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Old 08-31-2018, 08:03 AM   #1
yip
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Default 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
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Old 09-12-2018, 07:15 AM   #2
NGSMicro
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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.
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Old 09-12-2018, 07:56 AM   #3
yip
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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.

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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.
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