KeyError: "Unable to open object (object 'Partitions' doesn't exist)"

[star-lamp]

Hello, I want to use dfam38-1_full. 5. h5. gz as the Dfam database, but when I gunzip it and put it into the famdb folder (which only has this. h5 file), after using the Perl./configure command, I always get the error KeyError: "Cannot to open object (object 'Partitions' doesn't exist)". Both versions 4.1.6 and 4.1.7 are like this, and I still can't solve this problem, so I hope to get help.

[rmhubley]

I am sorry this isn't working for you. I haven't seen this type of error before. I wonder what your python environment looks like. I assume you have Python3.x.x? What about the version of h5py? The error seems to originate from numpy, what version of numpy do you have installed?

[NgocVuMinh]

I have the exact issue with dfam38-1_full.5.h5. I am running perl ./configure for RepeatMasker version 4.1.6 with Python 3.10.15, h5py 3.12.1, and numpy 1.26.4.

My environment:

Checking for libraries...

 - Found a FamDB root partition

Traceback (most recent call last):
  File "/Volumes/T7/RepeatMasker4.1.6/famdb.py", line 869, in <module>
    main()
  File "/Volumes/T7/RepeatMasker4.1.6/famdb.py", line 844, in main
    args.db_dir = FamDB(args.db_dir, mode)
  File "/Volumes/T7/RepeatMasker4.1.6/famdb_classes.py", line 698, in __init__
    self.files[idx] = FamDBRoot(f"{db_dir}/{file}", mode)
  File "/Volumes/T7/RepeatMasker4.1.6/famdb_classes.py", line 405, in __init__
    for partition in self.file[GROUP_TAXANAMES]
  File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
  File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
  File "/Users/ngoc/anaconda3/envs/genomeannot/lib/python3.10/site-packages/h5py/_hl/group.py", line 357, in __getitem__
    oid = h5o.open(self.id, self._e(name), lapl=self._lapl)
  File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
  File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
  File "h5py/h5o.pyx", line 257, in h5py.h5o.open
KeyError: "Unable to open object (object 'Partitions' doesn't exist)"
<PRESS ENTER TO CONTINUE>

The configuring command and everything else worked fine for the default min_init.0.h5.

Thank you in advance!

[rmhubley]

I wonder if something is corrupt in your copy of the root partition. Did you verify the md5 signature of the file after you downloaded from our site? I wonder what you get if you run:

% cd <your_repeatmasker_installation>
% ./famdb.py info

If you only have partitions 0 (root), and 5 it should look like this:

FamDB Directory     : /u3/home/rhubley/projects/distributions/tmp/RepeatMasker-4.1.6-test/Libraries/famdb
FamDB Generator     : famdb.py v1.0
FamDB Format Version: 1.0
FamDB Creation Date : 2023-11-15 11:30:15.311827

Database: Dfam withRBRM
Version : 3.8
Date    : 2023-11-14

Dfam - A database of transposable element (TE) sequence alignments and HMMs.
RBRM - RepBase RepeatMasker Edition - version 20181026

2 Partitions Present
Total consensus sequences present: 498368
Total HMMs present               : 472219


Partition Details
-----------------
 Partition 0 [dfam38_full.0.h5]: root - Mammalia, Amoebozoa, Bacteria <bacteria>, Choanoflagellata, Rhodophyta, Haptista, Metamonada, Fungi, Sar, Placozoa, Ctenophora <comb jellies>, Filasterea, Spiralia, Discoba, Cnidaria, Porifera, Viruses
     Consensi: 308186, HMMs: 295552

 Partition 1 [ Absent ]: Obtectomera 

 Partition 2 [ Absent ]: Euteleosteomorpha 

 Partition 3 [ Absent ]: Sarcopterygii - Sauropsida, Coelacanthimorpha, Amphibia, Dipnomorpha

 Partition 4 [ Absent ]: Diptera 

 Partition 5 [dfam38_full.5.h5]: Viridiplantae 
     Consensi: 190182, HMMs: 176667

 Partition 6 [ Absent ]: Deuterostomia - Chondrichthyes, Hemichordata, Cladistia, Holostei, Tunicata, Cephalochordata, Cyclostomata <vertebrates>, Osteoglossocephala, Otomorpha, Elopocephalai, Echinodermata, Chondrostei

 Partition 7 [ Absent ]: Hymenoptera 

 Partition 8 [ Absent ]: Ecdysozoa - Nematoda, Gelechioidea, Yponomeutoidea, Incurvarioidea, Chelicerata, Collembola, Polyneoptera, Tineoidea, Apoditrysia, Monocondylia, Strepsiptera, Palaeoptera, Neuropterida, Crustacea, Coleoptera, Siphonaptera, Trichoptera, Paraneoptera, Myriapoda, Scalidophora

It also appears that you are using the Conda installation of RepeatMasker. We have so many reports of problems with Conda that we do not support it currently. Please install RepeatMasker as described here: http://www.repeatmasker.org/RepeatMasker/