Description
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
Activity
oushujun commentedon Aug 12, 2019
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, thenRepeatMasker -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 commentedon Aug 13, 2019
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:
The outputs were:
Not sure if thats useful to you.
Thanks again
Dan
DanJeffries commentedon Aug 16, 2019
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.
Apparently I don't have the correct GLIBCXX version?
Any ideas?
Best
Dan