Cram files: failed to populate reference on Travis CI

[Wouter De Coster]

Hi,

When I process a cram file on my server everything works fine, no errors. When I do the same on Travis CI I get the following:

[E::cram_get_ref] Failed to populate reference for id 0

[E::cram_decode_slice] Unable to fetch reference #0 1..2100774

[E::cram_next_slice] Failure to decode slice

I reasoned that this is the case because it cannot find the reference fasta with which the cram file was made, so I included the reference in the test dataset.

My test data is a GitHub repo which gets cloned for testing on Travis CI (https://github.com/wdecoster/nanotest). 

However, the path in the cram header is an absolute path on my computer, and the path on Travis CI is obviously not the same.

I guess if I could specify in pysam which reference fasta to use everything would be fine? I guess pysam/samtools attempts to fetch the reference fasta.

Or should I manually adapt the cram header to get a relative path to the reference?

Do you have suggestions on how to fix this?

Cheers,

Wouter

[Andreas Heger]

Hi Wouter,

AlignmentFile() accepts to option 'reference_name':

reference_filename : string
Path to a FASTA-formatted reference file. Valid only for CRAM
files.
When reading a CRAM file, this overrides both ``$REF_PATH`` and
the URL
specified in the header (``UR`` tag), which are normally used
to find
the reference.

Best wishes,
Andreas

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[Wouter De Coster]

Hi Andreas,

Great, that should fix it. Thanks!

I've looked for something like this in the documentation, is it possible that it's undocumented? Or perhaps I just looked in the wrong places...

Cheers,

Wouter

[Wouter De Coster]

On second thought, that doesn't solve it. I can't hardcode a path to a reference file just for testing applications. Guess I'll see if I can convert the bam to cram on Travis CI.

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