error running seqtk with parallel
EduanWilkinson opened this issue · comments
Hi,
Im trying to run seqtk with parallel. My command looks as follows:
parallel '/Applications/biotools/seqtk/seqtk seq -aQ64 -q20 {}.fastq > {}.fasta' ::: $(ls *_L001_R.fastq | rev | cut -c 14- | rev | uniq)
Which produces the following error:
[E::stk_seq] failed to open the input file/stream.
[E::stk_seq] failed to open the input file/stream.
[E::stk_seq] failed to open the input file/stream.
When I try running it one by one it works. e.g. /Applications/biotools/seqtk/seqtk seq -aQ64 -q20 313507859_S20_L001_R.fastq > 313507859_S20_L001_R.fasta
Any idea what the problem may be? Much appreciated
With parallel
it might help to run it using the option --dry-run
to see what commands it was trying to run. Eg,
parallel --dry-run '/Applications/biotools/seqtk/seqtk seq -aQ64 -q20 {}.fastq > {}.fasta' ::: $(ls *_L001_R.fastq | rev | cut -c 14- | rev | uniq)
Maybe even add | head
at the end there if you have many files to run.