is this software alive?

[thedam]

Hey, are there any clear instructions how to run the software? After digging in Python files I built such command: charger --input tests/examples/10.1056_NEJMoa1508054_S4_AD_vep85.sorted.vcf.gz --pathogenic-variant tests/examples/annotations/grch37_pathogenic_variants.vcf.gz --inheritance-gene-table tests/examples/annotations/inheritance_gene_table.tsv.gz --PP2-gene-list tests/examples/annotations/pp2_gene_list.txt.gz --clinvar-table tests/examples/annotations/clinvar_chrom_22_only.b37.tsv.gz --output out.tsv

however I get no output file...

I only get messages like:

charger --input tests/examples/10.1056_NEJMoa1508054_S4_AD_vep85.sorted.vcf.gz --pathogenic-variant tests/examples/annotations/grch37_pathogenic_variants.vcf.gz --inheritance-gene-table tests/examples/annotations/inheritance_gene_table.tsv.gz --PP2-gene-list tests/examples/annotations/pp2_gene_list.txt.gz --clinvar-table tests/examples/annotations/clinvar_chrom_22_only.b37.tsv.gz --output out.tsv INFO | Running CharGer v0.6.0b1 with parameters: --input tests/examples/10.1056_NEJMoa1508054_S4_AD_vep85.sorted.vcf.gz --pathogenic-variant tests/examples/annotations/grch37_pathogenic_variants.vcf.gz --inheritance-gene-table tests/examples/annotations/inheritance_gene_table.tsv.gz --PP2-gene-list tests/examples/annotations/pp2_gene_list.txt.gz --clinvar-table tests/examples/annotations/clinvar_chrom_22_only.b37.tsv.gz --output out.tsv INFO | Validate the given config DEBUG | Given config: CharGerConfig(input=PosixPath('tests/examples/10.1056_NEJMoa1508054_S4_AD_vep85.sorted.vcf.gz'), output=PosixPath('out.tsv'), hotspot3d_cluster=None, pathogenic_variant=PosixPath('tests/examples/annotations/grch37_pathogenic_variants.vcf.gz'), override_variant_info=False, include_vcf_details=False, clinvar_table=PosixPath('tests/examples/annotations/clinvar_chrom_22_only.b37.tsv.gz'), rare_threshold=0.0005, common_threshold=0.005, acmg_module_scores={'PVS1': 8, 'PS1': 7, 'PS2': 4, 'PS3': 4, 'PS4': 4, 'PM1': 2, 'PM2': 2, 'PM3': 2, 'PM4': 2, 'PM5': 2, 'PM6': 2, 'PP1': 1, 'PP2': 1, 'PP3': 1, 'PP4': 1, 'PP5': 1, 'BP1': -1, 'BP2': -1, 'BP3': -1, 'BP4': -1, 'BP5': -1, 'BP6': -1, 'BP7': -1, 'BS1': -4, 'BS2': -4, 'BS3': -4, 'BS4': -4, 'BA1': -8}, charger_module_scores={'PSC1': 4, 'PMC1': 2, 'PPC1': 1, 'PPC2': 1, 'BMC1': -2, 'BSC1': -6}, min_pathogenic_score=9, min_likely_pathogenic_score=5, max_likely_benign_score=-4, max_benign_score=-8, disease_specific=False, inheritance_gene_table=PosixPath('tests/examples/annotations/inheritance_gene_table.tsv.gz'), PP2_gene_list=PosixPath('tests/examples/annotations/pp2_gene_list.txt.gz'), BP1_gene_list=None) INFO | Read input VCF from tests/examples/10.1056_NEJMoa1508054_S4_AD_vep85.sorted.vcf.gz DEBUG | VEP version 85 with CSQ format [62 fields]: Allele,Consequence,IMPACT,SYMBOL,Gene,Feature_type,Feature,BIOTYPE,EXON,INTRON,HGVSc,HGVSp,cDNA_position,CDS_position,Protein_position,Amino_acids,Codons,Existing_variation,DISTANCE,STRAND,FLAGS,VARIANT_CLASS,SYMBOL_SOURCE,HGNC_ID,CANONICAL,TSL,APPRIS,CCDS,ENSP,SWISSPROT,TREMBL,UNIPARC,GENE_PHENO,SIFT,PolyPhen,DOMAINS,HGVS_OFFSET,GMAF,AFR_MAF,AMR_MAF,EAS_MAF,EUR_MAF,SAS_MAF,AA_MAF,EA_MAF,ExAC_MAF,ExAC_Adj_MAF,ExAC_AFR_MAF,ExAC_AMR_MAF,ExAC_EAS_MAF,ExAC_FIN_MAF,ExAC_NFE_MAF,ExAC_OTH_MAF,ExAC_SAS_MAF,CLIN_SIG,SOMATIC,PHENO,PUBMED,MOTIF_NAME,MOTIF_POS,HIGH_INF_POS,MOTIF_SCORE_CHANGE SUCCESS | Read total 550 variants from the input VCF INFO | Read pathogenic VCF from tests/examples/annotations/grch37_pathogenic_variants.vcf.gz DEBUG | VEP version 84 with CSQ format [52 fields]: Allele,Consequence,IMPACT,SYMBOL,Gene,Feature_type,Feature,BIOTYPE,EXON,INTRON,HGVSc,HGVSp,cDNA_position,CDS_position,Protein_position,Amino_acids,Codons,Existing_variation,DISTANCE,STRAND,FLAGS,SYMBOL_SOURCE,HGNC_ID,TSL,APPRIS,SIFT,PolyPhen,GMAF,AFR_MAF,AMR_MAF,EAS_MAF,EUR_MAF,SAS_MAF,AA_MAF,EA_MAF,ExAC_MAF,ExAC_Adj_MAF,ExAC_AFR_MAF,ExAC_AMR_MAF,ExAC_EAS_MAF,ExAC_FIN_MAF,ExAC_NFE_MAF,ExAC_OTH_MAF,ExAC_SAS_MAF,CLIN_SIG,SOMATIC,PHENO,PUBMED,MOTIF_NAME,MOTIF_POS,HIGH_INF_POS,MOTIF_SCORE_CHANGE [W::vcf_parse] Contig '10' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '13' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '5' is not defined in the header. (Quick workaround: index the file with tabix.) INFO | Read total 1,819 pathogenic variants from the VCF INFO | Disable CharGer PMC1/PPC2 modules when inheritance gene table is provided INFO | Read inheritance gene table from tests/examples/annotations/inheritance_gene_table.tsv.gz INFO | Loaded inheritance mode of 152 genes INFO | Read PP2 gene list from tests/examples/annotations/pp2_gene_list.txt.gz INFO | Marked 152 genes for PP2 WARNING | CharGer cannot make BP1 calls without the given gene list. Disable BP1 module INFO | Match input variants with ClinVar table at tests/examples/annotations/clinvar_chrom_22_only.b37.tsv.gz SUCCESS | Matched 2 out of 550 input variants to a ClinVar record INFO | Run all ACMG modules INFO | Running PVS1 module INFO | Running PM4 module INFO | Run all CharGer modules INFO | Running PSC1 module INFO | Skipped PMC1 module INFO | Running PPC1 module INFO | Skipped PPC2 module

Are you planning to maintain this program?