-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_2/scaffold_2_13927101-14200292

-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 HiQ_model.g3361.t1
Valid prediction for snap_scaffold_2-snap.2725-T1
Valid prediction for Augustus_model.g3350.t1
Valid prediction for CodingQuarry_transcript_28659-T1
Valid prediction for GlimmerHMM_glimmerT_5001-T1
Valid prediction for pasa_asmbl_24913.p1
Valid prediction for CodingQuarry_transcript_28654-T1
Valid prediction for HiQ_model.g3354.t1
Valid prediction for pasa_asmbl_25453.p1
Valid prediction for snap_scaffold_2-snap.2718-T1
Valid prediction for snap_scaffold_2-snap.2739-T1
Valid prediction for pasa_asmbl_24920.p1
Valid prediction for GeneMark_model.8043_t
Valid prediction for GeneMark_model.8060_t
Valid prediction for snap_scaffold_2-snap.2735-T1
Valid prediction for GlimmerHMM_glimmerT_4998-T1
Valid prediction for snap_scaffold_2-snap.2746-T1
Valid prediction for GeneMark_model.8065_t
Valid prediction for snap_scaffold_2-snap.2731-T1
Valid prediction for GeneMark_model.8053_t
Valid prediction for GlimmerHMM_glimmerT_5004-T1
Valid prediction for snap_scaffold_2-snap.2744-T1
Valid prediction for CodingQuarry_transcript_28660-T1
Valid prediction for CodingQuarry_transcript_28667-T1
Valid prediction for GeneMark_model.8061_t
Valid prediction for GlimmerHMM_glimmerT_4989-T1
Valid prediction for pasa_asmbl_24902.p1
Valid prediction for Augustus_model.g3355.t1
Valid prediction for snap_scaffold_2-snap.2705-T1
Valid prediction for GlimmerHMM_glimmerT_4990-T1
Valid prediction for Augustus_model.g3359.t1
Valid prediction for GlimmerHMM_glimmerT_4992-T1
Valid prediction for snap_scaffold_2-snap.2719-T1
Valid prediction for snap_scaffold_2-snap.2706-T1
Valid prediction for HiQ_model.g3348.t1
Valid prediction for CodingQuarry_transcript_28663-T1
Couldn't classify 234162, 234244
Sorry, prediction pasa_asmbl_24918.p1 fails validation.
(ATG)	 CG	232917-233046	GT	GAG
(TCT)	 AG	233641-234039	GT	AGG
(GAG)	 AG	234162-234244	GC	ATG
-recovered pasa_asmbl_24918.p1, initial, 232917, 233046
-recovered pasa_asmbl_24918.p1, internal, 233641, 234039
-recovered pasa_asmbl_24918.p1, internal, 234162, 234244
Valid prediction for GeneMark_model.8038_t
Couldn't classify 173426, 174131
Sorry, prediction pasa_asmbl_24909.p1 fails validation.
(CTA)	 AA	173426-174131	GT	TGG
(TGG)	 AG	174250-174372	GT	ATG
(GTG)	 AG	174485-174600	TC	GAT
-recovered pasa_asmbl_24909.p1, terminal, 174485, 174600
-recovered pasa_asmbl_24909.p1, internal, 174250, 174372
Valid prediction for snap_scaffold_2-snap.2716-T1
Valid prediction for GeneMark_model.8057_t
Valid prediction for GlimmerHMM_glimmerT_4982-T1
Valid prediction for GlimmerHMM_glimmerT_4974-T1
Valid prediction for GeneMark_model.8046_t
Valid prediction for snap_scaffold_2-snap.2713-T1
Valid prediction for CodingQuarry_transcript_28658-T1
Valid prediction for GlimmerHMM_glimmerT_5005-T1
Valid prediction for CodingQuarry_transcript_28662-T1
Valid prediction for CodingQuarry_transcript_28668-T1
Valid prediction for GlimmerHMM_glimmerT_5000-T1
Valid prediction for pasa_asmbl_24896.p1
Valid prediction for GeneMark_model.8048_t
Valid prediction for GeneMark_model.8056_t
Valid prediction for Augustus_model.g3343.t1
Valid prediction for GeneMark_model.8032_t
Couldn't classify 223547, 223658
Sorry, prediction pasa_asmbl_24915.p1 fails validation.
(GTG)	 AT	223547-223658	GT	GCG
(GCT)	 AG	224107-224288	GT	AGG
(ATC)	 AG	224450-224605	GT	GTG
(GTG)	 AG	224929-225073	GT	TGG
(GTT)	 AG	226269-226453	GT	AGG
(GTG)	 AG	226585-226737	GT	AGG
(GTC)	 AG	227288-227431	CC	AGC
-recovered pasa_asmbl_24915.p1, terminal, 227288, 227431
-recovered pasa_asmbl_24915.p1, internal, 224107, 224288
-recovered pasa_asmbl_24915.p1, internal, 224450, 224605
-recovered pasa_asmbl_24915.p1, internal, 224929, 225073
-recovered pasa_asmbl_24915.p1, internal, 226269, 226453
-recovered pasa_asmbl_24915.p1, internal, 226585, 226737
Valid prediction for GlimmerHMM_glimmerT_4988-T1
Valid prediction for pasa_asmbl_24906.p1
Valid prediction for HiQ_model.g3341.t1
Valid prediction for Augustus_model.g3352.t1
Valid prediction for GeneMark_model.8041_t
Valid prediction for pasa_asmbl_24921.p1
Valid prediction for GlimmerHMM_glimmerT_4991-T1
Valid prediction for Augustus_model.g3351.t1
Valid prediction for GeneMark_model.8058_t
Valid prediction for snap_scaffold_2-snap.2741-T1
Valid prediction for snap_scaffold_2-snap.2734-T1
Valid prediction for snap_scaffold_2-snap.2726-T1
Valid prediction for GlimmerHMM_glimmerT_4987-T1
Valid prediction for GeneMark_model.8066_t
Valid prediction for snap_scaffold_2-snap.2729-T1
Valid prediction for HiQ_model.g3346.t1
Valid prediction for GeneMark_model.8047_t
Valid prediction for Augustus_model.g3349.t1
Valid prediction for GlimmerHMM_glimmerT_4996-T1
Valid prediction for GlimmerHMM_glimmerT_4986-T1
Valid prediction for GeneMark_model.8067_t
Valid prediction for GlimmerHMM_glimmerT_5006-T1
Valid prediction for snap_scaffold_2-snap.2727-T1
Valid prediction for GlimmerHMM_glimmerT_4980-T1
Valid prediction for snap_scaffold_2-snap.2707-T1
Valid prediction for snap_scaffold_2-snap.2732-T1
Valid prediction for GeneMark_model.8069_t
Valid prediction for pasa_asmbl_24912.p1
Valid prediction for GlimmerHMM_glimmerT_4973-T1
Couldn't classify 173024, 173416
Sorry, prediction pasa_asmbl_24908.p1 fails validation.
(GGT)	 AA	173024-173416	CA	ACC
Valid prediction for CodingQuarry_transcript_28653-T1
Valid prediction for snap_scaffold_2-snap.2730-T1
Valid prediction for snap_scaffold_2-snap.2723-T1
Valid prediction for Augustus_model.g3356.t1
Valid prediction for GeneMark_model.8054_t
Valid prediction for snap_scaffold_2-snap.2740-T1
Valid prediction for HiQ_model.g3347.t1
Valid prediction for snap_scaffold_2-snap.2712-T1
Valid prediction for snap_scaffold_2-snap.2724-T1
Valid prediction for CodingQuarry_transcript_28664-T1
Valid prediction for snap_scaffold_2-snap.2743-T1
Valid prediction for Augustus_model.g3358.t1
Valid prediction for GlimmerHMM_glimmerT_4985-T1
Valid prediction for GlimmerHMM_glimmerT_4995-T1
Valid prediction for GeneMark_model.8063_t
Valid prediction for snap_scaffold_2-snap.2737-T1
Valid prediction for snap_scaffold_2-snap.2736-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_4975-T1
Valid prediction for GlimmerHMM_glimmerT_4978-T1
Valid prediction for GeneMark_model.8045_t
Valid prediction for GeneMark_model.8037_t
Valid prediction for Augustus_model.g3342.t1
Valid prediction for Augustus_model.g3357.t1
Valid prediction for snap_scaffold_2-snap.2738-T1
Valid prediction for CodingQuarry_transcript_28657-T1
Valid prediction for Augustus_model.g3353.t1
Valid prediction for snap_scaffold_2-snap.2720-T1
Valid prediction for GeneMark_model.8036_t
Valid prediction for CodingQuarry_transcript_28656-T1
Valid prediction for CodingQuarry_transcript_28670-T1
Valid prediction for GeneMark_model.8064_t
Valid prediction for CodingQuarry_transcript_28665-T1
Valid prediction for snap_scaffold_2-snap.2721-T1
Valid prediction for GeneMark_model.8068_t
Valid prediction for GeneMark_model.8059_t
Valid prediction for snap_scaffold_2-snap.2733-T1
Valid prediction for GlimmerHMM_glimmerT_4977-T1
Valid prediction for GeneMark_model.8049_t
Valid prediction for CodingQuarry_transcript_28652-T1
Valid prediction for pasa_asmbl_23570.p1
Valid prediction for GlimmerHMM_glimmerT_4994-T1
Valid prediction for HiQ_model.g3345.t1
Valid prediction for snap_scaffold_2-snap.2742-T1
Valid prediction for GlimmerHMM_glimmerT_4976-T1
Valid prediction for CodingQuarry_transcript_28651-T1
Valid prediction for GeneMark_model.8050_t
Valid prediction for snap_scaffold_2-snap.2717-T1
Valid prediction for GeneMark_model.8044_t
Valid prediction for pasa_asmbl_23583.p1
Valid prediction for Augustus_model.g3362.t1
Valid prediction for Augustus_model.g3337.t1
Valid prediction for snap_scaffold_2-snap.2745-T1
Valid prediction for GeneMark_model.8034_t
Valid prediction for GlimmerHMM_glimmerT_5002-T1
Valid prediction for GlimmerHMM_glimmerT_4999-T1
Valid prediction for snap_scaffold_2-snap.2708-T1
Valid prediction for snap_scaffold_2-snap.2714-T1
Valid prediction for GlimmerHMM_glimmerT_4984-T1
Valid prediction for CodingQuarry_transcript_28650-T1
Valid prediction for CodingQuarry_transcript_28669-T1
Valid prediction for GeneMark_model.8042_t
Valid prediction for Augustus_model.g3340.t1
Valid prediction for Augustus_model.g3344.t1
Valid prediction for snap_scaffold_2-snap.2710-T1
Couldn't classify 221817, 221938
Couldn't classify 228599, 228694
Sorry, prediction pasa_asmbl_23567.p1 fails validation.
(GTG)	 CA	221817-221938	GT	AAG
(TAA)	 AG	222102-222213	GT	CGG
(GCG)	 AG	222743-222822	GT	AGG
(ACA)	 AG	222936-222999	GT	AGG
(AGT)	 AG	223266-223412	GT	AGG
(ACT)	 AG	223533-223560	GT	TGG
(GTC)	 AG	223709-223949	GT	AGG
(CTA)	 AG	225029-225151	GT	CTG
(GAT)	 AG	225284-225451	GT	CGG
(TGT)	 AG	225689-225797	GT	AGG
(GTG)	 AG	226104-226246	GT	GGG
(GTT)	 AG	226985-227173	GT	AAG
(GTT)	 AG	228348-228441	GT	AGG
(GCA)	 AG	228599-228694	TA	GGT
-recovered pasa_asmbl_23567.p1, internal, 222102, 222213
-recovered pasa_asmbl_23567.p1, internal, 222743, 222822
-recovered pasa_asmbl_23567.p1, internal, 222936, 222999
-recovered pasa_asmbl_23567.p1, internal, 223266, 223412
-recovered pasa_asmbl_23567.p1, internal, 223533, 223560
-recovered pasa_asmbl_23567.p1, internal, 223709, 223949
-recovered pasa_asmbl_23567.p1, internal, 225029, 225151
-recovered pasa_asmbl_23567.p1, internal, 225284, 225451
-recovered pasa_asmbl_23567.p1, internal, 225689, 225797
-recovered pasa_asmbl_23567.p1, internal, 226104, 226246
-recovered pasa_asmbl_23567.p1, internal, 226985, 227173
-recovered pasa_asmbl_23567.p1, internal, 228348, 228441
Valid prediction for CodingQuarry_transcript_28666-T1
Valid prediction for Augustus_model.g3338.t1
Valid prediction for GeneMark_model.8033_t
Valid prediction for snap_scaffold_2-snap.2711-T1
Couldn't classify 230434, 230563
Sorry, prediction pasa_asmbl_24044.p1 fails validation.
(GTT)	 AG	230434-230563	GT	AGG
(GCA)	 AG	230660-230796	GT	AGG
(GCG)	 AG	230900-231069	GT	AGG
(GGA)	 AG	231269-231425	GT	TGG
(ATG)	 AG	232039-232148	GT	AGG
(GTT)	 AG	232442-232649	GT	ACG
(ACC)	 AG	233004-233128	GT	GGG
(GTT)	 AG	233388-233505	GT	AGG
(TGT)	 AG	233596-233677	GC	TGG
(AGC)	 AG	233875-233984	GT	TGG
(GTC)	 AG	234089-234214	GT	TGG
(CTG)	 AG	234314-234496	AC	AGA
-recovered pasa_asmbl_24044.p1, initial, 232039, 232148
-recovered pasa_asmbl_24044.p1, terminal, 234314, 234496
-recovered pasa_asmbl_24044.p1, internal, 230434, 230563
-recovered pasa_asmbl_24044.p1, internal, 230660, 230796
-recovered pasa_asmbl_24044.p1, internal, 230900, 231069
-recovered pasa_asmbl_24044.p1, internal, 231269, 231425
-recovered pasa_asmbl_24044.p1, internal, 232039, 232148
-recovered pasa_asmbl_24044.p1, internal, 232442, 232649
-recovered pasa_asmbl_24044.p1, internal, 233004, 233128
-recovered pasa_asmbl_24044.p1, internal, 233388, 233505
-recovered pasa_asmbl_24044.p1, internal, 233596, 233677
-recovered pasa_asmbl_24044.p1, internal, 233875, 233984
-recovered pasa_asmbl_24044.p1, internal, 234089, 234214
Valid prediction for GlimmerHMM_glimmerT_4981-T1
Valid prediction for pasa_asmbl_23573.p1
Valid prediction for HiQ_model.g3339.t1
Valid prediction for GlimmerHMM_glimmerT_4979-T1
Valid prediction for GlimmerHMM_glimmerT_4983-T1
Valid prediction for GeneMark_model.8031_t
Valid prediction for snap_scaffold_2-snap.2715-T1
Valid prediction for GeneMark_model.8062_t
Valid prediction for GeneMark_model.8039_t
Valid prediction for pasa_asmbl_23560.p1
Valid prediction for GeneMark_model.8052_t
Valid prediction for GeneMark_model.8070_t
Valid prediction for pasa_asmbl_23569.p1
Valid prediction for snap_scaffold_2-snap.2728-T1
Valid prediction for GlimmerHMM_glimmerT_4993-T1
Valid prediction for GlimmerHMM_glimmerT_5003-T1
Valid prediction for GlimmerHMM_glimmerT_4997-T1
Valid prediction for GeneMark_model.8051_t
Valid prediction for GeneMark_model.8035_t
Valid prediction for snap_scaffold_2-snap.2722-T1
Valid prediction for CodingQuarry_transcript_28655-T1
Valid prediction for Augustus_model.g3360.t1
Valid prediction for snap_scaffold_2-snap.2709-T1
Couldn't classify 236075, 236106
Sorry, prediction pasa_asmbl_23564.p1 fails validation.
(ACC)	 CC	236075-236106	GT	GGG
(GAA)	 AG	236590-236638	GT	CTG
(TGG)	 AG	236778-236856	GT	TGG
(GTG)	 AG	237173-237342	GT	AGG
(GAC)	 AG	237675-237775	GT	TAG
(TGA)	 AG	238304-238337	GA	AAG
-recovered pasa_asmbl_23564.p1, terminal, 238304, 238337
-recovered pasa_asmbl_23564.p1, internal, 236590, 236638
-recovered pasa_asmbl_23564.p1, internal, 236778, 236856
-recovered pasa_asmbl_23564.p1, internal, 237173, 237342
-recovered pasa_asmbl_23564.p1, internal, 237675, 237775

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 49458, rend_intergenic: 42277  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152158, rend_intergenic: 148733  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 262454, rend_intergenic: 260081  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 266744, rend_intergenic: 264210  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 273192
-exon list size: 632


building trellis

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65.8    
65.9    
66.1    
66.2    
66.4    
66.6    
66.7    
66.9    
67.0    
67.2    
67.4    
67.5    
67.7    
67.8    
68.0    
68.1    
68.3    
68.5    
68.6    
68.8    
68.9    
69.1    
69.2    
69.4    
69.6    
69.7    
69.9    
70.0    
70.2    
70.3    
70.5    
70.7    
70.8    
71.0    
71.1    
71.3    
71.5    
71.6    
71.8    
71.9    
72.1    
72.2    
72.4    
72.6    
72.7    
72.9    
73.0    
73.2    
73.3    
73.5    
73.7    
73.8    
74.0    
74.1    
74.3    
74.4    
74.6    
74.8    
74.9    
75.1    
75.2    
75.4    
75.6    
75.7    
75.9    
76.0    
76.2    
76.3    
76.5    
76.7    
76.8    
77.0    
77.1    
77.3    
77.4    
77.6    
77.8    
77.9    
78.1    
78.2    
78.4    
78.5    
78.7    
78.9    
79.0    
79.2    
79.3    
79.5    
79.7    
79.8    
80.0    
80.1    
80.3    
80.4    
80.6    
80.8    
80.9    
81.1    
81.2    
81.4    
81.5    
81.7    
81.9    
82.0    
82.2    
82.3    
82.5    
82.6    
82.8    
83.0    
83.1    
83.3    
83.4    
83.6    
83.8    
83.9    
84.1    
84.2    
84.4    
84.5    
84.7    
84.9    
85.0    
85.2    
85.3    
85.5    
85.6    
85.8    
86.0    
86.1    
86.3    
86.4    
86.6    
86.8    
86.9    
87.1    
87.2    
87.4    
87.5    
87.7    
87.9    
88.0    
88.2    
88.3    
88.5    
88.6    
88.8    
89.0    
89.1    
89.3    
89.4    
89.6    
89.7    
89.9    
90.1    
90.2    
90.4    
90.5    
90.7    
90.9    
91.0    
91.2    
91.3    
91.5    
91.6    
91.8    
92.0    
92.1    
92.3    
92.4    
92.6    
92.7    
92.9    
93.1    
93.2    
93.4    
93.5    
93.7    
93.8    
94.0    
94.2    
94.3    
94.5    
94.6    
94.8    
95.0    
95.1    
95.3    
95.4    
95.6    
95.7    
95.9    
96.1    
96.2    
96.4    
96.5    
96.7    
96.8    
97.0    
97.2    
97.3    
97.5    
97.6    
97.8    
97.9    
98.1    
98.3    
98.4    
98.6    
98.7    
98.9    
99.1    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 49458, rend_intergenic: 42277  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152158, rend_intergenic: 148733  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 262454, rend_intergenic: 260081  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 266744, rend_intergenic: 264210  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

-building DP trellis

-building trellis in range 1 - 24091
-exon list size: 35


building trellis

2.7    
5.4    
8.1    
10.8    
13.5    
16.2    
18.9    
21.6    
24.3    
27.0    
29.7    
32.4    
35.1    
37.8    
40.5    
43.2    
45.9    
48.6    
51.4    
54.1    
56.8    
59.5    
62.2    
64.9    
67.6    
70.3    
73.0    
75.7    
78.4    
81.1    
83.8    
86.5    
89.2    
91.9    
94.6    
97.3    
-found 2 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 13679
-exon list size: 20


building trellis

4.5    
9.1    
13.6    
18.2    
22.7    
27.3    
31.8    
36.4    
40.9    
45.5    
50.0    
54.5    
59.1    
63.6    
68.2    
72.7    
77.3    
81.8    
86.4    
90.9    
95.5    
-found 2 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 12188
-exon list size: 14


building trellis

6.2    
12.5    
18.8    
25.0    
31.2    
37.5    
43.8    
50.0    
56.2    
62.5    
68.8    
75.0    
81.2    
87.5    
93.8    
-found 2 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 10516
-exon list size: 8


building trellis

10.0    
20.0    
30.0    
40.0    
50.0    
60.0    
70.0    
80.0    
90.0    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support