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jodyphelan / TBProfiler

Profiling tool for Mycobacterium tuberculosis to detect ressistance and strain type from WGS data
GNU General Public License v3.0
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fa2spoligotype() got an unexpected keyword argument 'kmer_counter' #316

Closed juliofdiaz closed 2 months ago

juliofdiaz commented 7 months ago

Hello,

I am trying to use Spolpred2, which I gather is implemented in tb-profiler, but I run into an error when the input is a fasta file

$ tb-profiler spoligotype --fasta $AMR_PRJS/assemblies/mtuberculosis/production/fasta/DRR290121.fasta 
[11:34:05] INFO     Using ref file: /well/aanensen/users/afk289/conda/skylake/envs/tbprofiler/share/tbprofiler//tbdb.fasta                                  db.py:594
           INFO     Using gff file: /well/aanensen/users/afk289/conda/skylake/envs/tbprofiler/share/tbprofiler//tbdb.gff                                    db.py:594
           INFO     Using bed file: /well/aanensen/users/afk289/conda/skylake/envs/tbprofiler/share/tbprofiler//tbdb.bed                                    db.py:594
           INFO     Using version file: /well/aanensen/users/afk289/conda/skylake/envs/tbprofiler/share/tbprofiler//tbdb.version.json                       db.py:594
           INFO     Using json_db file: /well/aanensen/users/afk289/conda/skylake/envs/tbprofiler/share/tbprofiler//tbdb.dr.json                            db.py:594
           INFO     Using variables file: /well/aanensen/users/afk289/conda/skylake/envs/tbprofiler/share/tbprofiler//tbdb.variables.json                   db.py:594
           INFO     Using spoligotype_spacers file:                                                                                                         db.py:594
                    /well/aanensen/users/afk289/conda/skylake/envs/tbprofiler/share/tbprofiler//tbdb.spoligotype_spacers.txt                                         
           INFO     Using spoligotype_annotations file:                                                                                                     db.py:594
                    /well/aanensen/users/afk289/conda/skylake/envs/tbprofiler/share/tbprofiler//tbdb.spoligotype_list.csv                                            
           INFO     Using bedmask file: /well/aanensen/users/afk289/conda/skylake/envs/tbprofiler/share/tbprofiler//tbdb.mask.bed                           db.py:594
           INFO     Using barcode file: /well/aanensen/users/afk289/conda/skylake/envs/tbprofiler/share/tbprofiler//tbdb.barcode.bed                        db.py:594
Traceback (most recent call last):
  File "/well/aanensen/users/afk289/conda/skylake/envs/tbprofiler/bin/tb-profiler", line 562, in <module>
    args.func(args)
  File "/well/aanensen/users/afk289/conda/skylake/envs/tbprofiler/bin/tb-profiler", line 244, in main_spoligotype
    "spoligotype":tbp.spoligotype(args),
  File "/well/aanensen/users/afk289/conda/skylake/envs/tbprofiler/lib/python3.10/site-packages/tbprofiler/spoligotyping.py", line 11, in spoligotype
    result = fa2spoligotype(args.fasta,args.files_prefix,args.conf,threads=args.threads,max_mem=args.ram,kmer_counter=args.kmer_counter)
TypeError: fa2spoligotype() got an unexpected keyword argument 'kmer_counter'
Cleaning up after failed run
           ERROR                                                                                                                                       tb-profiler:58

                    ################################# ERROR #######################################                                                                  

                    This run has failed. Please check all arguments and make sure all input files                                                                    
                    exist. If no solution is found, please open up an issue at                                                                                       
                    https://github.com/jodyphelan/TBProfiler/issues/new and paste or attach the                                                                      
                    contents of the error log (tbprofiler.errlog.txt)                                                                                                

                    ###############################################################################

When I look at this definition of fa2spoligotype , I can see that it doesn't need the kmer_counter argument. On the other hand the function spoligotype does feed the kmer_counter argument.

I installed tb-profiler with conda as described, and I am attaching the tbprofiler.errlog.txt:

# tb-profiler error report

* OS: linux
* Program version: 5.0.1
* Database version: {'name': 'tbdb', 'commit': 'c2fb9a2', 'Author': 'jodyphelan <jody.phelan@lshtm.ac.uk>', 'Date': 'Tue Oct 4 11:40:15 2022 +0100'}
* Program call:

{'logging': 'INFO', 'read1': None, 'read2': None, 'bam': None, 'fasta': '/well/aanensen/projects/amr-landscape/assemblies/mtuberculosis/production/fasta/DRR290121.fasta', 'prefix': 'tbprofiler', 'txt': False, 'csv': False, 'docx': False, 'text_template': None, 'kmer_counter': 'kmc', 'platform': 'illumina', 'db': 'tbdb', 'external_db': None, 'dir': '/gpfs3/users/aanensen/afk289', 'no_clean': False, 'threads': 1, 'ram': 2, 'temp': '.', 'func': <function main_spoligotype at 0x7fbdea69fc70>, 'software_name': 'tbprofiler', 'tmp_prefix': '721855c7-7052-4409-a8fb-ca67ff24a299', 'files_prefix': '/gpfs3/users/aanensen/afk289/721855c7-7052-4409-a8fb-ca67ff24a299', 'conf': {'snpEff_db': 'Mycobacterium_tuberculosis_h37rv', 'drugs': ['rifampicin', 'isoniazid', 'ethambutol', 'pyrazinamide', 'streptomycin', 'fluoroquinolones', 'moxifloxacin', 'ofloxacin', 'levofloxacin', 'ciprofloxacin', 'aminoglycosides', 'amikacin', 'capreomycin', 'kanamycin', 'cycloserine', 'ethionamide', 'clofazimine', 'para-aminosalicylic_acid', 'delamanid', 'bedaquiline', 'linezolid'], 'amplicon': False, 'files': {'ref': 'tbdb.fasta', 'gff': 'tbdb.gff', 'bed': 'tbdb.bed', 'version': 'tbdb.version.json', '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'}, 'ref': '/well/aanensen/users/afk289/conda/skylake/envs/tbprofiler/share/tbprofiler//tbdb.fasta', 'gff': '/well/aanensen/users/afk289/conda/skylake/envs/tbprofiler/share/tbprofiler//tbdb.gff', 'bed': '/well/aanensen/users/afk289/conda/skylake/envs/tbprofiler/share/tbprofiler//tbdb.bed', 'version': {'name': 'tbdb', 'commit': 'c2fb9a2', 'Author': 'jodyphelan <jody.phelan@lshtm.ac.uk>', 'Date': 'Tue Oct 4 11:40:15 2022 +0100'}, 'variables': {'snpEff_db': 'Mycobacterium_tuberculosis_h37rv', 'drugs': ['rifampicin', 'isoniazid', 'ethambutol', 'pyrazinamide', 'streptomycin', 'fluoroquinolones', 'moxifloxacin', 'ofloxacin', 'levofloxacin', 'ciprofloxacin', 'aminoglycosides', 'amikacin', 'capreomycin', 'kanamycin', 'cycloserine', 'ethionamide', 'clofazimine', 'para-aminosalicylic_acid', 'delamanid', 'bedaquiline', 'linezolid'], 'amplicon': False, 'files': {'ref': 'tbdb.fasta', 'gff': 'tbdb.gff', 'bed': 'tbdb.bed', 'version': 'tbdb.version.json', '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'}}, 'spoligotype_spacers': '/well/aanensen/users/afk289/conda/skylake/envs/tbprofiler/share/tbprofiler//tbdb.spoligotype_spacers.txt', 'spoligotype_annotations': '/well/aanensen/users/afk289/conda/skylake/envs/tbprofiler/share/tbprofiler//tbdb.spoligotype_list.csv', 'bedmask': '/well/aanensen/users/afk289/conda/skylake/envs/tbprofiler/share/tbprofiler//tbdb.mask.bed', 'barcode': '/well/aanensen/users/afk289/conda/skylake/envs/tbprofiler/share/tbprofiler//tbdb.barcode.bed'}}

## Traceback:

  File "/well/aanensen/users/afk289/conda/skylake/envs/tbprofiler/bin/tb-profiler", line 562, in <module>
    args.func(args)
  File "/well/aanensen/users/afk289/conda/skylake/envs/tbprofiler/bin/tb-profiler", line 244, in main_spoligotype
    "spoligotype":tbp.spoligotype(args),
  File "/well/aanensen/users/afk289/conda/skylake/envs/tbprofiler/lib/python3.10/site-packages/tbprofiler/spoligotyping.py", line 11, in spoligotype
    result = fa2spoligotype(args.fasta,args.files_prefix,args.conf,threads=args.threads,max_mem=args.ram,kmer_counter=args.kmer_counter)

## Value:

fa2spoligotype() got an unexpected keyword argument 'kmer_counter'

Thanks for your help!

jodyphelan commented 7 months ago

Hi @juliofdiaz

Looks like you found a bug. I'll get that fixed asap!

jodyphelan commented 2 months ago

Closing this now as the issue should be fixed