Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • "R Killed" when working with large BAM files

    I'm trying to work with large BAM files produced by bowtie alignment of illumina sequencing runs. I'm able to work with them fine with tools outside of R, but R seems to have some limitations or issues with the size.

    Issue: After reading 4 bam files of 650 MB (maybe 1 million reads each) with the function readAligned("path","bamfile.bam,"BAM") from the ShortRead package, R simply terminates with the message:

    /usr/lib64/R/bin/BATCH: line 60: 10315 Killed ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1

    I'm doing this on a linux-based grid engine, so it's not about the windows-specific memory limits. Also, this does not happen with small BAM files for testing. It night be about internal limits on table sizes, though?

    Any help would be greatly appreciated!

  • #2
    Hi. In lieu of other error msgs. Is it a possibility that the job timed out or was killed due to system admin set limits that are common for shared resources?
    Have u tried running just this command in a terminal?
    http://kevin-gattaca.blogspot.com/

    Comment


    • #3
      'Killed' is sometimes induced by running out of memory - the linux schedulder than kills processes until there is enough free memory again.

      How much swap space have you configured in addition to your RAM (and how much RAM is that)?

      Comment

      Latest Articles

      Collapse

      • seqadmin
        Strategies for Sequencing Challenging Samples
        by seqadmin


        Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
        03-22-2024, 06:39 AM
      • seqadmin
        Techniques and Challenges in Conservation Genomics
        by seqadmin



        The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

        Avian Conservation
        Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
        03-08-2024, 10:41 AM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, Yesterday, 06:37 PM
      0 responses
      8 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, Yesterday, 06:07 PM
      0 responses
      8 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-22-2024, 10:03 AM
      0 responses
      49 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-21-2024, 07:32 AM
      0 responses
      66 views
      0 likes
      Last Post seqadmin  
      Working...
      X