formatdb works but makeblastdb doesn't (BLAST)

[cdes79]

Dear all,

i am trying to format the non-redundant fasta database (nr) downloaded from the NCBI repository. I have initially formatted it with the program formatdb from blast 2.2.25 that i had installed on my machine and it worked fine

formatdb -p T -o T -i nr

However i have just upgraded to the latest blast 2.2.29+ version and i read that formatdb should no longer be used but makeblastdb should be used instead. So i tried to format the database again

 makeblastdb -in nr -dbtype prot

but i get the following error:
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.

I don't quite get the error and what could that be. Does anybody have any idea? Thanks

[GenoMax]

Why are you reformatting nr when you can get the pre-built indexes from: ftp://ftp.ncbi.nih.gov/blast/db/

[westerman]

While I agree with GenoMax's comment, I think that you can find the line causing the error at line #1431 of your input file. Also I find it interesting that your input file 'nr' does not have an extension -- are you sure this is correct?

[cdes79]

Why are you reformatting nr when you can get the pre-built indexes from: ftp://ftp.ncbi.nih.gov/blast/db/

I am new to it and that's how i thought it was done. As simple as that. So basically all the files in the main db directory are equivalent to the ones that i create during the formatting? Is that correct? I simply need to download all those nr.* and place them in my db directory?

Also I find it interesting that your input file 'nr' does not have an extension -- are you sure this is correct?

I simply downloaded the nr.gz file from the db/FASTA folder and unzipped it from the terminal using gzip. It had no extension and i used it as it was. And it worked with formatdb. Do you have any idea why it might be working with one and not the other if there is an error at that line? (will check tomorrow at work)

[GenoMax]

I am new to it and that's how i thought it was done. As simple as that. So basically all the files in the main db directory are equivalent to the ones that i create during the formatting? Is that correct? I simply need to download all those nr.* and place them in my db directory?

That is correct. Make sure you download all the nr* files. Be aware that this would be a large download and depending on bandwidth available could take some time.

[cdes79]

That is correct. Make sure you download all the nr* files. Be aware that this would be a large download and depending on bandwidth available could take some time.

Thanks very much. FYI i just figured that i can run the blast remotely on the ncbi server using the flag -remote. That doesn't require to download any databases as well as i can do it on my sloppy machine. :-)

Best,
Christian

[maubp]

However i have just upgraded to the latest blast 2.2.29+ version and ... i get the following error:
Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: Ignoring FASTA modifier(s) found because the input was not expected to have any.

I don't quite get the error and what could that be. Does anybody have any idea? Thanks

I just hit what is probably the same issue, and believe this is a new bug in BLAST+ 2.2.29 (the older versions I tested were fine) when FASTA query files which contain [key=value] tags in their description/title line: http://blastedbio.blogspot.co.uk/201...modifiers.html

I have reported this to the NCBI by email.

[shangzhong0619]

Thanks very much. FYI i just figured that i can run the blast remotely on the ncbi server using the flag -remote. That doesn't require to download any databases as well as i can do it on my sloppy machine. :-)

Best,
Christian

Hi, just a question, how many transcripts did you search using -remote? how is the speed? thanks.

[shangzhong0619]

That is correct. Make sure you download all the nr* files. Be aware that this would be a large download and depending on bandwidth available could take some time.

Hello, GenoMax, I have a question, there are 16 nr files in the ftp, can I use cat to concatenate the files with the same extension in those 16 folders and finally get only one big database? I don't want to blast 16 times for searching only one query.

[GenoMax]

Hello, GenoMax, I have a question, there are 16 nr files in the ftp, can I use cat to concatenate the files with the same extension in those 16 folders and finally get only one big database? I don't want to blast 16 times for searching only one query.

nr* files you download from NCBI are already formatted appropriately. You should only gunzip/untar them (make sure all the files are in the same folder) but leave them alone otherwise.

[rcrystal]

In case it helps anyone, I ran into this same issue and found this blogger who states that the error messages are irrelevant:

http://blastedbio.blogspot.com/2014/04/error-1431-fasta-reader-ignoring-modifiers.html

[maubp]

In case it helps anyone, I ran into this same issue and found this blogger who states that the error messages are irrelevant:

http://blastedbio.blogspot.com/2014/...modifiers.html

I posted a link to this earlier in the thread, but I'm glad it was useful

[rcrystal]

Thanks maubp! I see it now, I'm sorry I missed it before!