Error in blastx with nr database

Question

[mirza]

Hi, I have installed ncbi-blast-2.5.0+ in my ubuntu 16.04 system and downloaded the nr database using

$ wget ftp://ftp.ncbi.nlm.nih.gov/blast/db/nr.*.tar.gz

untared it,

$ ls *.gz |xargs -n1 tar -xzvf

and now I have nr db- nr.00 to nr.59.tar.gz (each having the 12 different files .phd,.phi, .phr upto .psq) But, when I try to run blastx, using the following command, for any -outfmt (like 0,1 or 6),

$ blastx -query test.fasta -db nr -outfmt 0 -out test_blastx -evalue 1e-10
It gives the following error.
Error: NCBI C++ Exception:
    T0 "/build/ncbi-blast+-bzPf_D/ncbi-blast+-2.2.31/c++/src/corelib/ncbiobj.cpp", line 926: Critical: ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL pointer.

I know there are similar posts her on biostar but none solved my issue or if there is an identical post, I might have missed so, kindly direct me to it? Blast+ is working fine as I have used it for analysis of my data, creating my own databases. I am facing problem with nr db only.

[GenoMax]

Looks like you have multiple versions of blast installed on your system. Running blastx the way you are doing it seems to be using an older version 2.2.31. Can you locate the version you want to run (2.5.0) and try providing full path to that executable?

[mirza]

ok, thanks, I'll look into it.

[Michael]

In addition, it is highly recommended to use update_blastdb.pl for updating your blast databases. The wget way does not verify the downloaded files, for example. Also, the latest version is now 2.6.0+.

[mirza]

thanks. I have blastx and blastdb added twice. Earlier, I had my softwares in Downloads/softwares dir so I added that to the path using vim .bashrc. The following the suggestions given to me on biostar only, I created a bin dir in my home copied all softwares there and added it to the path using vim .bashrc, again. So, now I have to different paths for blastx and blastdb. Everyone is suggesting that I should remove these from path. But, how to execute it, what commands to use precicely? I did used some of the commands from a few posts on stackoverflow.com. But, they didn't work for me. I am having trouble finding the right commands :(

[GenoMax]

We can't read your mind or see your terminal so you will need to spell out commands you are running and/or what your PATH variable looks like.

[mirza]

Yes of course, sorry. This is the link to my post in stackoverflow, http://askubuntu.com/questions/892239/how-to-remove-a-directory-path-from-path-permanently?noredirect=1#comment1395972_892239

I have written everything in detail. should I rewrite it here? I found that dd deletes a line in vim, but can't figure out how to actually use it.

[Michael]

If I remember correctly I have strongly advised against setting up your path this way. Never put a Downloads directory in your path. To fix this you simply need to remove the lines of your .profile, .bshrc starting with PATH= and setup a single clean PATH statement.

[mirza]

Yes, I followed your advice, made the bin dir in my home, copied all softwares to it and added it to the PATH. Hence, the duplication in PATH, 'coz I have added the Downloads/softwares to the PATH before this and I thought exporting the new PATH (/home/gjjha/bin) will override this one.

Can you please tell me exactly how to remove the lines. I found that dd deletes a line in vim, but can't figure out how to actually use it. I know the commands to edit and export a path but can you please tell me the commands to remove the lines? I'll be gratefull.

[GenoMax]

Use nano or pico text editor (if those are available) on your server. They are easier to understand than vi/vim.