ERROR: Failed while processing all repeats

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ERROR: Failed while processing all repeats


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.



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: [hidden email]


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