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Old 06-20-2014, 02:01 AM   #1
chris_s
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Default BLAST Database error: No alias or index file found for nucleotide database [nt]

Hi everyone,

I when I try to run BLAST+ on the nt database using a fasta file as query using the following command:

Code:
blastn -db nt -query /home/chris/Desktop/A1_R1.fasta -out results.out
I get the following error message:

BLAST Database error: No alias or index file found for nucleotide database [nt] in search path [/home/chris:$HOME/media/chris/Storage/Genomes_Transcriptomes_Proteomes/NCBI_databases/decompressed/nt:]

I have checked in the 'nt' folder for the nt.nal file, and it is indeed present, so I cannot understand why blast+ cannot find the index.

Any ideas?

Thank you,

Chris
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Old 06-20-2014, 03:45 AM   #2
chris_s
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Ok, I managed to solve the issue. The problem was that in the .bashrc file I had followed the guidelines specified by NCBI for the installation and configuration of the db folder and had entered the following line to specify its location:

export BLASTDB='$HOME/media/chris/Storage/Genomes_Transcriptomes_Proteomes/NCBI_databases/decompressed/nt'

However because in my computer setup (Ubuntu 14.04) the $HOME variable is set to my home directory, BLAST+ went searching in /home/chris then called the $HOME variable and added the path specified in the .bashrc file.

The issue was therefore solved by removing the $HOME variable in the path to the BLAST databases. My .bashrc file now has the following:

export BLASTDB='/media/chris/Storage/Genomes_Transcriptomes_Proteomes/NCBI_databases/decompressed/nt'

I hope this info may be of use to someone in the future.

Cheers,

Chris
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Old 06-11-2015, 06:11 AM   #3
jackfrost
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Default Similar Problem

Hi Chris,

I have the same error you received, although I don't think it is because $HOME (I didn't include that). In your /media/chris/Storage/Genomes_Transcriptomes_Proteomes/NCBI_databases/decompressed/nt directory, do you have a nt.nal file or some other index file? I have only the decompressed folders (nt.00, nt01, etc.) which each have a number of files, including nt.nal in each and otherwise look correct. I'm wondering if I accidentally deleted a central index file or something.
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Old 06-11-2015, 06:15 AM   #4
GenoMax
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There should be no "folders" after decompressing the tarred index files you obtained from NCBI.
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Old 06-11-2015, 06:17 AM   #5
jackfrost
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Ah, thanks GenoMax, I must have decompressed incorrectly
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Old 06-11-2015, 06:35 AM   #6
GenoMax
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If you do have folders, do you see 10 files in each folder with names in this format (e.g. nt.00.n**)?
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Old 06-11-2015, 07:52 AM   #7
jackfrost
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I do see the files. All of them are unique except for the nt.nai. Do you happen to know if I'm able to combine everything into a single folder (i.e. is the nt.nai file which is in each folder just a duplicate and so I only need one?).

I've found examples of how to extract the files properly; I had just done it via the interface instead of the command line which seems to not have worked. I could just re-download the NT database (I've already deleted the compressed files to save space) if I can't just merge all the files into a single directory.
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Old 06-11-2015, 07:58 AM   #8
GenoMax
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Try moving all nt.NN.n* files (out of the folders) into a common folder. Put the nt.nal file in the same folder. It describes the files pieces in the "nt" database. You should only need one.
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Old 06-11-2015, 08:12 AM   #9
jackfrost
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Thanks for the replies. Just tried that and blastn appears to be running fine. That saves me the bandwidth of transferring the files again from NCBI; thanks for the help. If my results look suspect I'll post a follow up but I'm guessing it will need to run for quite a while.

Thanks
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