Jeb Rosen
Jeb Rosen
Taxonomy::new() needs a path for a famdb file! at /usr/local/bin/RepeatMasker/RepeatMasker line 635.
Have you successfully run the `configure` program (or re-run it after installing `h5py`)? The "missing" file is `RepeatMaskerLib.h5`, which is created by that program.
Taxonomy::new() needs a path for a famdb file! at /usr/local/bin/RepeatMasker/RepeatMasker line 635.
> Building FASTA version of RepeatMasker.lib ...ERROR:main:Error reading file: Unable to open file (unable to open file: name = '/usr/local/bin/RepeatMasker/Libraries/RepeatMaskerLib.h5', errno = 2, error message = 'No such file or...
Taxonomy::new() needs a path for a famdb file! at /usr/local/bin/RepeatMasker/RepeatMasker line 635.
That is strange. What is the output of this command: `file /Users/utamiyd/Documents/repmas/RepeatMasker/Libraries/RepeatMaskerLib.h5` If the file does not exist, please try running this command as well to see if there is...
Taxonomy::new() needs a path for a famdb file! at /usr/local/bin/RepeatMasker/RepeatMasker line 635.
> As I remember, this file did not exist even before I run ./configure > Is this a file that should have come packed with RepBase tarball? No: this file...
Taxonomy::new() needs a path for a famdb file! at /usr/local/bin/RepeatMasker/RepeatMasker line 635.
> > can you try running addRepBase.pl separately (with no arguments) to see if there is an error with that process? > > Here is the result: > (...) >...
Taxonomy::new() needs a path for a famdb file! at /usr/local/bin/RepeatMasker/RepeatMasker line 635.
> I tried to repeat addRepBase.pl but the file content is still Zero bytes. Oh gosh, I missed this earlier in your `addRepBase.pl` output: > File: /usr/local/bin/RepeatMasker/Libraries/RepeatMaskerLib.h5 This looks like...
Taxonomy::new() needs a path for a famdb file! at /usr/local/bin/RepeatMasker/RepeatMasker line 635.
> /usr/local/bin/RepeatMasker/Libraries/RepeatMaskerLib.h5 I am confused again; I thought we were not using `/usr/local/bin` anymore. You cannot simply move or copy the RepeatMasker directory after running `configure`, because it will still...
Taxonomy::new() needs a path for a famdb file! at /usr/local/bin/RepeatMasker/RepeatMasker line 635.
> again it was "erased automatically" when I run ./configure again. This is totally bizarre. `configure` runs `addRepBase.pl`, which is apparently working fine when you run it manually but not...
Taxonomy::new() needs a path for a famdb file! at /usr/local/bin/RepeatMasker/RepeatMasker line 635.
In fact, the `configure` program itself seems to not work properly on macOS, and misconfigures `addRepBase.pl` and other files. I found an old report of this, and am in a...
Does the file `locust.fa` exist in the current directory? The `-fasta` option needs the original genome file that the `.out` file was generated from.