Does anyone know what would cause "No paris were aligned!" message during the scaffolding step in Redundans?
I am running it using this command:
redundans.py --identity 0.70 -v -i R1.fastq R2.fastq -f contigs.fa -o Results
I've checked all of the documentation and the examples to see if I am missing something and I cannot pinpoint what could be wrong. The only difference I see is the authors use compressed fastq files and I am not.
Any input would be greatly appreciated