Bowtie output zipped but not zipped

[thh32]

I have recently used Bowtie2 to separate out reads mapping to a set of genomes which which works fine however due to the size of my current dataset I had to input as zipped and output as zipped using the command below:

bowtie2 -f --threads 8THREADS -N 1 --un-gz NZ_bowtie_nonaligned_hungate_thread.done --al-gz NZ_bowtie_aligned_hungate_thread.done -x /ibers/ernie/home/thh32/thh32/mcCabe_qualtrimmed
_trimmed5P_files_.fastq/Hungate1000_index_bowtie -U /ibers/ernie/scratch/thh32/alldata.fa.gz -S /dev/null

The process itself worked fine except for the output zipping. The files themselves were not acknowledged as zipped and so could not be unzipped, however the data inside looked like this:

�95j����q�?�k�6��t��<^L����N� ��m��(N��k9ߟ4�|^��!�\/�߹��M����33���}^�6���۩s�}wsUo/��|.e^6{��\��Sf��sz̋��A���9H�%WLO���u~

Is there anyway to convert this into fasta format again?

Any help would be greatly appreciated.

Many thanks,
Tom

[dpryan]

That looks a lot like compressed data to me. Remember that zipping refers to gzip, not another zip variant. If you want to decompress then just use gunzip.

[thh32]

I thought it looked like compressed data so I tried using gunzip but gunzip wouldn't accept the file as a zipped file and so gave this error:

gzip: NZ_bowtie_nonaligned_hungate_thread.done: unknown suffix -- ignored

And with unzip it provided this answer:

Archive: NZ_bowtie_nonaligned_hungate_thread.done
End-of-central-directory signature not found. Either this file is not
a zipfile, or it constitutes one disk of a multi-part archive. In the
latter case the central directory and zipfile comment will be found on
the last disk(s) of this archive.

[thh32]

Managed to sort it out by using mv FILE FILE.gz and then was accepted and can be unzipped

[dpryan]

You just have to change the file name, since that's what gunzip is complaining about (the suffix in this case is "done", rather than "gz"). Try calling it "NZ_bowtie_nonaligned_hungate_thread.done.gz".

Edit: Ah, you just figured that out, good

[westerman]

One other methods aside from renaming the file is to use 'zcat'. As the manual says:

zcat will uncompress files that have the correct magic number whether they have a .gz suffix or not.