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morispi / HG-CoLoR

Hybrid method based on a variable-order de bruijn Graph for the error Correction of Long Reads
GNU Affero General Public License v3.0
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Error (core dumped) #13

Open Seajull opened 5 years ago

Seajull commented 5 years ago

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 commented 5 years ago

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 commented 5 years ago

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 commented 5 years ago

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 commented 4 years ago

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.