Does Bowtie2 accept compressed (.gz or .bz2) reads as input?

[Marc-Danie Nazaire]

The help text for the bowtie2 (bowtie2 --help) command states that it accepts compressed input:

"Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2)."

However when I try to run with compressed input I get the following error:

Error: reads file does not look like a FASTQ file
terminate called after throwing an instance of ‘int' bowtie2-align died with signal 6 (ABRT) (core dumped)).

Does Bowtie2 accept compressed (.gz or .bz2) reads as input? If so how should the command line look? 

Thanks.

[Marc-Danie Nazaire]

Any response would be appreciated. Has anyone tried this before?

Thanks.

[Flo]

Hello,

I am using bowtie2-2.2.9 and *fastq.gz reads are working fine as an unput.

Cheers,

Flo