jebrosen
commented
3 years ago The RepeatClassifier ran for 42 minutes and ended with an error missing RepeatMasker/libraries/RepeatMasker.lib.nsq
42 minutes sounds like the step for comparing the consensi against RepeatPeps.lib.psq, which should be generated at the same time and in the same way as RepeatMasker.lib.nsq. I'm a bit surprised one of those files was generated but not the other.
please re run the configure program in RepeatModeller directory.
Sorry about that; this should have said: please re-run the configure program in the RepeatMasker directory. This message will be fixed in the next release of RepeatModeler.
RepeatMasker version 4.1.1
This particular version of RepeatMasker is also known to produce some incorrect classifications (see issue #128). Can you try using a version of RepeatMasker without that bug (e.g. RepeatMasker 4.1.0 or RepeatMasker 4.1.2-p2)? If RepeatMasker's configure program still does not generate the file RepeatMasker.lib.nsq, you can try generating it manually which should explain why it failed:
.../rmblast/bin/makeblastdb -dbtype nucl -in .../RepeatMasker/Libraries/RepeatMasker.lib
It is not necessary to re-run all of RepeatModeler; RepeatClassifier is the last step. RepeatClassifier can be run separately as follow: RepeatClassifier -consensi consensi.fa -stockholm families.stk
Shrihariprasad
The repeat classifyer stops with an error message stating missing RepeatMasker.lib.nsq
Helpful context
I was trying to run RepeatModeller for a plant genome and the program ran for 47:50:23 (hh:mm:ss) completing all the 6 rounds
The RepeatClassifier ran for 42 minutes and ended with an error missing RepeatMasker/libraries/RepeatMasker.lib.nsq please re run the configure program in RepeatModeller directory. *I tried after re-configuring the program but still the error persists.
RepeatModeler Version 2.0.1 RepeatMasker version 4.1.1