lh3 / seqtk

Toolkit for processing sequences in FASTA/Q formats

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seqtk sample can't properly output fastq.gz

soappp9527 opened this issue · comments

I am trying to ramdomly extract 1000 reads from a fastq.gz

seqtk sample -s 999 all.fastq.gz 1000 > sub.fq.gz

but sub.fq.gz become readable just like a fastq text file which without gzip although with .gz suffix

$ gzip -l sub.fq.gz

gzip: sub.fq.gz: not in gzip format

seqtk sample seems can't gzip automatically

If you want gzip'd output, use pipe

seqtk sample -s 999 all.fastq.gz 1000 | gzip > sub.fq.gz