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loneknightpy / idba

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ShortSequence: Sequence is too long #55

Open sleepvet opened 4 years ago

sleepvet commented 4 years ago

I combined paired fq files into a fa file through " fq2fa --merge --filter 10.1.fa 10.2.fa 10.fa", then got the error hit when I run command "idba_ud -r 10.fa -o ../01assembly/". the sequences I used is 150-300 bp. the 10.fa file looks good. the error hit is:terminate called after throwing an instance of 'std::logic_error' what(): ShortSequence: Sequence is too long. Aborted (core dumped) I donot know what is wrong, could you please help me?

sleepvet commented 4 years ago

I assumed I should use fq files in fq2fa, then I run "" fq2fa --merge --filter 10.1.fq 10.2.fq 10.fa".Still, the fa file merged is not qualified.

mrxuzj commented 8 months ago

I combined paired fq files into a fa file through " fq2fa --merge --filter 10.1.fa 10.2.fa 10.fa", then got the error hit when I run command "idba_ud -r 10.fa -o ../01assembly/". the sequences I used is 150-300 bp. the 10.fa file looks good. the error hit is:terminate called after throwing an instance of 'std::logic_error' what(): ShortSequence: Sequence is too long. Aborted (core dumped) I donot know what is wrong, could you please help me?

same error, have you solved this problem？

gingerbuffy commented 8 months ago

I also got the same error and I followed the solution posted by akinori@jp in https://www.seqanswers.com/forum/bioinformatics/bioinformatics-aa/24625-250bp-reads-in-idba_ud and it works for me.

mrxuzj commented 8 months ago

您的邮件已收到，谢谢