Mismatch Issue with Analysis of direct cDNA data

[anatalex]

Hello,

I have used oxford nanopore's direct cDNA sequencing kit to obtain transcript information from 18 different samples. Right now I am trying to run a differential expression analysis between 6 of them as set up below:

sample_id condition
barcode01 untreated
barcode02 untreated
barcode03 untreated
barcode10 treated
barcode11 treated
barcode12 treated

When I run the differential expression analysis pipeline it gives me the following error:

• Join mismatch for the following entries:
• - key= values=[],[],[],[],[],[]
• - key=barcode02 values=[/mnt/c/Users/topas/epi2melabs/instances/wf-transcriptomes_eeff4573-1a2e-4ebc-976c-fd1466292ea2/work/7d/8eeebc22ec390d2c71666b1ac5f05d/barcode02.fastq]

This error repeats for all of my samples. I have checked the names and they are the same on the TSV as the files themselves. Does anyone know what might be causing this error?

Thank you!