Hello Michael,
On 5 Nov 2015, at 16:56, Michael Nuhn <[email protected]> wrote:
> I am using samtools 1.2. When I run the index command like this:
>
> /software/ensembl/funcgen/samtools index
> /lustre/scratch109/ensembl/funcgen/mn1/problem_bam/HEL9217:hist:BR2_WCE_3526_bwa_samse_1.unfiltered.bam
>
> samtools instantly terminates and generates no output. The exit code
> does not indicate a failure
The lack of error reporting here is something that has been improved since 1.2.
Samtools built from the current develop branch reports for this file:
[bam_index] corrupted or unsorted input file
and exits with failure. This was
https://github.com/samtools/samtools/issues/362 .
> -rw-r--r-- 1 mn1 ebiusers 34G Nov 5 11:20
> /lustre/scratch109/ensembl/funcgen/mn1/problem_bam/HEL9217:hist:BR2_WCE_3526_bwa_samse_1.unfiltered.bam
>
> and has headers and alignments in it. The bam file is generated by picard.
In this case, I suspect the problem is that your file is actually a SAM file!
This can't be indexed with samtools index, and I'll change the message for this
case to make it easier to diagnose. (A bgzipped SAM file could be indexed with
tabix, but unfortunately such an index can't be used with "samtools view FILE
REGION".)
John
--
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