What Is The Reason For Getting The "Max Hsp Reached" Error When Using The Ncbi Blast

Question

[Naren]

after this command :

blastall -p tblastx -d *1.txt* -i *2.txt* -o *ortholog.txt* -m 8 -a 3

this error:

[NULL_Caption] WARNING:  [000.000] 'gene|288336358|1037' : Reached max 200 HSPs in BlastSaveCurrentHsp, continuing with this limit

Answer 1

[Damian Kao]

It's just a warning. It should still continue to output your results. All it is saying is that it has found more than 200 HSPs and will stop outputting HSPs since the limit is set at 200.

[Naren]

Thanks, so far it is not affecting my output its okay.

Answer 2

[cdsouthan]

These may be caused by multiple domain match repeats

Answer 3

[vijay]

This happens when there are more than 200 significant alignments between the sequences. You can actually cut down your query sequences into small fragments and try running tblastx again .

The below tutorial addresses some of the issues confronted while running command line blast searches. Hope it would be useful for you!!

http://etutorials.org/Misc/blast/Part+IV+Industrial-Strength+BLAST/Chapter+10.+Installation+and+Command-Line+Tutorial/10.3+Command-Line+Tutorial/

[Naren]

thank you very much vijay