Error when running medaka_consensus

[rs-norman]

I recently updated to the newest version of Medaka and tried to run the medaka_consensus pipeline using:

medaka_consensus -i input.fastq.gz -d assembly.fasta -o output_folder -t 60 -m r1041_e82_400bps_sup_v4.3.0

This command generated the 'calls_to_draft.bam' and 'calls_to_draft.bam.bai' but then gave the following error:

"medaka: error: argument command: invalid choice: 'consensus'..... failed to run medaka consensus."

I understand that medaka consensus has changed to medaka inference but does that change prevent the running of medaka_consensus pipeline?

[cjw85]

This sounds like you have an incongruent version of the medaka_consensus script and the main medaka Python program. How have you install medaka?

[rs-norman]

Thanks for the quick response. The update was performed by University research computing personnel so I am not certain how it was installed. I will need to follow up with them.

[cjw85]

@rs-norman

Have you resolved this issue?