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Warning: [tblastn] Examining 5 or more matches is recommended

Hi, i am trying to run sma3s regarding annotation and it give following warning: is this warnings are ignorable or they will cause some issue in output file

./sma3s_v2.pl -i pan_genome_reference.fa -d uniref90.fasta -nucl -go -b  -p  -num_threads 20 -goslim 
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Starting Sma3s.v2 (annotator 123)
Nucleotide queries selected: identity and coverage thresholds have been reduced to 51%
Making initial calculations
Reading annotations from UniProt reference file
Reading sequences to annotate
Running Annotator 123

Warning: [tblastn] Examining 5 or more matches is recommended
Warning: [tblastn] Examining 5 or more matches is recommended
Warning: [tblastn] Examining 5 or more matches is recommended
Warning: [tblastn] Examining 5 or more matches is recommended
Warning: [tblastn] Examining 5 or more matches is recommended

Thank you!

sma3s
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written by Neel • Neel

1 answer

I don't know what sma3s_v2 is but, it's a warning from blast (any kind). This warning is generated when the command -max_target_seqs or -max_hsps is used to restrict the results for each query (in this case less than 5). It is recommended to examine 5 or more matches per query because the first results are not necessarily the best. However, it's just a warning, not an error.

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written by Buffo Buffo

Thank You for you time... Actually it the script is still running from past 3 days with this warning, i don't know when it gonna stop ..But anyway thank you for your reply.

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written by Neel • Neel

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