-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_19/scaffold_19_11512616-11722558

-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 snap_scaffold_19-snap.2268-T1
Valid prediction for GlimmerHMM_glimmerT_44950-T1
Valid prediction for snap_scaffold_19-snap.2258-T1
Valid prediction for Augustus_model.g29810.t1
Valid prediction for Augustus_model.g29796.t1
Valid prediction for snap_scaffold_19-snap.2269-T1
Valid prediction for GlimmerHMM_glimmerT_44941-T1
Valid prediction for GlimmerHMM_glimmerT_44948-T1
Valid prediction for Augustus_model.g29799.t1
Valid prediction for GlimmerHMM_glimmerT_44945-T1
Valid prediction for snap_scaffold_19-snap.2253-T1
Valid prediction for Augustus_model.g29807.t1
Valid prediction for Augustus_model.g29806.t1
Valid prediction for Augustus_model.g29803.t1
Valid prediction for snap_scaffold_19-snap.2245-T1
Valid prediction for snap_scaffold_19-snap.2256-T1
Couldn't classify 38607, 38963
Sorry, prediction pasa_asmbl_21709.p1 fails validation.
(GGA)	 TC	38607-38963	AA	AGA
Valid prediction for snap_scaffold_19-snap.2261-T1
Valid prediction for GlimmerHMM_glimmerT_44932-T1
Valid prediction for GlimmerHMM_glimmerT_44927-T1
Valid prediction for Augustus_model.g29808.t1
Valid prediction for GlimmerHMM_glimmerT_44923-T1
Valid prediction for Augustus_model.g29798.t1
Valid prediction for GlimmerHMM_glimmerT_44926-T1
Valid prediction for Augustus_model.g29800.t1
Valid prediction for GlimmerHMM_glimmerT_44937-T1
Valid prediction for snap_scaffold_19-snap.2241-T1
Valid prediction for GlimmerHMM_glimmerT_44952-T1
Valid prediction for Augustus_model.g29805.t1
Valid prediction for snap_scaffold_19-snap.2264-T1
Valid prediction for GlimmerHMM_glimmerT_44936-T1
Valid prediction for Augustus_model.g29813.t1
Valid prediction for snap_scaffold_19-snap.2247-T1
Valid prediction for GlimmerHMM_glimmerT_44946-T1
Valid prediction for GlimmerHMM_glimmerT_44940-T1
Valid prediction for Augustus_model.g29804.t1
Valid prediction for Augustus_model.g29795.t1
Valid prediction for snap_scaffold_19-snap.2266-T1
Valid prediction for GlimmerHMM_glimmerT_44943-T1
Valid prediction for snap_scaffold_19-snap.2251-T1
Valid prediction for Augustus_model.g29809.t1
Valid prediction for snap_scaffold_19-snap.2242-T1
Valid prediction for snap_scaffold_19-snap.2232-T1
Valid prediction for GlimmerHMM_glimmerT_44953-T1
Valid prediction for snap_scaffold_19-snap.2271-T1
Valid prediction for snap_scaffold_19-snap.2259-T1
Couldn't classify 168421, 168576
Couldn't classify 169998, 170221
Sorry, prediction pasa_asmbl_21713.p1 fails validation.
(GAA)	 CA	168421-168576	GT	AGG
(TCT)	 AG	169666-169756	GT	GAG
(ATC)	 AG	169998-170221	TA	GGT
-recovered pasa_asmbl_21713.p1, internal, 169666, 169756
Valid prediction for snap_scaffold_19-snap.2243-T1
Valid prediction for Augustus_model.g29811.t1
Valid prediction for snap_scaffold_19-snap.2254-T1
Valid prediction for GlimmerHMM_glimmerT_44947-T1
Valid prediction for GlimmerHMM_glimmerT_44933-T1
Valid prediction for Augustus_model.g29789.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 GlimmerHMM_glimmerT_44935-T1
Couldn't classify 163151, 163152
Couldn't classify 163942, 164286
Couldn't classify 164692, 165200
Couldn't classify 165846, 165936
Sorry, prediction CodingQuarry_transcript_25806-T1 fails validation.
(ATG)	 GA	163151-163152	GT	ATG
(GAA)	 AG	163528-163832	GT	AGG
(ACG)	 AG	163942-164286	AC	GGA
(CCG)	 GG	164692-165200	GT	GGG
(CTG)	 AG	165846-165936	TT	AGT
(GAG)	 AG	165969-165979	CC	AAC
-recovered CodingQuarry_transcript_25806-T1, terminal, 165969, 165979
-recovered CodingQuarry_transcript_25806-T1, internal, 163528, 163832
Valid prediction for snap_scaffold_19-snap.2255-T1
Valid prediction for CodingQuarry_transcript_25808-T1
Valid prediction for Augustus_model.g29812.t1
Valid prediction for snap_scaffold_19-snap.2260-T1
Valid prediction for snap_scaffold_19-snap.2239-T1
Couldn't classify 187188, 187277
Couldn't classify 187945, 188000
Sorry, prediction pasa_asmbl_22421.p1 fails validation.
(CTG)	 GA	187188-187277	GT	AGG
(GTA)	 AG	187437-187517	GT	GGG
(GAG)	 AG	187707-187857	GT	AGG
(CAC)	 AG	187945-188000	GG	AAG
-recovered pasa_asmbl_22421.p1, internal, 187437, 187517
-recovered pasa_asmbl_22421.p1, internal, 187707, 187857
Valid prediction for snap_scaffold_19-snap.2273-T1
Valid prediction for GlimmerHMM_glimmerT_44944-T1
Valid prediction for snap_scaffold_19-snap.2252-T1
Valid prediction for pasa_asmbl_22417.p2
Valid prediction for Augustus_model.g29788.t1
Valid prediction for snap_scaffold_19-snap.2231-T1
Valid prediction for snap_scaffold_19-snap.2234-T1
Couldn't classify 746, 1021
Sorry, prediction pasa_asmbl_22431.p1 fails validation.
(TTG)	 GA	746-1021	GT	AGG
(CTG)	 AG	1569-1746	GT	GGG
(TCC)	 AG	2115-2353	GT	AGG
(ATG)	 AG	2521-2682	AC	GAA
-recovered pasa_asmbl_22431.p1, terminal, 2521, 2682
-recovered pasa_asmbl_22431.p1, internal, 1569, 1746
-recovered pasa_asmbl_22431.p1, internal, 2115, 2353
Valid prediction for Augustus_model.g29797.t1
Valid prediction for GlimmerHMM_glimmerT_44951-T1
Valid prediction for GlimmerHMM_glimmerT_44929-T1
Valid prediction for CodingQuarry_transcript_25805-T1
Valid prediction for pasa_asmbl_22427.p1
Valid prediction for GlimmerHMM_glimmerT_44942-T1
Valid prediction for snap_scaffold_19-snap.2249-T1
Valid prediction for snap_scaffold_19-snap.2265-T1
Valid prediction for GlimmerHMM_glimmerT_44925-T1
Valid prediction for GlimmerHMM_glimmerT_44939-T1
Valid prediction for snap_scaffold_19-snap.2240-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for HiQ_model.g29790.t1
Valid prediction for snap_scaffold_19-snap.2272-T1
Valid prediction for GlimmerHMM_glimmerT_44938-T1
Valid prediction for HiQ_model.g29791.t1
Valid prediction for snap_scaffold_19-snap.2233-T1
Valid prediction for GlimmerHMM_glimmerT_44934-T1
Valid prediction for snap_scaffold_19-snap.2246-T1
Valid prediction for snap_scaffold_19-snap.2263-T1
Valid prediction for Augustus_model.g29802.t1
Valid prediction for snap_scaffold_19-snap.2257-T1
Valid prediction for pasa_asmbl_22423.p1
Valid prediction for GlimmerHMM_glimmerT_44928-T1
Valid prediction for snap_scaffold_19-snap.2248-T1
Valid prediction for snap_scaffold_19-snap.2250-T1
Couldn't classify 157753, 157849
Couldn't classify 157993, 158165
Sorry, prediction pasa_asmbl_22424.p1 fails validation.
(ATG)	 TA	151028-151105	GT	AGG
(GAG)	 AG	152713-152793	GT	AGG
(GTC)	 AG	153324-153516	GT	TGG
(ACG)	 AG	153610-153712	GT	TGG
(GAA)	 AG	153817-153913	GT	AGG
(ATC)	 AG	154042-154146	GT	AGG
(GCG)	 AG	154421-154543	GT	AGG
(CTA)	 AG	154817-154937	GT	TGG
(TCC)	 AG	155036-155123	GT	AGG
(CAA)	 AG	155223-155329	GT	CCG
(CTG)	 AG	155527-155651	GT	CTG
(CAC)	 AG	155831-155920	GT	AGG
(GTG)	 AG	156026-156199	GT	AGG
(TTG)	 AG	156333-156551	GT	AGG
(TTC)	 AG	156953-157036	GT	AGG
(ACG)	 AG	157158-157290	GT	CAG
(CCC)	 AG	157538-157659	GT	TGG
(GTG)	 AG	157753-157849	AT	TGA
(GTG)	 AC	157993-158165	GT	AGG
(TGC)	 AG	158306-158417	GT	CGG
(CCA)	 AG	158548-158603	GT	AGG
(GAC)	 AG	158728-158850	GT	TTG
(TGT)	 AG	159083-159302	GT	AGG
(AGG)	 AG	159403-159631	GT	AGG
(CAA)	 AG	159745-159886	GT	AGG
(GTC)	 AG	160009-160095	GG	GAG
-recovered pasa_asmbl_22424.p1, initial, 151028, 151105
-recovered pasa_asmbl_22424.p1, terminal, 160009, 160095
-recovered pasa_asmbl_22424.p1, internal, 152713, 152793
-recovered pasa_asmbl_22424.p1, internal, 153324, 153516
-recovered pasa_asmbl_22424.p1, internal, 153610, 153712
-recovered pasa_asmbl_22424.p1, internal, 153817, 153913
-recovered pasa_asmbl_22424.p1, internal, 154042, 154146
-recovered pasa_asmbl_22424.p1, internal, 154421, 154543
-recovered pasa_asmbl_22424.p1, internal, 154817, 154937
-recovered pasa_asmbl_22424.p1, internal, 155036, 155123
-recovered pasa_asmbl_22424.p1, internal, 155223, 155329
-recovered pasa_asmbl_22424.p1, internal, 155527, 155651
-recovered pasa_asmbl_22424.p1, internal, 155831, 155920
-recovered pasa_asmbl_22424.p1, internal, 156026, 156199
-recovered pasa_asmbl_22424.p1, internal, 156333, 156551
-recovered pasa_asmbl_22424.p1, internal, 156953, 157036
-recovered pasa_asmbl_22424.p1, internal, 157158, 157290
-recovered pasa_asmbl_22424.p1, internal, 157538, 157659
-recovered pasa_asmbl_22424.p1, internal, 158306, 158417
-recovered pasa_asmbl_22424.p1, internal, 158548, 158603
-recovered pasa_asmbl_22424.p1, internal, 158728, 158850
-recovered pasa_asmbl_22424.p1, internal, 159083, 159302
-recovered pasa_asmbl_22424.p1, internal, 159403, 159631
-recovered pasa_asmbl_22424.p1, internal, 159745, 159886
Valid prediction for snap_scaffold_19-snap.2244-T1
Valid prediction for snap_scaffold_19-snap.2270-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for Augustus_model.g29814.t1
Couldn't classify 188238, 188249
Couldn't classify 189572, 189742
Sorry, prediction pasa_asmbl_22420.p1 fails validation.
(GTA)	 AT	188238-188249	GT	CAG
(AGC)	 AG	188640-188748	GT	CGG
(CGT)	 AG	188934-189042	GT	GGG
(GTA)	 AG	189134-189287	GT	AGG
(GTG)	 AG	189572-189742	GT	AGG
-recovered pasa_asmbl_22420.p1, internal, 188640, 188748
-recovered pasa_asmbl_22420.p1, internal, 188934, 189042
-recovered pasa_asmbl_22420.p1, internal, 189134, 189287
-recovered pasa_asmbl_22420.p1, internal, 189572, 189742
Valid prediction for snap_scaffold_19-snap.2267-T1
Valid prediction for pasa_asmbl_22418.p1
Valid prediction for snap_scaffold_19-snap.2235-T1
Valid prediction for pasa_asmbl_22429.p1
Couldn't classify 146024, 146227
Couldn't classify 148285, 148472
Sorry, prediction pasa_asmbl_22426.p1 fails validation.
(ACG)	 GA	146024-146227	GT	AGG
(GTT)	 AG	146825-147388	GT	TGG
(GTC)	 AG	147923-148169	GT	AGG
(GTG)	 AG	148285-148472	GC	TCG
add_exon() Sorry, pasa_asmbl_22426.p1 147923-148169-terminal-3 is invalid.
-recovered pasa_asmbl_22426.p1, terminal, 147923, 148169
-recovered pasa_asmbl_22426.p1, internal, 146825, 147388
-recovered pasa_asmbl_22426.p1, internal, 147923, 148169
-recovered pasa_asmbl_22426.p1, internal, 148285, 148472
Valid prediction for GlimmerHMM_glimmerT_44924-T1
Valid prediction for CodingQuarry_transcript_25807-T1
Valid prediction for GlimmerHMM_glimmerT_44949-T1
Valid prediction for snap_scaffold_19-snap.2236-T1
Valid prediction for Augustus_model.g29794.t1
Valid prediction for snap_scaffold_19-snap.2262-T1
Valid prediction for HiQ_model.g29793.t1
Valid prediction for snap_scaffold_19-snap.2230-T1
Valid prediction for Augustus_model.g29801.t1
Valid prediction for GlimmerHMM_glimmerT_44931-T1
Couldn't classify 149002, 149142
Sorry, prediction pasa_asmbl_22425.p1 fails validation.
(TAT)	 GG	149002-149142	GT	AGG
(TTC)	 AG	149277-149459	CT	GAC
-recovered pasa_asmbl_22425.p1, terminal, 149277, 149459
Valid prediction for GlimmerHMM_glimmerT_44930-T1
Valid prediction for snap_scaffold_19-snap.2237-T1
Valid prediction for snap_scaffold_19-snap.2238-T1
Valid prediction for Augustus_model.g29792.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 90597, rend_intergenic: 85783  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93145, rend_intergenic: 91166  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97163, rend_intergenic: 93624  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113284, rend_intergenic: 102023  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119898, rend_intergenic: 113683  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127268, rend_intergenic: 123591  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128878, rend_intergenic: 127871  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132290, rend_intergenic: 130653  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138027, rend_intergenic: 132940  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147881, rend_intergenic: 146328  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154227, rend_intergenic: 148117  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159011, rend_intergenic: 154434  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165733, rend_intergenic: 159538  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170274, rend_intergenic: 165840  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182234, rend_intergenic: 175838  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185013, rend_intergenic: 182575  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186733, rend_intergenic: 185851  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 209943
-exon list size: 484


building trellis

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31.9    
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32.3    
32.5    
32.7    
32.9    
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33.3    
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34.6    
34.8    
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40.9    
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83.1    
83.3    
83.5    
83.7    
84.0    
84.2    
84.4    
84.6    
84.8    
85.0    
85.2    
85.4    
85.6    
85.8    
86.0    
86.2    
86.4    
86.6    
86.8    
87.0    
87.2    
87.4    
87.7    
87.9    
88.1    
88.3    
88.5    
88.7    
88.9    
89.1    
89.3    
89.5    
89.7    
89.9    
90.1    
90.3    
90.5    
90.7    
90.9    
91.2    
91.4    
91.6    
91.8    
92.0    
92.2    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
94.0    
94.2    
94.4    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.3    
97.5    
97.7    
97.9    
98.1    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 37 predictions from path traversal
Error with prediction: snap lend_intergenic: 90597, rend_intergenic: 85783  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93145, rend_intergenic: 91166  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97163, rend_intergenic: 93624  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113284, rend_intergenic: 102023  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119898, rend_intergenic: 113683  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127268, rend_intergenic: 123591  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128878, rend_intergenic: 127871  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132290, rend_intergenic: 130653  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138027, rend_intergenic: 132940  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147881, rend_intergenic: 146328  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154227, rend_intergenic: 148117  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159011, rend_intergenic: 154434  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165733, rend_intergenic: 159538  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170274, rend_intergenic: 165840  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182234, rend_intergenic: 175838  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185013, rend_intergenic: 182575  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186733, rend_intergenic: 185851  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