samtools sort: couldn't allocate memory for bam_mem

Question

[SushiRoll]

Dear all,

I'm running Snippy 4.6.0 and I'm having the following problem:

samtools sort: couldn't allocate memory for bam_mem [bam_mating_core] ERROR: Couldn't read header samtools sort: failed to read header from "-"

samtools sort runs as default:

samtools sort -n -l 0 -T /tmp --threads 3 -m 2000M | samtools fixmate -m --threads 3 - - | samtools sort -l 0 -T /tmp --threads 3 -m 2000M | samtools markdup -T /tmp --threads 3 -r -s - - > snps.bam 2>> snps.log

So I'm guessing it has to do with the 2000M. Is that correct? These tools run automatically when running snippy, should I modify the script? If that is indeed the problem, which would you suggest would be a reasonable amount of memory? I currently have 8Gb.

Thanks a lot!

[ATpoint]

I see no input file in the first sort command. Don't use /tmp as temporary directory, it's the physical memory, use any path on disk.

[SushiRoll]

Hi ATpoint,

Thanks for your help, in the end it was a server error, I'm using a VM hosted at our main server and after some maintenance, each VM was assigned Mb instead of Gb. With that fixed, it seems to be running smoothly. I'm nevertheless interested in not using /tmp as a directory, should it be changed? aren't the tools downstream the pipeline going to look for the files in /tmp? I'm not really familiar with the more "technical computer" stuff so I might be talking nonsense.

Thanks a lot!

[ATpoint]

Temporary files are created when the actual process (here sort) runs out of allocated memory. It will then spill intermediate files to -T location, and later merge them into the final file which is then piped to stdout. I personally find it bad practice to use /tmp as this is the physical memory so you are kind of defeating the purpose of tmp files.