Hi,
I struggle to sort whole-genome 110G BAM file. I run 8G RAM and 2CPU google
instance.
vmorozov@gstat:/disk/genomes$ samtools
Program: samtools (Tools for alignments in the SAM format)
Version: 1.2 (using htslib 1.2.1)
I tried:
nohup samtools sort -n -@ 2 -m 2G my_sample.bam sort > e&
the command crashed after 2 hours creating ~40G of sort.*.bam files. Empty
error/stdoutput. Now I have launched:
nohup samtools sort -n -@ 2 -m 1G my_sample.bam sort > e&
and I observe gradual increase of samtools occupied memory. After 30 min
run and creating 20Gb of temporary files, samtools occupied ~4G of memory:
top - 21:16:10 up 4:38, 2 users, load average: 2.15, 2.01, 1.70
Tasks: 94 total, 1 running, 93 sleeping, 0 stopped, 0 zombie
%Cpu(s): 89.2 us, 10.7 sy, 0.0 ni, 0.2 id, 0.0 wa, 0.0 hi, 0.0 si,
0.0 st
KiB Mem: 7660696 total, 7526644 used, 134052 free, 1244 buffers
KiB Swap: 0 total, 0 used, 0 free. 3234156 cached Mem
PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND
6045 vmorozov 20 0 4116052 3.769g 1796 S 196.5 51.6 49:14.03
samtools
26 root 39 19 0 0 0 S 2.3 0.0 0:10.80
khugepaged
39 root 20 0 0 0 0 S 1.0 0.0 3:13.44 kswapd0
Is it memory leakage? I guess it will crash eventually. Any suggestion how
to get the sort job done?
Thanks
Vlad
------------------------------------------------------------------------------
One dashboard for servers and applications across Physical-Virtual-Cloud
Widest out-of-the-box monitoring support with 50+ applications
Performance metrics, stats and reports that give you Actionable Insights
Deep dive visibility with transaction tracing using APM Insight.
http://ad.doubleclick.net/ddm/clk/290420510;117567292;y
_______________________________________________
Samtools-help mailing list
Samtools-help@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/samtools-help
