-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_26/scaffold_26_8492186-8668712

-reading genomic sequence.

** Processing features (+)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: +)
-loading gene prediction evidence. (strand: +)Valid prediction for GlimmerHMM_glimmerT_56264-T1
Couldn't classify 143781, 143834
Sorry, prediction pasa_asmbl_35184.p1 fails validation.
(ATG)	 AA	142832-142923	GT	GGG
(GAA)	 AG	143095-143201	GT	TGG
(TCA)	 AG	143469-143537	GT	AGG
(AAT)	 AG	143638-143681	GT	CAG
(CTC)	 AG	143781-143834	CA	ACC
-recovered pasa_asmbl_35184.p1, initial, 142832, 142923
-recovered pasa_asmbl_35184.p1, internal, 143095, 143201
-recovered pasa_asmbl_35184.p1, internal, 143469, 143537
-recovered pasa_asmbl_35184.p1, internal, 143638, 143681
Valid prediction for GlimmerHMM_glimmerT_56266-T1
Valid prediction for snap_scaffold_26-snap.1988-T1
Valid prediction for snap_scaffold_26-snap.1973-T1
Valid prediction for snap_scaffold_26-snap.1985-T1
Valid prediction for snap_scaffold_26-snap.1968-T1
Valid prediction for snap_scaffold_26-snap.1980-T1
Valid prediction for Augustus_model.g37272.t1
Valid prediction for snap_scaffold_26-snap.1965-T1
Valid prediction for HiQ_model.g37273.t1
Valid prediction for CodingQuarry_transcript_40415-T1
Valid prediction for CodingQuarry_transcript_40414-T1
Valid prediction for GlimmerHMM_glimmerT_56252-T1
Valid prediction for HiQ_model.g37280.t1
Valid prediction for GlimmerHMM_glimmerT_56254-T1
Valid prediction for snap_scaffold_26-snap.1955-T1
Valid prediction for GlimmerHMM_glimmerT_56262-T1
Valid prediction for Augustus_model.g37281.t1
Valid prediction for Augustus_model.g37278.t1
Valid prediction for snap_scaffold_26-snap.1984-T1
Valid prediction for GlimmerHMM_glimmerT_56261-T1
Valid prediction for snap_scaffold_26-snap.1975-T1
Valid prediction for snap_scaffold_26-snap.1990-T1
Valid prediction for snap_scaffold_26-snap.1974-T1
Valid prediction for GlimmerHMM_glimmerT_56243-T1
Valid prediction for snap_scaffold_26-snap.1970-T1
Valid prediction for Augustus_model.g37275.t1
Valid prediction for Augustus_model.g37266.t1
Valid prediction for GlimmerHMM_glimmerT_56246-T1
Valid prediction for pasa_asmbl_35181.p1
Valid prediction for snap_scaffold_26-snap.1956-T1
Valid prediction for GlimmerHMM_glimmerT_56256-T1
Valid prediction for snap_scaffold_26-snap.1987-T1
Valid prediction for snap_scaffold_26-snap.1977-T1
Valid prediction for snap_scaffold_26-snap.1981-T1

-loading the search evidence (protein and EST search results, strand: +)
-scoring exons (strand: +)

** Processing features (-)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: -)
-loading gene prediction evidence. (strand: -)Valid prediction for snap_scaffold_26-snap.1966-T1
Valid prediction for Augustus_model.g37277.t1
Valid prediction for Augustus_model.g37268.t1
Valid prediction for GlimmerHMM_glimmerT_56268-T1
Valid prediction for Augustus_model.g37282.t1
Valid prediction for Augustus_model.g37284.t1
Valid prediction for GlimmerHMM_glimmerT_56267-T1
Valid prediction for GlimmerHMM_glimmerT_56260-T1
Valid prediction for GlimmerHMM_glimmerT_56242-T1
Couldn't classify 79761, 79904
Couldn't classify 82227, 82411
Sorry, prediction pasa_asmbl_35734.p1 fails validation.
(CTC)	 GT	79761-79904	GT	AGG
(CAG)	 AG	80030-80161	GT	AGG
(GAG)	 AG	80652-80817	GT	GAG
(GTC)	 AG	80937-81041	GT	GGG
(TTA)	 AG	82227-82411	CG	ACC
add_exon() Sorry, pasa_asmbl_35734.p1 80652-80817-terminal-3 is invalid.
-recovered pasa_asmbl_35734.p1, terminal, 80652, 80817
-recovered pasa_asmbl_35734.p1, internal, 80030, 80161
-recovered pasa_asmbl_35734.p1, internal, 80652, 80817
-recovered pasa_asmbl_35734.p1, internal, 80937, 81041
Valid prediction for snap_scaffold_26-snap.1967-T1
Valid prediction for GlimmerHMM_glimmerT_56263-T1
Valid prediction for Augustus_model.g37270.t1
Valid prediction for Augustus_model.g37271.t1
Valid prediction for GlimmerHMM_glimmerT_56245-T1
Valid prediction for GlimmerHMM_glimmerT_56253-T1
Valid prediction for snap_scaffold_26-snap.1971-T1
Valid prediction for snap_scaffold_26-snap.1963-T1
Valid prediction for GlimmerHMM_glimmerT_56258-T1
Valid prediction for Augustus_model.g37269.t1
Valid prediction for snap_scaffold_26-snap.1976-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for Augustus_model.g37274.t1
Valid prediction for GlimmerHMM_glimmerT_56251-T1
Valid prediction for GlimmerHMM_glimmerT_56249-T1
Couldn't classify 88354, 88410
Couldn't classify 89671, 89735
Sorry, prediction pasa_asmbl_35918.p1 fails validation.
(GGG)	 TG	88354-88410	GT	CAG
(GAT)	 AG	88752-88881	GT	AGG
(ATG)	 AG	89366-89434	GT	AGG
(ACT)	 AG	89517-89576	GT	TGG
(CTG)	 AG	89671-89735	GT	ATG
add_exon() Sorry, pasa_asmbl_35918.p1 89366-89434-initial-1 is invalid.
-recovered pasa_asmbl_35918.p1, initial, 89366, 89434
-recovered pasa_asmbl_35918.p1, internal, 88752, 88881
-recovered pasa_asmbl_35918.p1, internal, 89366, 89434
-recovered pasa_asmbl_35918.p1, internal, 89517, 89576
-recovered pasa_asmbl_35918.p1, internal, 89671, 89735
Valid prediction for snap_scaffold_26-snap.1962-T1
Valid prediction for snap_scaffold_26-snap.1986-T1
Valid prediction for GlimmerHMM_glimmerT_56255-T1
Couldn't classify 82463, 82927
Sorry, prediction pasa_asmbl_35733.p1 fails validation.
(TCC)	 TC	82463-82927	CC	AAC
Valid prediction for HiQ_model.g37279.t1
Valid prediction for snap_scaffold_26-snap.1989-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_26-snap.1978-T1
Valid prediction for snap_scaffold_26-snap.1972-T1
Valid prediction for Augustus_model.g37267.t1
Valid prediction for snap_scaffold_26-snap.1957-T1
Couldn't classify 75281, 75483
Couldn't classify 78025, 78140
Sorry, prediction pasa_asmbl_35739.p1 fails validation.
(CAG)	 CG	75281-75483	GT	AGG
(GTC)	 AG	75647-75708	GT	AGG
(ACC)	 AG	76678-76731	GT	AGG
(AGC)	 AG	78025-78140	TT	TCT
-recovered pasa_asmbl_35739.p1, internal, 75647, 75708
-recovered pasa_asmbl_35739.p1, internal, 76678, 76731
Valid prediction for GlimmerHMM_glimmerT_56270-T1
Valid prediction for CodingQuarry_transcript_40416-T1
Valid prediction for Augustus_model.g37283.t1
Valid prediction for GlimmerHMM_glimmerT_56269-T1
Valid prediction for GlimmerHMM_glimmerT_56247-T1
Valid prediction for snap_scaffold_26-snap.1960-T1
Valid prediction for snap_scaffold_26-snap.1958-T1
Valid prediction for GlimmerHMM_glimmerT_56259-T1
Valid prediction for snap_scaffold_26-snap.1983-T1
Valid prediction for snap_scaffold_26-snap.1991-T1
Valid prediction for snap_scaffold_26-snap.1964-T1
Valid prediction for snap_scaffold_26-snap.1979-T1
Valid prediction for snap_scaffold_26-snap.1969-T1
Valid prediction for snap_scaffold_26-snap.1959-T1
Valid prediction for GlimmerHMM_glimmerT_56271-T1
Valid prediction for GlimmerHMM_glimmerT_56244-T1
Couldn't classify 33870, 34016
Sorry, prediction pasa_asmbl_35744.p1 fails validation.
(GTT)	 AC	33870-34016	GT	ATG
(AGT)	 AG	34295-34366	GT	AGG
(ACT)	 AG	34507-34623	GT	AGG
(TGG)	 AG	34734-34925	GT	TGG
(GTC)	 AG	35048-35236	GT	CGG
(GGT)	 AG	35402-35476	GT	CGG
(ATG)	 AG	35750-35857	GT	TGG
(GGT)	 AG	35972-36028	CC	GAC
-recovered pasa_asmbl_35744.p1, initial, 35750, 35857
-recovered pasa_asmbl_35744.p1, terminal, 35972, 36028
-recovered pasa_asmbl_35744.p1, internal, 34295, 34366
-recovered pasa_asmbl_35744.p1, internal, 34507, 34623
-recovered pasa_asmbl_35744.p1, internal, 34734, 34925
-recovered pasa_asmbl_35744.p1, internal, 35048, 35236
-recovered pasa_asmbl_35744.p1, internal, 35402, 35476
-recovered pasa_asmbl_35744.p1, internal, 35750, 35857
Valid prediction for GlimmerHMM_glimmerT_56248-T1
Valid prediction for GlimmerHMM_glimmerT_56257-T1
Valid prediction for GlimmerHMM_glimmerT_56250-T1
Valid prediction for Augustus_model.g37276.t1
Couldn't classify 25324, 25407
Sorry, prediction pasa_asmbl_35746.p1 fails validation.
(CGG)	 CA	25324-25407	GT	AGG
(GTC)	 AG	25569-25763	GT	AGG
(GTG)	 AG	25884-26423	GA	GAG
-recovered pasa_asmbl_35746.p1, terminal, 25884, 26423
-recovered pasa_asmbl_35746.p1, internal, 25569, 25763
Valid prediction for snap_scaffold_26-snap.1961-T1
Valid prediction for GlimmerHMM_glimmerT_56265-T1
Valid prediction for snap_scaffold_26-snap.1982-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 69589, rend_intergenic: 65445  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74047, rend_intergenic: 69668  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112401, rend_intergenic: 98941  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122517, rend_intergenic: 116058  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133900, rend_intergenic: 126796  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169258, rend_intergenic: 166139  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 176527
-exon list size: 414


building trellis

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34.6    
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35.8    
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37.3    
37.5    
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38.0    
38.2    
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38.7    
38.9    
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40.6    
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41.6    
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80.0    
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92.3    
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93.3    
93.5    
93.8    
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94.2    
94.5    
94.7    
95.0    
95.2    
95.4    
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95.9    
96.2    
96.4    
96.6    
96.9    
97.1    
97.4    
97.6    
97.8    
98.1    
98.3    
98.6    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 69589, rend_intergenic: 65445  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74047, rend_intergenic: 69668  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112401, rend_intergenic: 98941  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122517, rend_intergenic: 116058  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133900, rend_intergenic: 126796  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169258, rend_intergenic: 166139  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support