RepeatMasker database error

Question

[juliayork]

Hello! I am trying to run RepeatMasker on some genomic sequences from some various teleost fishes. RepeatMasker starts and gives me this:

RepeatMasker version 4.1.1
Search Engine: NCBI/RMBLAST [ 2.10.0+ ]

Using Master RepeatMasker Database: 
...path/bin/miniconda3/share/RepeatMasker/Libraries/RepeatMaskerLib.h5
  Title    :
  Version  :
  Date     :
  Families :


Species "teleost fish" is not known to RepeatMasker.  There may
not be any TE families defined in the libraries for this
species/clade or there may be an error in the spelling.
Please check your entry against the NCBI Taxonomy database
and/or try using a broader clade or related species instead.
The full list of species/clades defined in the library may be
obtained using the famdb.py script.

It does the same with any other species I've tried including danio and homo sapiens so I think the issue is the database. Please help! Thanks.

[lieven.sterck]

you will likely need to download/install the databases you want to use separately (this will be mentioned in the manual I guess). Normally you get them from RepBase. But in essence they are just fasta files of the repeat sequences you want to screen for.

[juliayork]

I've done that and I still cannot get it to work. I run the configuration, and then it says:

Building FASTA version of RepeatMasker.lib ...
Traceback (most recent call last): File "/mypath/RepeatMasker/famdb.py", line 51, in <module> import h5py File "/opt/apps/intel18/cray_mpich_7_7/python3/3.7.0/lib/python3.7/site-packages/h5py/__init__.py", line 26, in <module> from . import _errors ImportError: libhdf5.so.10: cannot open shared object file: No such file or directory . Building RMBlast frozen libraries.. The program is installed with a the following repeat libraries:

Further documentation on the program may be found here: /mypath/RepeatMasker/repeatmasker.help

I don't know what this "/opt/apps/intel18/cray_mpich_7_7/python3/..." path is, that isn't my path or anything I recognize.

What is going on?

[lieven.sterck]

Seems like something is not correct with the RepeatMasker install. Can you double check the install went OK? Also are you running the correct python version for it ?

[juliayork]

Yeah I think the issue is a python dependency. Python is running fine, and up to date. RepeatMasker says it needs Python3, I'm running 3.9. However, I think the issue is h5py. When I try to run RepeatMasker now it gives this:

Building FASTA version of RepeatMasker.lib ...[Fri Feb  5 14:10:42 2021] [unknown] Fatal error in PMPI_Init_thread: Other MPI error, error stack:
MPIR_Init_thread(537):
MPID_Init(246).......: channel initialization failed
MPID_Init(638).......:  PMI2 init failed: 1
aborting job:
Fatal error in PMPI_Init_thread: Other MPI error, error stack:
MPIR_Init_thread(537):
MPID_Init(246).......: channel initialization failed
MPID_Init(638).......:  PMI2 init failed: 1
.
Building RMBlast frozen libraries..
The program is installed with a the following repeat libraries:

Further documentation on the program may be found here:
  /work/05864/juliay/Notothenioids/TEs/RepeatMasker/repeatmasker.help

My cluster has hdf5 as a module so I do:

module load hdf5

which seems fine, but if I ask

which hdf5

it can't be found. I installed h5py using conda, but it didn't seem to work as

which h5py

also couldn't be found. So I uninstalled it and tried:

pip install h5py

But it says:

Requirement already satisfied: h5py in /opt/tacc_mounts/apps/intel18/cray_mpich_7_7/python3/3.7.0/lib/python3.7/site-packages (2.8.0)
Requirement already satisfied: numpy>=1.7 in ./miniconda3/lib/python3.7/site-packages (from h5py) (1.20.0)
Requirement already satisfied: six in ./miniconda3/lib/python3.7/site-packages (from h5py) (1.15.0)

But again

which h5py

Can't be found. Please help!!

[juliayork]

Ok, I had to run

module unload cray_mpich

And that now allows

import h5py

To work within the python interpreter. However! I still can't get RepeatMasker to recognize it. I run:

perl ./configure

And it allows set up of trf and the search engine, but then fails:

  File "/work/05864/juliay/Notothenioids/TEs/RepeatMasker/famdb.py", line 51, in <module>
    import h5py
ModuleNotFoundError: No module named 'h5py'

Running

./famdb.py

Gives the same error. Any ideas?

[chs.borges]

Hi,

I'm having the same issue with h5py. I've tried your solution and that's what I got:

Rebuilding RepeatMaskerLib.h5 master library

  Merging Dfam + RepBase into RepeatMaskerLib.h5 library....Traceback (most recent call last):
  File "/usr/local/RepeatMasker/famdb.py", line 55, in <module>
    import h5py
  File "/mypath/miniconda3/envs/repeat/lib/python3.9/site-packages/h5py/__init__.py", line 25, in <module>
    from . import _errors
ImportError: cannot import name '_errors' from 'h5py' (/mypath/miniconda3/envs/repeat/lib/python3.9/site-packages/h5py/__init__.py)
Failed to append /usr/local/RepeatMasker/Libraries/RMRB.embl to /usr/local/RepeatMasker/Libraries/RepeatMaskerLib.h5.writing.
Process exited with code 1.
.
Traceback (most recent call last):
  File "/usr/local/RepeatMasker/famdb.py", line 55, in <module>
    import h5py
  File "/mypath/miniconda3/envs/repeat/lib/python3.9/site-packages/h5py/__init__.py", line 25, in <module>
    from . import _errors
ImportError: cannot import name '_errors' from 'h5py' (/mypath/miniconda3/envs/repeat/lib/python3.9/site-packages/h5py/__init__.py)

Does anyone know what's going on? Thanks!

[oasiswho]

Thanks! It worked!

And I made a new environment for repeatmasker and solved this by reload conda evns

2 methods~

Answer 1

[juliayork]

I figured it out!!! RepeatMasker is running python3, so when I was running just python it was finding h5py but when I ran python3 it couldn't find it.

I fixed it by adding:

sys.path.append("/mypath/bin/miniconda3/lib/python3.7/site-packages")

directly to the famdb.py file, between import sys and import h5py

and it worked!! Hope this helps someone else