Unequal lengths in sequence

[bioramg]

I am trying to polish ONT contigs with Illumina reads. But getting an error while using the Illumina pair-end reads.

bwa mem -t 40 -x ont2d ./ont_assembly.fasta /home/Ill_paired.fastq >ont_mapping.sam

racon -m 8 -x -6 -g -8 -w 500 -t 14 /home/Ill_paired.fastq ./ont_mapping.sam ./ont_assembly.fasta > ./ont_polish_racon.fasta

[racon::Overlap::transmute] error: unequal lengths in sequence and overlap file for sequence ST-E00181:968:HGM7HCCX2:1:1101:20496:2610!

I am looking forward to hearing from you.

[rvaser]

Hello,
your Illumina pairs probably have the same name which is not supported in the current implementation. Please use this script to modify them before aligning and polishing.

Best regards,
Robert

[bioramg]

Thank you for your prompt response.

I am basic to use scripts and all. Is there any other option to modify using the basic commands?

Thank you.

[rvaser]

You can just run it with python racon_preprocess.py Ill_paired.fastq > Ill_paired.preproc.fastq.