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Old 03-25-2013, 12:44 PM   #1
pico
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Question Problem with making blast database

Hello,

I have a problem with makeblastdb in command line. I'm trying to make a database of a multi-fasta file containing 200 genes but the job is taking too much time, i have leave it for the week end but still no database created.

My file is in fasta format, i have checked it many times. I don't know where the problem can be, do you have a solution for that or i'm maybe missing something...

command line : makeblastdb -in genes.txt -dbtype nucl -out Db_genes.txt

Building a new DB, current time: 03/25/2013 21:06:33
New DB name: Db_genes.txt
New DB title: genes.txt
Sequence type: Nucleotide
Keep Linkouts: T
Keep MBits: T
Maximum file size: 1000000000B
.......it never finish the job...

Thank you very much
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Old 03-26-2013, 03:35 AM   #2
A.N.Other
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I would normally use:

Code:
makeblastdb -in <in_fa_file> -input_type fasta -title <title> -out <out_file>
-input_type defaults to fasta anyway, so the only issue I can see with your command is that you have '.txt' on the -out file name. makeblastdb will automatically give the extensions .nhr, .nin and .nsq to the three files it makes, so this is not necessary. Not sure if it's causing the problem, though. Make sure you've changed directory to the location would want the db created in before you run the script and make sure you've got the relevant permissions to do what you need.
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Old 03-26-2013, 03:36 AM   #3
GenoMax
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With just 200 genes this should not be taking a week. What OS are you doing this on? Did you create your multi-fasta file on a PC and then are trying to create the indexes on a unix machine?
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Old 03-26-2013, 08:12 AM   #4
pico
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i'm on a mac and always worked on it. I think i have a problem with my multi fasta file but i don't know what it can be...
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Old 03-26-2013, 02:00 PM   #5
danwiththeplan
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For 200 genes it should be done in seconds. Maybe check that there is no odd hidden line ending or wrapping on your fasta lines, although I don't know if this affects makeblastdb.
I.e. in a text editor, each fasta line should be the header and the sequence below it, both only on one line, with no extra line endings or word wrapping. Use a text editor that displays hidden characters (I use Geany on linux, not sure what works on mac). Check permissions as the other guy said.
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Old 03-26-2013, 06:42 PM   #6
Kennels
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can you paste an example of a gene with the header and sequence here?
It could be a problem with the header format, or as mentioned 'new line' format issue between different OS's.
Also, I'd use '-parse_seqids' options too.
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Old 03-26-2013, 11:22 PM   #7
Wallysb01
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Some text editors will input strange line brake characters. Look at your file using the "more" or "less" command, this will show the file how makeblastdb will see it.
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Old 03-27-2013, 09:48 AM   #8
pico
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Hello,

Thank you for all your answers, there was a line break in the middle of my text file!
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