Missing .qualities.npy file

[IoannaNika]

Hello, I have been trying to run viloca on some PacBio-Hifi amplicon reads. However, I am getting an error about files ending in .qualities.npy that are missing

The traceback of the error leads to viloca/local_haplotype_inference/use_quality_scores/preparation.py, line 103, in load_fasta_and_qualities

What could be the reason for this error and how could I solve it?

Thank you in advance for the help!

[LaraFuhrmann]

Hi Ioanna,

Were any files created ending in qualities.npy?
Also, could you specify which command you used to execute the tool?

[IoannaNika]

Hello @LaraFuhrmann, I think I resolved the previous issue, I use now for some files --mode learn_error_params

but I now get this error:

ERROR 2026/01/04 14:55:57 shotgun.py: run_dpm_wrapper() 142: 	Error in process for run_set ('w-MN908947.3-54-1182.reads.fas', 15075, 0.0001, array([0]), 'learn_error_params', 100, 1, True, 0.001, False): run_cavi() missing 1 required positional argument: 'seed_number'

my command:

viloca run -f $reference -b $in_path -z $zfile --mode learn_error_params

[IoannaNika]

Also, when I run it on some simulated datasets, I get (no other logs/files ):

b2w run not successful

(I filtered supplementary alignments)