Hi Jake,
BBDuk takes exponential time to process the reference when you increase the maximum number of substitutions. Specifically, allowing 3 substitutions with K=27 requires 82^3 or 551,368 times as long as normal for loading the reference, so may be the issue (it depends how big the reference is). During that time it will use roughly 7 threads. Processing 90,000 reads after the reference is loaded would take under 0.1 seconds.
I don't know all of the flags exposed by Geneious, but from what you've posted, I recommend these settings:
Adapters
Trim: Right End Only
Kmer Length: 23
Max Substitutions: 1 (I only go to 2 if the reads are very low quality, but never 3 for adapter trimming of paired reads)
Max Substitutions + INDELs: 0
Trim partial adapaters with kmer length: Yes, 11
Trim Low Quality - Yes
Right End Only
Minimum Quality: 12 (This varies; with very high coverage, this can be higher)
Discard Short Reads - Yes
Minimum Length: 75 bp (Again, this varies)
Keep Original Order - Yes
Additionally, you should add the flags "tbo" "tpe" to the custom flags area if they are not exposed in the GUI. So, please try that and let me know if the speed is still odd; with those settings it should take ~1 second, and result in less overtrimming.
BBDuk takes exponential time to process the reference when you increase the maximum number of substitutions. Specifically, allowing 3 substitutions with K=27 requires 82^3 or 551,368 times as long as normal for loading the reference, so may be the issue (it depends how big the reference is). During that time it will use roughly 7 threads. Processing 90,000 reads after the reference is loaded would take under 0.1 seconds.
I don't know all of the flags exposed by Geneious, but from what you've posted, I recommend these settings:
Adapters
Trim: Right End Only
Kmer Length: 23
Max Substitutions: 1 (I only go to 2 if the reads are very low quality, but never 3 for adapter trimming of paired reads)
Max Substitutions + INDELs: 0
Trim partial adapaters with kmer length: Yes, 11
Trim Low Quality - Yes
Right End Only
Minimum Quality: 12 (This varies; with very high coverage, this can be higher)
Discard Short Reads - Yes
Minimum Length: 75 bp (Again, this varies)
Keep Original Order - Yes
Additionally, you should add the flags "tbo" "tpe" to the custom flags area if they are not exposed in the GUI. So, please try that and let me know if the speed is still odd; with those settings it should take ~1 second, and result in less overtrimming.
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