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

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
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updated by vijay vijay • written by Naren Naren

3 answers

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.

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written by Damian Kao Damian Kao

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

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written by Naren Naren

These may be caused by multiple domain match repeats

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written by cdsouthan cdsouthan

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/

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written by vijay vijay

thank you very much vijay

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written by Naren Naren

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