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[pure6688]

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...

• Gathering up to 40000000 bp
• Final Sample Size = 40037628 bp ( 40026266 non ambiguous )
• Num Contigs Represented = 37
• Sequence extraction : 00:01:04 (hh:mm:ss) Elapsed Time
  --Running RepeatScout on the sequences...
• RepeatScout: Running build_lmer_table ( l = 14 )..
• RepeatScout: Running RepeatScout.. : 669 raw families identified
• RepeatScout: Running filtering stage.. 604 families remaining
• RepeatScout: 00:15:03 (hh:mm:ss) Elapsed Time
• Large Satellite Filtering.. : 9 found in 00:00:15 (hh:mm:ss) Elapsed Time
• Collecting repeat instances...: 00:02:51 (hh:mm:ss) Elapsed Time

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[duan12345678]

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
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rm: cannot remove ‘/home/try/RM_40457.TueApr22238162024/round-2/family-146-cons-8.fa.nin’: No such file or directory

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[pure6688]

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]

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]

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]

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

[pure6688]

Thanks for your help. I am using our software on CentOS Linux release 7.8.2003 (Core)

[rmhubley]

The currently supported version is 2.0.5 with perl 5.8 or newer. I would recommend using rmblast 2.14.1, but 2.14.0 is also ok. I have noticed that there are a few people having trouble using our pre-compiled releases of rmblast when running on older UNIX versions. I suspect that is what is happening with @duan12345678's runs. The remedy for that is to simply compile rmblast from source. The instructions for doing that may be found here: http://www.repeatmasker.org/rmblast/

[pure6688]

Thank you very much! I finished my work and rmblast 2.14.0 worked great. I will try to use the source compiled rmblast 2.14.1 on the next job.