Error when running coverM (genome mode): thread 'main' panicked at 'called `Option::unwrap()` on a `None` value'

[zehanna]

Hello,

I've encountered an error when trying to run coverM and I was wondering if you could help. I have installed coverM using conda like this:

conda install -c bioconda coverm

Now I'm trying to run it in genome mode with this command:

coverm genome --bam-files . --genome-fasta-directory bins --genome-fasta-extension fa -o coverm_output

And I'm getting this error:

[2021-07-21T13:03:07Z INFO coverm] CoverM version 0.6.1 [2021-07-21T13:03:07Z INFO coverm] Writing output to file: coverm_output [2021-07-21T13:03:07Z INFO coverm] Using min-covered-fraction 10% thread 'main' panicked at 'called Option::unwrap() on a None value', src/bam_generator.rs:280:18 note: run with RUST_BACKTRACE=1 environment variable to display a backtrace

Would you have any idea what's the problem?

Thanks a lot in advance,

Hanna

[wwood]

Hi,

I suspect this might be because you are specifying a directory (.) for --bam-files when it is expecting paths to one or more files. Dees that help?

[zehanna]

Thanks, indicating the bam files specifically worked (I thought it was enough to indicate the directory they're in). Best, Hanna