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