"The RMblast engine is not installed in RepeatMasker!" When specifying conda env installation --prefix

[DanJeffries]

Hi Shujun

I have been trying to install EDTA on my server but I have an annoying situation of a storage quota on my home directory meaning that the default location for the conda env isn't big enough to complete the installation. I am trying to get around it using:

conda create --prefix /scratch/djeffrie/EDTAenv

The installation seems to work fine. However when I run the pipeline I get the error:

The RMblast engine is not installed in RepeatMasker!

I see some issues for TIR_retriever with the same error but I can't figure out if its the same problem or not. I followed the suggestion [here]
(oushujun/LTR_retriever#43) of running

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

but I didn't get the expected output relating to the taxonomy data file, I got the error

RepeatMasker::setspecies: Could not find user specified library dummy060817.fa..

Would you have any solutions for how to get round this? Perhaps its a problem of using the --prefix argument? Or maybe just the server?

Best,

Dan

[oushujun]

Hi Dan,

I am sorry RepeatMasker is a pain to install. Please copy the dummy file at EDTA/bin/LTR_retriever/database/dummy060817.fa to a test directory, then RepeatMasker -e ncbi -q -pa 1 -no_is -norna -nolow dummy060817.fa -lib dummy060817.fa to see if this is the issue at oushujun/LTR_retriever#43.

Alternatively, if you have a working version of RepeatMasker, you can use the -repeatmasker parameter to tell EDTA where it is.

Best,
Shujun

[DanJeffries]

Hi Shujun,

many thanks for your quick reply!

Your idea to use my own version of RepeatMasker worked! The pipeline is now running, I'll update on its success.

FYI, the test for the RepeatMasker in your installation did not match the outcome of the issue mentioned above.

I copied the library as you said and ran the command as below:

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

The outputs were:

RepeatMasker version open-4.0.9
Search Engine: NCBI/RMBLAST [ 2.2.27+ ]
sh: line 1:  2893 Illegal instruction     /scratch/temporary/djeffrie/EDTAenv/bin/makeblastdb -out /stn4/djeffrie/EDTAtests/RM_2729.TueAug131100062019/dummy060817.fa -dbtype nucl -in dummy060817.fa > /stn4/djeffrie/EDTAtests/RM_2729.TueAug131100062019/makeblastdb.log 2>&1
Master RepeatMasker Database: /scratch/temporary/djeffrie/EDTAenv/share/RepeatMasker/Libraries/RepeatMaskerLib.embl ( Complete Database: CONS-Dfam_3.0 )
Custom Repeat Library: dummy060817.fa


Warning...unknown stuff <
>
Building general libraries in: /scratch/temporary/djeffrie/EDTAenv/share/RepeatMasker/Libraries/CONS-Dfam_3.0/general
sh: line 1:  2899 Illegal instruction     /scratch/temporary/djeffrie/EDTAenv/bin/makeblastdb -dbtype nucl -in /scratch/temporary/djeffrie/EDTAenv/share/RepeatMasker/Libraries/CONS-Dfam_3.0/general/l1.lib > /scratch/temporary/djeffrie/EDTAenv/share/RepeatMasker/Libraries/CONS-Dfam_3.0/general//rmblastdb.log 2>&1
RepeatMasker::createLib(): Error invoking /scratch/temporary/djeffrie/EDTAenv/bin/makeblastdb on file /scratch/temporary/djeffrie/EDTAenv/share/RepeatMasker/Libraries/CONS-Dfam_3.0/general/l1.lib.

Not sure if thats useful to you.

Thanks again

Dan

[DanJeffries]

hi Shujun,

Unfortunately I'm still having trouble with this. Following on from my previous comment, I am now using my own installed version of RepeatMasker and everthing seems to work until it gets to TIR learner, where I am now getting the below error.

Fri Aug 16 19:10:44 CEST 2019	Dependency checking:
		All passed!
Fri Aug 16 19:10:56 CEST 2019	Obtain raw TE libraries using various structure-based programs:
/stn4/djeffrie/EDTA/bin/TIR-Learner1.19/../GenericRepeatFinder/bin//grf-main: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by /stn4/djeffrie/EDTA/bin/TIR-Learner1.19/../GenericRepeatFinder/bin//grf-main)
/stn4/djeffrie/EDTA/bin/TIR-Learner1.19/../GenericRepeatFinder/bin//grf-main: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /stn4/djeffrie/EDTA/bin/TIR-Learner1.19/../GenericRepeatFinder/bin//grf-main)

Apparently I don't have the correct GLIBCXX version?

Any ideas?

Best

Dan