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lh3 / seqtk

Toolkit for processing sequences in FASTA/Q formats
MIT License
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ERROR: the 2nd file has fewer records #195

Closed mbk0asis closed 2 years ago

mbk0asis commented 2 years ago

Hi.

I'm trying to extract matching read pairs by following the commands in here.

but, seqtk mergepe R1 R2 gave me an error saying "the 2nd file has fewer records".

What could be the problem here?

Thank you!

shenwei356 commented 2 years ago

Make sure the R1 and R2 files are well paired with seqkit pair or fastq-pair.

seqkit pair -1 r1.fq.gz -2 r2.fq.gz -O paired

If the files are very big, like tens of GB, use another solution.