morispi
CONSENT-correction core dumped
Hi，when I use this fastq(https://github.com/lirr-lichen/1_testdata.git samle97.570.fastq )， with commond：CONSENT-correct --in samle97.570.fastq --out CONSENT.fasta --tmpdir ./ --nproc 12 --type ONT I meet this： CONSENT-correct: line 199: 297133 Segmentation fault (core dumped) $LRSCf/bin/CONSENT-correction -a $tmpdir/"$alignments" -s "$minSupport" -S "$maxSupport" -l "$windowSize" -k "$merSize" -c "$commonKMers" -A "$minAnchors" -f "$solid" -m "$windowOverlap" -j "$nproc" -r "$reads" -M "$maxMSA" -p "$LRSCf" >> "$out"
but when I use other fastq with the same commond, I do not meet this，and can run to the end。
Is there somethin wrong with this fastq?
Thank you
Hello,
This is strange, CONSENT works fine until the end on that file here. Not exactly sure what could be causing the issue.
Can you tell me a bit more about your computing environment? Operating systems, compilers versions, etc?
Best, Pierre
Sorry for getting back to you so late.
When I use other fastq with the same commond, CONSENT works fine. So I think this error may not due to the computing environment.
Finaly, I use seqtk software abstract fasta from samle97.570.fastq. And then use the same CONSENT commond, it works fine until the end.
I hope this information may help.
Best, Lichen
Hello,
Sorry for getting back to you so late as well.
If it does work with other files, it might not be a problem with the computing environment indeed. However, I tried running CONSENT on the file you encountered errors with, on two different computers, and I was unable to reproduce the issue.
I'm not exactly sure what could be causing it. Can you provide me the seqtk command you used to see if I can further help?
Best, Pierre