samtools sort

[EBER]

Hello,
I am trying to sort a large bam file, actually split in two, with samtools sort
I use -m 10000000000 so the job creates 8 sorted files of about the same size, plus a smaller last one.
At the end of the job, samtools sort give the message "core_sort_merge 9 bam files" and it stays like that for a while before the screen starts showing multiple caracters one after the other.

My question is, can I assume the job was completed?
My command-line was
samtools sort -no -m 10000000000 inpunt.bam output.prefix &

Any help appreciated.

[adaptivegenome]

Probably the best thing to do is just check to make sure you have the same number of reads in the output files as you do in your input.

Not sure if you are interested but we also have a parallelized implementation of "samtools sort" that combines the merge/sort step. Its at http://www.github.com/adaptivegenome/openge. It's open source and there are also binaries for convenience...