Running out of disk space with BWA, wrong CMD line?

[sindrle]

Hi!
I keep getting "out of disk space" errors , even with 800gb free space.

This is my code:

bwa samse -n4 reference.fa x.sai x.fastq.gz > x.sam

Somebody knows?

[GenoMax]

Have you checked to see if your /tmp is filling up? Are these very large files?

[sindrle]

Thats probably it..

All files is about 2-3gb. The x.sam file will be 16gb I guess..

Could I compress the sam to bam like this?

bwa samse -n4 reference.fa x.sai x.fastq.gz > x.sam | samtools view -Sb > x.bam

[GenoMax]

See this thread for examples of piping: http://www.biostars.org/p/43677/