BLAST Database error: No alias or index file found for nucleotide database [nt]

chris_s · 06-20-2014, 03:01 AM

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

chris_s · 06-20-2014, 04:45 AM

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

jackfrost · 06-11-2015, 07:11 AM

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.

GenoMax · 06-11-2015, 07:15 AM

There should be no "folders" after decompressing the tarred index files you obtained from NCBI.

jackfrost · 06-11-2015, 07:17 AM

Ah, thanks GenoMax, I must have decompressed incorrectly

GenoMax · 06-11-2015, 07:35 AM

If you do have folders, do you see 10 files in each folder with names in this format (e.g. nt.00.n**)?

jackfrost · 06-11-2015, 08:52 AM

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.

GenoMax · 06-11-2015, 08:58 AM

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.

jackfrost · 06-11-2015, 09:12 AM

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

varun S · 03-22-2019, 11:42 PM

Quote:

Originally Posted by jackfrost

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.

I have downloaded nt.NN.tar.gz files from ncbi, when i extract them into a single folder there is three files which are common to all the tar file that is nt.nal tax.db.btd and taxdb.bti. These files get replaced while extracting. Please help me how to extract them and setup nt database

GenoMax · 03-23-2019, 05:51 AM

Have you tried to use the index? It should be fine to have one copy of nt.nal for sure. If there is anything wrong you will get an error.

varun S · 03-23-2019, 06:01 AM

Can you please help me out, I don't know how to index. I have downloaded nt database which has 69 files and I have unzipped them into a folder. what should I do next?

jackfrost · 03-24-2019, 05:56 AM

That should be all you need to do (haven’t worked with NT in a while now).

Just download and decompress; the folder everything is now in is your complete index. Depending on what software you are using, you’ll have to tell it where that folder is at (or the index file). You’ll have to look at the help for your software for exactly how to do this since a lot of people develop it slightly differently.

The nt.nai is your ‘index file’ (as mentioned, it has a list of where all the other files are, but that’s the one you’ll enter into most programs).

As far as setting up the database, there is no way of installing it so programs automatically know where it is - you will have to manually provide its location at some point in any computations you run, depending on the specific software.

GenoMax · 03-24-2019, 07:59 AM

Quote:

Originally Posted by varun S

Can you please help me out, I don't know how to index. I have downloaded nt database which has 69 files and I have unzipped them into a folder. what should I do next?

Use the index for blast. Nothing else needs to be done beyond uncompressing files and making sure that all of them are in one folder. When you specify the index you only need to use the "basename" so it would be db=/path_to/nt

varun S · 03-24-2019, 08:11 AM

Quote:

Originally Posted by GenoMax

Use the index for blast. Nothing else needs to be done beyond uncompressing files and making sure that all of them are in one folder. When you specify the index you only need to use the "basename" so it would be db=/path_to/nt

Thank You, It worked.

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06-20-2014, 03:01 AM	#1
chris_s Junior Member Location: Belgium Join Date: May 2013 Posts: 9	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

06-11-2015, 07:11 AM	#3
jackfrost Junior Member Location: Washington DC Join Date: Jun 2015 Posts: 9	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.

03-23-2019, 06:01 AM	#12
varun S Junior Member Location: Bengaluru Join Date: Apr 2018 Posts: 3	I didnt do indexing, they have not mentioned that in blast manual Can you please help me out, I don't know how to index. I have downloaded nt database which has 69 files and I have unzipped them into a folder. what should I do next?

06-20-2014, 04:45 AM	#2
chris_s Junior Member Location: Belgium Join Date: May 2013 Posts: 9	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

06-11-2015, 07:15 AM	#4
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,080	There should be no "folders" after decompressing the tarred index files you obtained from NCBI.

06-11-2015, 07:17 AM	#5
jackfrost Junior Member Location: Washington DC Join Date: Jun 2015 Posts: 9	Ah, thanks GenoMax, I must have decompressed incorrectly

06-11-2015, 07:35 AM	#6
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,080	If you do have folders, do you see 10 files in each folder with names in this format (e.g. nt.00.n**)?

06-11-2015, 08:52 AM	#7
jackfrost Junior Member Location: Washington DC Join Date: Jun 2015 Posts: 9	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.

06-11-2015, 08:58 AM	#8
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,080	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.

06-11-2015, 09:12 AM	#9
jackfrost Junior Member Location: Washington DC Join Date: Jun 2015 Posts: 9	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

03-23-2019, 05:51 AM	#11
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,080	Have you tried to use the index? It should be fine to have one copy of nt.nal for sure. If there is anything wrong you will get an error.

03-24-2019, 05:56 AM	#13
jackfrost Junior Member Location: Washington DC Join Date: Jun 2015 Posts: 9	That should be all you need to do (haven’t worked with NT in a while now). Just download and decompress; the folder everything is now in is your complete index. Depending on what software you are using, you’ll have to tell it where that folder is at (or the index file). You’ll have to look at the help for your software for exactly how to do this since a lot of people develop it slightly differently. The nt.nai is your ‘index file’ (as mentioned, it has a list of where all the other files are, but that’s the one you’ll enter into most programs). As far as setting up the database, there is no way of installing it so programs automatically know where it is - you will have to manually provide its location at some point in any computations you run, depending on the specific software.