Re: [Biskit-general] database location

[Thomas E. <Tho...@po...>]

Raik,

>>> Interesting. I don't know what's going on here. My (meanwhile a  
>>> bit outdated)
>>> installation of blast and blast databases doesn't give this error.  
>>>  It could be
>>> that the blastclust version you are using has changed it's command-line
>>> parameters (There is a message like that in the log file). Please try using
>>> blastclust stand-alone with a bunch of fasta sequences. For example:
>>>
>>> cd biskit/Biskit/testdata/Mod/project/sequences
>>> blastclust -i nr.fasta
>>>
>>> this is just to test that the program itself is running.
>>>
>>> Then it could be that the new version of the nr database gives many more
>>> sequences for the test querry and this may sometimes crash blastclust.
>>>
>>> So it would be best if you could reproduce the error outside the   
>>> Biskit test case...
>>
>>
>> That's the output:
>>
>> $ blastclust -i nr.fasta
>> Dec 10, 2009  4:56 PM Start clustering of 14 queries
>> [blastclust] WARNING: Unable to open BLOSUM62
>> [blastclust] WARNING: BlastScoreBlkMatFill returned non-zero status
>> [blastclust] WARNING: SetUpBlastSearch failed.
>> [blastclust] ERROR: Failed to process query number 0
>
> looks like you don't have a properly setup .ncbirc in your home or  
> it is not used. See the instructions on the biskit web site: You  
> need a file that contains something like this:
>
> [NCBI]
> DATA=/usr/local/src/ncbi/data
>
> The folder is the one that contains the BLOSSUM and other matrix  
> files (not the databases!).
>
> Alternatively you can quickly try to set
> setenv BLASTMAT /usr/local/src/ncbi/data
> (or export...=)

I had a BLASTMAT and env variable but set to designate the ncbi/data  
directory created by apt-get. Then I read the section explaining that  
repository-packages are outdated and installed the stand-alone version  
without changing it. Another silliness of mine.

Anyway, that fixed WARNING: Unable to open BLOSUM62 but I still get  
*** buffer overflow detected *** with search_sequences.py

Thomas