Question: Why Is Samtools Colorspace Calmd Incredibly Slow?
0
gravatar for najoshi
9.5 years ago by
najoshi30
najoshi30 wrote:

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.
samtools • 2.2k views
ADD COMMENTlink written 9.5 years ago by najoshi30
3
gravatar for Nilshomer
9.5 years ago by
Nilshomer100
Nilshomer100 wrote:

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

ADD COMMENTlink written 9.5 years ago by Nilshomer100
1

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

ADD REPLYlink written 9.5 years ago by Casey Bergman18k

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."

ADD REPLYlink written 9.5 years ago by Istvan Albert ♦♦ 84k
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