badread error_model is not outputting anything and not giving an error

[evantroendle]

Describe the bug Hello, I have attempted to use badread to create a custom error model based on read data. I wanted to compare badread simulated samples using a custom error model to other badread simulated samples based from the included nanopore2020 error model (I also intend to create a custom qscore model).

To reproduce First I have aligned to a small set of reads data before attempting to create an error profile based on more reads. I have followed the instructions to create the alignments file: minimap2 -c -x map-ont nCoV-2019.reference.fasta Run_Name_barcode13.fastq.gz | gzip > alignments.paf.gz

To try to create an error model I have tried a few similar commands: badread error_model --reference nCoV-2019.reference.fasta --reads Run_Name_barcode13.fastq.gz --alignment alignments.paf.gz > new_error_model

badread error_model --reference nCoV-2019.reference.fasta --reads Run_Name_barcode13.fastq.gz --alignment alignments.paf.gz --k_size 15 > new_error_model

#^ takes a while and the PC runs out of memory,

badread error_model --reference nCoV-2019.reference.fasta --reads Run_Name_barcode13.fastq.gz --alignment alignments.paf.gz --k_size 2 --max_alignments 1 > new_error_model

^ tried to just get anything to output

files for reproducing alignments.paf.gz nCoV-2019.reference.fasta.gz Run_Name_barcode13.fastq.gz

Error message There is no error message (besides the case where k_size was 15 and the PC RAM couldn't support this). Any help as to what may be preventing analysis or output would be appreciated.

System info

• OS: [Ubuntu 20.04]
• Python version: [3.10.4]
• Conda version: [4.13.0]

Additional context minimap2 version: 2.17-r941 Badread v0.2.0

All the best, Evan