Hi everyone,
I encountered a strange problem with samtools sorting. A 37.6 GB sam file was generated by Stampy after mapping Illumina reads to hg19. It was converted to a 11.3 GB bam file with samtools. Then I tried to sort it and this where I hit the problem. I used fisrt default settings (1 thread, 756MB/thread):
After a while samtools started spitting chunks of out_sorted.bam000X.bam files, each new initiated after previous reached 130-160 MB; at 21st chunk I killed it.
Then I increased memory:
This time samtools spit out only 6 chunks of 1.5-2.5 GB, then started pouring binary gibberish to stdout, and eventually hang.
When I tried to run multithreaded sorting
the behavior was the same except chunks were spit in multiples of 8, with -@ 16 in multiples of 16, but eventually all ended up with binary gibberish to stdout.
I am using version 0.1.19-44428cd; the 2x4 cpu box has 96GB of memory, RHEL5.8.
Can anyone advise what is going on and why?
I encountered a strange problem with samtools sorting. A 37.6 GB sam file was generated by Stampy after mapping Illumina reads to hg19. It was converted to a 11.3 GB bam file with samtools. Then I tried to sort it and this where I hit the problem. I used fisrt default settings (1 thread, 756MB/thread):
Code:
samtools sort input.sam out_sorted.bam
Then I increased memory:
Code:
samtools sort -m 10G input.sam out_sorted.bam
When I tried to run multithreaded sorting
Code:
samtools sort -@ 8 -m 3G input.sam out_sorted.bam
I am using version 0.1.19-44428cd; the 2x4 cpu box has 96GB of memory, RHEL5.8.
Can anyone advise what is going on and why?
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