I was able to finish the job with -@ 2 -m 1G parameters. Though it
occupied about 4.5G memory by the end of the job
On Mon, Apr 27, 2015 at 9:33 PM, Colin Hercus <co...@novocraft.com> wrote:
> 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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