genomad annotate fastq file is empty or contains multiple entries

[skose82]

Hi I am getting the following error:

sample1.fastq.gz is either empty or contains multiple entries with the same identifier. Please check your input FASTA file and execute genomad annotate again.

Not sure what's happening as the file isn't empty and works fine with other scripts/programs.

Is there a way to run genomad with pair-end fastq files or do hey need to be interleavened first?

Command is: genomad end-to-end --cleanup --splits 20 sample1_R1.fastq.gz genomad_output genomad_db

Thanks