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Old 01-10-2016, 07:46 AM   #1
e.tortoli
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Default Use of cutomized blastn datagase

I have installed ncbi-blast-2.3.0 in my PC
I have created a custom database (I think it is made of the 6 new files named after my database name with different extensions: .nhr .nin .nog .nds .nsi nsq)
To interrogate this database with the sequence file abc.fsa, while within the directory containing the 6 files above I input:
blastn -db custom_database_name -query abc.fsa
I get the following message: Too many positional arguments (1), the offending value: -db
What did I make wrong?
Thanks in advance.

Enrico
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Old 01-10-2016, 03:06 PM   #2
GenoMax
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Are you using just the "basename" of the blast index as an argument for -db? Your query and database are both nucleotide sequences?
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Old 01-10-2016, 08:50 PM   #3
maubp
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Did you copy and paste the command, or type it directly? It should be a minus sign then db, but if you copied it from a PDF you can get a long dash symbol which looks like a minus sign but isn't. That would explain the error message.
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Old 01-11-2016, 01:18 AM   #4
GenoMax
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Good catch Peter. Smart hyphens (and related "smart" things) can cause unintended consequences on copy/paste. This is the most likely explanation here.
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Old 01-11-2016, 05:27 AM   #5
e.tortoli
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Quote:
Originally Posted by GenoMax View Post
Are you using just the "basename" of the blast index as an argument for -db? Your query and database are both nucleotide sequences?
Thanks for your reply,
yes the name of my database is MYCdb and I use such name as an argument of -db
Both query and database are nucleotide sequences
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Old 01-11-2016, 06:27 AM   #6
GenoMax
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Did you look into @Peter's (maubp) suggestion or does that not apply?
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Old 01-11-2016, 06:57 AM   #7
e.tortoli
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I tried again just now paying attention to use the minus;.
Now I have a different error message: Unknown argument: title
Actually typing
blastn -help
I do not see -title in the help-list
Thanks everibody
Enrico
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Old 01-11-2016, 07:08 AM   #8
e.tortoli
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It works now, I was using -title instead of -db.
Thanks everybody, sorry for my foolishness.

Enrico
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