Mark Currey

I'm also having issues with bamToWig: ERROR in file /packages/braker/2.1.4/scripts/braker.pl at line 10244 Failed to execute: /packages/python/3.6.7/bin/python3 /gpfs/packages/augustus/3.3.3/scripts/bamToWig.py -b /gpfs/projects/nereus/mcurrey/ptae/annotate/braker/rnaseq_plus.s.bam -g /gpfs/projects/nereus/mcurrey/ptae/annotate/braker/genome.fa -o /gpfs/projects/nereus/mcurrey/ptae/annotate/braker/rnaseq_plus.wig 2> /gpfs/projects/nereus/mcurrey/ptae/annotate/braker/errors/bamToWig_plus.err Traceback (most recent call...

We created custom libraries and used the -lib flag by running repeat modeler and combining the outputted consensus library with a teleost specific library retrieved by using queryRepeatDatabase.pl in version...

Sorry that I didn’t clarify this but yes we used —include-class-in-name while extracting the specific library. > On Dec 1, 2020, at 9:46 AM, Jeb Rosen wrote: > > >...

Using "equivalent" libraries these are the output tables. You can see the % masked is about the same however the elements listed are very different. [maker4.1.1_pttt_v1.1.fasta.tbl.txt](https://github.com/rmhubley/RepeatMasker/files/5626367/maker4.1.1_pttt_v1.1.fasta.tbl.txt) [maker4.70.7_pttt_1.1.fasta.tbl.txt](https://github.com/rmhubley/RepeatMasker/files/5626368/maker4.70.7_pttt_1.1.fasta.tbl.txt)

I think this is exactly what is happening. In the older versions of RepeatModeler and Masker it is querying an older Dfam library (maybe I'm interpreting the webpage wrong but...

Consensus Library 1 ("old") was generated with: - RepeatMasker version: 4.0.7 - RepBase RepeatMasker Edition version: RepBase-20170127 - RepeatModeler version: 1.0.11 - Total number of families: 11 families Consensus Library...