BWA exit issue

[vadoue]

Hi guys!

I am having troubles running BWA with ChIP-seq paired-end data (100bp from HiSeq2500).

It stop suddently without any specific error message. What is even more strange is that when I change the -t option sometimes it is running a little bit before the exit.

Any help is welcome, see below the output.

Thank you!


qsub -b Y bwa mem -M -t 4 ~/work/Genome/Bowtie-index/mm10.fa R1.fastq.gz R2.fastq.gz > output.sam

error file:
[M::main_mem] read 400000 sequences (40000000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (19, 144766, 1, 1)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (47, 53, 64)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (13, 98)
[M::mem_pestat] mean and std.dev: (55.94, 15.63)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 115)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (141, 153, 169)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (85, 225)
[M::mem_pestat] mean and std.dev: (156.32, 21.00)
[M::mem_pestat] low and high boundaries for proper pairs: (57, 253)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation FF
[M::worker2@2] performed mate-SW for 316058 reads
[M::worker2@1] performed mate-SW for 327210 reads
[M::worker2@0] performed mate-SW for 324144 reads
[M::worker2@3] performed mate-SW for 321252 reads
[M::main_mem] read 400000 sequences (40000000 bp)...
Your job has been killed.

And for all the other options (no -t; or -t 10; or anything to increase memory):
[M::main_mem] read 100000 sequences (10000000 bp)...
Your job has been killed.

[GenoMax]

Sounds like you need to request additional memory for your cluster job. (Something like qsub -l mem_free=16G). The default allocation is not enough and your job is getting killed.

[vadoue]

It seems to be a bwa version or compilation issue... I used same command but with full path to bwa (bwa-0.7.10) and now it is working.

Thanks!