Bowtie2 can not read input file

[aerlaut]

Hi,

I'm trying to use Bowtie2 to align some sequence. However, it seems that Bowtie2 failed to detect the input files:

I'm using the latest image of Bowtie2 from Bioconda, which seems to point to Bowtie2 version 2.5.0.

Can someone please help?

[aerlaut]

I think this issue is also referenced in this Stackoverflow question: https://stackoverflow.com/questions/73917347/directory-argument-for-bowtie2

[aerlaut]

I think the issue happens because the index was built using a different version of Bowtie2 than what I'm using. It turns out that the index files were built using Bowtie 2.4.5, while alignment was done using 2.5.0. Building the index again using Bowitie 2.5.0 fixes it.