The output data is now only an args file (previously several vcf files were generated).

[erarin]

Hello,

I would like to ask you a few questions.

I have been using nanocaller, and in the past, I was successfully generating multiple vcf files.

However, in the last few days, I have been getting only "args" in the output file, even though I tried to do the same thing.
In that case, there is no error message and the parsing is finished in a few seconds.

The contents of the args file are as follows
``
Command: python /Users/eura/miniconda3/envs/nanocaller_env/bin/Nanocaller -bam fastq_pass/20220413_Higuchi/220413_SP_q90_min5000_max18000.bam -p ont -o fastq_pass/output_0509_S -chrom chr9 -ref fastq_pass/Homo_sapiens_UCSC_hg38/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa -cpu 16

------Parameters Used For Variant Calling------
mode: both
sequencing: ont
cpu: 16
mincov: 8
maxcov: 160
keep_bam: False
output: fastq_pass/output_0509_S
prefix: variant_calls
sample: SAMPLE
include_bed: None
exclude_bed: None
start: None
end: None
preset: ont
bam: fastq_pass/20220413_Higuchi/220413_SP_q90_min5000_max18000.bam
ref: fastq_pass/Homo_sapiens_UCSC_hg38/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa
chrom: chr9
snp_model: ONT-HG002
min_allele_freq: 0.15
min_nbr_sites: 1
neighbor_threshold: 0.4,0.6
supplementary: False
indel_model: ONT-HG002
ins_threshold: 0.4
del_threshold: 0.6
win_size: 40
small_win_size: 4
impute_indel_phase: False
phase_bam: False
enable_whatshap: False
``

What are the possible causes of this problem?
Any advice would be greatly appreciated.

Best regards,
Yuka