samtools colorspace calmd is incredibly slow

[najoshi]

Hi all,

I'm running samtools version 0.1.14 (and bwa version 0.5.8c) and I am
trying to do solid colorspace analysis on some single-end reads. I
indexed the reference using colorspace and I also did the alignment
and samse using colorspace after converting the solid files using the
solid2fastq.pl script. Now I am trying to run samtools calmd on the bam files
and the process is incredibly slow. For example, I have a 1G
reference and a 2.4G bam file and the process has been running for
about 3 days now and only about 98M of data have been outputted. The
data does keep growing, however, so I know that the process is writing
and not hung, it's just writing at an incredibly slow rate. I am
running this on an 8 core, 144G ram machine. Am I doing something
wrong? Has anyone else seen this behavior?

Here is the calmd command I used:

samtools calmd -Ar input.bam reference.fa > output.calmd.bam

Any help would be highly appreciated. Thanks!

- Nik.

[nilshomer]

For those who didn't see the response on the samtools mailing list, try sorting your file first.

http://biostar.stackexchange.com/questions/7057/why-is-samtools-colorspace-calmd-incredibly-slow/7060

http://sourceforge.net/mailarchive/message.php?msg_id=27291513