Could not open refined model

[NicMAlexandre]

Hello,

I installed RepeatModeler with conda:

conda create -n repeatmodeler python=3.9 conda activate repeatmodeler conda install -c bioconda genometools-genometools repeatmodeler

I ran the following:

BuildDatabase -name Genome Genome_2022.fasta #No Errors

RepeatModeler -database Genome -pa 8 -LTRStruct

Then get the following error:

RepeatModeler Round # 1

Searching for Repeats -- Sampling from the database...

• Gathering up to 40000000 bp
• Final Sample Size = 40004123 bp ( 40004023 non ambiguous )
• Num Contigs Represented = 40
• Sequence extraction : 00:07:33 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences...
• RepeatScout: Running build_lmer_table ( l = 14 )..
• RepeatScout: Running RepeatScout.. : 462 raw families identified
• RepeatScout: Running filtering stage.. 418 families remaining
• RepeatScout: 00:17:11 (hh:mm:ss) Elapsed Time
• Large Satellite Filtering.. : 2 found in 00:00:39 (hh:mm:ss) Elapsed Time
• Collecting repeat instances... -- Refining Family R=147 / 0 ( RS Elements: 39629, Using 100 ) cannot read file /redser4/projects/Nicolas/Genomes/RM_1919395.WedDec142021572022/round-1/family-0.fa RepeatModeler: Could not open refined model /redser4/projects/Nicolas/Genomes/RM_1919395.WedDec142021572022/round-1/family-0.fa.refiner_cons!

I only see one issue online about this and it mentions installing from source instead. Is there a way around this if I use the conda installation.

[NicMAlexandre]

I reinstalled using the most recent version of RepeatModeler (2.0.4) and I no longer get this error and it seems to be progressing through each round smoothly. However, at the end of each round I have full output directories of fasta files, but the log file says 0 families discovered after each step.

RepeatModeler Round # 1

Searching for Repeats -- Sampling from the database...

• Gathering up to 40000000 bp
• Final Sample Size = 40028157 bp ( 40027857 non ambiguous )
• Num Contigs Represented = 43
• Sequence extraction : 00:04:15 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences...
• RepeatScout: 00:12:20 (hh:mm:ss) Elapsed Time Round Time: 00:21:03 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatModeler Round # 2

Searching for Repeats -- Sampling from the database...

• Gathering up to 10000000 bp
• Sequence extraction : 00:01:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence...
• TRFMask time 00:00:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10004948 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 10004848 bp After Masking: 9884687 bp Masked: 1.20 % -- Input Database Coverage: 10004948 bp out of 2501084987 bp ( 0.40 % ) Sampling Time: 00:01:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons...
  • Total Comparisons = 31375 Comparison Time: 01:06:52 (hh:mm:ss) Elapsed Time, 10510239 HSPs Collected Number of families returned by RECON: 4340 Round Time: 04:02:58 (hh:mm:ss) Elapsed Time : 0 families discovered.