Blastp -outfmt Problem With Format Specifiers

Question

[bearbob]

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!

[nadne]

Error could not be reproduced on my system.

Is genomax2's comments works for you?

[bearbob]

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)

[GenoMax]

It works for me so I am not sure that the problem is. Did you download the executable or compiled the program yourself?

[bearbob]

I used the ncbi-blast-2.2.31+-x64-linux.tar.gz, what did you use?

[colinwxl]

I think you may use the whole command as an argument, such as cmd ="...", if you really performed like what I said. You'd better add backslash before quote.

[Buffo]

std prints default parameters, after that you can add whatever you want..

-outfmt '6 std sscinames etc.etc.etc.......'

Answer 1

[GenoMax]

Have you tried single quotes

-outfmt '6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore staxids sscinames scomnames sblastnames sskingdoms'