Error while converting fastq to fasta

[PSchneeb]

Hi, I'm running seqtk seq on a centos 6.8 cluster (I have to load the module).

However, I get the following error when trying to convert a fastq to fasta:

[W::stk_seq] stdin is available; the input file is ignored!

I run the software with a perl script that first calls the sampling command (works well) and then calls the conversion command (fails).

I used the following command (I tried with both "-a" and "-A"):

system("seqtk seq -a $inputfile_conversion > $folder_temp/Filteredreads$outname$ext3");

Thanks in advance for the help! Pierre

[lh3]

To diagnose problems, it is better to run seqtk separately; otherwise, I don't know whether it is the problem with seqtk or the problem with the rest of your script.

[tseemann]

@PSchneeb i think you might have some strange characters in $inputfile_conversion. You should quote it in Perl as follows:

system("seqtk seq \Q$inputfile_conversion\E > \Q ... \E");