extractSequences.sh on gzipped input files

[You Me]

Hello,

I am trying to pull out the reads from my input file that were classified to a specific taxon. My input file is a gzipped fastq file, and I was able to run classify_metagenome.sh on this successfully with the --gzipped option. However, when I tried to run extractSequences.sh using this same input file, I encountered the following error:

Failed to recognize the file format: It does not look like a fastq/fasta format.

Is there an option to run extractSequences.sh on gzipped inputs? I would prefer not to unzip my input file if possible, as the compressed file is already very large (several GB). 

Thank you!

[Rachid]

Hi,

As for today, this script accepts only fast/fastq files. Please go ahead and uncompress your file behind running it,

Thank you,

Best,

Rachid