TrimOverlap: RuntimeError: Unexpected sample relationship about medaka

[cjw85]

Wouter,
If you can create a chr1-only bam and its not too big, I would like to have a look.

One curiosity, though not necessarily wrong and something medaka should handle, is that you have (at least one) read with a very long insert: the decimal places in the region string in your log above indicates insertion columns with respect to the reference.

[cjw85]

I'm just reviewing the changes we made between the pre-release and v0.7.0.

There was a commit which altered how chunks are sorted when they are read back from the HDF datastore. It looks to me in your case the chunks have indeed been read back incorrectly giving the Relationship.reverse_overlap error.

[wdecoster]

Could a structural variant explain the very long insert?

While attempting to share the data there are a few hurdles. One is "NA19240-chr1.cram has an invalid extension. Valid extension(s): zip, gz, 7z, tar, tgz, sqfs, hdf, fast5, xz." But okay, I can rename that one. But second: "I confirm that this data is not human genomic data, and that any necessary agreements and consents required to share this data with Oxford Nanopore are in place." -=> it's human, but I can share as it's from NA19240.

[cjw85]

I have run your data using the v0.7.0 release, It took around 30 mins to run the initial medaka consensus pass using a GPU and a further 10 minutes to create an unphased vcf. I believe the error you saw was therefore corrected between the pre-release and the release.

[wdecoster]

Alright then, I'll update again and see how it goes. Thanks!