-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_23/scaffold_23_5545719-5743937

-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_51042-T1
Valid prediction for snap_scaffold_23-snap.993-T1
Valid prediction for snap_scaffold_23-snap.991-T1
Valid prediction for CodingQuarry_transcript_35658-T1
Valid prediction for snap_scaffold_23-snap.988-T1
Valid prediction for snap_scaffold_23-snap.1020-T1
Valid prediction for Augustus_model.g34164.t1
Valid prediction for HiQ_model.g34144.t1
Valid prediction for snap_scaffold_23-snap.997-T1
Valid prediction for GlimmerHMM_glimmerT_51037-T1
Couldn't classify 175774, 176481
Sorry, prediction pasa_asmbl_31592.p1 fails validation.
(CAG)	 AG	175774-176481	GT	AGG
(GAG)	 AG	177332-177456	GT	AGG
(GAA)	 AG	177639-179037	CC	GAC
-recovered pasa_asmbl_31592.p1, terminal, 177639, 179037
-recovered pasa_asmbl_31592.p1, internal, 175774, 176481
-recovered pasa_asmbl_31592.p1, internal, 177332, 177456
Valid prediction for snap_scaffold_23-snap.1014-T1
Valid prediction for snap_scaffold_23-snap.1021-T1
Valid prediction for snap_scaffold_23-snap.998-T1
Valid prediction for snap_scaffold_23-snap.1016-T1
Valid prediction for snap_scaffold_23-snap.995-T1
Valid prediction for Augustus_model.g34142.t1
Valid prediction for Augustus_model.g34146.t1
Valid prediction for CodingQuarry_transcript_35659-T1
Valid prediction for snap_scaffold_23-snap.1030-T1
Valid prediction for snap_scaffold_23-snap.990-T1
Valid prediction for CodingQuarry_transcript_35660-T1
Couldn't classify 4314, 4403
Couldn't classify 8901, 9085
Sorry, prediction pasa_asmbl_31571.p1 fails validation.
(ACA)	 CA	4314-4403	GT	AGG
(AGC)	 AG	4560-4623	GT	TGG
(GTT)	 AG	4748-4891	GT	GAG
(ATG)	 AG	5158-5492	GT	TTG
(ATG)	 AG	5681-5802	GT	AAG
(TGG)	 AG	5954-6117	GT	AGG
(GTC)	 AG	7616-7703	GT	TGG
(GCC)	 AG	7794-7950	GT	AAG
(ACC)	 AG	8402-8768	GT	AGG
(ACT)	 AG	8901-9085	GT	AGG
add_exon() Sorry, pasa_asmbl_31571.p1 5158-5492-initial-1 is invalid.
-recovered pasa_asmbl_31571.p1, initial, 5158, 5492
-recovered pasa_asmbl_31571.p1, initial, 5681, 5802
-recovered pasa_asmbl_31571.p1, internal, 4560, 4623
-recovered pasa_asmbl_31571.p1, internal, 4748, 4891
-recovered pasa_asmbl_31571.p1, internal, 5158, 5492
-recovered pasa_asmbl_31571.p1, internal, 5681, 5802
-recovered pasa_asmbl_31571.p1, internal, 5954, 6117
-recovered pasa_asmbl_31571.p1, internal, 7616, 7703
-recovered pasa_asmbl_31571.p1, internal, 7794, 7950
-recovered pasa_asmbl_31571.p1, internal, 8402, 8768
-recovered pasa_asmbl_31571.p1, internal, 8901, 9085
Valid prediction for GlimmerHMM_glimmerT_51040-T1
Valid prediction for GlimmerHMM_glimmerT_51058-T1
Valid prediction for snap_scaffold_23-snap.1012-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for HiQ_model.g34143.t1
Valid prediction for HiQ_model.g34161.t1
Valid prediction for GlimmerHMM_glimmerT_51064-T1
Valid prediction for snap_scaffold_23-snap.1008-T1
Valid prediction for snap_scaffold_23-snap.1027-T1
Valid prediction for GlimmerHMM_glimmerT_51053-T1
Valid prediction for snap_scaffold_23-snap.1015-T1
Valid prediction for Augustus_model.g34158.t1
Valid prediction for snap_scaffold_23-snap.1026-T1
Valid prediction for Augustus_model.g34163.t1
Valid prediction for Augustus_model.g34147.t1
Valid prediction for GlimmerHMM_glimmerT_51043-T1
Couldn't classify 14399, 14600
Couldn't classify 18190, 18379
Sorry, prediction pasa_asmbl_31573.p1 fails validation.
(GAA)	 AG	14399-14600	GT	AGG
(GAT)	 AG	15731-15935	GC	AGG
(GAG)	 AG	16043-18067	GT	AGG
(CAG)	 AG	18190-18379	AG	CAA
-recovered pasa_asmbl_31573.p1, internal, 14399, 14600
-recovered pasa_asmbl_31573.p1, internal, 15731, 15935
-recovered pasa_asmbl_31573.p1, internal, 16043, 18067
Valid prediction for Augustus_model.g34165.t1
Valid prediction for GlimmerHMM_glimmerT_51067-T1
Valid prediction for snap_scaffold_23-snap.994-T1
Valid prediction for snap_scaffold_23-snap.999-T1
Valid prediction for GlimmerHMM_glimmerT_51066-T1
Valid prediction for snap_scaffold_23-snap.1025-T1
Valid prediction for GlimmerHMM_glimmerT_51046-T1
Valid prediction for snap_scaffold_23-snap.1010-T1
Valid prediction for GlimmerHMM_glimmerT_51039-T1
Couldn't classify 21506, 21619
Couldn't classify 27989, 28117
Sorry, prediction pasa_asmbl_31576.p1 fails validation.
(GAG)	 TT	21506-21619	GT	CTG
(GTG)	 AG	21807-21948	GT	AGG
(CCC)	 AG	24237-24313	GT	AGG
(GAT)	 AG	24618-24905	GT	ACG
(CCG)	 AG	25011-25112	GT	AGG
(ATG)	 AG	26332-26518	GT	GGG
(GTA)	 AG	26592-26689	GT	AGG
(GCA)	 AG	27989-28117	TA	GGT
-recovered pasa_asmbl_31576.p1, initial, 26332, 26518
-recovered pasa_asmbl_31576.p1, internal, 21807, 21948
-recovered pasa_asmbl_31576.p1, internal, 24237, 24313
-recovered pasa_asmbl_31576.p1, internal, 24618, 24905
-recovered pasa_asmbl_31576.p1, internal, 25011, 25112
-recovered pasa_asmbl_31576.p1, internal, 26332, 26518
-recovered pasa_asmbl_31576.p1, internal, 26592, 26689
Valid prediction for pasa_asmbl_31593.p1
Valid prediction for snap_scaffold_23-snap.1018-T1
Valid prediction for snap_scaffold_23-snap.1029-T1
Valid prediction for GlimmerHMM_glimmerT_51051-T1
Valid prediction for snap_scaffold_23-snap.1002-T1
Valid prediction for pasa_asmbl_31586.p1
Valid prediction for snap_scaffold_23-snap.1009-T1
Valid prediction for Augustus_model.g34140.t1
Valid prediction for Augustus_model.g34154.t1
Valid prediction for GlimmerHMM_glimmerT_51056-T1
Valid prediction for GlimmerHMM_glimmerT_51047-T1
Valid prediction for GlimmerHMM_glimmerT_51045-T1
Couldn't classify 31280, 31522
Sorry, prediction pasa_asmbl_31579.p1 fails validation.
(AGG)	 CC	31280-31522	GT	AGG
(GTA)	 AG	31638-31805	GT	AGG
(GCT)	 AG	32261-32337	GT	AGG
(GCC)	 AG	32434-32515	GT	AGG
(GTG)	 AG	33099-33308	GT	AGG
(AAT)	 AG	35565-35732	CA	AGC
-recovered pasa_asmbl_31579.p1, terminal, 35565, 35732
-recovered pasa_asmbl_31579.p1, internal, 31638, 31805
-recovered pasa_asmbl_31579.p1, internal, 32261, 32337
-recovered pasa_asmbl_31579.p1, internal, 32434, 32515
-recovered pasa_asmbl_31579.p1, internal, 33099, 33308
Valid prediction for CodingQuarry_transcript_35666-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 HiQ_model.g34151.t1
Valid prediction for Augustus_model.g34162.t1
Valid prediction for CodingQuarry_transcript_35662-T1
Valid prediction for GlimmerHMM_glimmerT_51063-T1
Valid prediction for snap_scaffold_23-snap.1024-T1
Valid prediction for GlimmerHMM_glimmerT_51049-T1
Valid prediction for snap_scaffold_23-snap.1017-T1
Valid prediction for snap_scaffold_23-snap.996-T1
Valid prediction for HiQ_model.g34155.t1
Valid prediction for snap_scaffold_23-snap.1000-T1
Valid prediction for pasa_asmbl_30935.p1
Valid prediction for GlimmerHMM_glimmerT_51061-T1
Valid prediction for GlimmerHMM_glimmerT_51052-T1
Valid prediction for snap_scaffold_23-snap.989-T1
Valid prediction for GlimmerHMM_glimmerT_51065-T1
Valid prediction for GlimmerHMM_glimmerT_51048-T1
Couldn't classify 177971, 178414
Sorry, prediction pasa_asmbl_31575.p1 fails validation.
(ATG)	 TA	177971-178414	TC	GGT
Valid prediction for GlimmerHMM_glimmerT_51062-T1
Valid prediction for snap_scaffold_23-snap.1007-T1
Valid prediction for snap_scaffold_23-snap.1013-T1
Valid prediction for pasa_asmbl_30938.p1
Valid prediction for pasa_asmbl_30926.p1
Valid prediction for snap_scaffold_23-snap.1001-T1
Sorry, intron length (9) is less than minimum required (10)
Couldn't classify 113142, 113483
Sorry, prediction pasa_asmbl_30934.p1 fails validation.
(ATG)	 GT	113142-113483	AC	CCA
Valid prediction for CodingQuarry_transcript_35664-T1
Valid prediction for snap_scaffold_23-snap.1003-T1
Valid prediction for GlimmerHMM_glimmerT_51059-T1
Valid prediction for GlimmerHMM_glimmerT_51055-T1
Valid prediction for HiQ_model.g34160.t1
Valid prediction for Augustus_model.g34149.t1
Valid prediction for Augustus_model.g34141.t1
Valid prediction for snap_scaffold_23-snap.1028-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g34145.t1
Valid prediction for GlimmerHMM_glimmerT_51041-T1
Valid prediction for CodingQuarry_transcript_35663-T1
Valid prediction for GlimmerHMM_glimmerT_51060-T1
Valid prediction for Augustus_model.g34156.t1
Valid prediction for GlimmerHMM_glimmerT_51054-T1
Valid prediction for GlimmerHMM_glimmerT_51057-T1
Valid prediction for Augustus_model.g34150.t1
Valid prediction for snap_scaffold_23-snap.992-T1
Valid prediction for CodingQuarry_transcript_35665-T1
Valid prediction for snap_scaffold_23-snap.1011-T1
Valid prediction for Augustus_model.g34153.t1
Valid prediction for GlimmerHMM_glimmerT_51038-T1
Valid prediction for GlimmerHMM_glimmerT_51044-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_23-snap.1019-T1
Valid prediction for GlimmerHMM_glimmerT_51050-T1
Valid prediction for snap_scaffold_23-snap.1005-T1
Valid prediction for Augustus_model.g34159.t1
Valid prediction for snap_scaffold_23-snap.1006-T1
Valid prediction for snap_scaffold_23-snap.1004-T1
Valid prediction for snap_scaffold_23-snap.1023-T1
Valid prediction for Augustus_model.g34148.t1
Valid prediction for Augustus_model.g34157.t1
Valid prediction for CodingQuarry_transcript_35661-T1
Valid prediction for Augustus_model.g34152.t1
Valid prediction for snap_scaffold_23-snap.1022-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 88481, rend_intergenic: 84834  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113570, rend_intergenic: 106651  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131161, rend_intergenic: 115433  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136622, rend_intergenic: 134391  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139791, rend_intergenic: 139538  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145566, rend_intergenic: 143487  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153707, rend_intergenic: 146440  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172813, rend_intergenic: 170449  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189504, rend_intergenic: 184065  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 198219
-exon list size: 435


building trellis

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14.9    
15.1    
15.3    
15.6    
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17.4    
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17.8    
18.1    
18.3    
18.5    
18.8    
19.0    
19.2    
19.5    
19.7    
19.9    
20.1    
20.4    
20.6    
20.8    
21.1    
21.3    
21.5    
21.7    
22.0    
22.2    
22.4    
22.7    
22.9    
23.1    
23.3    
23.6    
23.8    
24.0    
24.3    
24.5    
24.7    
24.9    
25.2    
25.4    
25.6    
25.9    
26.1    
26.3    
26.5    
26.8    
27.0    
27.2    
27.5    
27.7    
27.9    
28.1    
28.4    
28.6    
28.8    
29.1    
29.3    
29.5    
29.7    
30.0    
30.2    
30.4    
30.7    
30.9    
31.1    
31.4    
31.6    
31.8    
32.0    
32.3    
32.5    
32.7    
33.0    
33.2    
33.4    
33.6    
33.9    
34.1    
34.3    
34.6    
34.8    
35.0    
35.2    
35.5    
35.7    
35.9    
36.2    
36.4    
36.6    
36.8    
37.1    
37.3    
37.5    
37.8    
38.0    
38.2    
38.4    
38.7    
38.9    
39.1    
39.4    
39.6    
39.8    
40.0    
40.3    
40.5    
40.7    
41.0    
41.2    
41.4    
41.6    
41.9    
42.1    
42.3    
42.6    
42.8    
43.0    
43.2    
43.5    
43.7    
43.9    
44.2    
44.4    
44.6    
44.9    
45.1    
45.3    
45.5    
45.8    
46.0    
46.2    
46.5    
46.7    
46.9    
47.1    
47.4    
47.6    
47.8    
48.1    
48.3    
48.5    
48.7    
49.0    
49.2    
49.4    
49.7    
49.9    
50.1    
50.3    
50.6    
50.8    
51.0    
51.3    
51.5    
51.7    
51.9    
52.2    
52.4    
52.6    
52.9    
53.1    
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53.8    
54.0    
54.2    
54.5    
54.7    
54.9    
55.1    
55.4    
55.6    
55.8    
56.1    
56.3    
56.5    
56.8    
57.0    
57.2    
57.4    
57.7    
57.9    
58.1    
58.4    
58.6    
58.8    
59.0    
59.3    
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59.7    
60.0    
60.2    
60.4    
60.6    
60.9    
61.1    
61.3    
61.6    
61.8    
62.0    
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63.2    
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63.6    
63.8    
64.1    
64.3    
64.5    
64.8    
65.0    
65.2    
65.4    
65.7    
65.9    
66.1    
66.4    
66.6    
66.8    
67.0    
67.3    
67.5    
67.7    
68.0    
68.2    
68.4    
68.6    
68.9    
69.1    
69.3    
69.6    
69.8    
70.0    
70.3    
70.5    
70.7    
70.9    
71.2    
71.4    
71.6    
71.9    
72.1    
72.3    
72.5    
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73.0    
73.2    
73.5    
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73.9    
74.1    
74.4    
74.6    
74.8    
75.1    
75.3    
75.5    
75.7    
76.0    
76.2    
76.4    
76.7    
76.9    
77.1    
77.3    
77.6    
77.8    
78.0    
78.3    
78.5    
78.7    
78.9    
79.2    
79.4    
79.6    
79.9    
80.1    
80.3    
80.5    
80.8    
81.0    
81.2    
81.5    
81.7    
81.9    
82.2    
82.4    
82.6    
82.8    
83.1    
83.3    
83.5    
83.8    
84.0    
84.2    
84.4    
84.7    
84.9    
85.1    
85.4    
85.6    
85.8    
86.0    
86.3    
86.5    
86.7    
87.0    
87.2    
87.4    
87.6    
87.9    
88.1    
88.3    
88.6    
88.8    
89.0    
89.2    
89.5    
89.7    
89.9    
90.2    
90.4    
90.6    
90.8    
91.1    
91.3    
91.5    
91.8    
92.0    
92.2    
92.4    
92.7    
92.9    
93.1    
93.4    
93.6    
93.8    
94.1    
94.3    
94.5    
94.7    
95.0    
95.2    
95.4    
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95.9    
96.1    
96.3    
96.6    
96.8    
97.0    
97.3    
97.5    
97.7    
97.9    
98.2    
98.4    
98.6    
98.9    
99.1    
99.3    
99.5    
99.8    
-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 88481, rend_intergenic: 84834  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113570, rend_intergenic: 106651  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131161, rend_intergenic: 115433  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136622, rend_intergenic: 134391  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139791, rend_intergenic: 139538  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145566, rend_intergenic: 143487  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153707, rend_intergenic: 146440  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172813, rend_intergenic: 170449  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189504, rend_intergenic: 184065  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 32 predictions persist after filtering for low support