Overide default db Annovar

[zoeward-nz]

Hi,
I have just downloaded the latest version of Annovar I'm trying to run Cancervar with a config file using:

$ python ./CancerVar.py -c ./CancerVar/my.confi.ini -i my.sample.avinput -o my.sample.hg38_multianno.txt

$ cat my.confi.ini

[CancerVar]
buildver = hg38
# hg38
#inputfile =
inputfile_type = AVinput
database_cancervar = ./cancervardb
# the database location/dir for Intervar
lof_genes = %(database_cancervar)s/LOF.genes.exac_me_cancers
mim2gene = %(database_cancervar)s/mim2gene.txt
mim_pheno = %(database_cancervar)s/mim_pheno.txt
mim_orpha = %(database_cancervar)s/mim_orpha.txt
orpha = %(database_cancervar)s/orpha.txt
knowngenecanonical = %(database_cancervar)s/knownGeneCanonical.txt
exclude_snps = %(database_cancervar)s/ext.variants
cancervar_markers=%(database_cancervar)s/cancervar.out.txt
cancer_pathway=%(database_cancervar)s/cancers_genes.list_kegg.txt
cancers_genes=%(database_cancervar)s/cancer_census.genes
cancers_types=%(database_cancervar)s/cancervar.cancer.types
evidence_file = None
# add your own Evidence file for each Variant:
# evidence file as tab-delimited,format like this:
# Chr Pos Ref_allele Alt_allele  Evidence_list
disorder_cutoff = 0.01
#Allele frequency is greater than expected for disorder
[CancerVar_Bool]
onetranscript = TRUE
# TRUE or FALSE: print out only one transcript for exonic variants (default: FALSE/all transcripts)
otherinfo = TRUE
# TRUE or FALSE: print out otherinfo (information in fifth column in queryfile,default: TRUE)
# We want use the fifth column to provide the cancer types,
# this option only perform well with AVinput file,and the other information only can be put in the fifth column.  The information in >5th column will be lost.
# When input as  VCF or VCF_m files with otherinfo option, only het/hom will be kept, depth and qual will be lost, the cancer type should be provide by command option.
#When running on Nesi this is the path for the perl scripts after the module is loaded
[Annovar]
convert2annovar = ./annovar/convert2annovar.pl
#convert input file to annovar format
table_annovar = ./annovar/table_annovar.pl
#
#annotate_variation= ./annovar/annotate_variation.pl
#
database_locat = ./my.hg38.db/
# the database location/dir from annnovar  check if database file exists
database_names = refGeneWithVer gnomad312_genome dbnsfp42a cosmic91 icgc28
# specify the database_names from ANNOVAR or UCSC
[Other]
current_version = CancerVar_20230105
# pipeline version
public_dev = https://github.com/WGLab/CancerVar/releases

So I only want to annotate with refGeneWithVer gnomad312_genome dbnsfp42a cosmic91 icgc28

But I get the error:

Notice: Your command of CancerVar is ['./CancerVar.py', '-c', './CancerVar/my.confi.ini', '-i', 'my.sample.avinput', '-o', 'my.sample.hg38_multianno.txt']
Warning: Your specified evidence file [ None ], the analysis will take your additional evidence.
INFO: The options are {'buildver': 'hg38', 'inputfile_type': 'AVinput', 'database_cancervar': './cancervardb', 'lof_genes': './cancervardb/LOF.genes.exac_me_cancers', 'mim2gene': './cancervardb/mim2gene.txt', 'mim_pheno': './cancervardb/mim_pheno.txt', 'mim_orpha': './cancervardb/mim_orpha.txt', 'orpha': './cancervardb/orpha.txt', 'knowngenecanonical': './cancervardb/knownGeneCanonical.txt', 'exclude_snps': './cancervardb/ext.variants.hg38', 'cancervar_markers': './cancervardb/cancervar.out.txt', 'cancer_pathway': './cancervardb/cancers_genes.list_kegg.txt', 'cancers_genes': './cancervardb/cancer_census.genes', 'cancers_types': './cancervardb/cancervar.cancer.types', 'evidence_file': 'None', 'disorder_cutoff': '0.01', 'onetranscript': 'TRUE', 'otherinfo': 'TRUE', 'convert2annovar': ./annovar/convert2annovar.pl', 'table_annovar': './annovar/table_annovar.pl', 'annotate_variation': './annovar/annotate_variation.pl', 'database_locat': './my.hg38.db/', 'database_names': 'refGeneWithVer gnomad312_genome dbnsfp42a cosmic91 icgc28', 'current_version': 'CancerVar_20230105', 'public_dev': 'https://github.com/WGLab/CancerVar/releases', 'inputfile': 'my.sample.avinput', 'outfile': 'my.sample.hg38_multianno.txt'}
Warning: the folder of ./my.hg38.db is already created!
**perl ./annovar/table_annovar.pl my.sample.avinput ./my.hg38.db/ -buildver hg38 -remove -out my.sample.hg38_multianno.txt -protocol refGene,ensGene,knownGene,esp6500siv2_all,1000g2015aug_all,exac03,avsnp147,dbnsfp30a,dbscsnv11,dbnsfp31a_interpro,clinvar_20190305,cosmic91,icgc28,gnomad_genome  -operation  g,g,g,f,f,f,f,f,f,f,f,f,f,f  -nastring . --otherinfo --onetranscript**
NOTICE: the --polish argument is set ON automatically (use --nopolish to change this behavior)
Error: the required database file ./my.hg38.db/hg38_refGene.txt does not exist.
Warning: The CancerVar seems not run correctly, please check your inputs , options and configure file!
ERROR: The CancerVar did not find the annotation result file from ANNOVAR!
ERROR: The name of annotation result file should be like MEL0013T1_index14/vcf/MEL0013T1_index14.hg38_multianno.txt*.hg38_multianno.txt

Is there a way to override the 'default' options of Annovar and only annotate with refGeneWithVer gnomad312_genome dbnsfp42a cosmic91 icgc28????