-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_2/scaffold_2_3924685-4130101

-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_2-snap.940-T1
Valid prediction for GlimmerHMM_glimmerT_3617-T1
Valid prediction for CodingQuarry_transcript_28524-T1
Valid prediction for snap_scaffold_2-snap.926-T1
Valid prediction for GlimmerHMM_glimmerT_3608-T1
Valid prediction for pasa_asmbl_25442.p1
Valid prediction for GlimmerHMM_glimmerT_3618-T1
Valid prediction for HiQ_model.g2428.t1
Valid prediction for pasa_asmbl_24333.p1
Valid prediction for snap_scaffold_2-snap.930-T1
Valid prediction for snap_scaffold_2-snap.944-T1
Valid prediction for Augustus_model.g2432.t1
Valid prediction for snap_scaffold_2-snap.953-T1
Valid prediction for snap_scaffold_2-snap.932-T1
Valid prediction for GlimmerHMM_glimmerT_3611-T1
Valid prediction for Augustus_model.g2429.t1
Valid prediction for GlimmerHMM_glimmerT_3623-T1
Valid prediction for HiQ_model.g2426.t1
Valid prediction for GlimmerHMM_glimmerT_3603-T1
Valid prediction for GlimmerHMM_glimmerT_3605-T1
Valid prediction for CodingQuarry_transcript_28517-T1
Valid prediction for GlimmerHMM_glimmerT_3624-T1
Valid prediction for GlimmerHMM_glimmerT_3622-T1
Valid prediction for pasa_asmbl_24327.p1
Valid prediction for snap_scaffold_2-snap.950-T1
Valid prediction for CodingQuarry_transcript_28525-T1
Valid prediction for snap_scaffold_2-snap.931-T1
Valid prediction for snap_scaffold_2-snap.934-T1
Valid prediction for snap_scaffold_2-snap.933-T1
Valid prediction for pasa_asmbl_25340.p1
Valid prediction for HiQ_model.g2424.t1
Valid prediction for snap_scaffold_2-snap.938-T1
Valid prediction for Augustus_model.g2430.t1
Valid prediction for snap_scaffold_2-snap.956-T1
Valid prediction for snap_scaffold_2-snap.949-T1
Valid prediction for snap_scaffold_2-snap.958-T1
Valid prediction for GlimmerHMM_glimmerT_3626-T1
Valid prediction for snap_scaffold_2-snap.957-T1
Valid prediction for CodingQuarry_transcript_28519-T1
Valid prediction for CodingQuarry_transcript_28520-T1
Valid prediction for GlimmerHMM_glimmerT_3613-T1
Valid prediction for CodingQuarry_transcript_28515-T1
Valid prediction for CodingQuarry_transcript_28523-T1
Valid prediction for Augustus_model.g2431.t1
Valid prediction for HiQ_model.g2419.t1
Valid prediction for snap_scaffold_2-snap.927-T1
Valid prediction for snap_scaffold_2-snap.952-T1
Valid prediction for snap_scaffold_2-snap.925-T1
Valid prediction for GlimmerHMM_glimmerT_3615-T1
Valid prediction for snap_scaffold_2-snap.951-T1
Valid prediction for HiQ_model.g2421.t1
Valid prediction for HiQ_model.g2418.t1
Valid prediction for GlimmerHMM_glimmerT_3621-T1
Couldn't classify 123163, 123216
Sorry, prediction pasa_asmbl_24335.p1 fails validation.
(AAC)	 TC	123163-123216	GT	AGG
(GCT)	 AG	123489-123614	GT	AGG
(CTT)	 AG	124496-124635	GT	AGG
(CCC)	 AG	124852-124886	GT	AAG
(TCT)	 AG	125561-125664	GT	AGG
(ATG)	 AG	126150-126281	GG	AAG
-recovered pasa_asmbl_24335.p1, terminal, 126150, 126281
-recovered pasa_asmbl_24335.p1, internal, 123489, 123614
-recovered pasa_asmbl_24335.p1, internal, 124496, 124635
-recovered pasa_asmbl_24335.p1, internal, 124852, 124886
-recovered pasa_asmbl_24335.p1, internal, 125561, 125664
Couldn't classify 67903, 68001
Couldn't classify 68203, 68253
Sorry, prediction CodingQuarry_transcript_28516-T1 fails validation.
(ATG)	 CG	64789-64970	GT	AGG
(CCC)	 AG	65076-65130	GT	CTG
(GCT)	 AG	65226-65718	GT	GAG
(CTC)	 AG	66184-66311	GT	AGG
(TTT)	 AG	66445-66549	GT	CGG
(TAC)	 AG	67705-67792	GT	CGG
(ACG)	 AG	67903-68001	GA	CGG
(GAG)	 GA	68203-68253	GT	CAG
(GTG)	 AG	68756-68841	AC	AGA
-recovered CodingQuarry_transcript_28516-T1, initial, 64789, 64970
-recovered CodingQuarry_transcript_28516-T1, terminal, 68756, 68841
-recovered CodingQuarry_transcript_28516-T1, internal, 65076, 65130
-recovered CodingQuarry_transcript_28516-T1, internal, 65226, 65718
-recovered CodingQuarry_transcript_28516-T1, internal, 66184, 66311
-recovered CodingQuarry_transcript_28516-T1, internal, 66445, 66549
-recovered CodingQuarry_transcript_28516-T1, internal, 67705, 67792
Valid prediction for snap_scaffold_2-snap.936-T1
Valid prediction for pasa_asmbl_24325.p1
Valid prediction for GlimmerHMM_glimmerT_3627-T1
Valid prediction for Augustus_model.g2417.t1
Valid prediction for snap_scaffold_2-snap.946-T1
Valid prediction for snap_scaffold_2-snap.937-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 snap_scaffold_2-snap.954-T1
Valid prediction for snap_scaffold_2-snap.939-T1
Valid prediction for pasa_asmbl_23036.p1
Couldn't classify 76344, 76397
Couldn't classify 77551, 77699
Sorry, prediction pasa_asmbl_23046.p2 fails validation.
(CAT)	 AA	76344-76397	GT	AAG
(GAT)	 AG	76973-77072	GT	TGG
(GCT)	 AG	77551-77699	GG	GGG
-recovered pasa_asmbl_23046.p2, internal, 76973, 77072
Valid prediction for GlimmerHMM_glimmerT_3616-T1
Valid prediction for GlimmerHMM_glimmerT_3606-T1
Valid prediction for Augustus_model.g2425.t1
Valid prediction for GlimmerHMM_glimmerT_3620-T1
Valid prediction for snap_scaffold_2-snap.947-T1
Valid prediction for snap_scaffold_2-snap.924-T1
Valid prediction for GlimmerHMM_glimmerT_3607-T1
Valid prediction for HiQ_model.g2420.t1
Valid prediction for GlimmerHMM_glimmerT_3612-T1
Valid prediction for Augustus_model.g2415.t1
Valid prediction for Augustus_model.g2414.t1
Valid prediction for GlimmerHMM_glimmerT_3619-T1
Valid prediction for snap_scaffold_2-snap.928-T1
Couldn't classify 198206, 198258
Sorry, prediction pasa_asmbl_23025.p1 fails validation.
(GTG)	 CA	198206-198258	GT	AGG
(GAC)	 AG	198525-198650	GT	AAG
(GAG)	 AG	198859-198994	GT	AGG
(CTT)	 AG	199252-199397	GT	AAG
(GAC)	 AG	199799-199838	AC	AAA
-recovered pasa_asmbl_23025.p1, terminal, 199799, 199838
-recovered pasa_asmbl_23025.p1, internal, 198525, 198650
-recovered pasa_asmbl_23025.p1, internal, 198859, 198994
-recovered pasa_asmbl_23025.p1, internal, 199252, 199397
Valid prediction for CodingQuarry_transcript_28514-T1
Valid prediction for HiQ_model.g2422.t1
Valid prediction for GlimmerHMM_glimmerT_3604-T1
Valid prediction for Augustus_model.g2413.t1
Valid prediction for GlimmerHMM_glimmerT_3609-T1
Valid prediction for GlimmerHMM_glimmerT_3614-T1
Couldn't classify 90149, 90263
Couldn't classify 91334, 91524
Sorry, prediction pasa_asmbl_23975.p1 fails validation.
(CAT)	 TC	90149-90263	GT	AGG
(AAT)	 AG	91334-91524	AG	GCA
Valid prediction for snap_scaffold_2-snap.942-T1
Valid prediction for snap_scaffold_2-snap.945-T1
Couldn't classify 125510, 125542
Sorry, prediction pasa_asmbl_23033.p1 fails validation.
(ATG)	 CC	124169-124304	GT	CAG
(ATC)	 AG	124459-124553	GT	GGG
(AAA)	 AG	124679-124795	GT	TGG
(GAT)	 AG	124992-125132	GT	AAG
(CCC)	 AG	125510-125542	CG	AGC
-recovered pasa_asmbl_23033.p1, initial, 124169, 124304
-recovered pasa_asmbl_23033.p1, internal, 124459, 124553
-recovered pasa_asmbl_23033.p1, internal, 124679, 124795
-recovered pasa_asmbl_23033.p1, internal, 124992, 125132
Valid prediction for CodingQuarry_transcript_28518-T1
Valid prediction for Augustus_model.g2416.t1
Couldn't classify 188989, 189063
Couldn't classify 195086, 195181
Sorry, prediction pasa_asmbl_23918.p1 fails validation.
(AAC)	 TC	188989-189063	GT	AGG
(GTG)	 AG	191232-191332	GT	TGG
(CTG)	 AG	191839-191973	GT	GGG
(GTT)	 AG	193941-194058	GT	AGG
(ATC)	 AG	194339-194431	GT	AGG
(GAG)	 AG	195086-195181	GG	AAG
-recovered pasa_asmbl_23918.p1, internal, 191232, 191332
-recovered pasa_asmbl_23918.p1, internal, 191839, 191973
-recovered pasa_asmbl_23918.p1, internal, 193941, 194058
-recovered pasa_asmbl_23918.p1, internal, 194339, 194431
Valid prediction for snap_scaffold_2-snap.955-T1
Couldn't classify 170939, 170993
Sorry, prediction pasa_asmbl_23030.p1 fails validation.
(CAG)	 AC	170939-170993	GT	AGG
(AGG)	 AG	171297-171386	GT	GGG
(GTA)	 AG	172361-172424	GT	AAG
(GGT)	 AG	172671-172833	GT	TGG
(GAC)	 AG	173332-173433	TG	AAT
-recovered pasa_asmbl_23030.p1, terminal, 173332, 173433
-recovered pasa_asmbl_23030.p1, internal, 171297, 171386
-recovered pasa_asmbl_23030.p1, internal, 172361, 172424
-recovered pasa_asmbl_23030.p1, internal, 172671, 172833
Couldn't classify 88830, 88886
Sorry, prediction pasa_asmbl_23043.p1 fails validation.
(ATG)	 TA	86076-86188	GT	AGG
(CGT)	 AG	87862-87942	GT	AGG
(GTG)	 AG	88213-88261	GT	AGG
(AAT)	 AG	88830-88886	GG	AGG
-recovered pasa_asmbl_23043.p1, initial, 86076, 86188
-recovered pasa_asmbl_23043.p1, internal, 87862, 87942
-recovered pasa_asmbl_23043.p1, internal, 88213, 88261
Couldn't classify 125654, 125739
Sorry, prediction pasa_asmbl_23032.p1 fails validation.
(CTG)	 GC	125654-125739	GT	ATG
(AGT)	 AG	125839-126043	GT	AGG
(TCA)	 AG	126695-126860	GT	AGG
(GCT)	 AG	127142-127267	GT	TGG
(ACT)	 AG	127372-127422	GT	CGG
(GAA)	 AG	127526-127633	GT	CGG
(ATT)	 AG	127806-127859	GT	TGG
(AAC)	 AG	128031-128203	GT	AGG
(TGT)	 AG	128928-129144	GT	AGG
(ACT)	 AG	129382-129517	GT	CGG
(AGA)	 AG	129834-129900	GT	TGG
(AAT)	 AG	130077-130181	CA	GAC
-recovered pasa_asmbl_23032.p1, terminal, 130077, 130181
-recovered pasa_asmbl_23032.p1, internal, 125839, 126043
-recovered pasa_asmbl_23032.p1, internal, 126695, 126860
-recovered pasa_asmbl_23032.p1, internal, 127142, 127267
-recovered pasa_asmbl_23032.p1, internal, 127372, 127422
-recovered pasa_asmbl_23032.p1, internal, 127526, 127633
-recovered pasa_asmbl_23032.p1, internal, 127806, 127859
-recovered pasa_asmbl_23032.p1, internal, 128031, 128203
-recovered pasa_asmbl_23032.p1, internal, 128928, 129144
-recovered pasa_asmbl_23032.p1, internal, 129382, 129517
-recovered pasa_asmbl_23032.p1, internal, 129834, 129900
Valid prediction for snap_scaffold_2-snap.929-T1
Valid prediction for snap_scaffold_2-snap.948-T1
Valid prediction for snap_scaffold_2-snap.941-T1
Valid prediction for GlimmerHMM_glimmerT_3610-T1
Valid prediction for snap_scaffold_2-snap.943-T1
Valid prediction for CodingQuarry_transcript_28522-T1
Valid prediction for Augustus_model.g2427.t1
Valid prediction for Augustus_model.g2423.t1
Valid prediction for CodingQuarry_transcript_28521-T1
Valid prediction for snap_scaffold_2-snap.935-T1
Valid prediction for GlimmerHMM_glimmerT_3625-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 25714, rend_intergenic: 4077  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51284, rend_intergenic: 32527  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63133, rend_intergenic: 59898  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174711, rend_intergenic: 170820  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 205417
-exon list size: 392


building trellis

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10.9    
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14.5    
14.7    
15.0    
15.2    
15.5    
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16.0    
16.2    
16.5    
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17.0    
17.3    
17.5    
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18.0    
18.3    
18.5    
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19.3    
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20.1    
20.3    
20.6    
20.8    
21.1    
21.3    
21.6    
21.8    
22.1    
22.3    
22.6    
22.8    
23.1    
23.4    
23.6    
23.9    
24.1    
24.4    
24.6    
24.9    
25.1    
25.4    
25.6    
25.9    
26.1    
26.4    
26.6    
26.9    
27.2    
27.4    
27.7    
27.9    
28.2    
28.4    
28.7    
28.9    
29.2    
29.4    
29.7    
29.9    
30.2    
30.5    
30.7    
31.0    
31.2    
31.5    
31.7    
32.0    
32.2    
32.5    
32.7    
33.0    
33.2    
33.5    
33.8    
34.0    
34.3    
34.5    
34.8    
35.0    
35.3    
35.5    
35.8    
36.0    
36.3    
36.5    
36.8    
37.1    
37.3    
37.6    
37.8    
38.1    
38.3    
38.6    
38.8    
39.1    
39.3    
39.6    
39.8    
40.1    
40.4    
40.6    
40.9    
41.1    
41.4    
41.6    
41.9    
42.1    
42.4    
42.6    
42.9    
43.1    
43.4    
43.7    
43.9    
44.2    
44.4    
44.7    
44.9    
45.2    
45.4    
45.7    
45.9    
46.2    
46.4    
46.7    
47.0    
47.2    
47.5    
47.7    
48.0    
48.2    
48.5    
48.7    
49.0    
49.2    
49.5    
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50.0    
50.3    
50.5    
50.8    
51.0    
51.3    
51.5    
51.8    
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52.3    
52.5    
52.8    
53.0    
53.3    
53.6    
53.8    
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54.6    
54.8    
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55.6    
55.8    
56.1    
56.3    
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56.9    
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57.6    
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58.1    
58.4    
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64.2    
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66.0    
66.2    
66.5    
66.8    
67.0    
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67.5    
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68.0    
68.3    
68.5    
68.8    
69.0    
69.3    
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70.1    
70.3    
70.6    
70.8    
71.1    
71.3    
71.6    
71.8    
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72.3    
72.6    
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73.4    
73.6    
73.9    
74.1    
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75.4    
75.6    
75.9    
76.1    
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76.6    
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77.2    
77.4    
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77.9    
78.2    
78.4    
78.7    
78.9    
79.2    
79.4    
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79.9    
80.2    
80.5    
80.7    
81.0    
81.2    
81.5    
81.7    
82.0    
82.2    
82.5    
82.7    
83.0    
83.2    
83.5    
83.8    
84.0    
84.3    
84.5    
84.8    
85.0    
85.3    
85.5    
85.8    
86.0    
86.3    
86.5    
86.8    
87.1    
87.3    
87.6    
87.8    
88.1    
88.3    
88.6    
88.8    
89.1    
89.3    
89.6    
89.8    
90.1    
90.4    
90.6    
90.9    
91.1    
91.4    
91.6    
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92.1    
92.4    
92.6    
92.9    
93.1    
93.4    
93.7    
93.9    
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94.4    
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95.4    
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95.9    
96.2    
96.4    
96.7    
97.0    
97.2    
97.5    
97.7    
98.0    
98.2    
98.5    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 25714, rend_intergenic: 4077  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51284, rend_intergenic: 32527  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63133, rend_intergenic: 59898  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174711, rend_intergenic: 170820  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support