Dfam-consortium / RepeatModeler

De-Novo Repeat Discovery Tool

Other

182 stars 23 forks source link

RepeatClassifier: ERROR from search engine (2) #183

Open wjq1981 opened 1 year ago

wjq1981 commented 1 year ago

Hi, When I run RepeatModeler, I end up with RepeatClassifier: ERROR from search engine (2). There is no final families.fa, but the log file shows that it runs completely. Also when I run RepeatClassifier -consensi consensi.fa -stockholm families.stk, RepeatClassifier Version 2.0.1

Search Engine = rmblast

Looking for Simple and Low Complexity sequences..
Looking for similarity to known repeat proteins..
Looking for similarity to known repeat consensi.. RepeatClassifier: ERROR from search engine (2)

Can you help me to see what it is? It was working fine until 1 month ago.

rmhubley commented 1 year ago

This is a generic error caused by the failure of the aligner tool (RMBlast, or ABBlast). I am not sure which version of these tools you are using but certainly RepeatModeler is a bit out of date ( 2.0.1 vs 2.0.3 ). RepeatClassifier performs a large comparison of all families vs the TE protein database and separately the TE consensi database provided to RepeatMasker. It looks like the failure occurred in this last step. What is the version of the RepeatMasker database installed on this system? I will be releasing a new version of RepeatModeler 2.0.4 in a few weeks time which has many speed improvements, you may want to wait to update your software if you are not in a rush.

wjq1981 commented 1 year ago

This is a generic error caused by the failure of the aligner tool (RMBlast, or ABBlast). I am not sure which version of these tools you are using but certainly RepeatModeler is a bit out of date ( 2.0.1 vs 2.0.3 ). RepeatClassifier performs a large comparison of all families vs the TE protein database and separately the TE consensi database provided to RepeatMasker. It looks like the failure occurred in this last step. What is the version of the RepeatMasker database installed on this system? I will be releasing a new version of RepeatModeler 2.0.4 in a few weeks time which has many speed improvements, you may want to wait to update your software if you are not in a rush.

Thank you for your response and I look forward to your updates.

rmhubley commented 1 year ago

I will need more information from you before I can look into this further. Please provide the versions of the tools you are using and the version of the RepeatMasker database you installed.

wjq1981 commented 1 year ago

I will need more information from you before I can look into this further. Please provide the versions of the tools you are using and the version of the RepeatMasker database you installed.

Thank you for your careful guidance. The version of RepeatMasker is 4.1.2-p1 and the version of RepeatModeler is 2.0.1. Release: Dfam_3.3 Date : 2020-11-09