bwa, faidx command not found

Question

bwa, faidx command not found

Closed this issue 9 months ago · 5 comments

Based on Metapro tutorial while indexing ChocoPhlAn database for BWA and DIAMOND getting error bwa and faidx command not found.

Answer 1 · 2024-01-18T17:32:35.000Z

what's the command you typed?
Sounds like the command is wrong, or docker/singularity wasn't installed correctly.
Not a MetaPro issue.

Answer 2 · 2024-01-19T04:45:59.000Z

this is below command i have used
bwa index -a bwtsw - samtools faidx
i put chocophlan path as well.

Answer 3 · 2024-01-19T16:08:36.000Z

You're not invoking any of the docker/singularity image. Metapro doesn't install these tools for you. We package it inside a container.

You need to use singularity/docker. Please take another look at our documentation, and perhaps the tutorial too.

Please also consult the documentation docker/singularity provide.

Answer 4 · 2024-02-12T06:45:39.000Z

Can you please guide me how to invoke because I am new to docker. I followed each step in metapro tutorial.

Answer 5 · 2024-02-12T18:35:47.000Z

This level of support is beyond my capacity to provide. I suggest that you contact a more senior bioinformatician at your institution or signup for the Canadian Bioinformatics workshop https://bioinformatics.ca/