Most probably the basecalling option was not selected during the run set up. There could be however unexpected error that prevented to generate fastq files.

To recover your data, you can rerun the fastq file/s through the “Analysis” tab on MinKNOW to demultiplex it. Or you can rebasecall and demultiplex the fast5 files again through MinKNOW.

Another way of rebasecalling is to use the command line. Follow the instructions below:

Access guppy_basecaller through the Terminal (either on Linux or Windows). A general basecalling command looks something like this
$ guppy_basecaller -i -s -c dna_r9.4.1_450bps_hac.cfg –barcode_kits SQK-RBK110-96 –q_score 7 –trim_barcodes -x cuda:all

The would need to be a completed file path to the data you want to analyse e.g. /data/omixon_experiment/no_sample/Run_ID/fast5_pass, and likewise the -s would also need to be the path to where you want the data to be outputted to.

More information about guppy basecaller can be found here.