silent bwa mem crash

[cuidaniel]

I am running something along these lines: bwa mem -M -T 45 -t 8 hg38.fa sample.r1.fq sample.r2.fq > sample.sam 2> mem.err

The job starts normally, [M::bwa_idx_load_from_disk] read 0 ALT contigs [M::process] read 648150 sequences (80000124 bp)... [M::process] read 638744 sequences (80000167 bp)...

But then silently stops, and produces no error.

Any help would be greatly appreciated! This behavior was the same with both the SourceForge bwa and the bioconda bwa.

[SunYong0821]

@cuidaniel you need write bwa version

[cuidaniel]

I'm using this version: 0.7.17-r1188. What version should I be using then?

[mgb217]

hi, I meet the same problem, have you solved it ?

[cuidaniel]

No. Got nothing after the Dec 15th reply.

[ripanea]

I did receive this kind of error as well once, when aligning to the hg19 reference. In my case the problem was the lack of memory. I believe BWA tries to read the sequences in the memory and it runs out of memory,

I simply increased the memory on the server and everything ran fine.

[KennethLim314]

I've tried the same thing on hg38. Bumping up the memory to 30 GB failed to succeed here on small (20000 reads!) files on bwa 0.7.17-r1188. Silent failures, as per OP.

[medcelerate]

Question, what processor are you using when you get these issues?