alignment.bam output file seems to be missing

[irc47]

Ask away!

The workflow completes but I'm not able to locate the alignment.bam file that is listed as one of the outputs. I've had the same issue running in EPI2me desktop and in the command line and using both the V1.4.1 and with earlier versions of the workflow. Is there something specific I need to do to get this file as an output?

[cjalder]

Hi @irc47 - this seems to be an oversight on our part and they aren't currently output. We'll address this for the next release. For now I can suggest looking in the work directory for them using the following command find ./ -name '*.reads2ref.bam'

[irc47]

Thank you for such a quick reply- I was able to find the file using this suggestion.

[forty2wallabyway]

Also looking forward to getting a .bam alignment output but for now was able to use the suggested workaround!

What is the reference file that these reads are being aligned against?

[cjalder]

For de novo mode it will be the draft assembly from Flye (pre-medaka polishing) and for reference based mode it will be the provided reference file.

[forty2wallabyway]

Thanks, that makes sense. When reference_based is used, are gaps/ambiguities due to no/low coverage pulled through from the reference to the final consensus? (This seems to be the case when looking at .medaka.fasta outputs in Geneious, but I could be mistaken.)

[cjalder]

Hi @forty2wallabyway - you are correct, we're exploring the idea of masking regions of low/no-coverage in a future release to mitigate bias to the reference in these cases.

[forty2wallabyway]

Thanks @cjalder - that would be super helpful for completing genomes from unknown isolates, I think.