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Dfam-consortium / RepeatModeler

De-Novo Repeat Discovery Tool
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"RepeatScout did not return any models" because nseg is missing in RepModelConfig.pm #125

Closed xiaoyezao closed 3 years ago

xiaoyezao commented 3 years ago

I modified RepModelConfig.pm to set the tool paths (I cannot run the configure because of Perl module issues). There are no lines for the tool nseg in RepModelConfig.pm, and RepeatModeler does not check the availability of nseg, however, this will result in RepeatScout did not return any models in round-1. RepeatScout (specifically filter-stage-1.prl) will filter out all identified repeats if nseg is not available without error message. In such case, RepeatModeler seems can finish the job smoothly without results from round-1. Will some repeats are missing in such a run?

jebrosen commented 3 years ago

What versions of RepeatModeler and RepeatScout are you using? The most recent releases of RepeatScout and RepeatModeler replaced that usage of nseg with dustmasker, because dustmasker is more actively supported and is already distributed alongside RMBlast.

RepeatScout (specifically filter-stage-1.prl) will filter out all identified repeats if nseg is not available without error message. In such case, RepeatModeler seems can finish the job smoothly without results from round-1. Will some repeats are missing in such a run?

RepeatScout and RECON have different strengths, so it is possible that the results are missing repetitive elements that RepeatScout could find but not RECON. Exactly what kind of difference this has on the final results would depend on the composition of repeats within the particular genome/assembly.

xiaoyezao commented 3 years ago

I use RepeatModeler-2.0.1 and RepeatScout-1.0.5 which are both the latest release I think. However, in the round-1 folder of RepeatModeler result, I see filter-stage-1.log which is the log file of filter-stage-1.prl (RepeatScout script). filter-stage-1.prl calls trf and nseg rather than dustmaker. Is there another version of RepeatScout which calls dustmaker?

jebrosen commented 3 years ago

The latest version of RepeatScout is 1.0.6, linked from the RepeatModeler download page: http://www.repeatmasker.org/RepeatModeler/

xiaoyezao commented 3 years ago

Thank you very much!!