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Old 04-22-2013, 10:35 AM   #1
utagenomics
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Default Making a Blast Script for FASTA files

Hi I am trying to BLAST one large genome file with a specific set of sequences and I cannot figure out what is wrong with my script (I am obviously new to scripting). Any help would be greatly appreciated.

This is my script:

-in P.reformat.CDS.transcripts.fa -out p.full dbtype=nucl

blastn -query=NGF.fasta -db=p.full -outfmt="6" -out=blast


I want to search the "P.reformat.CDS.transcripts.fa" file for anything similar to the sequences in the "NGF.fasta" file.
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Old 04-22-2013, 11:19 AM   #2
GenoMax
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Are you referring to a script (that may contain multiple lines of code/options) or a command line where you are providing multiple options?

What you have posted above does not quite look like either (perhaps there is something missing from the copy/paste). Seems like you are creating the database on the first line and the searching on the second?

What seems to be the error (if any) that you are getting? Are you sure the database was created successfully?

Last edited by GenoMax; 04-22-2013 at 11:23 AM.
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Old 04-23-2013, 02:54 AM   #3
Ciaran
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In your blast call you do not need the "=" characters
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Old 04-26-2013, 08:21 AM   #4
utagenomics
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Hey everyone,

So I successfully made my database in the correct folder, but then when I actually try to run my blast, it isn't working...

#I used the following to make the db

makeblastdb -in supercontigs.fasta.txt -dbtype 'nucl' -out p.full

#I then tried to run this the next step, with and without the '=' sign

query=NGF.fasta -db=p.full -outfmt="6" -out=blast

Any ideas how I can change my second step to successfully run the blast search?

Thanks,
Kyle
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Old 04-26-2013, 09:25 AM   #5
mastal
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Default Making a Blast Script for FASTA files

Have a look at the blast commandline applications manual,

http://www.ncbi.nlm.nih.gov/books/NBK1763/

particularly the sample queries in the Cookbook section,

and the use of the 'blastdbcmd' command for checking that
the database you created is OK, and that your computer knows
where to find the blast databases.
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Old 04-26-2013, 10:02 AM   #6
kbradnam
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It always helps to provide the error message that you get when something "isn't working". The more information you provide, the more likely that someone can help you.
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Old 04-26-2013, 10:27 AM   #7
utagenomics
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When I posted the above command to run the blast search I received the following error message.


Command line argument error: Argument "out". File is not accessible: `blast'
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Old 04-26-2013, 10:41 AM   #8
kbradnam
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This suggests that you might not have permission to create output files in whatever directory you are running this command in.
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Old 04-26-2013, 11:29 AM   #9
GenoMax
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Quote:
Originally Posted by utagenomics View Post
When I posted the above command to run the blast search I received the following error message.


Command line argument error: Argument "out". File is not accessible: `blast'
Check the command line examples from the link Maria posted in #5.

Please post the entire command line when asking for help. So something like this will work.

Code:
blast(n/p/x) -query NGF.fasta -db p.full -outfmt 6 -out blast_output_file
What kind (nucleotide/protein/translated) of blast search are you trying to run?
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