-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_3/scaffold_3_2139065-2354361

-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: +)Couldn't classify 187040, 187372
Sorry, prediction pasa_asmbl_38741.p1 fails validation.
(GCA)	 AG	187040-187372	CG	GAC
Valid prediction for Augustus_model.g4001.t1
Valid prediction for snap_scaffold_3-snap.504-T1
Valid prediction for Augustus_model.g4002.t1
Valid prediction for snap_scaffold_3-snap.514-T1
Valid prediction for snap_scaffold_3-snap.534-T1
Valid prediction for GlimmerHMM_glimmerT_6128-T1
Valid prediction for HiQ_model.g4000.t1
Valid prediction for snap_scaffold_3-snap.518-T1
Valid prediction for Augustus_model.g4008.t1
Valid prediction for GlimmerHMM_glimmerT_6147-T1
Valid prediction for snap_scaffold_3-snap.509-T1
Valid prediction for GlimmerHMM_glimmerT_6129-T1
Valid prediction for snap_scaffold_3-snap.522-T1
Valid prediction for GlimmerHMM_glimmerT_6149-T1
Valid prediction for pasa_asmbl_39898.p1
Valid prediction for CodingQuarry_transcript_46100-T1
Valid prediction for GlimmerHMM_glimmerT_6134-T1
Valid prediction for snap_scaffold_3-snap.528-T1
Valid prediction for snap_scaffold_3-snap.537-T1
Valid prediction for GlimmerHMM_glimmerT_6135-T1
Valid prediction for CodingQuarry_transcript_46101-T1
Valid prediction for HiQ_model.g3998.t1
Valid prediction for pasa_asmbl_39894.p1
Valid prediction for GlimmerHMM_glimmerT_6140-T1
Valid prediction for GlimmerHMM_glimmerT_6142-T1
Valid prediction for GlimmerHMM_glimmerT_6131-T1
Valid prediction for HiQ_model.g3996.t1
Couldn't classify 79568, 79830
Couldn't classify 80145, 80165
Sorry, prediction CodingQuarry_transcript_46098-T1 fails validation.
(ATG)	 CG	70327-70501	GT	TGG
(CCA)	 AG	70739-70839	GT	ATG
(GAA)	 AG	71089-71122	GT	ACG
(CTG)	 AG	71579-71803	GT	AGG
(GAA)	 AG	72010-72237	GT	AGG
(CTG)	 AG	72336-74596	GT	CGG
(ACT)	 AG	74771-75001	GT	AGG
(ATG)	 AG	75191-75412	GT	AGG
(GCT)	 AG	75834-75921	GT	AGG
(GCT)	 AG	76030-76176	GT	AGG
(GGG)	 AG	76448-76510	GT	GGG
(GAG)	 AG	76927-77103	GT	AGG
(GCA)	 AG	77542-77754	GT	ATG
(CAT)	 AG	77939-78553	GT	AGG
(GCC)	 AG	78824-78966	GT	AGG
(ATT)	 AG	79157-79331	GT	CGG
(CTG)	 AG	79568-79830	TA	AGT
(TAT)	 TT	80145-80165	AA	AGA
-recovered CodingQuarry_transcript_46098-T1, initial, 70327, 70501
-recovered CodingQuarry_transcript_46098-T1, initial, 75191, 75412
-recovered CodingQuarry_transcript_46098-T1, internal, 70739, 70839
-recovered CodingQuarry_transcript_46098-T1, internal, 71089, 71122
-recovered CodingQuarry_transcript_46098-T1, internal, 71579, 71803
-recovered CodingQuarry_transcript_46098-T1, internal, 72010, 72237
-recovered CodingQuarry_transcript_46098-T1, internal, 72336, 74596
-recovered CodingQuarry_transcript_46098-T1, internal, 74771, 75001
-recovered CodingQuarry_transcript_46098-T1, internal, 75191, 75412
-recovered CodingQuarry_transcript_46098-T1, internal, 75834, 75921
-recovered CodingQuarry_transcript_46098-T1, internal, 76030, 76176
-recovered CodingQuarry_transcript_46098-T1, internal, 76448, 76510
-recovered CodingQuarry_transcript_46098-T1, internal, 76927, 77103
-recovered CodingQuarry_transcript_46098-T1, internal, 77542, 77754
-recovered CodingQuarry_transcript_46098-T1, internal, 77939, 78553
-recovered CodingQuarry_transcript_46098-T1, internal, 78824, 78966
-recovered CodingQuarry_transcript_46098-T1, internal, 79157, 79331
Valid prediction for Augustus_model.g4003.t1
Valid prediction for snap_scaffold_3-snap.515-T1
Valid prediction for snap_scaffold_3-snap.517-T1
Valid prediction for snap_scaffold_3-snap.523-T1
Valid prediction for HiQ_model.g4007.t1
Couldn't classify 72336, 74229
Couldn't classify 74264, 74294
Sorry, prediction CodingQuarry_transcript_46097-T1 fails validation.
(ATG)	 CG	70327-70501	GT	TGG
(CCA)	 AG	70739-70839	GT	ATG
(GAA)	 AG	71089-71122	GT	ACG
(CTG)	 AG	71579-71803	GT	AGG
(GAA)	 AG	72010-72237	GT	AGG
(CTG)	 AG	72336-74229	AT	GAA
(ATC)	 CC	74264-74294	AC	GAA
-recovered CodingQuarry_transcript_46097-T1, initial, 70327, 70501
-recovered CodingQuarry_transcript_46097-T1, internal, 70739, 70839
-recovered CodingQuarry_transcript_46097-T1, internal, 71089, 71122
-recovered CodingQuarry_transcript_46097-T1, internal, 71579, 71803
-recovered CodingQuarry_transcript_46097-T1, internal, 72010, 72237
Couldn't classify 109169, 109342
Couldn't classify 116376, 116422
Sorry, prediction pasa_asmbl_39901.p1 fails validation.
(GAA)	 CT	109169-109342	GT	AGG
(GTA)	 AG	110845-110913	GT	AGG
(GAT)	 AG	112421-112582	GT	AGG
(CTG)	 AG	112972-113097	GT	AAG
(GAG)	 AG	113488-113835	GT	AGG
(GCC)	 AG	113951-114025	GT	CAG
(GCT)	 AG	115845-115920	GT	AGG
(AAG)	 AG	116207-116227	GT	AGG
(ATG)	 AG	116376-116422	GA	GAG
-recovered pasa_asmbl_39901.p1, internal, 110845, 110913
-recovered pasa_asmbl_39901.p1, internal, 112421, 112582
-recovered pasa_asmbl_39901.p1, internal, 112972, 113097
-recovered pasa_asmbl_39901.p1, internal, 113488, 113835
-recovered pasa_asmbl_39901.p1, internal, 113951, 114025
-recovered pasa_asmbl_39901.p1, internal, 115845, 115920
-recovered pasa_asmbl_39901.p1, internal, 116207, 116227
Valid prediction for GlimmerHMM_glimmerT_6126-T1
Valid prediction for GlimmerHMM_glimmerT_6132-T1
Valid prediction for pasa_asmbl_39906.p1
Valid prediction for snap_scaffold_3-snap.516-T1
Valid prediction for snap_scaffold_3-snap.529-T1
Valid prediction for snap_scaffold_3-snap.513-T1
Valid prediction for snap_scaffold_3-snap.526-T1
Valid prediction for snap_scaffold_3-snap.531-T1
Valid prediction for GlimmerHMM_glimmerT_6143-T1
Valid prediction for Augustus_model.g4004.t1
Valid prediction for GlimmerHMM_glimmerT_6136-T1
Couldn't classify 89700, 89788
Couldn't classify 90560, 90650
Sorry, prediction pasa_asmbl_40866.p1 fails validation.
(AAC)	 TG	89700-89788	GT	AGG
(GAA)	 AG	89971-90102	GT	AAG
(GTT)	 AG	90560-90650	AA	GGA
-recovered pasa_asmbl_40866.p1, internal, 89971, 90102
Couldn't classify 105707, 106114
Couldn't classify 106289, 106456
Sorry, prediction pasa_asmbl_39899.p1 fails validation.
(GCA)	 AC	105707-106114	GT	AGG
(ATT)	 AG	106289-106456	AA	GGA
Couldn't classify 63548, 63655
Sorry, prediction pasa_asmbl_39895.p1 fails validation.
(ATG)	 GT	60876-60989	GC	AGG
(GAG)	 AG	61178-61406	GT	AGG
(AGA)	 AG	63007-63056	GT	CGG
(GGG)	 AG	63548-63655	AT	CCA
-recovered pasa_asmbl_39895.p1, initial, 60876, 60989
add_exon() Sorry, pasa_asmbl_39895.p1 61178-61406-terminal-3 is invalid.
-recovered pasa_asmbl_39895.p1, terminal, 61178, 61406
-recovered pasa_asmbl_39895.p1, internal, 61178, 61406
-recovered pasa_asmbl_39895.p1, internal, 63007, 63056
Valid prediction for snap_scaffold_3-snap.510-T1
Valid prediction for GlimmerHMM_glimmerT_6123-T1
Valid prediction for Augustus_model.g4009.t1
Valid prediction for GlimmerHMM_glimmerT_6146-T1
Valid prediction for snap_scaffold_3-snap.501-T1
Valid prediction for Augustus_model.g4006.t1
Valid prediction for GlimmerHMM_glimmerT_6138-T1
Valid prediction for snap_scaffold_3-snap.507-T1
Valid prediction for snap_scaffold_3-snap.506-T1
Valid prediction for CodingQuarry_transcript_46099-T1
Valid prediction for snap_scaffold_3-snap.535-T1
Valid prediction for GlimmerHMM_glimmerT_6133-T1
Couldn't classify 123776, 123999
Sorry, prediction pasa_asmbl_39902.p2 fails validation.
(GAG)	 TT	123776-123999	GT	AGG
(GGT)	 AG	124317-124482	GA	GAG
-recovered pasa_asmbl_39902.p2, terminal, 124317, 124482
Valid prediction for snap_scaffold_3-snap.502-T1
Valid prediction for GlimmerHMM_glimmerT_6144-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_3-snap.521-T1
Valid prediction for GlimmerHMM_glimmerT_6141-T1
Valid prediction for snap_scaffold_3-snap.512-T1
Valid prediction for snap_scaffold_3-snap.525-T1
Valid prediction for Augustus_model.g4011.t1
Valid prediction for GlimmerHMM_glimmerT_6139-T1
Valid prediction for GlimmerHMM_glimmerT_6148-T1
Valid prediction for Augustus_model.g4010.t1
Valid prediction for Augustus_model.g3999.t1
Valid prediction for snap_scaffold_3-snap.532-T1
Valid prediction for snap_scaffold_3-snap.524-T1
Valid prediction for GlimmerHMM_glimmerT_6145-T1
Valid prediction for GlimmerHMM_glimmerT_6127-T1
Valid prediction for snap_scaffold_3-snap.508-T1
Valid prediction for snap_scaffold_3-snap.505-T1
Valid prediction for snap_scaffold_3-snap.519-T1
Valid prediction for GlimmerHMM_glimmerT_6137-T1
Valid prediction for snap_scaffold_3-snap.500-T1
Couldn't classify 168969, 169025
Sorry, prediction pasa_asmbl_38733.p1 fails validation.
(AAC)	 CG	168969-169025	GT	AGG
(ATC)	 AG	169322-169442	GT	GGG
(AGA)	 AG	170060-170197	GT	TGG
(AGA)	 AG	170446-170532	GT	CGG
(TGG)	 AG	170950-170966	AT	GAA
-recovered pasa_asmbl_38733.p1, terminal, 170950, 170966
-recovered pasa_asmbl_38733.p1, internal, 169322, 169442
-recovered pasa_asmbl_38733.p1, internal, 170060, 170197
-recovered pasa_asmbl_38733.p1, internal, 170446, 170532
Valid prediction for snap_scaffold_3-snap.511-T1
Valid prediction for snap_scaffold_3-snap.536-T1
Valid prediction for snap_scaffold_3-snap.533-T1
Valid prediction for pasa_asmbl_38736.p1
Valid prediction for snap_scaffold_3-snap.530-T1
Valid prediction for Augustus_model.g4005.t1
Valid prediction for CodingQuarry_transcript_46096-T1
Valid prediction for snap_scaffold_3-snap.503-T1
Valid prediction for snap_scaffold_3-snap.520-T1
Valid prediction for GlimmerHMM_glimmerT_6130-T1
Valid prediction for Augustus_model.g4012.t1
Valid prediction for snap_scaffold_3-snap.527-T1
Valid prediction for GlimmerHMM_glimmerT_6125-T1
Valid prediction for GlimmerHMM_glimmerT_6124-T1
Valid prediction for Augustus_model.g3997.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15566, rend_intergenic: 12958  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49024, rend_intergenic: 44755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56185, rend_intergenic: 50477  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124482, rend_intergenic: 110695  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144688, rend_intergenic: 134382  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169299, rend_intergenic: 163671  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196434, rend_intergenic: 187933  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199761, rend_intergenic: 196538  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 214481, rend_intergenic: 202644  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 215297
-exon list size: 382


building trellis

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1.0    
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2.6    
2.9    
3.1    
3.4    
3.6    
3.9    
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4.4    
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4.9    
5.2    
5.5    
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6.2    
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10.2    
10.4    
10.7    
10.9    
11.2    
11.5    
11.7    
12.0    
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14.6    
14.8    
15.1    
15.4    
15.6    
15.9    
16.1    
16.4    
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16.9    
17.2    
17.4    
17.7    
18.0    
18.2    
18.5    
18.8    
19.0    
19.3    
19.5    
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20.1    
20.3    
20.6    
20.8    
21.1    
21.4    
21.6    
21.9    
22.1    
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22.7    
22.9    
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23.7    
24.0    
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25.3    
25.5    
25.8    
26.0    
26.3    
26.6    
26.8    
27.1    
27.3    
27.6    
27.9    
28.1    
28.4    
28.6    
28.9    
29.2    
29.4    
29.7    
29.9    
30.2    
30.5    
30.7    
31.0    
31.2    
31.5    
31.8    
32.0    
32.3    
32.6    
32.8    
33.1    
33.3    
33.6    
33.9    
34.1    
34.4    
34.6    
34.9    
35.2    
35.4    
35.7    
35.9    
36.2    
36.5    
36.7    
37.0    
37.2    
37.5    
37.8    
38.0    
38.3    
38.5    
38.8    
39.1    
39.3    
39.6    
39.8    
40.1    
40.4    
40.6    
40.9    
41.1    
41.4    
41.7    
41.9    
42.2    
42.4    
42.7    
43.0    
43.2    
43.5    
43.8    
44.0    
44.3    
44.5    
44.8    
45.1    
45.3    
45.6    
45.8    
46.1    
46.4    
46.6    
46.9    
47.1    
47.4    
47.7    
47.9    
48.2    
48.4    
48.7    
49.0    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.0    
51.3    
51.6    
51.8    
52.1    
52.3    
52.6    
52.9    
53.1    
53.4    
53.6    
53.9    
54.2    
54.4    
54.7    
54.9    
55.2    
55.5    
55.7    
56.0    
56.2    
56.5    
56.8    
57.0    
57.3    
57.6    
57.8    
58.1    
58.3    
58.6    
58.9    
59.1    
59.4    
59.6    
59.9    
60.2    
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60.7    
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62.0    
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63.0    
63.3    
63.5    
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64.1    
64.3    
64.6    
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65.1    
65.4    
65.6    
65.9    
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66.9    
67.2    
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68.0    
68.2    
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68.8    
69.0    
69.3    
69.5    
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70.1    
70.3    
70.6    
70.8    
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71.6    
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72.1    
72.4    
72.7    
72.9    
73.2    
73.4    
73.7    
74.0    
74.2    
74.5    
74.7    
75.0    
75.3    
75.5    
75.8    
76.0    
76.3    
76.6    
76.8    
77.1    
77.3    
77.6    
77.9    
78.1    
78.4    
78.6    
78.9    
79.2    
79.4    
79.7    
79.9    
80.2    
80.5    
80.7    
81.0    
81.2    
81.5    
81.8    
82.0    
82.3    
82.6    
82.8    
83.1    
83.3    
83.6    
83.9    
84.1    
84.4    
84.6    
84.9    
85.2    
85.4    
85.7    
85.9    
86.2    
86.5    
86.7    
87.0    
87.2    
87.5    
87.8    
88.0    
88.3    
88.5    
88.8    
89.1    
89.3    
89.6    
89.8    
90.1    
90.4    
90.6    
90.9    
91.1    
91.4    
91.7    
91.9    
92.2    
92.4    
92.7    
93.0    
93.2    
93.5    
93.8    
94.0    
94.3    
94.5    
94.8    
95.1    
95.3    
95.6    
95.8    
96.1    
96.4    
96.6    
96.9    
97.1    
97.4    
97.7    
97.9    
98.2    
98.4    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 15566, rend_intergenic: 12958  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49024, rend_intergenic: 44755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56185, rend_intergenic: 50477  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124482, rend_intergenic: 110695  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144688, rend_intergenic: 134382  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169299, rend_intergenic: 163671  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196434, rend_intergenic: 187933  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199761, rend_intergenic: 196538  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 214481, rend_intergenic: 202644  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support