[maker-devel] ERROR: Failed while processing all repeats

[Xiong, Wei]

Dear Colleague,

I had encountered an ERROR when I used MAKER to annotate my genome.
It is a large plant genome (more than 3Gb), I included a TE (gff) data, one Transcriptome data (fasta), and four protein sequences (fasta) for the homology annotation. There are in total 29 scaffolds. Three scaffolds faced the "ERROR: Failed while processing all repeats," while the other 26 finished successfully.
I have tried the following methods from the online forum. However, I still cannot fix the error.


  *   Check the RepeatMasker configuration
  *   Check the maker_exe.ctl
  *   replace .../maker/lib/Widget/RepeatMasker.pm http://gmod.827538.n3.nabble.com/MAKER-v3-ERROR-Failed-while-processing-all-repeats-td4059410.html
  *   increase the try_count in the maker_opt.ctl

Could you please help me to solve this problem?
Thank you for reading my email. I look forward to hearing from you.
Best wishes and stay healthy,


Met vriendelijke groet,
With kind regards,

Wei Xiong
PhD candidate | Wageningen University & Research
Plant Science Group | Biosystematics Group Radix Building 107 Droevendaalsesteeg 1
6708 PB Wageningen
The Netherlands
Email: wei.xiong at wur.nl<mailto:wei.xiong at wur.nl>

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