Non bins with nanopore reads

[gilmahu]

Wishing everyone a productive new year.
I have been encountering some challenges with metawrap with nanopore reads.
While it works perfectly with illumina reads, I have been unable to use it successfully with any of the binners with nanopore data that were assembled with metaflye.
The wonder is even more confusing as i receive no error file.

Here are examples of the commands

metawrap binning -o /bins/mca_182 -t 40 -a /mca_182/assembly.fasta --single-end /decompressed_reads/mca_182.fastq --metabat2 --concoct --maxbin2

I also tried without the single end option
metawrap binning -o /bins/mca_182 -t 40 -a /mca_182/assembly.fasta /decompressed_reads/mca_182.fastq --metabat2 --concoct --maxbin2

In all cases, i never get any output.

I also tried directly with one binner like this:
minimap2 -ax map-ont assembly.fasta mca_182.fastq | samtools sort -o aligned_reads.bam -T temp
samtools index aligned_reads.bam
metabat2 -i assembly.fasta -a aligned_reads.bam -o /bin -t 40

Has anyone experienced anything like this with nanopore data and could advice? or is the issue from the metaflye assemblies?