-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_7/scaffold_7_11996231-12344961

-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 Augustus_model.g12262.t1
Valid prediction for snap_scaffold_7-snap.2273-T1
Valid prediction for CodingQuarry_transcript_57656-T1
Valid prediction for GlimmerHMM_glimmerT_18197-T1
Valid prediction for GlimmerHMM_glimmerT_18202-T1
Valid prediction for HiQ_model.g12263.t1
Valid prediction for CodingQuarry_transcript_57655-T1
Valid prediction for snap_scaffold_7-snap.2295-T1
Valid prediction for GlimmerHMM_glimmerT_18204-T1
Valid prediction for Augustus_model.g12260.t1
Valid prediction for pasa_asmbl_50206.p1
Valid prediction for GlimmerHMM_glimmerT_18212-T1
Valid prediction for snap_scaffold_7-snap.2287-T1
Valid prediction for snap_scaffold_7-snap.2278-T1
Valid prediction for snap_scaffold_7-snap.2296-T1
Valid prediction for pasa_asmbl_50238.p1
Valid prediction for GlimmerHMM_glimmerT_18220-T1
Valid prediction for snap_scaffold_7-snap.2277-T1
Couldn't classify 268543, 269415
Sorry, prediction pasa_asmbl_50228.p1 fails validation.
(TCA)	 CA	268543-269415	CT	ACC
Valid prediction for Augustus_model.g12261.t1
Valid prediction for Augustus_model.g12265.t1
Couldn't classify 338827, 339382
Couldn't classify 339931, 339961
Sorry, prediction pasa_asmbl_50243.p1 fails validation.
(GAG)	 TG	338827-339382	GT	GGG
(GGC)	 AG	339536-339752	GT	AGG
(GGA)	 AG	339931-339961	CA	TGC
-recovered pasa_asmbl_50243.p1, internal, 339536, 339752
Valid prediction for snap_scaffold_7-snap.2280-T1
Valid prediction for snap_scaffold_7-snap.2293-T1
Couldn't classify 238431, 238527
Couldn't classify 239333, 239400
Sorry, prediction pasa_asmbl_50222.p1 fails validation.
(GAC)	 TT	238431-238527	GT	ATG
(ATC)	 AG	238673-238869	GT	TAG
(GAA)	 AG	239063-239237	GT	ATG
(ATG)	 AG	239333-239400	GG	CAG
-recovered pasa_asmbl_50222.p1, internal, 238673, 238869
-recovered pasa_asmbl_50222.p1, internal, 239063, 239237
Valid prediction for CodingQuarry_transcript_57650-T1
Valid prediction for CodingQuarry_transcript_57647-T1
Valid prediction for GlimmerHMM_glimmerT_18210-T1
Couldn't classify 270757, 270840
Sorry, prediction pasa_asmbl_50235.p1 fails validation.
(GAT)	 TA	270757-270840	GT	AGG
(AAA)	 AG	271064-271231	GT	AGG
(AGA)	 AG	271607-271653	GT	AAG
(AGA)	 AG	271980-272094	GT	AGG
(CTG)	 AG	272316-272441	GT	AGG
(GGG)	 AG	272558-272752	GT	AGG
(CTG)	 AG	274124-274219	GT	CGG
(CAA)	 AG	274975-275027	GT	ATG
(TTT)	 AG	275204-275310	GT	TGG
(GTA)	 AG	275618-275685	CA	AAC
-recovered pasa_asmbl_50235.p1, terminal, 275618, 275685
-recovered pasa_asmbl_50235.p1, internal, 271064, 271231
-recovered pasa_asmbl_50235.p1, internal, 271607, 271653
-recovered pasa_asmbl_50235.p1, internal, 271980, 272094
-recovered pasa_asmbl_50235.p1, internal, 272316, 272441
-recovered pasa_asmbl_50235.p1, internal, 272558, 272752
-recovered pasa_asmbl_50235.p1, internal, 274124, 274219
-recovered pasa_asmbl_50235.p1, internal, 274975, 275027
-recovered pasa_asmbl_50235.p1, internal, 275204, 275310
Valid prediction for CodingQuarry_transcript_57651-T1
Valid prediction for HiQ_model.g12256.t1
Couldn't classify 292861, 293008
Sorry, prediction pasa_asmbl_50242.p1 fails validation.
(ATT)	 AG	292861-293008	GT	GAG
(ATG)	 AG	293148-293227	GT	AGG
(GTA)	 AG	293414-293542	GT	CAG
(GTG)	 AG	293633-293721	GT	ATG
(CAT)	 AG	293928-294036	GT	AGG
(GCC)	 AG	294153-294251	GT	AGG
(CTA)	 AG	294337-294483	GT	AGG
(TAT)	 AG	294648-294886	GT	CGG
(AGT)	 AG	294985-295131	GT	AGG
(CAT)	 AG	295252-295372	GT	TGG
(GGA)	 AG	295483-295620	GC	GAG
add_exon() Sorry, pasa_asmbl_50242.p1 293148-293227-initial-1 is invalid.
-recovered pasa_asmbl_50242.p1, initial, 293148, 293227
add_exon() Sorry, pasa_asmbl_50242.p1 292861-293008-terminal-3 is invalid.
-recovered pasa_asmbl_50242.p1, terminal, 292861, 293008
-recovered pasa_asmbl_50242.p1, terminal, 295483, 295620
-recovered pasa_asmbl_50242.p1, internal, 292861, 293008
-recovered pasa_asmbl_50242.p1, internal, 293148, 293227
-recovered pasa_asmbl_50242.p1, internal, 293414, 293542
-recovered pasa_asmbl_50242.p1, internal, 293633, 293721
-recovered pasa_asmbl_50242.p1, internal, 293928, 294036
-recovered pasa_asmbl_50242.p1, internal, 294153, 294251
-recovered pasa_asmbl_50242.p1, internal, 294337, 294483
-recovered pasa_asmbl_50242.p1, internal, 294648, 294886
-recovered pasa_asmbl_50242.p1, internal, 294985, 295131
-recovered pasa_asmbl_50242.p1, internal, 295252, 295372
-recovered pasa_asmbl_50242.p1, internal, 295483, 295620
Valid prediction for snap_scaffold_7-snap.2284-T1
Valid prediction for snap_scaffold_7-snap.2268-T1
Valid prediction for Augustus_model.g12268.t1
Valid prediction for GlimmerHMM_glimmerT_18219-T1
Valid prediction for HiQ_model.g12254.t1
Valid prediction for GlimmerHMM_glimmerT_18218-T1
Valid prediction for snap_scaffold_7-snap.2286-T1
Valid prediction for HiQ_model.g12252.t1
Valid prediction for snap_scaffold_7-snap.2267-T1
Valid prediction for HiQ_model.g12250.t1
Valid prediction for pasa_asmbl_50217.p1
Valid prediction for snap_scaffold_7-snap.2294-T1
Valid prediction for pasa_asmbl_50213.p1
Valid prediction for GlimmerHMM_glimmerT_18201-T1
Valid prediction for pasa_asmbl_50212.p1
Valid prediction for CodingQuarry_transcript_57653-T1
Valid prediction for snap_scaffold_7-snap.2272-T1
Valid prediction for GlimmerHMM_glimmerT_18223-T1
Valid prediction for HiQ_model.g12251.t1
Couldn't classify 340198, 340372
Sorry, prediction pasa_asmbl_50616.p1 fails validation.
(GAG)	 AG	340198-340372	GT	AAG
(ACA)	 AG	340554-340648	GT	TTG
(ATT)	 AG	340734-340815	GT	TGG
(GCG)	 AG	340944-341236	AC	GAA
-recovered pasa_asmbl_50616.p1, terminal, 340944, 341236
-recovered pasa_asmbl_50616.p1, internal, 340198, 340372
-recovered pasa_asmbl_50616.p1, internal, 340554, 340648
-recovered pasa_asmbl_50616.p1, internal, 340734, 340815
Valid prediction for snap_scaffold_7-snap.2276-T1
Valid prediction for CodingQuarry_transcript_57646-T1
Valid prediction for GlimmerHMM_glimmerT_18206-T1
Valid prediction for CodingQuarry_transcript_57648-T1
Valid prediction for pasa_asmbl_50205.p1
Valid prediction for GlimmerHMM_glimmerT_18214-T1
Valid prediction for Augustus_model.g12269.t1
Valid prediction for CodingQuarry_transcript_57654-T1
Valid prediction for snap_scaffold_7-snap.2291-T1
Valid prediction for HiQ_model.g12264.t1
Valid prediction for snap_scaffold_7-snap.2285-T1
Valid prediction for CodingQuarry_transcript_57652-T1
Valid prediction for snap_scaffold_7-snap.2289-T1
Valid prediction for GlimmerHMM_glimmerT_18224-T1
Valid prediction for GlimmerHMM_glimmerT_18222-T1
Valid prediction for snap_scaffold_7-snap.2288-T1
Valid prediction for Augustus_model.g12267.t1
Valid prediction for snap_scaffold_7-snap.2279-T1
Valid prediction for pasa_asmbl_50215.p1

-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_18208-T1
Valid prediction for CodingQuarry_transcript_57657-T1
Valid prediction for snap_scaffold_7-snap.2292-T1
Valid prediction for snap_scaffold_7-snap.2281-T1
Valid prediction for GlimmerHMM_glimmerT_18203-T1
Valid prediction for Augustus_model.g12257.t1
Valid prediction for pasa_asmbl_51195.p1
Valid prediction for Augustus_model.g12248.t1
Valid prediction for snap_scaffold_7-snap.2266-T1
Valid prediction for pasa_asmbl_51194.p1
Valid prediction for HiQ_model.g12270.t1
Valid prediction for GlimmerHMM_glimmerT_18213-T1
Valid prediction for GlimmerHMM_glimmerT_18207-T1
Valid prediction for GlimmerHMM_glimmerT_18211-T1
Valid prediction for GlimmerHMM_glimmerT_18198-T1
Valid prediction for snap_scaffold_7-snap.2265-T1
Valid prediction for CodingQuarry_transcript_57649-T1
Valid prediction for Augustus_model.g12247.t1
Valid prediction for pasa_asmbl_51185.p1
Valid prediction for GlimmerHMM_glimmerT_18196-T1
Valid prediction for snap_scaffold_7-snap.2297-T1
Valid prediction for snap_scaffold_7-snap.2290-T1
Valid prediction for snap_scaffold_7-snap.2271-T1
Valid prediction for GlimmerHMM_glimmerT_18226-T1
Valid prediction for GlimmerHMM_glimmerT_18221-T1
Couldn't classify 346714, 347115
Sorry, prediction pasa_asmbl_51183.p1 fails validation.
(GCT)	 CA	346714-347115	TG	AGT
Valid prediction for HiQ_model.g12259.t1
Valid prediction for snap_scaffold_7-snap.2264-T1
Valid prediction for GlimmerHMM_glimmerT_18227-T1
Valid prediction for GlimmerHMM_glimmerT_18205-T1
Valid prediction for Augustus_model.g12255.t1
Valid prediction for HiQ_model.g12253.t1
Valid prediction for pasa_asmbl_51192.p1
Valid prediction for Augustus_model.g12258.t1
Valid prediction for snap_scaffold_7-snap.2282-T1
Valid prediction for GlimmerHMM_glimmerT_18200-T1
Valid prediction for GlimmerHMM_glimmerT_18209-T1
Valid prediction for GlimmerHMM_glimmerT_18216-T1
Valid prediction for snap_scaffold_7-snap.2270-T1
Couldn't classify 130232, 130321
Sorry, prediction pasa_asmbl_51190.p1 fails validation.
(ATG)	 AA	127897-128133	GT	AAG
(AAA)	 AG	128335-128425	GT	AGG
(TTA)	 AG	128614-128656	GT	AGG
(AGA)	 AG	128888-128990	GT	AGG
(TCC)	 AG	130232-130321	GT	AGG
-recovered pasa_asmbl_51190.p1, initial, 127897, 128133
-recovered pasa_asmbl_51190.p1, internal, 128335, 128425
-recovered pasa_asmbl_51190.p1, internal, 128614, 128656
-recovered pasa_asmbl_51190.p1, internal, 128888, 128990
-recovered pasa_asmbl_51190.p1, internal, 130232, 130321
Valid prediction for snap_scaffold_7-snap.2283-T1
Valid prediction for HiQ_model.g12266.t1
Valid prediction for GlimmerHMM_glimmerT_18199-T1
Valid prediction for snap_scaffold_7-snap.2275-T1
Valid prediction for GlimmerHMM_glimmerT_18215-T1
Couldn't classify 276060, 276104
Sorry, prediction pasa_asmbl_51184.p1 fails validation.
(TTG)	 CA	276060-276104	GT	CTG
(GCA)	 AG	276470-276584	GT	CAG
(ATG)	 AG	276730-276871	GT	TTG
(CAC)	 AG	276967-277102	GT	AGG
(ACA)	 AG	277299-277402	GT	AGG
(GGG)	 AG	277489-277654	GT	CGG
(ATC)	 AG	277746-277796	GC	AGG
add_exon() Sorry, pasa_asmbl_51184.p1 276730-276871-initial-1 is invalid.
-recovered pasa_asmbl_51184.p1, initial, 276730, 276871
-recovered pasa_asmbl_51184.p1, terminal, 277746, 277796
-recovered pasa_asmbl_51184.p1, internal, 276470, 276584
-recovered pasa_asmbl_51184.p1, internal, 276730, 276871
-recovered pasa_asmbl_51184.p1, internal, 276967, 277102
-recovered pasa_asmbl_51184.p1, internal, 277299, 277402
-recovered pasa_asmbl_51184.p1, internal, 277489, 277654
-recovered pasa_asmbl_51184.p1, internal, 277746, 277796
Valid prediction for snap_scaffold_7-snap.2274-T1
Valid prediction for snap_scaffold_7-snap.2269-T1
Valid prediction for GlimmerHMM_glimmerT_18225-T1
Valid prediction for Augustus_model.g12249.t1
Valid prediction for GlimmerHMM_glimmerT_18217-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12567, rend_intergenic: 11987  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 348731
-exon list size: 469


building trellis

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20.8    
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21.2    
21.4    
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21.9    
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22.3    
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22.7    
22.9    
23.1    
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23.6    
23.8    
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24.2    
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24.8    
25.1    
25.3    
25.5    
25.7    
25.9    
26.1    
26.3    
26.5    
26.8    
27.0    
27.2    
27.4    
27.6    
27.8    
28.0    
28.2    
28.5    
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28.9    
29.1    
29.3    
29.5    
29.7    
29.9    
30.1    
30.4    
30.6    
30.8    
31.0    
31.2    
31.4    
31.6    
31.8    
32.1    
32.3    
32.5    
32.7    
32.9    
33.1    
33.3    
33.5    
33.8    
34.0    
34.2    
34.4    
34.6    
34.8    
35.0    
35.2    
35.5    
35.7    
35.9    
36.1    
36.3    
36.5    
36.7    
36.9    
37.2    
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37.6    
37.8    
38.0    
38.2    
38.4    
38.6    
38.9    
39.1    
39.3    
39.5    
39.7    
39.9    
40.1    
40.3    
40.6    
40.8    
41.0    
41.2    
41.4    
41.6    
41.8    
42.0    
42.3    
42.5    
42.7    
42.9    
43.1    
43.3    
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43.9    
44.2    
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44.6    
44.8    
45.0    
45.2    
45.4    
45.6    
45.9    
46.1    
46.3    
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46.9    
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47.6    
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48.2    
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48.6    
48.8    
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50.1    
50.3    
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51.2    
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51.6    
51.8    
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58.8    
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59.2    
59.4    
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59.9    
60.1    
60.3    
60.5    
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60.9    
61.1    
61.4    
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61.8    
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64.1    
64.3    
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65.0    
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65.6    
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66.0    
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67.3    
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68.8    
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69.2    
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77.9    
78.1    
78.3    
78.6    
78.8    
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79.2    
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80.0    
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81.3    
81.5    
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82.0    
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82.6    
82.8    
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83.4    
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83.9    
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84.3    
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84.9    
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85.4    
85.6    
85.8    
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87.3    
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87.9    
88.1    
88.3    
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88.7    
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89.8    
90.0    
90.2    
90.4    
90.7    
90.9    
91.1    
91.3    
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91.9    
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92.4    
92.6    
92.8    
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96.6    
96.8    
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97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.2    
99.4    
99.6    
99.8    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 12567, rend_intergenic: 11987  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 28 predictions persist after filtering for low support