TypeError: unsupported operand type(s) for +: 'int' and 'NoneType'

[Janehol]

Hi! I am trying to use the krisp_vcf command but I am running into the below error message over and over again no matter how I alter my VCF file.

$ krisp_vcf krisp_metadata.csv Race_1.masked.fa --vcf SNPs_exclude_nonetype_merged_DNAs.vcf.gz --groups NA2 NA3 NA4 NA5 NA6 OTHR --out_csv krisp_SNPs_diagnostic_variants.csv
Traceback (most recent call last):
File "/home/holmesj/data/miniconda3/envs/py311/bin/krisp_vcf", line 8, in
sys.exit(main())
^^^^^^
File "/home/holmesj/genomics/2-MISC-BY-USER/Janesse/krisp/src/krisp/krisp_vcf/krisp_vcf.py", line 1393, in main
run_all()
File "/home/holmesj/genomics/2-MISC-BY-USER/Janesse/krisp/src/krisp/krisp_vcf/krisp_vcf.py", line 1383, in run_all
for result in report_diag_region(args.vcf, contig, groups, reference, args,
File "/home/holmesj/genomics/2-MISC-BY-USER/Janesse/krisp/src/krisp/krisp_vcf/krisp_vcf.py", line 1193, in report_diag_region
for region in find_diag_region(variants, groups, reference, **kwargs):
File "/home/holmesj/genomics/2-MISC-BY-USER/Janesse/krisp/src/krisp/krisp_vcf/krisp_vcf.py", line 791, in find_diag_region
for region in windower:
File "/home/holmesj/genomics/2-MISC-BY-USER/Janesse/krisp/src/krisp/krisp_vcf/krisp_vcf.py", line 204, in sliding_window
for index, variant in enumerate(variants):
File "/home/holmesj/genomics/2-MISC-BY-USER/Janesse/krisp/src/krisp/krisp_vcf/find_diag_var.py", line 196, in from_vcf
out = cls(var, groups, check_groups=False, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/holmesj/genomics/2-MISC-BY-USER/Janesse/krisp/src/krisp/krisp_vcf/find_diag_var.py", line 169, in init
self.allele_counts = self._allele_counts(variant, self.groups,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/holmesj/genomics/2-MISC-BY-USER/Janesse/krisp/src/krisp/krisp_vcf/find_diag_var.py", line 304, in _allele_counts
output[group] = GroupedVariant._count_genotypes(variant,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/holmesj/genomics/2-MISC-BY-USER/Janesse/krisp/src/krisp/krisp_vcf/find_diag_var.py", line 256, in _count_genotypes
min_depth = sum(data['AD']) * min_freq
^^^^^^^^^^^^^^^
TypeError: unsupported operand type(s) for +: 'int' and 'NoneType'

According to Google, "The NoneType object is a special type in Python that represents the absence of a value. In other words, NoneType is the type for the None object, which is an object that contains no value or defines a null value. It is used to indicate that a variable or expression does not have a value or has an undefined value."

So, I tried to filter out any undefined/missing data with the following command (I specified to keep MQ values as I received a previous error message saying "KeyError: 'invalid FORMAT: MQ"):

$vcftools --gzvcf SNPs_filtered_merged_DNAs.vcf.gz --max-missing 1.00 --recode --recode-INFO MQ --stdout | bgzip -c > SNPs_exclude_nonetype_merged_DNAs.vcf.gz

Even after the data is filtered, I still keep getting the "TypeError: unsupported operand type(s) for +: 'int' and 'NoneType'" message whenever I use the above krisp_vcf command. I am at a loss for how to fix this error. Can anyone provide some advice on what I am doing wrong?