outfmt 6 BLAST column names

Question

[Paula]

Hi!

I am using the command line BLAST tool to search sequences against a custom database. I ran the following command:

blastp -query . /s3_protein_Sequences_sol_1_10.faa -db ./database/nr -outfmt 6 -num_threads 16 -max_target_seqs 5 -evalue 1e-30 -out s3_protein_Sequequences_taxonomy.txt

Here is the first line of the output table :

NODE_101_length_82643_cov_14.288202_80  / seq_85 /  98.925  / 93    / 1 /   0 / 146 / 238 / 1   93/     1.72E-63 /  191

As you can see, the names of the columns are not included. Do you know what each number means? I have searched in the documentation but I cannot find the information.

Thanks a lot!

Answer 1

[lieven.sterck]

yes, use outfmt 7 , that will include header lines.

or, you can have a look in the blast -help where it is explained what each of the default output outfmt 6 columns means.

few other points:

• use that much num_threads will likely not speed up your analysis much, at that number you are already on the plateau of speed gain (moreover only limited parts of the blast analysis is multithreaded anyway)
• be careful when using the max_target_seq parameter, it might not return what you think it will (for details google or look around here on biostars)

Answer 2

[GenoMax]

https://www.metagenomics.wiki/tools/blast/blastn-output-format-6

https://www.ncbi.nlm.nih.gov/books/NBK279684/table/appendices.T.options_common_to_all_blast/

When not provided, the default value is:

'qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore', which is equivalent to the keyword 'std'