No results from get_sequence_type

[VoronDM]

I download MLST database by download_mlst_databases and make export MLST_DATABASES=/export/data/user/MLSTdb

(base) [user@bigmem01 STRP-2020]$ get_sequence_type -a
Achromobacter spp
Acinetobacter baumannii 1
Acinetobacter baumannii 2
Aeromonas spp
Aggregatibacter actinomycetemcomitans
Anaplasma phagocytophilum
Arcobacter spp
Aspergillus fumigatus
Bacillus cereus
Bacillus licheniformis
Bacillus subtilis
Bartonella bacilliformis
Bartonella henselae
Bartonella washoensis
Bordetella spp
Borrelia spp
Brachyspira hampsonii
Brachyspira hyodysenteriae
Brachyspira intermedia
Brachyspira pilosicoli
Brachyspira spp
Brucella spp
Burkholderia cepacia complex
Burkholderia pseudomallei
Campylobacter concisus curvus
Campylobacter fetus
Campylobacter helveticus
Campylobacter hyointestinalis
Campylobacter insulaenigrae
Campylobacter jejuni
Campylobacter lanienae
Campylobacter lari
Campylobacter sputorum
Campylobacter upsaliensis
Candida albicans
Candida glabrata
Candida krusei
Candida tropicalis
Candidatus Liberibacter solanacearum
Carnobacterium maltaromaticum
Chlamydiales spp
Citrobacter freundii
Clonorchis sinensis
Clostridioides difficile
Clostridium botulinum
Clostridium perfringens
Clostridium septicum
Corynebacterium diphtheriae
Cronobacter spp
Dichelobacter nodosus
Edwardsiella spp
Enterobacter cloacae
Enterococcus faecalis
Enterococcus faecium
Escherichia coli 1
Escherichia coli 2
Flavobacterium psychrophilum
Gallibacterium anatis
Geotrichum spp
Glaesserella parasuis
Haemophilus influenzae
Helicobacter cinaedi
Helicobacter pylori
Helicobacter suis
Kingella kingae
Klebsiella aerogenes
Klebsiella oxytoca
Klebsiella pneumoniae
Kudoa septempunctata
Lactobacillus salivarius
Leptospira spp
Leptospira spp  2
Leptospira spp  3
Listeria monocytogenes
Macrococcus canis
Macrococcus caseolyticus
Mannheimia haemolytica
Melissococcus plutonius
Moraxella catarrhalis
Mycobacteria spp
Mycobacterium abscessus
Mycobacterium massiliense
Mycoplasma agalactiae
Mycoplasma bovis
Mycoplasma flocculare
Mycoplasma gallisepticum 1
Mycoplasma gallisepticum 2
Mycoplasma hominis
Mycoplasma hyopneumoniae
Mycoplasma hyorhinis
Mycoplasma iowae
Mycoplasma pneumoniae
Mycoplasma synoviae
Neisseria spp
Orientia tsutsugamushi
Ornithobacterium rhinotracheale
Paenibacillus larvae
Pasteurella multocida 1
Pasteurella multocida 2
Photobacterium damselae
Piscirickettsia salmonis
Porphyromonas gingivalis
Propionibacterium acnes
Pseudomonas aeruginosa
Pseudomonas fluorescens
Pseudomonas putida
Rhodococcus spp
Riemerella anatipestifer
Salmonella enterica
Saprolegnia parasitica
Shewanella spp
Sinorhizobium spp
Staphylococcus aureus
Staphylococcus chromogenes
Staphylococcus epidermidis
Staphylococcus haemolyticus
Staphylococcus hominis
Staphylococcus lugdunensis
Staphylococcus pseudintermedius
Stenotrophomonas maltophilia
Streptococcus agalactiae
Streptococcus bovis equinus complex  SBSEC
Streptococcus canis
Streptococcus dysgalactiae equisimilis
Streptococcus gallolyticus
Streptococcus oralis
Streptococcus pneumoniae
Streptococcus pyogenes
Streptococcus suis
Streptococcus thermophilus
Streptococcus thermophilus 2
Streptococcus uberis
Streptococcus zooepidemicus
Streptomyces spp
Taylorella spp
Tenacibaculum spp
Treponema pallidum
Trichomonas vaginalis
Ureaplasma spp
Vibrio cholerae
Vibrio cholerae 2
Vibrio parahaemolyticus
Vibrio spp
Vibrio tapetis
Vibrio vulnificus
Wolbachia
Xylella fastidiosa
Yersinia pseudotuberculosis
Yersinia ruckeri

But there is no results for my file:

(base) [user@bigmem01 STRP-2020]$get_sequence_type -s "Streptococcus pneumoniae" -c /export/data/user/STRP-2020/Strp101_assembly_lg500.fasta
Couldn't find a single MLST profile
No message received from child process 147113!
Attribute (header) does not pass the type constraint because: Validation failed for 'ArrayRef' with value undef at constructor Bio::MLST::Spreadsheet::File::new (defined at /export/home/user/miniconda3/lib/site_perl/5.26.2/Bio/MLST/Spreadsheet/File.pm line 44) line 39
        Bio::MLST::Spreadsheet::File::new('Bio::MLST::Spreadsheet::File', 'header', undef, 'spreadsheet_allele_numbers_rows', 'ARRAY(0x56215e250fc0)', 'spreadsheet_genomic_rows', 'ARRAY(0x56215dae19b0)', 'output_directory', '/export/data/user/STRP-2020', 'spreadsheet_basename', 'mlst_results') called at /export/home/user/miniconda3/lib/site_perl/5.26.2/Bio/MLST/Check.pm line 108
        Bio::MLST::Check::create_result_files('Bio::MLST::Check=HASH(0x56215e2aef10)') called at /export/home/user/miniconda3/bin/get_sequence_type line 144

[ZhangDengwei]

the same issue I encountered, have you figured it out?

[neelam19051]

I am also facing same issue, can you please tell me how to solve it?

Thank you, if possible please reply.

[fino0000]

I all. I am facing this issue. Did you by nay chance solved it?

Thank you :)

[VoronDM]

Three years have passed and there is no issue to this problem.

[mohsamir2023]

Have you figured that out ?