ERROR: No valid secondary alignments found in bam file. Were the reads aligned with minimap `-p 0 -N 10` options ?

Hello,

thank you for the software! I am testing it as we speak it throwing an error which I cannot seem to fix following the instructions.

## Checking options and input files ##
## Initialise Nanocount ##
        Parse Bam file and filter low quality alignments
        Summary of alignments parsed in input bam file
                Discarded unmapped alignments: 543,714
                Discarded negative strand alignments: 5,949
                Discarded alignment with invalid 3 prime end: 2,667
                Discarded supplementary alignments: 2,273
                Valid alignments: 582
                Discarded short alignments: 6
ERROR: No valid secondary alignments found in bam file. Were the reads aligned with minimap `-p 0 -N 10` options ?
        Summary of reads filtered
                Reads with valid best alignment: 516
                Reads with low query fraction aligned: 66
        Generate initial read/transcript compatibility index
## Start EM abundance estimate ##
        Progress: 2.00 rounds [00:00, 1.21k rounds/s]
        Exit EM loop after 2 rounds
        Convergence value: 0.0
## Summarize data ##
        Convert results to dataframe
        Compute estimated counts and TPM
        Write file

NanoCount v1.0.0.post6 I am using a small portion of the reads is this the reason why it's not working?

best,

Loïc

a-slide / NanoCount

ERROR: No valid secondary alignments found in bam file. Were the reads aligned with minimap `-p 0 -N 10` options ? #35