I did alignment with Hisat2 Human RNA-Seq sample from Illumina average sam file ~15.00GB in size I converted to bam file by using code
samtools view -S -b input. sam > output.bam
This created bam files with average size ~4.00GB size I checked the bam files for headers are othe stat which is looking good and don't think files are corrapted
now when I am trying to sort them with
samtools sort input.bam -o output.bam
it worked for a while and generated temporary bam files then start spitting on terminal with binary codes. and further no work even if I leave it to finishe. I also tried this code as felt may be this is due to memory problem
samtools sort @ 5 -m10G input.bam -o output.bam
Didn't work. I tried with other similar parameter to make it work but non working for me.
I am using CentOS7 with ~100GB ram and ~12TB on HDD
what I am doing wrong? please help.