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Dfam-consortium / RepeatMasker

RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
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Error building FASTA version of RepeatMasker.lib during configuration #141

Closed charlesfeigin closed 2 years ago

charlesfeigin commented 2 years ago

Hi, I am trying to install the most current version of RepeatMasker (4.1.2-p1) and am encountering the following error during configuration:

Enter Selection: 5 Building FASTA version of RepeatMasker.lib ...........................................Traceback (most recent call last): File "/home/cfeigin/src/RepeatMasker/famdb.py", line 1841, in main() File "/home/cfeigin/src/RepeatMasker/famdb.py", line 1834, in main args.func(args) File "/home/cfeigin/src/RepeatMasker/famdb.py", line 1623, in command_families print_families(args, families, True, target_id) File "/home/cfeigin/src/RepeatMasker/famdb.py", line 1565, in print_families buffer=buffer_spec File "/home/cfeigin/src/RepeatMasker/famdb.py", line 398, in to_fasta for clade_id in self.clades: TypeError: 'NoneType' object is not iterable .. Building RMBlast frozen libraries.. The program is installed with a the following repeat libraries: File: /home/cfeigin/src/RepeatMasker/Libraries/Dfam.h5 Database: Dfam Version: 3.5 Date: 2021-10-08

Dfam - A database of transposable element (TE) sequence alignments and HMMs.

Total consensus sequences: 285580 Total HMMs: 285542

Further documentation on the program may be found here: /home/cfeigin/src/RepeatMasker/repeatmasker.help

I followed the instructions found here when installing: http://www.repeatmasker.org/RepeatMasker/ and have repeated the process several times to no avail. I see another user had encountered the same error in 2020 (https://github.com/rmhubley/RepeatMasker/issues/84) however based on the thread, their issue may have been due to installing RepeatMasker in a directory containing an old install. In my case though, I am doing this in a fresh directory and not overwriting any old files. Its a clean install.

If you have any sense of why the configuration is failing I would greatly appreciate it.

charlesfeigin commented 2 years ago

Apologies, it was a Dfam version issue

jebrosen commented 2 years ago

Hi @charlesfeigin, what was the issue and what did you do to solve it? It could help someone else solve the same problem, or help us to fix it if there really is a problem with RepeatMasker or Dfam.

Lvmingjie commented 2 years ago

I have the same error in merging Dfam 3.6 and Repbase20181026, is these two database incompatible？

hyoj-seo commented 2 years ago

I have the same error too. I downloaded Dfam 3.6 (Dfam.h5.gz in https://www.dfam.org/releases/Dfam_3.6/families/) and unzipped in Libraries folder. Then I ran the code 'perl ./configure'. But I got this error. Has anyone solved it?

TobyBaril commented 2 years ago

I am also having the same issue with Dfam 3.6, all other installations with Dfam 3.4 are working perfectly.

Did you find a solution @charlesfeigin ?

TobyBaril commented 2 years ago

@jebrosen I have found that this is an issue with Dfam 3.6. I can successfully configure RepeatMasker with all versions up to Dfam 3.5, so the issue is with the latest h5 file rather than the RepBase libraries, not sure if this helps?

rmhubley commented 2 years ago

Thanks everyone for reporting this. I have identified this as a problem particular to the merging of RepBase libraries (RepBase RepeatMasker Edition) and Dfam 3.6. The problem occurs in 3.6 due to updates in the NCBI Taxonomy that shifted some scientific names to synonyms. We do not currently store synonyms in our h5 exports causing problems with merging in specific RepBase entries. To fix this I regenerated the Dfam 3.6 .h5 exports and updated a file in the RepeatMasker distribution "Libraries/RMRBMeta.embl". If both of these files are updated, the merger should proceed normally and RepeatMasker can be setup. Here are the steps:

I will update the instructions on the RepeatMasker website and prioritize getting a new RepeatMasker release and containers out soon so this won't be necessary in the future. NOTE that this shouldn't be necessary at all if you only intend to use Dfam 3.6 with RepeatMasker.

caonetto commented 2 years ago

Hi, I tried following your instructions but I now get the following error while configuring RepeatMasker. Sorry for the screenshot.

Any ideas what could be going on?

Thanks.

Screenshot from 2022-08-05 11-54-21

gamzeozbay commented 2 years ago

Screen Shot 2022-08-17 at 16 56 05 I am having the following error during configuration. Building FASTA version of RepeatMasker.lib .../usr/bin/env: python3: 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: /okyanus/users/gozbay/RepeatMasker/repeatmasker.help

rmhubley commented 2 years ago

@gamzeozbay, Python is a dependency of RepeatMasker. You will need to make sure it's installed on your system (including the H5py library), and that Python is in your path before running the RepeatMasker configure program.

rmhubley commented 2 years ago

@caonetto, I am about to release RepeatMasker 4.1.3 which should fix this issue for you and others.

WeiZhangVivi commented 1 year ago

Hi, I have the similar problem in installing RepeatMasker-4.1.5, I followed the instructions found here when installing: https://www.repeatmasker.org/RepeatMasker/.

the following error during configuration:

Enter Selection: 5

Building FASTA version of RepeatMasker.lib ...........................................

Building RMBlast frozen libraries.. The program is installed with a the following repeat libraries: File: /home/cfeigin/src/RepeatMasker/Libraries/Dfam.h5 Database: Dfam Version: 3.7 Date: 2023-1-10

Dfam - A database of transposable element (TE) sequence alignments and HMMs.

Total consensus sequences: 825549 Total HMMs: 825492

Further documentation on the program may be found here: /home/cfeigin/src/RepeatMasker/repeatmasker.help

Hoping anyone can hlep me to solve this.

rmhubley commented 11 months ago

@WeiZhangVivi, could you try running running the following command to see if we can reproduce the issue:

cd /home/cfeigin/src/RepeatMasker
./famdb.py -i  /home/cfeigin/src/RepeatMasker/Libraries/Dfam.h5 families --descendants 1 --curated --format fasta_name --include-class-in-name > test_rmlib.fa

And capture the screen output?