Error in bwa mem and samtools sort, return code: 256

[myco-bradshaw]

Error in bwa mem and samtools sort, return code: 256

[bistace]

Hello,

it seems that the samtools step crashed, could you please show me what is inside logs/samtools_sort.e?

[myco-bradshaw]

Yes, the error from logs/samtools_sort.e:

samtools sort: couldn't allocate memory for bam_mem

[bistace]

It means that the samtools sort ran out of RAM. As we allocate 5G of RAM per samtools sort thread, you should relaunch hapo-g with a lower number of threads.