[Samtools-help] Error when converting cram to bam

[Yvonne T. <yh...@ca...>]

Hi,

I have using samtools on a standalone computer and encountered this 
error while trying to convert cram files to bam files. These cram files 
were previously converted successfully by my colleague when using 
samtools through iRODs (Sanger).

Error message:
Slice ends beyond reference end.
ERROR: md5sum reference mismatch for ref 1 pos 26310..47257971
CRAM: 6f3d18602e7dc00eb80e6245904f7e36
Ref : 4e80faaa9678ef991b5f9f5fc8ec6bcb
Failure to decode slice
[main_samview] truncated file.

I am using Version: 1.3.1 (using htslib 1.3.1). I have tried 
reinstalling samtools but same error happened.

Can I ask how can I solve this problem?

Thanks!

Best wishes,
Yvonne