sambamba (release 0.6.7) had abnormally finished with error code 35584

[gskrasnov]

Dear Authors,

sambamba (release 0.6.7) had abnormally finished with error code 35584
I tried to sort my BAM file (available here) and got segmentation fault error.

However, sambamba has produced normally sorted final BAM file (available here) + index *.bai

command line:
/sambamba_v0.6.7 sort --memory-limit 12000000000 --nthreads 6 --tmpdir ./MME03.temp --out MME03.bam MME03.sn.bam

There are 1870 reference scaffolds/contigs and a large proportion of reads from the mitochondrial genome

[pjotrp]

On running latest I get no errors:

~/sambamba-0.6.8-pre1 sort --memory-limit 12000000000 --tmpdir ./MME03.temp --out MME03.bam MME03.sn.bam    

penguin2:~/data/sambamba/issue346$ ls -lrt 
-rw-r--r-- 1 pjotr pjotr 1439421481 Apr  1 07:47 MME03.sn.bam
-rw-r--r-- 1 pjotr pjotr       7896 Apr  2 09:12 MME03.sn.bam.bai
-rw-r--r-- 1 pjotr pjotr  890369670 Apr  2 09:16 MME03.bam
-rw-r--r-- 1 pjotr pjotr     475792 Apr  2 09:16 MME03.bam.bai

Are you running on a Xeon E5 per chance? See #335

[pjotrp]

DL http://files.genenetwork.org/software/contrib/sambamba-0.6.8-pre1

[gskrasnov]

Thank you, Pjotrp!

No, I'm running sambamba on Xeon E7- 8837 @8 threads

I tried the updated 0.6.8-pre1 and everything went fine.