Why Is Samtools Colorspace Calmd Incredibly Slow?

Question

[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 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.

Answer 1

[Nilshomer]

Answers to your question since you posted it elsewhere: Here & Here

[Casey Bergman]

Thanks Nils for linking all three posts. Vigilence like this really can help prevent redundant effort.

[Istvan Albert]

Let me also add the answer linked in those posts just in case this forum happens to outlive those ;-) "You should sort the alignment first."