Yesterday (20190625) I generated a subset of the first 18 FastA sequences from the Pgenerosa_v070.fa file. This subset has been designated as Pgenerosa_v074 by Steven. It’s available on our Genomic Resources wiki:

• Pgenerosa_v074.fa

He’s asked me to annotate this assembly using MAKER - this will be detailed in another notebook entry at some point.

In preparation for that, I need to run the assembly through RepeatModeler and provide the output to MAKER. I ran RepeatModeler v1.0.11 on Emu (Apple Xserve running Ubuntu 16.04LTS).

All of it is detailed in this Jupyter Notebook (GitHub):

• 20190626_emu_Pgenerosa_v074_repeatmodeler.ipynb

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RESULTS

Run time was 1974 minutes (~32.4hrs).

Output folder:

• 20190626_Pgenerosa_v074_repeatmodeler

RepeatModeler FastA:

• 20190626_Pgenerosa_v074_repeatmodeler/Pgenerosa_v074-families.fa