[maker-devel] <MAKER Trac Server> #27: high-scoring blastx hit disappears

[MAKER]

#27: high-scoring blastx hit disappears
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 Reporter:  sspao at ucdavis.edu  |       Owner:       
     Type:  defect             |      Status:  new  
 Priority:  major              |   Milestone:       
Component:  Code               |     Version:  0.001
 Keywords:                     |  
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 There's a high-scoring blastx hit that was present in a maker run aka
 RUN1. But it disappears in a second maker run aka RUN2, which has a much
 larger database. Both protein databases contain the sequence (aka
 CAN65888). This is verifiable because there are intermediate files created
 and both maker runs contain the hits in the blastx file (with same
 score/evalue/etc), but only RUN2 has a protein2genome intermediate file
 with the CAN65888 sequence. maker_bopts.ctl options are the same for both
 runs. When comparing the GFF files from the two runs, there is a blastx
 and a protein2genome hit in RUN1, but in RUN2 those two hits are not
 there.

 copy of maker_bopts.ctl
 #-----BLAST and Exonerate statistics thresholds
 percov_blastn:0.80 #Blastn Percent Coverage Threhold EST-Genome Alignments
 percid_blastn:0.85 #Blastn Percent Identity Threshold EST-Genome Aligments
 eval_blastn:1e-10 #Blastn eval cutoff
 bit_blastn:40 #Blastn bit cutoff
 percov_blastx:0.50 #Blastx Percent Coverage Threhold Protein-Genome
 Alignments
 percid_blastx:0.40 #Blastx Percent Identity Threshold Protein-Genome
 Aligments
 eval_blastx:1e-6 #Blastx eval cutoff
 bit_blastx:30 #Blastx bit cutoff
 e_perc_cov:50 #Exonerate Percent Coverage Thresshold EST_Genome Alignments
 ep_score_limit:20 #Report  alignments scoring at least this percentage of
 the maximal score exonerate nucleotide
 en_score_limit:20 #Report  alignments scoring at least this percentage of
 the maximal score exonerate protein

-- 
Ticket URL: <http://malachite.genetics.utah.edu/projects/maker/ticket/27>
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