bioconda-recipes: ERROR: Could not determine if RepBase is installed
Hi @abretaud, @nathanweeks, @johanneskoester, @kastman, @pvanheus, @jerowe, @bgruening and @ArneKr,
I ran Maker but I got the following error:
> qpeek 4702790.pbs
Possible precedence issue with control flow operator at /lustre/work-lustre/waterhouse_team/miniconda2/envs/maker/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 805.
STATUS: Parsing control files...
ERROR: Could not determine if RepBase is installed
--> rank=NA, hostname=cl4n008
Where do I install RepBase with this package?
Thank you in advance,
Michal
About this issue
- Original URL
- State: open
- Created 5 years ago
- Comments: 24 (6 by maintainers)
According to This Reply, MASKER checks
xxx/RepeatMasker/Libraries/RepeatMaskerLib.emblfor Repbase.However, RepeatMasker no more creates
RepeatMaskerLib.embl, instead it usesDfam.h5to createRepeatMaskerLib.h5. Even though you may download old version of Repbase somewhere, (e.g.RMRBSeqs.embl), RM will only add it intoRepeatMaskerLib.h5, thus it won’t help if you setREPEATMASKER_LIB_DIR. BTW, RM usesLIBDIRinstead ofREPEATMASKER_LIB_DIRin newer versions.So there are two ways to solve this:
model_org=empty inmaker_opts.ctl, and it won’t check if Repbase was installed.RMRBSeqs.embl, create symlink inxxx/RepeatMasker/Libraries/. For example,ln -s RMRBSeqs.embl RepeatMaskerLib.embl. But in that case,model_org=should be set to the org that exists in the database, instead ofall. CAUTION: I don’t know whether the result is reliable enough in this way.Last but not least, for the sake that Repbase now provides repeat_db in fasta format, if you have newer version of db, just provide it by setting
rmlib=xxx.fain MASKER config.Hi @abretaud I tried to follow the solutions you provided but I still encounter a similar issue.
Here are what I have tried:
I found the Maker bioconda package seems to already have the libraries, so I downloaded the updated library “RepBaseRepeatMaskerEdition-20181026.tar.gz” from RepBase and then I uncompressed it at my Bioconda environment directory: /sd/MAKER_py2/share/RepeatMasker/Libraries
Set up the environment variable for the library: export REPEATMASKER_LIB_DIR=sd/MAKER_py2/share/RepeatMasker/Libraries
I found the Maker bioconda package also seems to already have the Matrices, so I set up the environment variable for the matrices as: export REPEATMASKER_MATRICES_DIR=sd/MAKER_py2/share/RepeatMasker/Matrices I echoed both variables and they look correct.
However, when I tried the Maker, it shows:
Could you help see which step might go wrong? Thank you so much.
I also met this problem, the problem can be resolved. Firstly, you need use the command line $which -a RepeatMasker, if the information show that ~/anaconda3/bin/RepeatMasker, this may be the source of the problem. Y’d better install RepeatMasker software manually. Meanwhile, you need download the Repbase database and decompress it in the RepeatMasker working directory in order to update the library files. Finally, you need change the RepeatMasker software path in the file of maker_exe.ctl. Then maker will be working correctly.
@xonq : you can set the environment variables in your shell (script) before invoking
maker; e.g.:Hi, i avoided this error by running “$ RepeatMasker ./configure” from within the environment conda installed maker in
@gbdias : that post was a while ago; the inline C issue should have been resolved: https://github.com/bioconda/bioconda-recipes/pull/15001
@phhsieh1329: the warning is harmless, and is fixed in newer versions of bioperl: https://github.com/bioperl/bioperl-live/pull/251 (MAKER is pinned to bioperl 1.7.2, since bioperl 1.7.3 removed many modules, which were separated into different distributions)
You have to get a license for the program and install.