Question: Blastp -outfmt Problem With Format Specifiers
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bearbob • 0 wrote:
Hi,
I'm using the 2.2.31+ version of the blast+ executable in a bash command line to execute a blastp task:
blastp -db /local/brandjoe/bjorn/data/input/nr -query headlines -out blastshellout -num_threads 80 -evalue 0.001 -matrix "BLOSUM62" -outfmt "6" -max_target_seqs 1
While this works just fine, I want to customize the output with some of the format specifiers:
blastp -db /local/brandjoe/bjorn/data/input/nr -query headlines -out blastshellout -num_threads 80 -evalue 0.001 -matrix "BLOSUM62" -outfmt "6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore staxids sscinames scomnames sblastnames sskingdoms" -max_target_seqs 1
This, however, results in an error:
Error: Too many positional arguments (1), the offending value: qseqid
I've tried it with -outfmt 6,7 and 10, none of these options work.
Thank you very much!
Have you tried single quotes
Error could not be reproduced on my system.
Is genomax2's comments works for you?
Unfortunately single quotes don't work either, it produces the very same error. So far it only works if i use -outfmt with the single number argument ("6", or '10' and the likes)
It works for me so I am not sure that the problem is. Did you download the executable or compiled the program yourself?
I used the ncbi-blast-2.2.31+-x64-linux.tar.gz, what did you use?
std prints default parameters, after that you can add whatever you want..