SPAdes assembler error "The number of reads in file with interlaced reads is ODD"

Question

[Neil]

Hello. I try to assembly genomes from this project with SPAdes assembler with parameters --12 ( File with interlaced forward and reverse paired-end reads.) but I get the error "The number of reads in file with interlaced reads is ODD"! What I do wrong? I read manual many times but this didn't help.

[GenoMax]

The error is telling you what is wrong. There is an odd number of reads belonging to either R1/R2. This generally happens if you scan/trim the two read files independently and a read is dropped out of one file but not its mate.

You can fix the original files by using repair.sh from BBMap suite.