racon: layer begin and positions are invalid

Hi! I am currently trying to run the following command: racon -u -f -w 50 -q 9 ../trim50_dem_q9/barcode02.fastq ../minimap2_output_x_map_ont/aln_2.sam ../gene_references/msp2_pf3d7_02026800.fasta

but I get the error: layer begin and positions are invalid

I am basically trying to get a set of fastq or fasta corrected sequences so I can tell the difference between sequencing errors from SNPs. My project consists of analysis of haplotypes, where SNP calling is crucial for this. The genes I sequenced using nanopore are short, around 550 bp and 800 bp (two different genes). I was looking at #118 and it seems that my error is a little bit different. I tried running it with both .sam and .paf and I am getting similar errors (ran an alignment using minimap2 previous to this, hence the .sam file I used).

However it works fine when I run this one: racon ../trim50_dem_q9/barcode01.fastq ../minimap2_output_x_map_ont/aln_01.paf ../gene_references/msp2_pf3d7_02026800.fasta > test , where I get a consensus fasta sequence, but I am looking forward to get a fasta set of corrected sequences.

Thanks for your help,

Daniel