Error at final shred and polish stage

[Hoberti]

Hello,

First, thank you very much for this tool. I am using rebaler for chloroplast genome assembly and it crashed at the final shred and polish stage.

Full traceback:

Final shred and polish (2021-04-17 17:39:00) To get the best possible consensus, Rebaler now shreds the previous polished assemblies to make "reads" for a final couple rounds of polishing.

Traceback (most recent call last): File "/home/Rebaler/rebaler-runner.py", line 9, in main() File "/home/Rebaler/rebaler/main.py", line 97, in main final_assembly = final_shred_and_polish(ref_names, circularity, polish_dir, args.threads) File "/home/Rebaler/rebaler/main.py", line 179, in final_shred_and_polish final_assembly = polish_assembly_with_racon(ref_names, unpolished_sequences, circularity, File "/home/Rebaler/rebaler/main.py", line 396, in polish_assembly_with_racon unitig_graph = UnitigGraph(names, unpolished_sequences, circularity) File "/home/Rebaler/rebaler/unitig_graph.py", line 30, in init sequence = seqs[name] KeyError: 'm54259_190626_092626/4391152/46555_65897'

I used python version 3.7 and the following line to call it

python3.7 /Rebaler/rebaler-runner.py -t 3 assembly.fasta corrected_reads.fasta.gz > assembly_rebaler.fasta

The assembly_rebaler.fasta is empty.

Could you help me with this?

Thanks in advance