bwa aln fails

[mike2vandy]

I'm running bwa verision 0.5.9

I have 6 fastq files each 33 GB.

I'm running:

bwa aln -l 28 -t 6 <ref_file> <in_file> -f <out_file>

Four of the six fastq files align to the indexed genome correctly. All six files were generated from the same library, adapters have been clipped. However 2 fastq files run through:

[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9

then stall here (for hours) like its frozen. I'm not getting a segmentation fault or any error. The program just ceases to continue.

Has anybody seen this before or have a fix???

[xied75]

First reasonable check, are those two really look the same as the other four? If it's fastq.gz, unzip it first, then head or tail on it.

[tahamasoodi]

Are you running them at the same time, if so try to rerun the 2 files separately?

[Richard Finney]

How big is your machine?
Have you checked your inputs?
Bad input and/or not enough memory causes problems with BWA.

See my response in this thread for an explanation:

http://seqanswers.com/forums/showthread.php?t=2895

[mike2vandy]

Well, not really sure what I did. I changed my pbs script, dropped number of threads from 6 to 4 and it seems to be running....whatever works man.