Question: Blastp -outfmt Problem With Format Specifiers
0
gravatar for bearbob
3.3 years ago by
bearbob0
Germany
bearbob0 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!

blastp output outfmt format blast • 2.7k views
ADD COMMENTlink modified 23 months ago by colinwxl0 • written 3.3 years ago by bearbob0
1

Have you tried single quotes

-outfmt '6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore staxids sscinames scomnames sblastnames sskingdoms' 
ADD REPLYlink written 3.3 years ago by genomax64k

Error could not be reproduced on my system.

Is genomax2's comments works for you?

ADD REPLYlink written 3.3 years ago by nadne30

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)

ADD REPLYlink written 3.3 years ago by bearbob0

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

ADD REPLYlink written 3.3 years ago by genomax64k

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

ADD REPLYlink written 3.3 years ago by bearbob0

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

-outfmt '6 std sscinames etc.etc.etc.......'
ADD REPLYlink modified 23 months ago • written 23 months ago by Buffo1.4k
0
gravatar for colinwxl
23 months ago by
colinwxl0
Peking,Chian
colinwxl0 wrote:

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

ADD COMMENTlink written 23 months ago by colinwxl0
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