Errors with getblast/blastread built-in functions

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Aneesh on 21 Oct 2014
Answered: Bruno Pop-Stefanov on 22 Oct 2014
I'm trying to retrieve a BLAST job that I submitted through the web interface (not from MATLAB). I have the RID, and when I run even the simple function:
data = getblast(RID)
I am consistently returned with the following error:
Attempted to access stats_start(0); index must be a positive integer or logical.
Error in blastread (line 125) statstext = blasttext(stats_start(size(stats_start,1)):size(blasttext,2));
Error in getblast (line 218) blastdata = blastread(blasttext);
Of course, if I run simply blastread with a local copy of the report, I also see the same error. Does anybody have any ideas as to how I can troubleshoot this? Thanks so much in advance!

Answers (1)

Bruno Pop-Stefanov
Bruno Pop-Stefanov on 22 Oct 2014
What release of Bioinformatics Toolbox are you using?
There was a bug in R2009a and earlier in which the blastread function did not handle server errors on the NCBI side correctly in that it still tried to parse the report, resulting in the same error as you are getting. This bug was fixed in R2009b.
Is there a way you could check whether the report is correct and does not contain any error?

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