error.converter: unsupported operand type

[loipf]

hi all,

I am trying to annotate a project .vcf file retrieved from GLnexus with OpenCRAVAT. the .bcf file file gets converted to an .vcf file with: bcftools view <bcf_file> | bgzip -c > pvcf_all_glnexus.vcf.gz

oc is installed with conda install open-cravat==2.2.1. if I run this file with oc run -l hg38 -t csv -x pvcf_all_glnexus.vcf.gz for most of the lines it works perfectly but for some I get the following errors in the err log for multiple lines:

SOURCE:error.converter      
LINE:530
INPUT:1	925408	1_925408_TTGGCGCCTGC_T	TTGGCGCCTGC	T	20	MONOALLELIC	AF=0.1;AQ=20	GT:DP:AD:GQ:PL:RNC	./.:0:.,0:1:0,0,0:11	./.:0:.,0:1:0,0,0:11	./.:0:.,0:0:0,0,0:II	./1:2:.,2:3:0,0,0:1.	./.:3:.,0:7:0,0,0:11	./.:5:.,0:13:0,0,0:11	./.:5:.,0:12:0,0,0:11	./.:0:.,0:0:0,0,0:II	./.:4:.,0:9:0,0,0:11	./.:0:.,0:0:0,0,0:II
ERROR:unsupported operand type(s) for +: 'int' and 'NoneType'
#
SOURCE:error.converter      
LINE:705
INPUT:1	976745	1_976745_CG_C	CG	C	17	.	AF=0.5;AQ=17	GT:DP:AD:GQ:PL:RNC	./.:13:.:.:0,0,0:OO	./1:20:.,8:.:0,0,0:O.	1/1:19:3,15:10:13,15,0:..	1/1:23:2,20:12:15,22,0:..	1/1:20:0,18:14:17,35,0:..	./.:10:.:.:0,0,0:OO	1/1:31:4,24:2:5,13,0:..	./1:8:.,4:.:0,0,0:O.	./.:21:15,4:7:0,5,21:II	./.:17:14,3:4:0,1,14:II
ERROR:unsupported operand type(s) for +: 'int' and 'NoneType'

the subset of the input .vcf file looks like this (2. and 5. line are problematic, one line before and after the error is included for comparison) :

##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##GLnexusVersion=v1.2.7-0-g0e74fc4
##GLnexusConfigName=DeepVariant
##GLnexusConfigCRC32C=2857227159
##GLnexusConfig={unifier_config: {drop_filtered: false, min_allele_copy_number: 1, min_AQ1: 10, min_AQ2: 10, min_GQ: 0, max_alleles_per_site: 32, monoallelic_sites_for_lost_alleles: true, preference: common}, genotyper_config: {revise_genotypes: true, min_assumed_allele_frequency: 9.99999975e-05, required_dp: 0, allow_partial_data: true, allele_dp_format: AD, ref_dp_format: MIN_DP, output_residuals: false, more_PL: true, squeeze: false, trim_uncalled_alleles: true, output_format: BCF, liftover_fields: [{orig_names: [MIN_DP, DP], name: DP, description: "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">", type: int, number: basic, default_type: missing, count: 1, combi_method: min, ignore_non_variants: true}, {orig_names: [AD], name: AD, description: "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">", type: int, number: alleles, default_type: zero, count: 0, combi_method: min, ignore_non_variants: false}, {orig_names: [GQ], name: GQ, description: "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">", type: int, number: basic, default_type: missing, count: 1, combi_method: min, ignore_non_variants: true}, {orig_names: [PL], name: PL, description: "##FORMAT=<ID=PL,Number=G,Type=Integer,Description=\"Phred-scaled genotype Likelihoods\">", type: int, number: genotype, default_type: missing, count: 0, combi_method: missing, ignore_non_variants: true}]}}
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency estimate for each alternate allele">
##INFO=<ID=AQ,Number=A,Type=Integer,Description="Allele Quality score reflecting evidence for each alternate allele (Phred scale)">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##FILTER=<ID=MONOALLELIC,Description="Site represents one ALT allele in a region with multiple variants that could not be unified into non-overlapping multi-allelic sites">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=RNC,Number=2,Type=Character,Description="Reason for No Call in GT: . = n/a, M = Missing data, P = Partial data, I = gVCF input site is non-called, D = insufficient Depth of coverage, - = unrepresentable overlapping deletion, L = Lost/unrepresentable allele (other than deletion), U = multiple Unphased variants present, O = multiple Overlapping variants present, 1 = site is Monoallelic, no assertion about presence of REF or ALT allele">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Phred-scaled genotype Likelihoods">
##contig=<ID=1,length=248956422>
##contig=<ID=10,length=133797422>
##contig=<ID=11,length=135086622>
##contig=<ID=12,length=133275309>
##contig=<ID=13,length=114364328>
##contig=<ID=14,length=107043718>
##contig=<ID=15,length=101991189>
##contig=<ID=16,length=90338345>
##contig=<ID=17,length=83257441>
##contig=<ID=18,length=80373285>
##contig=<ID=19,length=58617616>
##contig=<ID=2,length=242193529>
##contig=<ID=20,length=64444167>
##contig=<ID=21,length=46709983>
##contig=<ID=22,length=50818468>
##contig=<ID=3,length=198295559>
##contig=<ID=4,length=190214555>
##contig=<ID=5,length=181538259>
##contig=<ID=6,length=170805979>
##contig=<ID=7,length=159345973>
##contig=<ID=8,length=145138636>
##contig=<ID=9,length=138394717>
##contig=<ID=MT,length=16569>
##contig=<ID=X,length=156040895>
##contig=<ID=Y,length=57227415>
##bcftools_viewVersion=1.11+htslib-1.11
##bcftools_viewCommand=view pvcf_all_glnexus.bcf; Date=Thu Jan 14 22:27:57 2021
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	sample_1	sample_2	sample_3	sample_4	sample_5	sample_6	sample_7	sample_8	sample_9	sample_10
1	925408	1_925408_TTGG_T	TTGG	T	36	.	AF=0.4;AQ=36	GT:DP:AD:GQ:PL:RNC	0/0:0:0,0:1:0,3,29:..	0/0:0:0,0:1:0,3,29:..	./.:0:0,0:0:0,0,0:II	./.:2:0,0:7:0,0,0:--	1/1:3:0,3:3:25,7,0:..	1/1:5:0,5:9:32,13,0:..	1/1:5:0,5:9:34,13,0:..	./.:0:0,0:0:0,0,0:II	1/1:4:0,4:8:36,12,0:..	./.:0:0,0:0:0,0,0:II
1	925408	1_925408_TTGGCGCCTGC_T	TTGGCGCCTGC	T	20	MONOALLELIC	AF=0.1;AQ=20	GT:DP:AD:GQ:PL:RNC	./.:0:.,0:1:0,0,0:11	./.:0:.,0:1:0,0,0:11	./.:0:.,0:0:0,0,0:II	./1:2:.,2:3:0,0,0:1.	./.:3:.,0:7:0,0,0:11	./.:5:.,0:13:0,0,0:11	./.:5:.,0:12:0,0,0:11	./.:0:.,0:0:0,0,0:II	./.:4:.,0:9:0,0,0:11	./.:0:.,0:0:0,0,0:II
1	925412	1_925412_CGCCTGCG_C	CGCCTGCG	C	32	.	AF=0.4;AQ=32	GT:DP:AD:GQ:PL:RNC	0/0:0:0,0:1:0,3,29:..	0/0:0:0,0:1:0,3,29:..	./.:0:0,0:0:0,0,0:II	./.:2:.:.:0,0,0:UU	1/1:3:0,3:3:24,7,0:..	1/1:5:0,5:9:30,13,0:..	1/1:5:0,5:8:32,12,0:..	./.:0:0,0:0:0,0,0:II	1/1:4:0,4:5:31,9,0:..	./.:0:0,0:0:0,3,29:II
1	976723	1_976723_G_A	G	A	39	.	AF=0.75;AQ=39	GT:DP:AD:GQ:PL:RNC	0/1:29:16,10:22:21,0,40:..	0/1:26:12,14:24:27,0,26:..	1/1:23:0,21:29:30,46,0:..	1/1:31:0,31:38:39,57,0:..	1/1:29:0,29:37:38,58,0:..	0/1:34:14,19:28:29,0,32:..	1/1:45:0,43:28:29,46,0:..	0/1:11:5,6:27:27,0,41:..	1/1:37:1,33:27:28,31,0:..	0/1:29:21,8:16:16,0,26:..
1	976745	1_976745_CG_C	CG	C	17	.	AF=0.5;AQ=17	GT:DP:AD:GQ:PL:RNC	./.:13:.:.:0,0,0:OO	./1:20:.,8:.:0,0,0:O.	1/1:19:3,15:10:13,15,0:..	1/1:23:2,20:12:15,22,0:..	1/1:20:0,18:14:17,35,0:..	./.:10:.:.:0,0,0:OO	1/1:31:4,24:2:5,13,0:..	./1:8:.,4:.:0,0,0:O.	./.:21:15,4:7:0,5,21:II	./.:17:14,3:4:0,1,14:II
1	976747	1_976747_C_A	C	A	23	.	AF=0.45;AQ=23	GT:DP:AD:GQ:PL:RNC	./.:9:3,6:10:0,9,20:II	./.:10:.:.:0,0,0:OO	1/1:17:2,15:14:17,30,0:..	1/1:22:2,20:14:17,32,0:..	1/1:18:2,16:20:23,39,0:..	./.:10:.:.:0,0,0:OO	1/1:25:1,24:6:9,28,0:..	./.:3:.:.:0,0,0:OO	0/1:19:15,4:10:9,0,31:..	./.:4:1,3:12:0,13,16:II

I cant really see any obvious difference between these lines. can you help me if this error is already in the .vcf file and OpenCRAVAT is supposed to skip these cases or just a bug ? Thank you in advance !

[kmoad]

Well look into this and get back to you. Thanks a lot for the detail here.