problem running Blast

Question

[nagem7]

Hi! I installed Blast in my computer, but I'm having troubles to use it.

I want to Blast my protein sequence against nr database using the -remote option. Here is the command I'm using

blastp.exe -query FILE LOCATION\seqs2.aa -out FILE LOCATION\resultado.blast -remote -db nr -evalue 1e-5 -num_alignments 50 -num_descriptions 50

However, when I try to run that command I see the message:

Warning: Error initializing local BLAST database data loader: "No alias or index file found for protein database [nr] in search path [C:\Program Files\NCBI\blast-2.2.29+\bin;;]"

Can anyone help me with that?

Thanks a lot!

[Ram]

Did you download the NR database earlier by any chance? Os does the bin folder have a nr.fa or nr file?

[nagem7]

No, I didn't download the NR database earlier. In the bin folder there are only files ending in .exe, such a blastp.exe, blastn.exe and others.

As suggested in the post below, by airan, I took a look in that post, but in that post Blast can't find a local database. I'm not using a local database....I'm using the -remote option so I can use databases stored in the NCBI server. I'm not understanding why blast is trying to find a database if I'm using the -remote option!

Thanks for your help!! If you have anything else that could help me, please let me know!

[Ram]

I wish I knew why you're facing this error, but everything seems fine with your command. I was just making sure that left over files from previous analyses were not hindering your current analysis. Just a quirky suggestion - could you try moving the -remote to the end of the command?

[nagem7]

I did it, but it did not work! Same problem....

I'm using a windows 8. I did the same in a windows 7 laptop, and the problem was the same. When I ran in a Ubuntu laptop the error was different. Problem there is a problem with NCBI server....that is all I can think! :-(

[Ram]

What was the error in Ubuntu?

[nagem7]

I'm not in the ubuntu righ now. But it was also a problem to connect! I can send it later here!!

Thanks!!

[Istvan Albert]

the problem is what the tool reports - you don't have the data where the program is trying to access it from.

this is a classic problem that plagues all of computing, be that a bash command that does not run, an class path for java, a python import path

it is an annoying problem but the solution is always the same: meticulously investigate the impossible - why is it that a place that clearly is on the path is not found on the path. Then you'll find all kinds of wierd things - a space in the path name, a location that is different in just one character, a 1 that looks like an l etc

[nagem7]

I checked and everything is right. The problem is: I'm not trying to access a local database...I'm trying to use the -remote option, that is why I'm not understanding the reason the program is trying to find a database in my computer.

Also, after a few minutes a new error message shows up:

Error: (311.26) SOCK#1000[700]@130.15.19.110:80 [SOCK::Connect] Failed pending connect():Closed {error=10060,Operation timed out}
Error: (303.7) [URL_Connect] Failed to connect to www.ncbi.nlm.nih.gov:80: Closed

I'm not sure, but it seems I'm having trouble to connect to NCBI server....

[Ram]

This discussion is along the problem you're facing right now: http://seqanswers.com/forums/archive/index.php/t-29820.html

Also, check if you can access ftp://ftp.ncbi.nlm.nih.gov/ from your network.

Answer 1

[iraun]

Take a look to this post: Blast Can'T Find Databases

[Ram]

I saw this one too, but OP is using the right database (Proteins and NR), so the post doesn't help OP's problem.

[iraun]

Mmm... yes, you're right. I did not realize.

Answer 2

[onuralp]

It seems to me that this is either proxy configuration / firewall problem (on your part) or it just happens that you submitted your query in the midst of busy traffic.

If it is just busy traffic, you should be fine when you retry a bit later.

Regarding the configuration issues, do you experience any problem processing your query from the browser?