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  • Trimmomatic memory use

    I assume that Trimmomatic processes the reads sequentially, so I don't understand why a run with paired-end fastq input could take >10GB of memory easily. Does anyone know what I am missing?

    I'm using trimmomatic-0.36 with 4 threads for a job. The input fastq files are about 4GB in size each.

    Thank you!
    yip

  • #2
    I don't know for certain, but it could be that trimmomatic is opening 4 of the files at a time, as it has 4 threads working.

    Comment


    • #3
      Thank you for your comments. I can understand if multi-threading results in more I/O, but why would the run be so memory-hungry?
      Next time I could try running my command single-threaded to see whether it makes a difference.

      Originally posted by NGSMicro View Post
      I don't know for certain, but it could be that trimmomatic is opening 4 of the files at a time, as it has 4 threads working.

      Comment

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