-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_18978416-19156950

-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_3-snap.3766-T1
Valid prediction for GlimmerHMM_glimmerT_8599-T1
Valid prediction for snap_scaffold_3-snap.3769-T1
Valid prediction for Augustus_model.g5714.t1
Couldn't classify 161644, 161761
Couldn't classify 164822, 164870
Sorry, prediction pasa_asmbl_40722.p1 fails validation.
(TCC)	 TC	161644-161761	GT	GGG
(AGA)	 AG	161941-162096	GT	TGG
(TGT)	 AG	163485-163645	GT	AGG
(GGC)	 AG	163917-164119	GT	AGG
(AGG)	 AG	164822-164870	GG	TGG
-recovered pasa_asmbl_40722.p1, internal, 161941, 162096
-recovered pasa_asmbl_40722.p1, internal, 163485, 163645
-recovered pasa_asmbl_40722.p1, internal, 163917, 164119
Valid prediction for Augustus_model.g5724.t1
Valid prediction for snap_scaffold_3-snap.3771-T1
Valid prediction for GeneMark_model.13979_t
Valid prediction for GlimmerHMM_glimmerT_8608-T1
Valid prediction for GlimmerHMM_glimmerT_8605-T1
Valid prediction for Augustus_model.g5717.t1
Valid prediction for snap_scaffold_3-snap.3790-T1
Valid prediction for GeneMark_model.13988_t
Valid prediction for GeneMark_model.14005_t
Valid prediction for snap_scaffold_3-snap.3764-T1
Valid prediction for GeneMark_model.13997_t
Valid prediction for GlimmerHMM_glimmerT_8616-T1
Valid prediction for snap_scaffold_3-snap.3746-T1
Valid prediction for GeneMark_model.14002_t
Valid prediction for snap_scaffold_3-snap.3773-T1
Valid prediction for snap_scaffold_3-snap.3772-T1
Valid prediction for GeneMark_model.13992_t
Valid prediction for snap_scaffold_3-snap.3760-T1
Valid prediction for GeneMark_model.13971_t
Valid prediction for GlimmerHMM_glimmerT_8619-T1
Valid prediction for snap_scaffold_3-snap.3751-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.13975_t
Couldn't classify 81980, 82137
Couldn't classify 86259, 86411
Sorry, prediction pasa_asmbl_40799.p1 fails validation.
(CAA)	 AG	81980-82137	GT	AGG
(GAT)	 AG	83445-83524	GT	TGG
(CTC)	 AG	84991-85106	GT	TGG
(GCC)	 AG	85673-85722	GT	GGG
(GTT)	 AG	85813-85900	GT	AGG
(GTA)	 AG	86259-86411	CC	CTC
-recovered pasa_asmbl_40799.p1, internal, 81980, 82137
-recovered pasa_asmbl_40799.p1, internal, 83445, 83524
-recovered pasa_asmbl_40799.p1, internal, 84991, 85106
-recovered pasa_asmbl_40799.p1, internal, 85673, 85722
-recovered pasa_asmbl_40799.p1, internal, 85813, 85900
Valid prediction for snap_scaffold_3-snap.3784-T1
Valid prediction for GeneMark_model.13984_t
Valid prediction for CodingQuarry_transcript_46375-T1
Valid prediction for snap_scaffold_3-snap.3775-T1
Valid prediction for snap_scaffold_3-snap.3782-T1
Valid prediction for GeneMark_model.13982_t
Valid prediction for Augustus_model.g5718.t1
Couldn't classify 158231, 158265
Couldn't classify 160312, 160517
Sorry, prediction pasa_asmbl_40721.p1 fails validation.
(GTC)	 TG	158231-158265	GT	AGG
(TGA)	 AG	158994-159068	GT	AAG
(ACT)	 AG	159191-159428	GT	AGG
(GAT)	 AG	159714-159776	GT	GGG
(CAG)	 AG	159904-160048	GT	AGG
(GCC)	 AG	160312-160517	AA	GCA
-recovered pasa_asmbl_40721.p1, internal, 158994, 159068
-recovered pasa_asmbl_40721.p1, internal, 159191, 159428
-recovered pasa_asmbl_40721.p1, internal, 159714, 159776
-recovered pasa_asmbl_40721.p1, internal, 159904, 160048
Couldn't classify 149697, 149790
Couldn't classify 153682, 153738
Sorry, prediction pasa_asmbl_40720.p1 fails validation.
(GAG)	 CA	149697-149790	GT	GGG
(CTG)	 AG	149894-149955	GT	AGG
(GAG)	 AG	150309-150374	GT	AGG
(GCT)	 AG	151177-151242	GT	AGG
(GAT)	 AG	151797-151841	GT	AGG
(GAG)	 AG	152121-152147	GT	TGG
(GAA)	 AG	153339-153404	GT	AGG
(GAG)	 AG	153682-153738	AG	GGA
-recovered pasa_asmbl_40720.p1, internal, 149894, 149955
-recovered pasa_asmbl_40720.p1, internal, 150309, 150374
-recovered pasa_asmbl_40720.p1, internal, 151177, 151242
-recovered pasa_asmbl_40720.p1, internal, 151797, 151841
-recovered pasa_asmbl_40720.p1, internal, 152121, 152147
-recovered pasa_asmbl_40720.p1, internal, 153339, 153404
Valid prediction for GlimmerHMM_glimmerT_8612-T1
Valid prediction for Augustus_model.g5723.t1
Valid prediction for GlimmerHMM_glimmerT_8613-T1
Valid prediction for snap_scaffold_3-snap.3786-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g5716.t1
Valid prediction for snap_scaffold_3-snap.3747-T1
Valid prediction for GlimmerHMM_glimmerT_8618-T1
Valid prediction for GlimmerHMM_glimmerT_8602-T1
Valid prediction for Augustus_model.g5711.t1
Valid prediction for GeneMark_model.14000_t
Valid prediction for GeneMark_model.13970_t
Valid prediction for snap_scaffold_3-snap.3761-T1
Valid prediction for snap_scaffold_3-snap.3763-T1
Valid prediction for snap_scaffold_3-snap.3767-T1
Valid prediction for GeneMark_model.14004_t
Valid prediction for GeneMark_model.13986_t
Valid prediction for snap_scaffold_3-snap.3777-T1
Valid prediction for GeneMark_model.13967_t
Valid prediction for snap_scaffold_3-snap.3755-T1
Valid prediction for GeneMark_model.13976_t
Valid prediction for Augustus_model.g5720.t1
Valid prediction for Augustus_model.g5721.t1
Valid prediction for GlimmerHMM_glimmerT_8617-T1
Valid prediction for pasa_asmbl_40718.p1
Valid prediction for GeneMark_model.13969_t
Valid prediction for GeneMark_model.13991_t
Valid prediction for GeneMark_model.13994_t
Valid prediction for GlimmerHMM_glimmerT_8609-T1
Valid prediction for snap_scaffold_3-snap.3780-T1
Valid prediction for snap_scaffold_3-snap.3787-T1
Valid prediction for snap_scaffold_3-snap.3748-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 GeneMark_model.13972_t
Valid prediction for GeneMark_model.13990_t
Valid prediction for Augustus_model.g5722.t1
Valid prediction for GeneMark_model.13995_t
Valid prediction for GeneMark_model.14003_t
Valid prediction for GeneMark_model.13981_t
Couldn't classify 130427, 130641
Sorry, prediction pasa_asmbl_39585.p1 fails validation.
(ATG)	 GG	127831-127929	GT	AGG
(ACG)	 AG	128407-128512	GT	AGG
(GAG)	 AG	128661-128743	GT	AGG
(GAG)	 AG	129562-129626	GT	AAG
(CAA)	 AG	129709-129827	GT	CGG
(AGC)	 AG	130427-130641	AA	GGA
-recovered pasa_asmbl_39585.p1, initial, 127831, 127929
-recovered pasa_asmbl_39585.p1, internal, 128407, 128512
-recovered pasa_asmbl_39585.p1, internal, 128661, 128743
-recovered pasa_asmbl_39585.p1, internal, 129562, 129626
-recovered pasa_asmbl_39585.p1, internal, 129709, 129827
Valid prediction for Augustus_model.g5710.t1
Valid prediction for snap_scaffold_3-snap.3789-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_3-snap.3745-T1
Valid prediction for GlimmerHMM_glimmerT_8606-T1
Valid prediction for GeneMark_model.14001_t
Valid prediction for GlimmerHMM_glimmerT_8604-T1
Valid prediction for GlimmerHMM_glimmerT_8600-T1
Valid prediction for snap_scaffold_3-snap.3791-T1
Valid prediction for GeneMark_model.13985_t
Valid prediction for snap_scaffold_3-snap.3770-T1
Valid prediction for GlimmerHMM_glimmerT_8614-T1
Valid prediction for GeneMark_model.13993_t
Valid prediction for GeneMark_model.13999_t
Valid prediction for GeneMark_model.13977_t
Valid prediction for snap_scaffold_3-snap.3762-T1
Valid prediction for snap_scaffold_3-snap.3788-T1
Valid prediction for snap_scaffold_3-snap.3779-T1
Valid prediction for snap_scaffold_3-snap.3781-T1
Valid prediction for snap_scaffold_3-snap.3754-T1
Valid prediction for snap_scaffold_3-snap.3759-T1
Valid prediction for GeneMark_model.13998_t
Valid prediction for HiQ_model.g5712.t1
Valid prediction for snap_scaffold_3-snap.3749-T1
Couldn't classify 130427, 130607
Couldn't classify 130644, 130776
Couldn't classify 130849, 131100
Sorry, prediction CodingQuarry_transcript_46373-T1 fails validation.
(ATG)	 GG	127831-127929	GT	AGG
(ACG)	 AG	128407-128512	GT	AGG
(GAG)	 AG	128661-128743	GT	AGG
(GAG)	 AG	129562-129626	GT	AAG
(CAA)	 AG	129709-129827	GT	CGG
(AGC)	 AG	130427-130607	CC	GCC
(GGA)	 AA	130644-130776	CT	ACC
(CTG)	 AC	130849-131100	GT	AGG
(CCT)	 AG	131771-131932	CT	AAC
-recovered CodingQuarry_transcript_46373-T1, initial, 127831, 127929
-recovered CodingQuarry_transcript_46373-T1, terminal, 131771, 131932
-recovered CodingQuarry_transcript_46373-T1, internal, 128407, 128512
-recovered CodingQuarry_transcript_46373-T1, internal, 128661, 128743
-recovered CodingQuarry_transcript_46373-T1, internal, 129562, 129626
-recovered CodingQuarry_transcript_46373-T1, internal, 129709, 129827
Valid prediction for snap_scaffold_3-snap.3776-T1
Valid prediction for GlimmerHMM_glimmerT_8601-T1
Valid prediction for Augustus_model.g5715.t1
Couldn't classify 130427, 130607
Couldn't classify 130644, 130776
Couldn't classify 130903, 131100
Sorry, prediction CodingQuarry_transcript_46374-T1 fails validation.
(ATG)	 GG	127831-127929	GT	AGG
(ACG)	 AG	128407-128512	GT	AGG
(GAG)	 AG	128661-128743	GT	AGG
(GAG)	 AG	129562-129626	GT	AAG
(CAA)	 AG	129709-129827	GT	CGG
(AGC)	 AG	130427-130607	CC	GCC
(GGA)	 AA	130644-130776	CT	ACC
(CTG)	 AC	130903-131100	GT	AGG
(CCT)	 AG	131771-131932	CT	AAC
-recovered CodingQuarry_transcript_46374-T1, initial, 127831, 127929
-recovered CodingQuarry_transcript_46374-T1, terminal, 131771, 131932
-recovered CodingQuarry_transcript_46374-T1, internal, 128407, 128512
-recovered CodingQuarry_transcript_46374-T1, internal, 128661, 128743
-recovered CodingQuarry_transcript_46374-T1, internal, 129562, 129626
-recovered CodingQuarry_transcript_46374-T1, internal, 129709, 129827
Valid prediction for GlimmerHMM_glimmerT_8615-T1
Valid prediction for GeneMark_model.13968_t
Valid prediction for snap_scaffold_3-snap.3753-T1
Valid prediction for GlimmerHMM_glimmerT_8611-T1
Valid prediction for Augustus_model.g5709.t1
Valid prediction for GlimmerHMM_glimmerT_8603-T1
Valid prediction for snap_scaffold_3-snap.3768-T1
Valid prediction for Augustus_model.g5713.t1
Valid prediction for GeneMark_model.13973_t
Valid prediction for snap_scaffold_3-snap.3774-T1
Valid prediction for GeneMark_model.13983_t
Valid prediction for snap_scaffold_3-snap.3757-T1
Valid prediction for GlimmerHMM_glimmerT_8607-T1
Valid prediction for snap_scaffold_3-snap.3750-T1
Valid prediction for GeneMark_model.13978_t
Valid prediction for GeneMark_model.13996_t
Valid prediction for snap_scaffold_3-snap.3778-T1
Valid prediction for snap_scaffold_3-snap.3783-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_3-snap.3765-T1
Valid prediction for GlimmerHMM_glimmerT_8610-T1
Valid prediction for snap_scaffold_3-snap.3758-T1
Valid prediction for GeneMark_model.13989_t
Valid prediction for snap_scaffold_3-snap.3785-T1
Valid prediction for snap_scaffold_3-snap.3756-T1
Valid prediction for Augustus_model.g5719.t1
Valid prediction for GeneMark_model.13987_t
Valid prediction for GeneMark_model.13974_t
Valid prediction for snap_scaffold_3-snap.3752-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11897, rend_intergenic: 2636  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48091, rend_intergenic: 46604  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63782, rend_intergenic: 60308  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75883, rend_intergenic: 74423  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84125, rend_intergenic: 75885  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88069, rend_intergenic: 84286  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109185, rend_intergenic: 104625  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120540, rend_intergenic: 114736  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126432, rend_intergenic: 123921  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131195, rend_intergenic: 128138  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137077, rend_intergenic: 131442  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143814, rend_intergenic: 140061  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148341, rend_intergenic: 144620  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148858, rend_intergenic: 148369  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153792, rend_intergenic: 151494  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156430, rend_intergenic: 153947  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168170, rend_intergenic: 158096  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177531, rend_intergenic: 172455  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 178535
-exon list size: 577


building trellis

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73.6    
73.7    
73.9    
74.1    
74.3    
74.4    
74.6    
74.8    
75.0    
75.1    
75.3    
75.5    
75.6    
75.8    
76.0    
76.2    
76.3    
76.5    
76.7    
76.9    
77.0    
77.2    
77.4    
77.5    
77.7    
77.9    
78.1    
78.2    
78.4    
78.6    
78.8    
78.9    
79.1    
79.3    
79.4    
79.6    
79.8    
80.0    
80.1    
80.3    
80.5    
80.7    
80.8    
81.0    
81.2    
81.3    
81.5    
81.7    
81.9    
82.0    
82.2    
82.4    
82.6    
82.7    
82.9    
83.1    
83.2    
83.4    
83.6    
83.8    
83.9    
84.1    
84.3    
84.5    
84.6    
84.8    
85.0    
85.1    
85.3    
85.5    
85.7    
85.8    
86.0    
86.2    
86.4    
86.5    
86.7    
86.9    
87.0    
87.2    
87.4    
87.6    
87.7    
87.9    
88.1    
88.3    
88.4    
88.6    
88.8    
88.9    
89.1    
89.3    
89.5    
89.6    
89.8    
90.0    
90.2    
90.3    
90.5    
90.7    
90.8    
91.0    
91.2    
91.4    
91.5    
91.7    
91.9    
92.1    
92.2    
92.4    
92.6    
92.7    
92.9    
93.1    
93.3    
93.4    
93.6    
93.8    
94.0    
94.1    
94.3    
94.5    
94.6    
94.8    
95.0    
95.2    
95.3    
95.5    
95.7    
95.9    
96.0    
96.2    
96.4    
96.5    
96.7    
96.9    
97.1    
97.2    
97.4    
97.6    
97.8    
97.9    
98.1    
98.3    
98.4    
98.6    
98.8    
99.0    
99.1    
99.3    
99.5    
99.7    
99.8    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 11897, rend_intergenic: 2636  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48091, rend_intergenic: 46604  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63782, rend_intergenic: 60308  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75883, rend_intergenic: 74423  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84125, rend_intergenic: 75885  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88069, rend_intergenic: 84286  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109185, rend_intergenic: 104625  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120540, rend_intergenic: 114736  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126432, rend_intergenic: 123921  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131195, rend_intergenic: 128138  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137077, rend_intergenic: 131442  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143814, rend_intergenic: 140061  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148341, rend_intergenic: 144620  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148858, rend_intergenic: 148369  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153792, rend_intergenic: 151494  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156430, rend_intergenic: 153947  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168170, rend_intergenic: 158096  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177531, rend_intergenic: 172455  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support