FileNotFoundError: No such file or directory when using pre-trained model

[florenmartino]

Hi NanoSim team,

I'm encountering an issue when trying to run NanoSim with a pre-trained model. I'm using the human_giab_hg002_sub1M_kitv14_dorado pre-trained model, but I keep getting the following error:

FileNotFoundError: [Errno 2] No such file or directory: '/home/fmartino/NanoSim/pre-trained_models/human_giab_hg002_sub1M_kitv14_dorado_strandness_rate'

Steps I've taken:

I downloaded the pre-trained model human_giab_hg002_sub1M_kitv14_dorado.tar.gz from the repository.
I extracted the files using tar -xzvf human_giab_hg002_sub1M_kitv14_dorado.tar.gz.
I verified that the files are present in the folder:

(nanosim):~/NanoSim/pre-trained_models/human_giab_hg002_sub1M_kitv14_dorado$ ls
hg002_nanosim_sub1M_aligned_region.pkl hg002_nanosim_sub1M_gap_length.pkl hg002_nanosim_sub1M_model_profile human_giab_hg002_sub1M_kitv14_dorado_error_rate.tsv
hg002_nanosim_sub1M_chimeric_info hg002_nanosim_sub1M_ht_length.pkl hg002_nanosim_sub1M_reads_alignment_rate human_giab_hg002_sub1M_kitv14_dorado_strandness_rate
hg002_nanosim_sub1M_error_markov_model hg002_nanosim_sub1M_ht_ratio.pkl hg002_nanosim_sub1M_unaligned_length.pkl
hg002_nanosim_sub1M_first_match.hist hg002_nanosim_sub1M_match_markov_model human_giab_hg002_sub1M_kitv14_dorado_aligned_reads.pkl

I renamed the files to match what NanoSim expects and same error.

I ran the simulation command:

simulator.py genome \
    -rg /home/fmartino/Ref_seq/Simulation_DC0135_anellos/Annelovirus_AllRefs.part_AB303554_circular.fasta \
    -o /home/fmartino/Ref_seq/Simulation_DC0135_anellos/simulation_Annelovirus_AllRefs.part_AB303554 \
    -n 55 \
    -dna_type circular \
    -c /home/fmartino/NanoSim/pre-trained_models/human_giab_hg002_sub1M_kitv14_dorado/ \
    -med 1000 \
    -sd 0.2 \
    --fastq \
    -t 22

Despite these steps, I still get the FileNotFoundError. Could you please help me understand what I might be doing wrong?

Additional information:

NanoSim version: Installed via conda install -c bioconda nanosim.
Environment: Python 3.7, Conda environment.
Pre-trained model: human_giab_hg002_sub1M_kitv14_dorado.tar.gz. (I also tried with the v3.2.1)

Thank you for your help!

Best regards,

Flor