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  • bedtools makes ubuntu 14.04 slow

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

    Code:
    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.

  • #2
    You are probably running into I/O bottleneck depending on what else is happening on the system.

    Comment


    • #3
      Thanks, I am moving to a cluster server soon that has dedicated PCIe SSD to help with I/o issues. Thanks.

      Comment


      • #4
        Look into iostat command if you are curious about checking if this indeed is causing the bottleneck.

        Comment


        • #5
          I will definitely take a look at iostat. Thank you .

          Comment


          • #6
            Here is the output:

            Code:
            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 .
            Last edited by cmccabe; 07-14-2016, 10:16 AM. Reason: added details

            Comment


            • #7
              I'd like to watch disk activity on my USB external hard drive. I know that I can use iotop to monitor disk I/O for each running process, but is there a way to get a measure per filesystem?

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