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rmhubley / RepeatMasker

RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
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No RepeatMasker.lib.* files created with FamDB HDF5 partitions #255

Closed carolindahms closed 2 months ago

carolindahms commented 2 months ago

Hello, after configuring RepeatMasker on Linux with Dfam libraries, no RepeatMasker.lib files are created in the the Libraries directory, and running RepeatClassifier it gives me the error 'Missing RepeatMasker.lib.nsq!'

I have manually installed different RepeatMasker versions per instructions ( now working with 4.1.6) and the configure output doesn't show any errors, although it does not mention any use of RepeatMasker.embl, which is not present in any of my directories. I have downloaded Dfam partition 0 and 6, which are in my /Libraries/famdb directory. Based on previous issues (https://github.com/Dfam-consortium/RepeatModeler/issues/10) I have also downloaded the full Dfam_3.8.embl database and reconfigured, to no avail.

My /Libraries/ content:

Artefacts.embl Dfam.embl famdb README.meta RepeatPeps.lib.pdb RepeatPeps.lib.pin RepeatPeps.lib.pot RepeatPeps.lib.ptf RepeatPeps.readme RMRB_spec_to_tax.json CONS-Dfam_3.8 Dfam.h5 general RepeatAnnotationData.pm RepeatPeps.lib RepeatPeps.lib.phr RepeatPeps.lib.pjs RepeatPeps.lib.psq RepeatPeps.lib.pto RMRBMeta.embl taxonomy.dat

Configuration output: ####### Building RMBlast frozen libraries.. The program is installed with a the following repeat libraries:

FamDB Directory : /home/marevo/Softwares/RepeatMasker/RepeatMasker/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 Version : 3.8 Date : 2023-11-14

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

2 Partitions Present Total consensus sequences present: 576140 Total HMMs present : 576140

Partition Details

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

Partition 1 [ Absent ]: Obtectomera

Partition 2 [ Absent ]: Euteleosteomorpha

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

Partition 4 [ Absent ]: Diptera

Partition 5 [ Absent ]: Viridiplantae

Partition 6 [dfam38_full.6.h5]: Deuterostomia - Chondrichthyes, Hemichordata, Cladistia, Holostei, Tunicata, Cephalochordata, Cyclostomata , Osteoglossocephala, Otomorpha, Elopocephalai, Echinodermata, Chondrostei Consensi: 280588, HMMs: 280588

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

What am I missing here? Thank you for any advice!

carolindahms commented 2 months ago

Apologies, I just found this issue solved at #238