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What do you need to know about makeblastdb?
makeblastdb is an EMBOSS “wrapper” program for the program makeblastdb from the NCBI’s BLAST (Basic Local Alignment Search Tool) suite. It must be used in order to format protein or nucleic acid source databases before these databases can be searched by blast, psiblast or phiblast.
Why is makeblastdb…-hash _ index causing the ” BLAST database creation error?
So makeblastdb -hash_index was causing the “BLAST Database creation error: Error: Duplicate seq_ids are found: GNL|BL_ORD_ID:3299542” error? If so, that is good to clarify, but does seem to be unrelated to the original -max_file_sz problem.
Why does makeblastdb fail in the same way outside galaxy?
Or, that the Galaxy admin adds the database to the *.loc file. Reproducing this outside Galaxy would be really instructive – does the failing command line string Galaxy used (read this via a fail makeblastdb history entry) fail in the same way outside Galaxy?
Why is makeblastdb-MAX _ file _ SZ still failing?
This is still failing with BLAST Database creation error: Error: Duplicate seq_ids are found: GNL|BL_ORD_ID|18349221. One of our users is also now running into this. @bgruening do you recall if increasing -max_file_sz fixed this? I’m trying 10GB now, but this isn’t exactly a quick process.
How to create BLAST database in mhahsler / rblast?
Try Sys.which (“makeblastdb”) to see if the program is properly installed. Use blast_help (“makeblastdb”) to see all possible extra arguments. Arguments need to be formated in exactly the way as they would be used for the command line tool. BLAST+ http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download
How to create a BLAST database in FASTA?
Create a BLAST database. First you need to create a BLAST database for your genome or transcriptome. For your reference sequences in a FASTA file, use this command line: makeblastdb -in -dbtype nucl -parse_seqids -out -title “Database title”. The -parse_seqids option is required to keep the original sequence
How to create a BLAST database in NCBI?
Otherwise makeblastdb will generate its own identifiers, -title is optional. For more information on makeblastdb see NCBI BLAST+ Command Line User Manual. Magic-BLAST will work with a genome in a FASTA file, but will be very slow for anything larger than a bacterial genome, so we do not recommend it.