Closed kcleal closed 1 year ago
Hi there, thanks for raising this issue. Unfortunately at the moment SAVANA doesn't support the use of .cram
files - only .bam
. This is functionality I can look into adding though.
For now, if you convert your cram files to bam does this resolve the issue?
I converted a few Mb to bam and I think it works, thanks. I had a go at changing some of the source code to get it working but not luck yet. Thanks for the quick reply
Hi there, I've implemented CRAM support in the latest commit (v1.0.3 - I'll create a release for it soon). However, SAVANA will run much more slowly on CRAM files than BAM files. This is because I rely on the get_index_statistics
functionality of pysam to optimise memory usage. This information isn't available for CRAM files though (see: https://github.com/pysam-developers/pysam/issues/1060).
So I'd still recommend converting to BAM if you'd like faster speeds, but if that's not a concern, CRAM files should now work. If you know your chromosomes of interest, it's highly recommended that you supply them via the --contigs
argument. This will prevent worker threads being spawned for thousands of contigs which have no reads mapped to them.
Hi, Thanks for the nice tool. Im running into this error which pops up straight away after running: