cannot run - BLAST issue

[Becks555]

I am new to BRIG using Mac OS 10.14. I have installed the latest version of BLAST, located it in my directory, and have BRIG pointed to NCBI blast folder in the correct place. However, every time I try to run the program, it says it cannot find BLAST and to make sure BLAST is installed and in the correct location. Does BRIG require that BLAST be in a different location that /usr/local/ncbi/blast? Please help. I am trying to illustrate some amazing work kids in middle school and high school have done for our research project using the MinION, generating complete genomes. I think BRIG is exactly what we need, as we want to show differences between Illumina data based assembly and nanopore read assembly of same species.

[oolawole0621]

Hi, were you able to solve this problem? I am currently having a similar challenge.

[Becks555]

Aloha, no. I did not solve it. Sorry!

[bgka2009]

Hi there, did somebody solve this problem? i am struggling now because of similar problem. I am using Window10, BRIG v0.95 and the latest blast. but my BRIG programm give an error message " Could not run BLAST, please check it is installed and BRIG's location is correct.
i need your help.

[ramadatta]

Hi, I ran into same problem with this today, for some strange reason, brig.jar could not detect the blastn from /user/path/ncbi-blast-2.9.0+/bin and kept on getting error. It resolved only after I have put in legacy binaries of blastall and formatdb into the path. Hope this helps someone.

[jerrydodo1]

Hi, I ran into same problem with this today, for some strange reason, brig.jar could not detect the blastn from /user/path/ncbi-blast-2.9.0+/bin and kept on getting error. It resolved only after I have put in legacy binaries of blastall and formatdb into the path. Hope this helps someone.

I have the same problem... What do you mean put those two files in the path. I couldn't find /user/path/ncbi-blast-2.9.0+/bin in my Mac.
Thank you

[ramadatta]

@jerrydodo1 You can try putting the legacy binary files of blastall and formatdb in your downloaded ncbi-blast-2.9.0+/bin folder and set that as a path in BRIG.jar. Check if that works.

[Aciole-David]

After installing (again) blast+ and legacy
and few frustrating minutes, I was able to run BRIG only as sudo, like

sudo java -Xmx8000M -jar BRIG.jar

dad gummit

@happykhan, we could use some help from any documentation.

[emmannaemeka]

Hi,
I am having a similar issue. I have installed blast+ and legacy, tried sudo java -Xmx3000M -jar BRIG.jar.

The error
Error: Too many positional arguments (1), the offending value: /Users/emmannaemeka/Documents/bioiformatics_program/ncbi-blast-2.2.26+/bin
Error: (CArgException::eSynopsis) Too many positional arguments (1), the offending value: /Users/emmannaemeka/Documents/bioiformatics_program/ncbi-blast-2.2.26+/bin
makeblastdb -dbtype nucl -in /Users/emmannaemeka/Documents/Nale_phage/20181119_Nale1/reads/brig/fasta/Shigella_shfl1.fasta
Success!
blastn -outfmt 6 -query /Users/emmannaemeka/Documents/Nale_phage/20181119_Nale1/reads/brig/fasta/Escherichia_phage_vB_EcoS_UP19.fa -db /Users/emmannaemeka/Documents/Nale_phage/20181119_Nale1/reads/brig/fasta/Shigella_shfl1.fasta -out /Users/emmannaemeka/Documents/Nale_phage/20181119_Nale1/reads/brig/fasta/scratch/Escherichia_phage_vB_EcoS_UP19.faVsShigella_shfl1.fasta.tab /Users/emmannaemeka/Documents/bioiformatics_program/ncbi-blast-2.2.26+/bin -task blastn
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] [-mt_mode int_value] [-remote] [-version]

DESCRIPTION
Nucleotide-Nucleotide BLAST 2.13.0+

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

Error: Too many positional arguments (1), the offending value: /Users/emmannaemeka/Documents/bioiformatics_program/ncbi-blast-2.2.26+/bin
Error: (CArgException::eSynopsis) Too many positional arguments (1), the offending value: /Users/emmannaemeka/Documents/bioiformatics_program/ncbi-blast-2.2.26+/bin
makeblastdb -dbtype nucl -in /Users/emmannaemeka/Documents/Nale_phage/20181119_Nale1/reads/brig/fasta/Shigella_shfl1.fasta
Success!
blastn -outfmt 6 -query /Users/emmannaemeka/Documents/Nale_phage/20181119_Nale1/reads/brig/fasta/Escherichia_phage_vB_EcoS_UP30.fasta -db /Users/emmannaemeka/Documents/Nale_phage/20181119_Nale1/reads/brig/fasta/Shigella_shfl1.fasta -out /Users/emmannaemeka/Documents/Nale_phage/20181119_Nale1/reads/brig/fasta/scratch/Escherichia_phage_vB_EcoS_UP30.fastaVsShigella_shfl1.fasta.tab /Users/emmannaemeka/Documents/bioiformatics_program/ncbi-blast-2.2.26+/bin -task blastn
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] [-mt_mode int_value] [-remote] [-version]

DESCRIPTION
Nucleotide-Nucleotide BLAST 2.13.0+

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

@happykhan any help please?

[Aciole-David]

Hi, @emmannaemeka,
Are you passing absolute paths? Can you show us your commands or any other info?

[emmannaemeka]

java -Xmx30000M -jar BRIG.jar

BLAST version 2.13.0+

Blast option /usr/local/bin/

Error message

Error: Too many positional arguments (1), the offending value: /usr/local/bin/
Error: (CArgException::eSynopsis) Too many positional arguments (1), the offending value: /usr/local/bin/
Shigella_shfl1.fasta.nin exists, skipping ..
blastn -outfmt 6 -query /Users/emmannaemeka/Documents/Nale_phage/20181119_Nale1/reads/brig/fasta/Escherichia_phage_vB_EcoS_UP30.fasta -db /Users/emmannaemeka/Documents/Nale_phage/20181119_Nale1/reads/brig/fasta/Shigella_shfl1.fasta -out /Users/emmannaemeka/Documents/Nale_phage/20181119_Nale1/reads/brig/fasta//scratch/Escherichia_phage_vB_EcoS_UP30.fastaVsShigella_shfl1.fasta.tab /usr/local/bin/ -task blastn
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] [-mt_mode int_value] [-remote] [-version]

DESCRIPTION
Nucleotide-Nucleotide BLAST 2.13.0+

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

Error: Too many positional arguments (1), the offending value: /usr/local/bin/
Error: (CArgException::eSynopsis) Too many positional arguments (1), the offending value: /usr/local/bin/

Parsing BLAST Results...

Rendering CGVIEW image...
java -Xmx1500m -jar cgview/cgview.jar -f jpg -i /Users/emmannaemeka/Documents/Nale_phage/20181119_Nale1/reads/brig/fasta//scratch/Shigella_shfl1.fasta.xml -o /Users/emmannaemeka/Documents/Nale_phage/20181119_Nale1/reads/brig/fasta//Shigella_shfl1.fasta.jpg
Parsing XML input.
Drawing features.....
Positioning and drawing 0 labels..........................
0 labels were removed.
Drawing tick marks.
Drawing legends.
The map has been drawn.

[Aciole-David]

Ok. Can you provide screenshots of your parameters?
I think you may be passing the blast path to the "BLAST options" field

instead of "Preferences>BRIG options>BLAST binary folder" field.

Also, if you have blastn in your system default path, maybe you can try not specifying it (that's how I'm currently running my BRIG test).

[emmannaemeka]

It worked.

I followed this

Also, if you have blastn in your system default path, maybe you can try not specifying it (that's how I'm currently running my BRIG test).

Thanks

[Aciole-David]

Great!
You're welcome

[ramadatta]

I used binary files from ncbi-blast-2.7.1+-x64-linux.tar.gz and set path in preferences > Brig options > save & close. That also worked for me!