Hi Vladimir, You could try using novosort, it's included in download at http://www.novocraft.com/support/download/
novosort -m 4G -t . my_sample.bam >sorted.bam
To get multi-threading you need a license and I've attached a 1 month
trial. Just extract the file novoalign.lic from the attached tar and save
into the folder with novosort program. You can freely use without a license
but only 1 thread.
Kind Regards, Colin
Colin Hercus,
*Novocraft Technologies Sdn Bhd* <http://www.novocraft.com/>
C-23A-05, 3 Two Square, Jalan 19/1, Section 19,
46300 Petaling Jaya, Selangor Darul Ehsan, Malaysia
Tel: +6016 2482 668 Fax: +603 7960 0540
www.novocraft.com
On 28 April 2015 at 05:19, Vladimir Morozov <vmmoro...@gmail.com> wrote:
> 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
>
>
>
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