-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_28/scaffold_28_5829724-6035590

-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_60331-T1
Valid prediction for snap_scaffold_28-snap.1329-T1
Valid prediction for Augustus_model.g40179.t1
Valid prediction for snap_scaffold_28-snap.1350-T1
Valid prediction for GeneMark_model.104995_t
Valid prediction for GeneMark_model.104984_t
Valid prediction for GeneMark_model.105001_t
Valid prediction for CodingQuarry_transcript_43591-T1
Valid prediction for GeneMark_model.104989_t
Valid prediction for snap_scaffold_28-snap.1324-T1
Valid prediction for snap_scaffold_28-snap.1317-T1
Valid prediction for Augustus_model.g40162.t1
Valid prediction for Augustus_model.g40172.t1
Valid prediction for GlimmerHMM_glimmerT_60302-T1
Valid prediction for GlimmerHMM_glimmerT_60312-T1
Valid prediction for snap_scaffold_28-snap.1335-T1
Valid prediction for snap_scaffold_28-snap.1323-T1
Valid prediction for GeneMark_model.105007_t
Valid prediction for GlimmerHMM_glimmerT_60308-T1
Valid prediction for GlimmerHMM_glimmerT_60318-T1
Valid prediction for snap_scaffold_28-snap.1341-T1
Valid prediction for GeneMark_model.104991_t
Valid prediction for snap_scaffold_28-snap.1346-T1
Valid prediction for snap_scaffold_28-snap.1354-T1
Couldn't classify 88947, 89036
Sorry, prediction pasa_asmbl_38308.p1 fails validation.
(ATG)	 CC	84613-84619	GT	AGG
(GCG)	 AG	85241-85309	GT	AGG
(CTG)	 AG	85694-85791	GT	AGG
(AGC)	 AG	85888-86053	GT	TGG
(ATA)	 AG	86148-86260	GT	GGG
(GTA)	 AG	86418-86595	GT	TAG
(ACA)	 AG	86694-86858	GT	ATG
(TGT)	 AG	87215-87384	GT	AGG
(GTC)	 AG	88947-89036	AG	ACA
-recovered pasa_asmbl_38308.p1, initial, 84613, 84619
-recovered pasa_asmbl_38308.p1, internal, 85241, 85309
-recovered pasa_asmbl_38308.p1, internal, 85694, 85791
-recovered pasa_asmbl_38308.p1, internal, 85888, 86053
-recovered pasa_asmbl_38308.p1, internal, 86148, 86260
-recovered pasa_asmbl_38308.p1, internal, 86418, 86595
-recovered pasa_asmbl_38308.p1, internal, 86694, 86858
-recovered pasa_asmbl_38308.p1, internal, 87215, 87384
Valid prediction for GlimmerHMM_glimmerT_60309-T1
Valid prediction for GlimmerHMM_glimmerT_60314-T1
Valid prediction for HiQ_model.g40164.t1
Valid prediction for Augustus_model.g40161.t1
Valid prediction for snap_scaffold_28-snap.1344-T1
Valid prediction for Augustus_model.g40165.t1
Valid prediction for pasa_asmbl_38311.p1
Valid prediction for GeneMark_model.104976_t
Valid prediction for GlimmerHMM_glimmerT_60294-T1
Valid prediction for snap_scaffold_28-snap.1328-T1
Valid prediction for GeneMark_model.104981_t
Valid prediction for GlimmerHMM_glimmerT_60306-T1
Valid prediction for GeneMark_model.104987_t
Valid prediction for GlimmerHMM_glimmerT_60333-T1
Valid prediction for GeneMark_model.104982_t
Valid prediction for snap_scaffold_28-snap.1332-T1
Valid prediction for pasa_asmbl_38313.p1
Valid prediction for GlimmerHMM_glimmerT_60332-T1
Valid prediction for snap_scaffold_28-snap.1330-T1
Valid prediction for GlimmerHMM_glimmerT_60304-T1
Valid prediction for snap_scaffold_28-snap.1355-T1
Valid prediction for GlimmerHMM_glimmerT_60293-T1
Valid prediction for GlimmerHMM_glimmerT_60295-T1
Valid prediction for GlimmerHMM_glimmerT_60300-T1
Valid prediction for snap_scaffold_28-snap.1331-T1
Valid prediction for GlimmerHMM_glimmerT_60329-T1
Valid prediction for GeneMark_model.104983_t
Valid prediction for GlimmerHMM_glimmerT_60310-T1
Valid prediction for GeneMark_model.104969_t
Valid prediction for HiQ_model.g40157.t1
Valid prediction for GlimmerHMM_glimmerT_60324-T1
Valid prediction for GeneMark_model.104993_t
Valid prediction for GlimmerHMM_glimmerT_60311-T1
Valid prediction for GlimmerHMM_glimmerT_60316-T1
Couldn't classify 19311, 19452
Sorry, prediction pasa_asmbl_38304.p1 fails validation.
(AAC)	 AG	19311-19452	GT	ACG
(ACA)	 AG	19745-19826	GT	AAG
(CTA)	 AG	19917-20001	GT	CTG
(ACT)	 AG	20115-20201	GT	TGG
(GAC)	 AG	20288-20464	GT	AGG
(GCA)	 AG	20654-20737	GT	AGG
(ATC)	 AG	20872-21009	GT	TGG
(CCC)	 AG	21275-21426	GT	GAG
(CAG)	 AG	22239-22386	GT	AGG
(CTC)	 AG	22522-22672	GT	CAG
(GTT)	 AG	23048-23166	GT	AGG
(TTC)	 AG	23317-23400	AA	AGA
-recovered pasa_asmbl_38304.p1, terminal, 23317, 23400
-recovered pasa_asmbl_38304.p1, internal, 19311, 19452
-recovered pasa_asmbl_38304.p1, internal, 19745, 19826
-recovered pasa_asmbl_38304.p1, internal, 19917, 20001
-recovered pasa_asmbl_38304.p1, internal, 20115, 20201
-recovered pasa_asmbl_38304.p1, internal, 20288, 20464
-recovered pasa_asmbl_38304.p1, internal, 20654, 20737
-recovered pasa_asmbl_38304.p1, internal, 20872, 21009
-recovered pasa_asmbl_38304.p1, internal, 21275, 21426
-recovered pasa_asmbl_38304.p1, internal, 22239, 22386
-recovered pasa_asmbl_38304.p1, internal, 22522, 22672
-recovered pasa_asmbl_38304.p1, internal, 23048, 23166
Valid prediction for GlimmerHMM_glimmerT_60299-T1
Valid prediction for HiQ_model.g40168.t1
Valid prediction for GeneMark_model.104979_t
Valid prediction for GeneMark_model.104999_t
Valid prediction for Augustus_model.g40163.t1
Couldn't classify 17892, 17981
Sorry, prediction pasa_asmbl_38303.p1 fails validation.
(ATG)	 AG	15918-16061	GT	AAG
(TTT)	 AG	16232-16317	GT	ACG
(GCT)	 AG	16611-16767	GT	TTG
(AAC)	 AG	16962-17002	GT	CGG
(ATA)	 AG	17120-17210	GT	AGG
(TGG)	 AG	17381-17500	GT	AAG
(ATG)	 AG	17892-17981	GT	TGG
-recovered pasa_asmbl_38303.p1, initial, 15918, 16061
-recovered pasa_asmbl_38303.p1, initial, 17892, 17981
-recovered pasa_asmbl_38303.p1, internal, 15918, 16061
-recovered pasa_asmbl_38303.p1, internal, 16232, 16317
-recovered pasa_asmbl_38303.p1, internal, 16611, 16767
-recovered pasa_asmbl_38303.p1, internal, 16962, 17002
-recovered pasa_asmbl_38303.p1, internal, 17120, 17210
-recovered pasa_asmbl_38303.p1, internal, 17381, 17500
-recovered pasa_asmbl_38303.p1, internal, 17892, 17981
Valid prediction for HiQ_model.g40175.t1
Valid prediction for Augustus_model.g40170.t1
Valid prediction for Augustus_model.g40156.t1
Valid prediction for GlimmerHMM_glimmerT_60330-T1
Valid prediction for GeneMark_model.104974_t
Valid prediction for snap_scaffold_28-snap.1321-T1
Valid prediction for snap_scaffold_28-snap.1316-T1
Valid prediction for GlimmerHMM_glimmerT_60319-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.105006_t
Valid prediction for Augustus_model.g40159.t1
Valid prediction for snap_scaffold_28-snap.1325-T1
Valid prediction for Augustus_model.g40167.t1
Couldn't classify 35029, 35103
Couldn't classify 35703, 35774
Sorry, prediction pasa_asmbl_37655.p1 fails validation.
(CCG)	 AG	35029-35103	GT	AGG
(GAG)	 AG	35232-35312	GT	AGG
(ATT)	 AG	35525-35608	GT	AGG
(AGC)	 AG	35703-35774	AC	AGA
-recovered pasa_asmbl_37655.p1, internal, 35029, 35103
-recovered pasa_asmbl_37655.p1, internal, 35232, 35312
-recovered pasa_asmbl_37655.p1, internal, 35525, 35608
Valid prediction for GlimmerHMM_glimmerT_60303-T1
Valid prediction for GeneMark_model.104996_t
Valid prediction for Augustus_model.g40177.t1
Valid prediction for snap_scaffold_28-snap.1352-T1
Valid prediction for GeneMark_model.104986_t
Valid prediction for GlimmerHMM_glimmerT_60323-T1
Valid prediction for GlimmerHMM_glimmerT_60296-T1
Valid prediction for GlimmerHMM_glimmerT_60307-T1
Valid prediction for snap_scaffold_28-snap.1339-T1
Valid prediction for Augustus_model.g40178.t1
Valid prediction for GlimmerHMM_glimmerT_60322-T1
Valid prediction for HiQ_model.g40174.t1
Valid prediction for GeneMark_model.104992_t
Valid prediction for snap_scaffold_28-snap.1340-T1
Valid prediction for GeneMark_model.104972_t
Valid prediction for pasa_asmbl_37653.p1
Valid prediction for GeneMark_model.104998_t
Valid prediction for snap_scaffold_28-snap.1353-T1
Couldn't classify 35703, 35809
Sorry, prediction pasa_asmbl_37654.p1 fails validation.
(AGC)	 AG	35703-35809	GT	ATG
(GTG)	 AG	35918-36036	GT	TGG
(GTG)	 AG	36193-36347	GT	AGG
(GTG)	 AG	36460-36649	GT	GTG
(CCT)	 AG	36823-36996	GT	GGG
(TGT)	 AG	37200-37360	GT	AGG
(GTG)	 AG	37568-37795	GT	GGG
(CCG)	 AG	37907-38098	GT	AGG
(GGC)	 AG	38259-38437	GT	AGG
(GTT)	 AG	38541-38692	GT	TGG
(GTG)	 AG	38805-38913	GT	GCG
(GTA)	 AG	39043-39151	GT	AGG
(GAT)	 AG	39343-39532	GT	GGG
(GCA)	 AG	39760-39924	GT	CGG
(AGT)	 AG	40060-40181	GT	AGG
(CTG)	 AG	40275-40418	GT	AGG
(GCG)	 AG	40524-40700	GT	AGG
(GGT)	 AG	40832-40992	GT	AGG
(TGG)	 AG	41116-41197	GT	AGG
(AAA)	 AG	41334-41426	GT	AGG
(GTG)	 AG	41539-41688	GG	GAG
-recovered pasa_asmbl_37654.p1, terminal, 41539, 41688
-recovered pasa_asmbl_37654.p1, internal, 35703, 35809
-recovered pasa_asmbl_37654.p1, internal, 35918, 36036
-recovered pasa_asmbl_37654.p1, internal, 36193, 36347
-recovered pasa_asmbl_37654.p1, internal, 36460, 36649
-recovered pasa_asmbl_37654.p1, internal, 36823, 36996
-recovered pasa_asmbl_37654.p1, internal, 37200, 37360
-recovered pasa_asmbl_37654.p1, internal, 37568, 37795
-recovered pasa_asmbl_37654.p1, internal, 37907, 38098
-recovered pasa_asmbl_37654.p1, internal, 38259, 38437
-recovered pasa_asmbl_37654.p1, internal, 38541, 38692
-recovered pasa_asmbl_37654.p1, internal, 38805, 38913
-recovered pasa_asmbl_37654.p1, internal, 39043, 39151
-recovered pasa_asmbl_37654.p1, internal, 39343, 39532
-recovered pasa_asmbl_37654.p1, internal, 39760, 39924
-recovered pasa_asmbl_37654.p1, internal, 40060, 40181
-recovered pasa_asmbl_37654.p1, internal, 40275, 40418
-recovered pasa_asmbl_37654.p1, internal, 40524, 40700
-recovered pasa_asmbl_37654.p1, internal, 40832, 40992
-recovered pasa_asmbl_37654.p1, internal, 41116, 41197
-recovered pasa_asmbl_37654.p1, internal, 41334, 41426
Valid prediction for GeneMark_model.105005_t
Valid prediction for snap_scaffold_28-snap.1327-T1
Valid prediction for GeneMark_model.104997_t
Valid prediction for GeneMark_model.104988_t
Valid prediction for snap_scaffold_28-snap.1320-T1
Valid prediction for Augustus_model.g40160.t1
Valid prediction for GeneMark_model.105002_t
Valid prediction for snap_scaffold_28-snap.1336-T1
Valid prediction for snap_scaffold_28-snap.1334-T1
Valid prediction for GeneMark_model.105003_t
Valid prediction for GeneMark_model.104977_t
Valid prediction for GeneMark_model.104985_t
Valid prediction for GlimmerHMM_glimmerT_60297-T1
Valid prediction for CodingQuarry_transcript_43590-T1
Valid prediction for GeneMark_model.104994_t
Valid prediction for GlimmerHMM_glimmerT_60317-T1
Valid prediction for Augustus_model.g40169.t1
Valid prediction for GeneMark_model.104973_t
Valid prediction for snap_scaffold_28-snap.1349-T1
Valid prediction for GlimmerHMM_glimmerT_60301-T1
Valid prediction for Augustus_model.g40173.t1
Valid prediction for GeneMark_model.104990_t
Valid prediction for GeneMark_model.104980_t
Valid prediction for snap_scaffold_28-snap.1351-T1
Valid prediction for GlimmerHMM_glimmerT_60305-T1
Valid prediction for snap_scaffold_28-snap.1345-T1
Valid prediction for GlimmerHMM_glimmerT_60327-T1
Valid prediction for snap_scaffold_28-snap.1348-T1
Valid prediction for GeneMark_model.104970_t
Valid prediction for GlimmerHMM_glimmerT_60320-T1
Valid prediction for Augustus_model.g40171.t1
Valid prediction for snap_scaffold_28-snap.1337-T1
Valid prediction for GlimmerHMM_glimmerT_60313-T1
Valid prediction for snap_scaffold_28-snap.1333-T1
Valid prediction for Augustus_model.g40166.t1
Valid prediction for Augustus_model.g40158.t1
Valid prediction for snap_scaffold_28-snap.1319-T1
Valid prediction for GlimmerHMM_glimmerT_60325-T1
Valid prediction for GlimmerHMM_glimmerT_60328-T1
Valid prediction for GlimmerHMM_glimmerT_60321-T1
Valid prediction for snap_scaffold_28-snap.1318-T1
Valid prediction for snap_scaffold_28-snap.1343-T1
Valid prediction for GlimmerHMM_glimmerT_60315-T1
Couldn't classify 31702, 31842
Sorry, prediction pasa_asmbl_37656.p1 fails validation.
(ATG)	 CC	29035-29079	GT	CGG
(AAC)	 AG	29390-29553	GT	AAG
(GCG)	 AG	29655-29826	GT	AGG
(CCT)	 AG	29966-30158	GT	GGG
(ATG)	 AG	30410-30465	GT	AGG
(GAG)	 AG	30547-30645	GT	ACG
(CTG)	 AG	30795-30947	GT	AGG
(ACG)	 AG	31080-31179	GT	GAG
(TCC)	 AG	31298-31434	GT	GGG
(GAG)	 AG	31535-31615	GT	AGG
(TCC)	 AG	31702-31842	GC	CCG
-recovered pasa_asmbl_37656.p1, initial, 29035, 29079
add_exon() Sorry, pasa_asmbl_37656.p1 30410-30465-initial-1 is invalid.
-recovered pasa_asmbl_37656.p1, initial, 30410, 30465
-recovered pasa_asmbl_37656.p1, terminal, 31080, 31179
-recovered pasa_asmbl_37656.p1, internal, 29390, 29553
-recovered pasa_asmbl_37656.p1, internal, 29655, 29826
-recovered pasa_asmbl_37656.p1, internal, 29966, 30158
-recovered pasa_asmbl_37656.p1, internal, 30410, 30465
-recovered pasa_asmbl_37656.p1, internal, 30547, 30645
-recovered pasa_asmbl_37656.p1, internal, 30795, 30947
-recovered pasa_asmbl_37656.p1, internal, 31080, 31179
-recovered pasa_asmbl_37656.p1, internal, 31298, 31434
-recovered pasa_asmbl_37656.p1, internal, 31535, 31615
-recovered pasa_asmbl_37656.p1, internal, 31702, 31842
Valid prediction for GlimmerHMM_glimmerT_60326-T1
Valid prediction for GeneMark_model.104978_t
Valid prediction for snap_scaffold_28-snap.1322-T1
Valid prediction for snap_scaffold_28-snap.1342-T1
Valid prediction for Augustus_model.g40176.t1
Valid prediction for GlimmerHMM_glimmerT_60298-T1
Valid prediction for snap_scaffold_28-snap.1326-T1
Valid prediction for snap_scaffold_28-snap.1338-T1
Valid prediction for snap_scaffold_28-snap.1347-T1
Valid prediction for GeneMark_model.105000_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 133136, rend_intergenic: 131814  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136514, rend_intergenic: 133836  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138805, rend_intergenic: 136674  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151735, rend_intergenic: 139851  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 205867
-exon list size: 674


building trellis

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50.6    
50.7    
50.9    
51.0    
51.2    
51.3    
51.5    
51.6    
51.8    
51.9    
52.1    
52.2    
52.4    
52.5    
52.7    
52.8    
53.0    
53.1    
53.3    
53.4    
53.6    
53.7    
53.8    
54.0    
54.1    
54.3    
54.4    
54.6    
54.7    
54.9    
55.0    
55.2    
55.3    
55.5    
55.6    
55.8    
55.9    
56.1    
56.2    
56.4    
56.5    
56.7    
56.8    
57.0    
57.1    
57.2    
57.4    
57.5    
57.7    
57.8    
58.0    
58.1    
58.3    
58.4    
58.6    
58.7    
58.9    
59.0    
59.2    
59.3    
59.5    
59.6    
59.8    
59.9    
60.1    
60.2    
60.4    
60.5    
60.7    
60.8    
60.9    
61.1    
61.2    
61.4    
61.5    
61.7    
61.8    
62.0    
62.1    
62.3    
62.4    
62.6    
62.7    
62.9    
63.0    
63.2    
63.3    
63.5    
63.6    
63.8    
63.9    
64.1    
64.2    
64.3    
64.5    
64.6    
64.8    
64.9    
65.1    
65.2    
65.4    
65.5    
65.7    
65.8    
66.0    
66.1    
66.3    
66.4    
66.6    
66.7    
66.9    
67.0    
67.2    
67.3    
67.5    
67.6    
67.8    
67.9    
68.0    
68.2    
68.3    
68.5    
68.6    
68.8    
68.9    
69.1    
69.2    
69.4    
69.5    
69.7    
69.8    
70.0    
70.1    
70.3    
70.4    
70.6    
70.7    
70.9    
71.0    
71.2    
71.3    
71.4    
71.6    
71.7    
71.9    
72.0    
72.2    
72.3    
72.5    
72.6    
72.8    
72.9    
73.1    
73.2    
73.4    
73.5    
73.7    
73.8    
74.0    
74.1    
74.3    
74.4    
74.6    
74.7    
74.9    
75.0    
75.1    
75.3    
75.4    
75.6    
75.7    
75.9    
76.0    
76.2    
76.3    
76.5    
76.6    
76.8    
76.9    
77.1    
77.2    
77.4    
77.5    
77.7    
77.8    
78.0    
78.1    
78.3    
78.4    
78.6    
78.7    
78.8    
79.0    
79.1    
79.3    
79.4    
79.6    
79.7    
79.9    
80.0    
80.2    
80.3    
80.5    
80.6    
80.8    
80.9    
81.1    
81.2    
81.4    
81.5    
81.7    
81.8    
82.0    
82.1    
82.2    
82.4    
82.5    
82.7    
82.8    
83.0    
83.1    
83.3    
83.4    
83.6    
83.7    
83.9    
84.0    
84.2    
84.3    
84.5    
84.6    
84.8    
84.9    
85.1    
85.2    
85.4    
85.5    
85.7    
85.8    
85.9    
86.1    
86.2    
86.4    
86.5    
86.7    
86.8    
87.0    
87.1    
87.3    
87.4    
87.6    
87.7    
87.9    
88.0    
88.2    
88.3    
88.5    
88.6    
88.8    
88.9    
89.1    
89.2    
89.3    
89.5    
89.6    
89.8    
89.9    
90.1    
90.2    
90.4    
90.5    
90.7    
90.8    
91.0    
91.1    
91.3    
91.4    
91.6    
91.7    
91.9    
92.0    
92.2    
92.3    
92.5    
92.6    
92.8    
92.9    
93.0    
93.2    
93.3    
93.5    
93.6    
93.8    
93.9    
94.1    
94.2    
94.4    
94.5    
94.7    
94.8    
95.0    
95.1    
95.3    
95.4    
95.6    
95.7    
95.9    
96.0    
96.2    
96.3    
96.4    
96.6    
96.7    
96.9    
97.0    
97.2    
97.3    
97.5    
97.6    
97.8    
97.9    
98.1    
98.2    
98.4    
98.5    
98.7    
98.8    
99.0    
99.1    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 133136, rend_intergenic: 131814  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136514, rend_intergenic: 133836  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138805, rend_intergenic: 136674  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151735, rend_intergenic: 139851  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 30 predictions persist after filtering for low support