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???
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???
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