Error in RepeatClassifier step: Missing RepeatPeps.lib.psq

[athenasyarifa]

Hi @rmhubley and everyone,

I finished several rounds of RepeatModeler, but I have an error in the RepeatClassifier step. It seems I am missing several required files for RepeatClassifier: RepeatPeps.lib.psq, RepeatMasker.lib, RepeatMasker.lib.nsq. I tried running again configure in RepeatMasker directory with successful installation of Dfam library according to the instruction in the website. See below the final part of the configuration:

Add a Search Engine:
   1. Crossmatch: [ Un-configured ]
   2. RMBlast: [ Configured, Default ]
   3. HMMER3.1 & DFAM: [ Un-configured ]
   4. ABBlast: [ Un-configured ]

   5. Done

Enter Selection: 5
Building RMBlast frozen libraries..
The program is installed with a the following repeat libraries:

FamDB Directory     : /dss/dsslegfs01/pr53da/pr53da-dss-0026/projects/2023__Pmon_pop_gen/0__repeatmasking/tools/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.

1 Partitions Present
Total consensus sequences present: 295552
Total HMMs present               : 295552

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: 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 [ 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

Further documentation on the program may be found here:
  /dss/dsslegfs01/pr53da/pr53da-dss-0026/projects/2023__Pmon_pop_gen/0__repeatmasking/tools/RepeatMasker/repeatmasker.help

But after that, there is no RepeatMasker.lib files in the RepeatMasker/Libraries/ directory.

I ran RepeatModeler v.2.0.5 with installed dependencies: rmblast 2.14.1+, TRF 4.09, RECON, RepeatScout 1.0.6, RepeatMasker 4.1.6 along with the Dfam libraries installed according to the website instructions. I attached below the log file of RepeatModeler run:

00_repeatmodeler.log

I run the following command to run RepeatModeler:

${RepeatModelerDIR}/BuildDatabase -name poeMon1 poeMon1.fa
${RepeatModelerDIR}/RepeatModeler -LTRStruct -threads 4 -database poeMon1 2>&1 | tee 00_repeatmodeler.log

This is what inside my RepeatMasker/Libraries directory:

$ ls RepeatMasker/Libraries/
Artefacts.embl  famdb  README.meta  RepeatAnnotationData.pm  RepeatPeps.lib  RepeatPeps.readme  RMRBMeta.embl  RMRB_spec_to_tax.json  taxonomy.dat

$ ls RepeatMasker/Libraries/famdb
dfam38_full.0.h5  rmlib.config

I am running on a Linux machine 4.12.14-197.108-default (this is the login node).

I saw some other issues with missing RepeatMasker.lib such as #137 but they have the RepeatPeps.lib and issue #128 about how to generate my own RepeatMasker.lib but from my understanding the configuration step should automatically make this RepeatMasker.lib file from the downloaded Dfam libraries. Did I do something wrong?

Any help would be much appreciated. Thank you so much! Best, Rifa

[malvaradol]

Hi @athenasyarifa

I'm currently having the same issue, and after multiple attempts I was able to generate the RepeatMasker.lib, here's what I did:

• Create a fresh RepeatMasker directory. This means delete the existing directory of RepeatMasker and create a new one by decompressing the release file (RepeatMasker-4.1.7-p1.tar.gz.
• Download the necessary dfam partitions and decompress them before running the configuration script. I downloaded the partitions directly into the Libraries/famdb directory.
• Run the configure script. I noticed that when you are done configuring the search engines, this message "Building RMBlast frozen libraries.." takes way longer that it used to.
• After this I was able to find the RepeatMasker.lib file in the Libraries directory.

I'm still waiting for the output of RepeatModeler, as when RepeatMasker.lib did not exist the program did not execute RepeatClassifier for the exact same reasons that you are pointing out. I will let you know how it goes.

Hope this helps in any way.