Input should be a valid string error

[enes-ak]

I am getting this error when I run the TB-profiler. I checked my fasta file and it seems okay. What can be the problem?

Here is my command:
tb-profiler profile --fasta barcode05.fasta -t 12 -p barcode05 --spoligotype --csv

tb-profiler version: 6.2.1

# tb-profiler error report

* OS: linux
* Program version: 6.2.1
* Database version: {'name': 'tbdb', 'commit': '620fb05', 'Author': 'Jody Phelan <jody.phelan@lshtm.ac.uk>', 'Date': 'Mon Oct 14 22:19:31 2024 +0100'}
* Program call:

{'logging': 'INFO', 'read1': None, 'read2': None, 'bam': None, 'fasta': 'barcode05.fasta', 'vcf': '/home/enes/Desktop/bioinfo_pipelines/tb_pipeline/data/raw_fasta/barcode05/78bc9512-b939-48c7-8c14-ffe53f7902d7.vcf.gz', 'platform': 'illumina', 'db': 'tbdb', 'external_db': None, 'prefix': 'barcode05', 'csv': True, 'txt': False, 'text_template': None, 'docx': False, 'docx_template': None, 'add_columns': None, 'add_mutation_metadata': False, 'dir': '/home/enes/Desktop/bioinfo_pipelines/tb_pipeline/data/raw_fasta/barcode05', 'depth': '0,0', 'af': '0,0.1', 'strand': '0,0', 'sv_depth': '0,10', 'sv_af': '0.5,0.9', 'sv_len': '100000,50000', 'mapper': 'bwa', 'caller': 'freebayes', 'calling_params': None, 'kmer_counter': 'kmc', 'coverage_tool': 'samtools', 'suspect': False, 'spoligotype': True, 'update_phylo': False, 'call_whole_genome': False, 'snp_dist': None, 'snp_diff_db': None, 'snp_diff_no_store': False, 'no_trim': False, 'no_coverage_qc': False, 'no_samclip': False, 'no_delly': False, 'no_lineage': False, 'add_variant_annotations': False, 'threads': 12, 'ram': 2, 'delly_vcf': None, 'supplementary_bam': None, 'no_clean': False, 'temp': '.', 'func': <function main_profile at 0x711ea6ed40d0>, 'software_name': 'tbprofiler', 'version': '6.2.1', 'tmp_prefix': '78bc9512-b939-48c7-8c14-ffe53f7902d7', 'files_prefix': '/home/enes/Desktop/bioinfo_pipelines/tb_pipeline/data/raw_fasta/barcode05/78bc9512-b939-48c7-8c14-ffe53f7902d7', 'conf': {'db-schema-version': '1.0.0', 'snpEff_db': 'Mycobacterium_tuberculosis_h37rv', 'drugs': ['rifampicin', 'isoniazid', 'ethambutol', 'pyrazinamide', 'moxifloxacin', 'levofloxacin', 'bedaquiline', 'delamanid', 'pretomanid', 'linezolid', 'streptomycin', 'amikacin', 'kanamycin', 'capreomycin', 'clofazimine', 'ethionamide', 'para-aminosalicylic_acid', 'cycloserine'], 'tb-profiler-version': '>=6.0.0,<7.0.0', 'version': {'name': 'tbdb', 'commit': '620fb05', 'Author': 'Jody Phelan jody.phelan@lshtm.ac.uk', 'Date': 'Mon Oct 14 22:19:31 2024 +0100'}, 'amplicon': False, 'files': {'ref': 'tbdb.fasta', 'gff': 'tbdb.gff', 'bed': 'tbdb.bed', 'json_db': 'tbdb.dr.json', 'variables': 'tbdb.variables.json', 'spoligotype_spacers': 'tbdb.spoligotype_spacers.txt', 'spoligotype_annotations': 'tbdb.spoligotype_list.csv', 'bedmask': 'tbdb.mask.bed', 'barcode': 'tbdb.barcode.bed', 'rules': 'tbdb.rules.txt'}, 'ref': '/home/enes/miniconda3/envs/tools/share/tbprofiler//tbdb.fasta', 'gff': '/home/enes/miniconda3/envs/tools/share/tbprofiler//tbdb.gff', 'bed': '/home/enes/miniconda3/envs/tools/share/tbprofiler//tbdb.bed', 'variables': {'db-schema-version': '1.0.0', 'snpEff_db': 'Mycobacterium_tuberculosis_h37rv', 'drugs': ['rifampicin', 'isoniazid', 'ethambutol', 'pyrazinamide', 'moxifloxacin', 'levofloxacin', 'bedaquiline', 'delamanid', 'pretomanid', 'linezolid', 'streptomycin', 'amikacin', 'kanamycin', 'capreomycin', 'clofazimine', 'ethionamide', 'para-aminosalicylic_acid', 'cycloserine'], 'tb-profiler-version': '>=6.0.0,<7.0.0', 'version': {'name': 'tbdb', 'commit': '620fb05', 'Author': 'Jody Phelan jody.phelan@lshtm.ac.uk', 'Date': 'Mon Oct 14 22:19:31 2024 +0100'}, 'amplicon': False, 'files': {'ref': 'tbdb.fasta', 'gff': 'tbdb.gff', 'bed': 'tbdb.bed', 'json_db': 'tbdb.dr.json', 'variables': 'tbdb.variables.json', 'spoligotype_spacers': 'tbdb.spoligotype_spacers.txt', 'spoligotype_annotations': 'tbdb.spoligotype_list.csv', 'bedmask': 'tbdb.mask.bed', 'barcode': 'tbdb.barcode.bed', 'rules': 'tbdb.rules.txt'}}, 'spoligotype_spacers': '/home/enes/miniconda3/envs/tools/share/tbprofiler//tbdb.spoligotype_spacers.txt', 'spoligotype_annotations': '/home/enes/miniconda3/envs/tools/share/tbprofiler//tbdb.spoligotype_list.csv', 'bedmask': '/home/enes/miniconda3/envs/tools/share/tbprofiler//tbdb.mask.bed', 'barcode': '/home/enes/miniconda3/envs/tools/share/tbprofiler//tbdb.barcode.bed', 'rules': ['Variant(gene_name=mmpL5,type=lof) inactivates_resistance Variant(gene_name=mmpR5)', 'Variant(gene_name=eis,type=lof) inactivates_resistance Variant(gene_name=eis)'], 'variant_filters': {'depth_hard': 0, 'depth_soft': 0, 'af_hard': 0, 'af_soft': 0.1, 'strand_hard': 0, 'strand_soft': 0, 'sv_depth_hard': 0, 'sv_depth_soft': 10, 'sv_af_hard': 0.5, 'sv_af_soft': 0.9, 'sv_len_hard': 100000, 'sv_len_soft': 50000}}, 'run_delly': True, 'samclip': True, 'coverage_qc': True, 'data_source': 'fasta', 'call_lineage': True, 'paf': '/home/enes/Desktop/bioinfo_pipelines/tb_pipeline/data/raw_fasta/barcode05/78bc9512-b939-48c7-8c14-ffe53f7902d7.paf', 'barcode_snps': None}

## Traceback:

File "/home/enes/miniconda3/envs/tools/bin/tb-profiler", line 587, in
args.func(args)
File "/home/enes/miniconda3/envs/tools/bin/tb-profiler", line 118, in main_profile
spoligotype = tbp.spoligotype(args)
File "/home/enes/miniconda3/envs/tools/lib/python3.10/site-packages/tbprofiler/spoligotyping.py", line 20, in spoligotype
return Spoligotype(**result)
File "/home/enes/miniconda3/envs/tools/lib/python3.10/site-packages/pydantic/main.py", line 214, in init
validated_self = self.pydantic_validator.validate_python(data, self_instance=self)

## Value:

3 validation errors for Spoligotype
family
Input should be a valid string [type=string_type, input_value=None, input_type=NoneType]
For further information visit https://errors.pydantic.dev/2.10/v/string_type
SIT
Input should be a valid string [type=string_type, input_value=None, input_type=NoneType]
For further information visit https://errors.pydantic.dev/2.10/v/string_type
countries
Input should be a valid string [type=string_type, input_value=None, input_type=NoneType]
For further information visit https://errors.pydantic.dev/2.10/v/string_type```