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Dfam-consortium / RepeatModeler

De-Novo Repeat Discovery Tool
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ERROR from search engine (0) #239

Open pure6688 opened 3 months ago

pure6688 commented 3 months ago

When I used RepeatModeler, the Round-1 phase encountered an error in the search engine, but the Round-2 phase worked correctly. Here are my code and errors :

RepeatModeler -database /home/PMO/DB1/PMOGEN1 -threads 16 -LTRStruct

RepeatModeler Round # 1

Searching for Repeats -- Sampling from the database...

ERROR from search engine (0)

duan12345678 commented 3 months ago

Hello, I encountered the same problem in the process of running the program, I would like to know how you solve the problem, the following is my running code and error logs, can you help me see how to solve it? Thank you for your help.

~/miniconda3/envs/repeat/bin/RepeatModeler -threads 40 -database try.fna.db -LTRStruct > repeatmodeler2.run.out ERROR from search engine (0)

ERROR from search engine (0)

ERROR from search engine (0) rm: cannot remove ‘/home/try/RM_40457.TueApr22238162024/round-2/family-146-cons-8.fa.nin’: No such file or directory

ERROR from search engine (1)

ERROR from search engine (0)

ERROR from search engine (0)

ERROR from search engine (0)

ERROR from search engine (0)

ERROR from search engine (0)

pure6688 commented 2 months ago

I noticed that you used conda to install the software. In my subsequent revisions, I gave up the conda installation Repeatmodeler, and compiled RepeatMasker and Repeatmodelr from the source code. Although this problem has been solved, new problems have arisen in ROUND5. But I still recommend that you compile the two software from the source code and avoid using conda, which will reduce a lot of problems.

duan12345678 commented 2 months ago

Thanks for your reply, As you suggested, I tried to re-download the software and source code after installing it. I noticed that you posted a new question.There is the new error reported in ROUND 6. Here is my log file LANGUAGE = (unset), LC_ALL = (unset), LC_ALL = (unset) LC_ALL = (unset), LANG = "en_US.UTF-8" are supported and installed on your system. perl: warning: Falling back to the standard locale ("C"). rm: cannot remove '/home/try/RM_18804.ThuApr41547492024/round-6/family-4572-cons-5.fa.nin': No such file or directory

ERROR from search engine (1) I am using RepeatModeler version 2.0.1. Can you help me with this? Regards,

pure6688 commented 2 months ago

Hello, I am also a beginner in bioinformatics. I haven't encountered this problem yet, but I can suggest that you upgrade the software to the latest version. Version 2.0.1 is really too old. I've also seen in other issues on GitHub that the software authors recommend upgrading from versions that are too outdated. For the first problem with Perl running, you can try setting in bashrc: export LC_ALL=en_US.UTF-8. But I still recommend you upgrade the software. Thank you.

rmhubley commented 2 weeks ago

Please let me know what kind of system you are running this on (e.g which flavor of unix and which version).