BLAST error, out_aminoglycoside.xml, did not exist.

[Samir Vargas da Fonseca Atum]

I’ve found a couple of reports of this issue but none were solved.

My input is:

python3 ~/git/resfinder/run_resfinder.py -o finder -ifa assembly_GUA1312.fasta -b /bin/blastn -db_res ~/git/resfinder/db_resfinder -acq

The output is:

Error: BLAST did not run as expected. The expected output file, /home/samir/Área de trabalho/phd/metagen/gua/finder/resfinder_blast/tmp/out_aminoglycoside.xml, did not exist.
BLAST 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]
[-sum_stats bool_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] [-sorthits sort_hits][-sorthsps sort_hsps] [-max_target_seqs num_sequences]
[-num_threads int_value] [-remote] [-version]

DESCRIPTION
Nucleotide-Nucleotide BLAST 2.11.0+

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

Error: Too many positional arguments (1), the offending value: de
Error:  (CArgException::eSynopsis) Too many positional arguments (1), the offending value: de

I appreciate any help

[CGE Helpdesk]

Dear Samir, 

Thank you for the interest in ResFinder and sorry for the late response.

The program outputs the error message: Error: Too many positional arguments (1), the offending value: de

I suspect that the issue is the name of the path /home/samir/Área de trabalho/phd/metagen/gua/finder/resfinder_blast/tmp/out_aminoglycoside.xmlmight cause the problem. 

I could be wrong, but the whitespaces in the directory Área de trabalho might be causing issues, as the error suggests that de is the problem, as well as too may positional arguments, suggesting that the program reads the arguments as not only one value (due to the whitespace). I suggest you try to change the directory name, so it does not include whitespaces. For example Area_de_trabalho instead (I have also removed the accent, as special characters also could cause problems in some cases). 

I hope this makes sense. If this does not work, please do not hesitate to write us again, and I will look further into the issue. 

Kind regards,

Malene, CGE Helpdesk

[Samir Vargas da Fonseca Atum]

Thank you for the answer, the directory name is default for the system language, but moving to a directory without the spaces corrected the problem.

[Samir Vargas da Fonseca Atum]

directory names can't have whitespaces

[CGE Helpdesk]

Dear Samir,

Glad to hear, that you made it work. If you encounter any other issues or have questions, please do not hesitate to write us again.

Kind regards

Malene, CGE Helpdesk