Mismatching csv output and text alignment output

[buchanri]

Hello! I'm running into a problem where the csv and text alignment file that krisp_vcf gives as outputs, are not agreeing with each other. They agree with the group region but not the chromosome.

After running krisp via this command:
krisp_vcf /nfs5/BPP/Grunwald_Lab/home/buchanri/crispr_dx_pinf_lineages/data/metadata/not_specific_USEU_metasata.csv /nfs5/BPP/Grunwald_Lab/home/buchanri/crispr_dx_pinf_lineages/data/ref_genome/2023-06-23_Pinf1306_UCR_assembly.fna --vcf /nfs5/BPP/Grunwald_Lab/home/buchanri/crispr_dx_pinf_lineages/results/merged_EUandUS/merged_vcf_with_T2Tref_us_and_eu_lineages --vcf --cores 8 --groups EU US --out_csv "/nfs5/BPP/Grunwald_Lab/home/buchanri/crispr_dx_pinf_lineages/results/merged_EUandUS/krisp_gatk/T2T/USEU_krisp_all.csv" --out_align "/nfs5/BPP/Grunwald_Lab/home/buchanri/crispr_dx_pinf_lineages/results/merged_EUandUS/krisp_gatk/T2T/USEU_krisp_all_out.txt" --log "/nfs5/BPP/Grunwald_Lab/home/buchanri/crispr_dx_pinf_lineages/results/merged_EUandUS/krisp_gatk/T2T/log.USEU" --amp_size 80 140 --min_samples 12 --min_reads 10 --min_samp_prop 0.97 --min_map_qual 33 --min_geno_qual 33

For one of the csv outputs I get:
CM047791.1:20306902-20306987,US,CM047791.1,1,0,20306887,20307058,20306932,20306959,20306902,20306931,
20306960,20306987,,aagccacttcgttcg,ttgatgaagtcccgtccaactcgagTgatg,,cttccagcacagaTaaggactggaccac,,gtctgaatgtgtagttccggtcaagaac,caaggccagtgtggttcctgctgggccttcgcagctgtggcagctctcgagagcgccatttgtctgtctgg,86,12.770494778911825,ttgatgaagtcccgtccaactcgagTgatg,gttcttgaccggaactacacattcagac,7.446905935403322,5.323588843508503,67.94690593540332,63.8235888435085,50.0,46.42857142857143,20.849039674039034,9.463168145811721,17.26840787235949,0.0,0.0,39.68132369827515,3.07,3.51,0.0,2.5861112917269793

But in the alignment text file it shows the same region but different chromosome:
## CM047790.1:20306902-20306987 is diagnostic for US

After viewing these in IGV the csv file output shows the correct chromosome for the variant site and not the alignment file one. This also happened in multiple other runs but using different parameters.