search

Dfam-consortium / RepeatModeler

De-Novo Repeat Discovery Tool
Other
183 stars 23 forks source link

Can't locate WUBlastSearchEngine.pm #106

Closed ohan-Bioinfo closed 3 years ago

ohan-Bioinfo commented 3 years ago 
Can't locate WUBlastSearchEngine.pm in @INC (you may need to install the WUBlastSearchEngine module) (@INC contains: /usr/local/bin /Users/ohon_ad/Documents/Tools/RepeatModeler/RepeatModeler-2.0.1 /usr/local/Cellar/perl/5.30.3/lib/perl5/site_perl/5.30.3/darwin-thread-multi-2level /usr/local/Cellar/perl/5.30.3/lib/perl5/site_perl/5.30.3 /usr/local/Cellar/perl/5.30.3/lib/perl5/5.30.3/darwin-thread-multi-2level /usr/local/Cellar/perl/5.30.3/lib/perl5/5.30.3 /usr/local/lib/perl5/site_perl/5.30.3/darwin-thread-multi-2level /usr/local/lib/perl5/site_perl/5.30.3) at /Users/ohon_ad/Documents/Tools/RepeatModeler/RepeatModeler-2.0.1/RepeatUtil.pm line 78.
BEGIN failed--compilation aborted at /Users/ohon_ad/Documents/Tools/RepeatModeler/RepeatModeler-2.0.1/RepeatUtil.pm line 78.
Compilation failed in require at ./RepeatModeler line 126.
BEGIN failed--compilation aborted at ./RepeatModeler line 126.

I used Cpan to install all the dependencies need it by Perl but still having this error when I run RepeatModeler

Can you advice please

jebrosen commented 3 years ago

WUBlastSearchEngine.pm is part of the RepeatMasker dependency, which is missing from @INC. The ./configure program should have asked for a path to the RepeatMasker directory, or it can also be hand-edited in RepModelConfig.pm.

yangkaiyanyangkaiyan commented 1 year ago

i set the path of RMBlast to the RepeatMakser, and i have not configured Wublast, finally this error was still here . how to handed edit in RepModelConfig.pm

yangkaiyanyangkaiyan commented 1 year ago

Can't locate WUBlastSearchEngine.pm in @INC (you may need to install the WUBlastSearchEngine module) (@INC contains: /home/yangkaiyan/miniconda3/envs/repeat/bin /home/yangkaiyan/miniconda3/envs/repeat/share/RepeatModeler /home/yangkaiyan/miniconda3/envs/repeat/lib/perl5/5.32/site_perl /home/yangkaiyan/miniconda3/envs/repeat/lib/perl5/site_perl /home/yangkaiyan/miniconda3/envs/repeat/lib/perl5/5.32/vendor_perl /home/yangkaiyan/miniconda3/envs/repeat/lib/perl5/vendor_perl /home/yangkaiyan/miniconda3/envs/repeat/lib/perl5/5.32/core_perl /home/yangkaiyan/miniconda3/envs/repeat/lib/perl5/core_perl .) at /home/yangkaiyan/miniconda3/envs/repeat/share/RepeatModeler/RepeatUtil.pm line 78. BEGIN failed--compilation aborted at /home/yangkaiyan/miniconda3/envs/repeat/share/RepeatModeler/RepeatUtil.pm line 78. Compilation failed in require at /home/yangkaiyan/miniconda3/envs/repeat/bin/RepeatModeler line 126. BEGIN failed--compilation aborted at /home/yangkaiyan/miniconda3/envs/repeat/bin/RepeatModeler line 126.

BioHlT commented 1 year ago

I ran in to the same error message, Is the issue resolved yet?

Carrefour-pirate commented 11 months ago

I met this error too. I fixed this creating soft links for all the XXXXX.pm needed in a path contained by "@ INC", XXX/XX/XX/RepeatModeler. Actually, all the XXXX.pm are located in ~/miniconda3/envs/???/share/RepeatMasker, setting "@ INC" to contain that path shoud be a better/easer way.

YuzhouGong commented 9 months ago

I have met this error too. My solution is to copy all the .pm files in the ~/xxx/RepeatMasker to the ~/xxx/RepeatModeler.

aberaslop commented 5 months ago

@YuzhouGong's solution works perfectly for me. Thank you!

YuzhouGong commented 4 months ago

@YuzhouGong's solution works perfectly for me. Thank you!

Glad to help, mate!