gz paired end reads

[Former user]

I usually run Illumina paired end gz files in CGE website. I downloaded the command line but it is giving me an error.

Command ran:

 python3 ~/Downloads/Software/resfinder/resfinder.py -i MDB159_S2_L001_R1_001.fastq.gz MDB159_S2_L001_R2_001.fastq.gz -o . -p /usr/db/resfinder_db -mp blast -x  

But I got an error message that looks like a blastn error.

Error:  (CArgException::eInvalidArg) Unknown argument: "t_db"

Any suggestion why?

[Sofie Theisen Honoré]

Dear user.
Thank you for your question and interest in using ResFinder.

I think the problem is that you should provide the path to an executable blastn file after -mp (not just write blast). If you haven’t already installed blastn, you can do it here: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/

I hope this helps. If not, please do not hesitate to write us again!

Best,
Sofie, CGE Helpdesk

[Dyana]

Hi,

Thank you for you reply.

I have downloaded blast. If I run it with fasta as an input, it works perfectly fine.

python3 ~/Downloads/Software/resfinder/resfinder.py -i ../DBWGS15_S12_47077DX_3_MDB90/spades/DBWGS15_S12_47077DX_3_MDB90_contigs.fasta -o . -p /usr/db/resfinder_db -mp /usr/Software/ncbi-blast-2.8.1+/bin/blastn -x

Found: lsa(A)_3_AY737526
Saving: NODE_2_length_460353_cov_84.569986:355115..356611:lsa(A)_3_AY737526:98.663995
Found: lsa(A)_1_AY225127
Same contig: NODE_2_length_460353_cov_84.569986 == NODE_2_length_460353_cov_84.569986
lsa(A)_1_AY225127 vs lsa(A)_3_AY737526
overlap found (1496): lsa(A)_1_AY225127
{'resfinder': {'results': {'Aminoglycoside': {'aminoglycoside': 'No hit found'},
'Beta-lactam': {'beta-lactam': 'No hit found'},
'Colistin': {'colistin': 'No hit found'},
'Fosfomycin': {'fosfomycin': 'No hit found'},
'Fusidicacid': {'fusidicacid': 'No hit found'},
'Glycopeptide': {'glycopeptide': 'No hit found'},
'Macrolide': {'macrolide': {'NODE_2_length_460353_cov_84.569986:355115..356611:lsa(A)_3_AY737526:98.663995': {'HSP_length': 1497,
'accession': 'AY737526',
'contig_name': 'NODE_2_length_460353_cov_84.569986',
'coverage': 100.0,
'hit_id': 'NODE_2_length_460353_cov_84.569986:355115..356611:lsa(A)_3_AY737526:98.663995',
'identity': 98.66,
'note': '3',
'position_in_ref': '1..1497',
'positions_in_contig': '355115..356611',
'predicted_phenotype': 'Macrolide '
'resistance '
'Alternate '
'name; '
'abc-23',
'resistance_gene': 'lsa(A)',
'subject_header': 'lsa(A)_3_AY737526',
'template_length': 1497}}},
'Nitroimidazole': {'nitroimidazole': 'No hit found'},
'Oxazolidinone': {'oxazolidinone': 'No hit found'},
'Phenicol': {'phenicol': 'No hit found'},
'Quinolone': {'quinolone': 'No hit found'},
'Rifampicin': {'rifampicin': 'No hit found'},
'Sulphonamide': {'sulphonamide': 'No hit found'},
'Tetracycline': {'tetracycline': 'No hit found'},
'Trimethoprim': {'trimethoprim': 'No hit found'}},
'run_info': {'date': '06.07.2020', 'time': '09:51:06'},
'user_input': {'file_format': 'fasta',
'filename(s)': ['../DBWGS15_S12_47077DX_3_MDB90/spades/DBWGS15_S12_47077DX_3_MDB90_contigs.fasta'],
'method': 'blast'}}}

But if the input is paired reads, I will get an error message.

python3 ~/Downloads/Software/resfinder/resfinder.py -i ATCC_DBWGS19_fasta/MDB159_S2_L001_R1_001.fastq.gz ATCC_DBWGS19_fasta/MDB159_S2_L001_R2_001.fastq.gz -o . -p /usr/db/resfinder_db -mp /usr/Software/ncbi-blast-2.8.1+/bin/blastn -x
Error: KMA did not run as expected.
KMA finished with the following response:

USAGE
blastn [-h] [-help] [-import_search_strategy filename]
[-export_search_strategy filename] [-task task_name] [-db database_name]
[-dbsize num_letters] [-gilist filename] [-seqidlist filename]
[-negative_gilist filename] [-negative_seqidlist filename]
[-taxids taxids] [-negative_taxids taxids] [-taxidlist filename]
[-negative_taxidlist filename] [-entrez_query entrez_query]
[-db_soft_mask filtering_algorithm] [-db_hard_mask filtering_algorithm]
[-subject subject_input_file] [-subject_loc range] [-query input_file]
[-out output_file] [-evalue evalue] [-word_size int_value]
[-gapopen open_penalty] [-gapextend extend_penalty]
[-perc_identity float_value] [-qcov_hsp_perc float_value]
[-max_hsps int_value] [-xdrop_ungap float_value] [-xdrop_gap float_value]
[-xdrop_gap_final float_value] [-searchsp int_value] [-penalty penalty]
[-reward reward] [-no_greedy] [-min_raw_gapped_score int_value]
[-template_type type] [-template_length int_value] [-dust DUST_options]
[-filtering_db filtering_database]
[-window_masker_taxid window_masker_taxid]
[-window_masker_db window_masker_db] [-soft_masking soft_masking]
[-ungapped] [-culling_limit int_value] [-best_hit_overhang float_value]
[-best_hit_score_edge float_value] [-subject_besthit]
[-window_size int_value] [-off_diagonal_range int_value]
[-use_index boolean] [-index_name string] [-lcase_masking]
[-query_loc range] [-strand strand] [-parse_deflines] [-outfmt format]
[-show_gis] [-num_descriptions int_value] [-num_alignments int_value]
[-line_length line_length] [-html] [-max_target_seqs num_sequences]
[-num_threads int_value] [-remote] [-version]

DESCRIPTION
Nucleotide-Nucleotide BLAST 2.8.1+

Use '-help' to print detailed descriptions of command line arguments

Error: (CArgException::eInvalidArg) Unknown argument: "t_db"

‌

Not exactly sure why it

‌

[Sofie Theisen Honoré]

Hi again.

Thank you for your answer.

The problem arises because Blast can’t handle fastq files. If you want to run ResFinder with fastq files you should use kma as method instead of Blast. You can download kma here: https://bitbucket.org/genomicepidemiology/kma/src/master/

When running ResFinder, you should then specify the path to the executable kma file with the -mp flag (instead of the Blast path).

I can see that this is not quite clear in the README so I’ll update that - thank you for making us aware of it.

Best,
Sofie, CGE Helpdesk