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oushujun / LTR_retriever

LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5813529/
GNU General Public License v3.0
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Dependency checking: The RMblast engine is not installed in RepeatMasker! #43

Closed Donbbit closed 5 years ago

Donbbit commented 5 years ago

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.

oushujun commented 5 years ago

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

nm100 commented 5 years ago

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 commented 5 years ago

@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

oushujun commented 5 years ago

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!

  2. 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*

  3. 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

aaronphillips7493 commented 4 years ago

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 commented 4 years ago

@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 commented 3 years ago

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 commented 3 years ago

@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 commented 3 years ago

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 commented 3 years ago

Hi BRs,

If you have a working RepeatMasker, you can provid its path to LTR_retriever. Please check -help for more instructions.

Best, Shujun

On Sat, Mar 20, 2021 at 5:05 AM Elkan Chang @.***> wrote:

Hi Shujun,

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

However, I'm pretty sure 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 thing 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

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JiyangChang commented 3 years ago

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 commented 3 years ago

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

oushujun commented 2 years ago

Thank you for sharing this. - Shujun

On Tue, Jan 11, 2022 at 10:34 AM zzz @.***> wrote:

Hi all, I also got into this error that RMblast engine is not installed in RepeatMasker, after several months I made a successful run with LTR_retriever. I guess the new RepeatMasker does not include RMBlast by default. It took me a bit to find out how to re-configure the RepeatMasker in miniconda environment, and would like to share here, in case anyone needs it.

First thing is to conda install rmblast, and then in the environment that repeatMasker was build find the path where contain the configure file of RepeatMasker (e.g. /miniconda3/envs/EDTA/share/RepeatMasker/configure ), then run perl ./configure and follow the instruction. Some info can be found here https://supcom.hgc.jp/english/utili_info/manual/RepeatMasker.html

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