bedtools makes ubuntu 14.04 slow

[cmccabe]

When I run bedtools 2.25.0 covereBed, the command below does run.

coverageBed -d -g custom.genome.txt -a targets.bed -b file.txt > base_counts.txt

There are 11.5 millino bases in each file and when I am running bedTools any other process is very slow.

I am using ubuntu 14.04, 64 bit witn 64GB, Xeon processor with 8 cores and 20MB cache.

Is this normal? Thanks.

[GenoMax]

You are probably running into I/O bottleneck depending on what else is happening on the system.

[cmccabe]

Thanks, I am moving to a cluster server soon that has dedicated PCIe SSD to help with I/o issues. Thanks.

[GenoMax]

Look into iostat command if you are curious about checking if this indeed is causing the bottleneck.

[cmccabe]

I will definitely take a look at iostat. Thank you .

[cmccabe]

Here is the output:

iostat -d
Linux 3.19.0-64-generic (DTV-A5211QLM) 	07/14/2016 	_x86_64_	(16 CPU)

Device:            tps    kB_read/s    kB_wrtn/s    kB_read    kB_wrtn
sda              70.83      3703.23      1938.31 2606232340 1364127572
sdb               0.93        61.37       302.07   43187620  212588268
dm-0             24.97      2691.32       680.78 1894076305  479110996
dm-1            567.33      1011.80      1257.50  712076724  884995480
sdc               6.68       332.42       177.86  233944508  125173544

Not sure what everything means the manual is kind of difficult to read.

Thank you .

[GenoMax]

http://askubuntu.com/questions/3561/...specific-drive