Closed YingHu-jlau closed 5 years ago
Hi Ying,
Sorry that RepeatMasker is not working for you. I added more detailed guidelines in #43, hopefully you can follow them through and fix the issue. Please let me know if you encounter new issues.
Best, Shujun
Hi, Shujun,
I followed your suggestions to try to fix the problem. However, the dependency checking is still failed. Then I tried to use version 1.6 and it works. I am wondering version 2.5 may need to compare with 1.6 to fix this dependency problem.
Thanks,
Ying
Hi Ying,
For dependency checking, the difference between v1.6 and v2.5 is the use of a random number generator to avoid interference between LTR_retriever runs in the same directory. From your initial post, the random number generator seems working in your system, so there should be no difference.
I tried a new clone of v2.5 and followed the fix instruction in #43, didn't have a failure for the RepeatMasker dependency. You may start fresh and try again. If you already did, can you paste the output of running this command?
RepeatMasker -e ncbi -q -pa 1 -no_is -norna -nolow dummy060817.fa* -lib dummy060817.fa*
Can you please let me know your system platform?
Best, Shujun
Hi, Shujun,
I run the following script: module load ltrretriever/2.5 B73="B73Ref4.fa" LTR_retriever \ -genome $B73 \ -infinder ../01_ltrfinder/B73.finder.1.scn \ -inharvest ../02_ltrharvest/B73.harvest.scn \ -nonTGCA ../02_ltrharvest/B73.harvest.nonTGCA.scn \ -threads 8
The job failed due to the following error: Dependency checking: The RMblast engine is not installed in RepeatMasker! There is one output file generated, which is dummy060817.fa.946456.
Then I run the command: RepeatMasker -e ncbi -q -pa 1 -no_is -norna -nolow dummy060817.fa -lib dummy060817.fa Here is the output: (I need to load module repeatmasker/4.0.3 or repeatmasker/4.0.5)
dummy060817.fa.946456.masked
dummy060817.fa.946456.nsq
dummy060817.fa.946456.tbl
dummy060817.fa.946456
dummy060817.fa.946456.nhr
dummy060817.fa.946456.ori.out
dummy060817.fa.946456.cat
dummy060817.fa.946456.nin
dummy060817.fa.946456.out
I am running on the supercomputer of my university.
Thanks for your help!
Ying
Hi Ying,
The output confirms that you have RepeatMasker in your HPC, however LTR_retriever is complaining the missing of RepeatMasker, which means the RepeatMasker path is not properly passed down to LTR_retriever. You may need to double check the installation of LTR_retriever. If you didn't change the path file and rely on finding denpendent programs from bash, then you also need to load RepeatMasker to your job.
module load repeatmasker/4.0.5 module load ltrretriever/2.5 B73="B73Ref4.fa" LTR_retriever -genome $B73 -infinder ../01_ltrfinder/B73.finder.1.scn -inharvest ../02_ltrharvest/B73.harvest.scn -nonTGCA ../02_ltrharvest/B73.harvest.nonTGCA.scn -threads 8
Best, Shujun
Hi, Shujun,
I am facing the same problem with dependency of RMblast engine. I tried to follow Nancy's suggestions #43 . I don't have Taxononmy::new() error but successfully got the following files:
dummy060817.fa.926962 dummy060817.fa.926962.masked dummy060817.fa.926962.nin dummy060817.fa.926962.ori.out dummy060817.fa.926962.tbl dummy060817.fa.926962.cat dummy060817.fa.926962.nhr dummy060817.fa.926962.nsq dummy060817.fa.926962.out
However, when I run ltrretriever 2.5 and ltrretriever 2.1 , I still got error: Dependency checking: The RMblast engine is not installed in RepeatMasker!
I don't have this error when I use ltrretriever 1.6 and 20170514.
Best,
Ying