Skip to content
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

Dependency checking: The RMblast engine is not installed in RepeatMasker! #43

Closed
Donbbit opened this issue Mar 26, 2019 · 13 comments
Closed

Dependency checking: The RMblast engine is not installed in RepeatMasker! #43

Donbbit opened this issue Mar 26, 2019 · 13 comments
Labels
help wanted

Comments

@Donbbit
Copy link

Donbbit commented Mar 26, 2019

I use conda to install LTR_retriever ：
conda create -n LTR_retriever
source activate LTR_retriever
conda install -c conda-forge perl perl-text-soundex
conda install -c bioconda cd-hit repeatmasker
git clone https://github.com/oushujun/LTR_retriever.git
./LTR_retriever/LTR_retriever -h

But when I run it with : LTR_retriever -genome Athaliana_167_TAIR9.fa -infinder Athaliana_167_TAIR9.fa.LTR.fa -verbose
the error occurs.
@Donbbit Donbbit closed this as completed Mar 26, 2019
@oushujun
Copy link
Owner

Hello @Donbbit ,

Thank you for using LTR_retriever. Have you solved this issue? If so, could you post how you solve it? Other users may benefit from your experience, thanks!

Best,
Shujun

@oushujun oushujun added the bug label Apr 13, 2019
@nm100
Copy link

nm100 commented Apr 13, 2019

Hi @Donbbit,

Not sure if you were able to solve this issue, but here's a quick solution to this problem:

Try to run RepeatMasker independently with the following command first:
RepeatMasker -e ncbi -q -pa 1 -no_is -norna -nolow dummy060817.fa.$rand -lib dummy060817.fa.$rand

if you are getting the following error on running the above command:
Taxononmy::new() Could not locate the taxonomy data file!

Then, you need to go to the RepeatMasker lib directory and unzip the taxonomy.data.gz file.

This will solve the RepeatMasker dependency issue.

Thanks!

@oushujun
Copy link
Owner

@nm100 Thanks Nancy!

The RepeatMasker lib directory is located here:
$path/miniconda2/envs/LTR_retriever/share/RepeatMasker/Libraries/, where $path is the installation path of your conda.

Best,
Shujun

@YingHu-jlau YingHu-jlau mentioned this issue Apr 26, 2019
Closed
@oushujun
Copy link
Owner

Summary for the fix and with more details:

  1. If you install dependencies via conda and encounter this error in LTR_retriever:

Dependency checking: The RMblast engine is not installed in RepeatMasker!

  1. Your RepeatMasker is likely improperly installed. To test out, simply run this command in your LTR_retriever working directory:
    RepeatMasker -e ncbi -q -pa 1 -no_is -norna -nolow dummy060817.fa* -lib dummy060817.fa*

  2. If you enounter this error:

RepeatMasker version development-$Id: RepeatMasker,v 1.332 2017/04/17 19:01:11 rhubley Exp $
Search Engine: NCBI/RMBLAST [ 2.6.0+ ]
Taxononmy::new() Could not locate the taxonomy data file!
at /home/oushujun/las/bin/miniconda2/envs/LTR_retriever/share/RepeatMasker/RepeatMasker line 638.

Then yes, it confirms that your RepeatMasker is improperly installed.

  1. To fix RepeatMasker, list this directory:
    ls -l $path/miniconda2/envs/LTR_retriever/share/RepeatMasker/Libraries/
    where $path is the installation path of your conda.
    You should see this file: taxonomy.dat.gz

  2. Do these three steps (remember to replace $path with your actual path). It just simply copies it out, unzip it, and move the unzipped version back:
    cp $path/miniconda2/envs/LTR_retriever/share/RepeatMasker/Libraries/taxonomy.dat.gz ./
    gunzip taxonomy.dat.gz
    mv taxonomy.dat $path/miniconda2/envs/LTR_retriever/share/RepeatMasker/Libraries/

Your RepeatMasker should be fixed. To test out:

  1. Rerun: $ RepeatMasker -e ncbi -q -pa 1 -no_is -norna -nolow dummy060817.fa* -lib dummy060817.fa*
    You should see something like:

RepeatMasker version development-$Id: RepeatMasker,v 1.332 2017/04/17 19:01:11 rhubley Exp $
Search Engine: NCBI/RMBLAST [ 2.6.0+ ]
Master RepeatMasker Database: /home/oushujun/las/bin/miniconda2/envs/LTR_retriever/share/RepeatMasker/Libraries/RepeatMaskerLib.embl ( Complete Database: dc20181026 )
Custom Repeat Library: dummy060817.fa.818966
Warning...unknown stuff
Building general libraries in: /home/oushujun/las/bin/miniconda2/envs/LTR_retriever/share/RepeatMasker/Libraries/dc20181026/general
analyzing file dummy060817.fa.818966
identifying matches to dummy060817.fa.818966 sequences in batch 1 of 1
processing output:
cycle 1
cycle 2
Generating output...
masking
done

@DanJeffries DanJeffries mentioned this issue Aug 12, 2019
Closed
@oushujun oushujun mentioned this issue Nov 14, 2019
Closed
@aaronphillips7493
Copy link

Hello,

I am getting the same error about RMblast engine when I try to run LTR_retriever.

When I try to run:
RepeatMasker -e ncbi -q -pa 1 -no_is -norna -nolow dummy060817.fa* -lib dummy060817.fa*

I get the error:
RepeatMasker can not handle filenames with the special character "*" as in the file "dummy060817.fa*"

Is there a fix for this?

Thank you :)

@oushujun
Copy link
Owner

@aaronphillips7493 "*" is the file extension of your dummy file. LTR_retriever will add the system date as an extension to avoid corruption. You may copy the dummy file from the LTR_retriever folder to another place for this test. Or you may simply reinstall RepeatMasker from conda.

@aaronphillips7493
Copy link

aaronphillips7493 commented Aug 6, 2020 •
edited

Hey,

I am trying to run this code:
LTR_retriever/LTR_retriever -genome ragtag_nuclear_assemblyhypo_polishingragoo_scaffolds/ragtag.scaffolds.fasta -inharvest ragtag_nuclear_assemblyhypo_polishingragoo_scaffolds/ragtag.scaffolds.fasta.rawLTR.scn -threads 10

Now when I try to run LTR_Retriever I get the error:
Dependency checking: Error: The RMblast engine is not installed in RepeatMasker!

I have tried re-installing everything as per the online instructions, and followed the steps above to resolve the issue.

When I run:
RepeatMasker -e ncbi -q -pa 1 -no_is -norna -nolow dummy060817.fa* -lib dummy060817.fa*

I see the error:
RepeatMasker version open-4.0.8 which: no rmblastn in (/usr/local/rmblast) NCBIBlastSearchEngine::setPathToEngine( /usr/local/rmblast/rmblastn ): Program does not exist! at /apps/software/RepeatMasker/4.0.8-foss-2016b-Perl-5.24.0-HMMER/RepeatMasker line 527.

I don't know what the solution to this is...all I know is that this was working for me back in June and now it is not. Please, can you provide some insight into what is happening here?

Thank you,
Aaron :)

@oushujun oushujun added help wanted and removed bug labels Aug 6, 2020
@oushujun oushujun pinned this issue Aug 6, 2020
@oushujun
Copy link
Owner

oushujun commented Aug 6, 2020

@aaronphillips7493

You may need to reinstall RMblast as suggested in this thread #15 by @Weihankk:

My LTR_retriever version is 2.9.0, my RepeatMasker version is 4.0.9, and my rmblast version is 2.2.28. So I try to reinstall rmblast in another version by conda:

conda install rmblast=2.6.0

Fortunately, the error was resolved. I run LTR_retriever successfully!

@JiyangChang
Copy link

JiyangChang commented Mar 19, 2021 •
edited

Hi Shujun,

I'm not using a conda version but I still met this problem with LTR_retriever-2.9.0.

However, I think my RepeatMasker is properly installed, and when I try the protocol you mentioned above:

RepeatMasker -e ncbi -q -pa 1 -no_is -norna -nolow dummy060817.fa* -lib dummy060817.fa*

Everything is normal,

RepeatMasker -e ncbi -q -pa 1 -no_is -norna -nolow dummy060817.fa.458191 -lib dummy060817.fa.458191 
RepeatMasker version 4.1.1
Search Engine: NCBI/RMBLAST [ 2.10.0+ ]
Using Custom Repeat Library: dummy060817.fa.458191


analyzing file dummy060817.fa.458191
identifying matches to dummy060817.fa.458191 sequences in batch 1 of 1
processing output: 
cycle 1 
cycle 2 
Generating output... 
masking
done

It just didn't work within the LTR_retriever, can you help me with this ?

BRs

@oushujun
Copy link
Owner

oushujun commented Mar 22, 2021 via email

@JiyangChang
Copy link

Hi Shujun,

I have tried the -repeatmasker parameter and still got the same error...

##########################
### LTR_retriever v2.9.0 ###
##########################

Contributors: Shujun Ou, Ning Jiang

For LTR_retriever, please cite:

	Ou S and Jiang N (2018). LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons. Plant Physiol. 176(2): 1410-1422.

For LAI, please cite:

	Ou S, Chen J, Jiang N (2018). Assessing genome assembly quality using the LTR Assembly Index (LAI). Nucleic Acids Res. 2018;46(21):e126.

Parameters: -genome genomic.fna -infinder finder.scn -inharvest harvest.scn -repeatmasker /home/elkan/MyFiles/software/RepeatMasker


Thu Apr  1 18:32:33 CEST 2021	Dependency checking: Error: The RMblast engine is not installed in RepeatMasker!

BRs
Elkan

@oushujun
Copy link
Owner

oushujun commented Apr 7, 2021

Hi Elkan,

Sorry for the delayed reply. It seems that the RepeatMasker you were providing did not have the RMblast engine deployed. You may want to reconfigure the program to use the RMblast engine.

Best,
Shujun

@JackyHess JackyHess mentioned this issue Apr 30, 2021
Closed
@oushujun
Copy link
Owner

oushujun commented Jan 12, 2022 via email

@Shokusei Shokusei mentioned this issue Oct 6, 2022
Closed
@zpliu1126 zpliu1126 mentioned this issue Dec 8, 2022
Closed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
help wanted
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
5 participants
@oushujun @Donbbit @JiyangChang @nm100 @aaronphillips7493