Hi,
Running into a problem with samtools 1.0 sort, specifically the merging phase.
It's very slow compared to the previous version. I have a 965MB bam file (which
is already sorted) but I use it here as an example:
Version 0.1.19:
$ time samtools sort test.bam test.0.1.19.sorted
[bam_sort_core] merging from 8 files...
real 7m9.964s
user 6m54.334s
sys 0m8.205s
Version 1.0:
$ time samtools sort test.bam test.1.0.sorted
[bam_sort_core] merging from 8 files...
Terminated
real 60m40.508s
user 60m27.051s
sys 0m6.612s
(This didn't actually complete, I killed the process).
This happens on different servers (both running Ubuntu), both with over 100G
RAM. I am using the precompiled samtools in the
samtools-bcftools-htslib-1.0_x64-linux tarball.
Cheers,
Adam Skarshewski.
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