Re: [Samtools-help] Error when converting cram to bam

[James B. <jk...@sa...>]

Hello Yvonne,

On Wed, Jun 22, 2016 at 03:58:21PM +0100, Yvonne Teng wrote:
> 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).

If they've been processed at Sanger (here) I think they should have
a reasonable chain of @PG headers outlining the commands used to
create the CRAM.

Perhaps that gives a clue as to what software versions created the
CRAM.

Do happen to have the file name or irods run/lane numbers?  I may be
able to debug it locally then.

> 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.

It's also possible that your problem is something to do with the
references loaded up.   We found an issue where references could be
corrupted during interrupted downloads and not detected by samtools.
That issue is now fixed, but it could leave invalid references cached
locally.

There isn't a trivial check, but by default it'll be saving references
in ~/.cache/hts-ref/.  You could md5sum the suspected sequences
(whatever ref 1 is; the second @SQ line IIRC) and validate that it
matches the saved filename.

James
-- 
James Bonfield (jk...@sa...) | Hora aderat briligi. Nunc et Slythia Tova
                                  | Plurima gyrabant gymbolitare vabo;
  A Staden Package developer:     | Et Borogovorum mimzebant undique formae,
https://sf.net/projects/staden/   | Momiferique omnes exgrabure Rathi. 


-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE.