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epi2me-labs / wf-human-variation

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The genome build detected in the BAM is not compatible with this workflow. #172

Closed selmapichot closed 2 months ago

selmapichot commented 2 months ago

Ask away!

Hi, I am trying to run this workflow with the T2T reference genome, but I had this error message : The genome build detected in the BAM is not compatible with this workflow. Is the issue due to the T2T reference ? if so, is there a way to work around it ? Many thanks. All the best, Selma.

vlshesketh commented 2 months ago

Hi @selmapichot, this is because you are most likely attempting to run a sub-workflow that is not currently supported for the T2T genome. Please refer to the documentation for the options that are compatible with this genome (i.e. the Other human section): https://github.com/epi2me-labs/wf-human-variation#10-genome-compatibility-and-running-the-workflow-on-non-human-genomes

selmapichot commented 2 months ago

Hi, Many thanks for your reply. I'm calling snp (it seems that the correct flag is --snv instead of --snp as written in the documentation ...?). If I understand correctly the documentation, it should be possible to call --snv with another human reference genome, which is what I am trying to do with the T2T, but I am still having this error message " The genome build detected in the BAM is not compatible with this workflow." Any advise on how to work around it will be greatly appreciated. All the best, Selma.

vlshesketh commented 2 months ago

Hi, the correct parameter for calling SNVs is indeed --snp

For T2T, the parameters that should enable you to analyse your data are:

--snp --sv --mod --annotation false

Can you please let me know if you are still getting the error message, with these options? I wonder if you are not including --annotation false as this can only be carried out with hg19/hg38.

selmapichot commented 2 months ago

Hi, many thanks again for the reply. I got another arror message when using the --annotation false which is : The exit status of the task that caused the workflow execution to fail was: 0.

The full error message was:

Error executing process > 'snv:wf_build_regions (1)'

Caused by: Missing output file(s) snv_TB23_00177_T1/tmp/CONTIGS expected by process snv:wf_build_regions (1)

vlshesketh commented 2 months ago

Hi @selmapichot from your recent message, I wonder if you meant to open this ticket for the wf-somatic-variation workflow instead? snv:wf_build_regions is a process from that workflow, not wf-human-variation. The wf-somatic-variation issue page is here: https://github.com/epi2me-labs/wf-somatic-variation/issues. That would also explain the --snp vs. --snv discrepancy, as we use the former in wf-human-variation and the latter in wf-somatic-variation.

selmapichot commented 2 months ago

Many thanks for your reply.