatLR" -a $tmpdir/"$aln" $tmpdir/"$K-mers.fa.pgsa" > "$out.fasta"

Thanks in advance.

[morispi]

Hi,

The error actually seems to happen during the HG-CoLoR / correction step.
It happened to me a few times too, usually because the size of the stack was too small.

Did the ulimit -s 65536 command included in the main script work?
Otherwhise, can you try to run it yourself, maybe with a higher max stack value, and rerun the program?

Also if your data is public, I could take a look as to where / why this segfault happens, if you want.

Cheers,
Pierre

[Seajull]

Thanks for the quick answer !

The ulimit command appear to work (ulimit -s return 65536 when executed in script) but i try to double it (to 131072) and the same error happen.
Should i try with higher value ?

[morispi]

Hi,

Very late answer this time, sorry.

Well, if the command does work, the problem probably doesn't come from that.
Can you please provide me the command line you used to run HG-CoLoR?

Cheers,
Pierre

[baishengjun]

Hello,,
I have the same problem.
It is my command:../HG-CoLoR --longreads ~/data/P_deltoides_nano.fasta --shortreads ~/worka/deltoides_PE/SRR3204673_merge_filtered.fastq --out corr -K 100 --nproc 40 --kmcmem 6
How to solve it?
Thanks in advance.