Question: problem running Blast
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nagem7 • 0 wrote:
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!
Did you download the NR database earlier by any chance? Os does the bin folder have a "nr.fa" or "nr" file?
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!
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
-remoteto the end of the command?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! :-(
What was the error in Ubuntu?
I'm not in the ubuntu righ now. But it was also a problem to connect! I can send it later here!! Thanks!!
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
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....
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.