How can I monitor the progress of BWA?

[Azazel]

When aligning a fastq file with BWA, I would like to monitor the progres, to know how long it approx. will take until the alignment of the whole file is finished.

Is there any way to do this?

I was thinking about using pv (process viewer) but can't figure out how. Is it possible with pv, or maybe is there another way?

[davidblaney]

Hi,

I'm guessing that you would like to see progress of the bwa aln command.
I looked into this before for version 0.6.2 of bwa and found every so often the program will print this information.

[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 26188815 sequences have been processed.

The ' X sequences have been processed' seems to be

X = number of reads in the fastq file.

So I took the the number of lines in the fastq file and divide it by 4 to get the number of reads. I could then write a script to capture the this information and the bwa progress information and calculate how far through the fastq file I was.

Hope this helps,
David