Skip to content

RepeatProteinMask error in LIBDIR location #41

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom
Closed
mdoellma opened this issue Nov 26, 2019 · 3 comments
Closed

RepeatProteinMask error in LIBDIR location #41

mdoellma opened this issue Nov 26, 2019 · 3 comments
Labels
bug fixed

Comments

@mdoellma
Copy link

Should line 192 of RepeatProteinMask read

my $LIBDIR = $config->{'LIBDIR'}->{'value'};

instead of

my $LIBDIR = $config->{'LIBDIR_DIR'}->{'value'};

? The variable $LIBDIR_DIR does not appear in RepeatMaskerConfig.pm; $LIBDIR is used instead. As written, RepeatProteinMask gives me ##the error:

NCBIBlastXSearchEngine::search: Error...compressed subject database (/RepeatPeps.lib) does not exist! at /RepeatProteinMask line 371.

After making the suggested correction, RepeatProteinMask finished running without error.

Apologies for a repeat posting, if someone else has already brought this to your attention. Thank you!
@jebrosen jebrosen added the bug label Nov 26, 2019
@jebrosen
Copy link
Member

This has been fixed and the fix will make it into the next release. Thank you for reporting this.

@jebrosen jebrosen added the fixed label Dec 23, 2019
@sadikmu
Copy link

sadikmu commented Nov 20, 2020

I am experiencing the same error on v 4.1.1 couldn't get what I've missed.

RepeatProteinMask assembly.fasta -engine ncbi -noLowSimple -pvalue 0.0001 -libdir ../Repbase/RepBase*.fasta

str.err

Identifying Simple and Low Complexity Repeats...(masking turned off)
Tandem Repeats: 0
Masking Repeat Proteins...
NCBIBlastXSearchEngine::search: Error...compressed subject database (../Repbase/RepBase*.fasta/RepeatPeps.lib) does not exist! at /miniconda3/envs/repeatmasker/bin/RepeatProteinMask line 371.

Any suggestions please?

@jebrosen
Copy link
Member

Closing, since this issue has been fixed in a more recent version of RepeatMasker.

@sadikmu This is an unrelated issue: -libdir should be a path to a RepeatMasker Libraries directory, not a fasta file. Please open a new issue if this is still a problem for you.

@mbeavitt mbeavitt mentioned this issue Jul 23, 2024
Closed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
bug fixed
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
3 participants
@jebrosen @mdoellma @sadikmu