-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_8/scaffold_8_14498144-14778800

-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_20863-T1
Valid prediction for Augustus_model.g13898.t1
Valid prediction for snap_scaffold_8-snap.2677-T1
Valid prediction for GlimmerHMM_glimmerT_20850-T1
Valid prediction for GlimmerHMM_glimmerT_20872-T1
Valid prediction for snap_scaffold_8-snap.2674-T1
Valid prediction for snap_scaffold_8-snap.2648-T1
Valid prediction for Augustus_model.g13895.t1
Valid prediction for GlimmerHMM_glimmerT_20862-T1
Valid prediction for GlimmerHMM_glimmerT_20865-T1
Valid prediction for snap_scaffold_8-snap.2659-T1
Valid prediction for GlimmerHMM_glimmerT_20852-T1
Valid prediction for GlimmerHMM_glimmerT_20851-T1
Valid prediction for snap_scaffold_8-snap.2679-T1
Valid prediction for GlimmerHMM_glimmerT_20869-T1
Valid prediction for snap_scaffold_8-snap.2647-T1
Valid prediction for snap_scaffold_8-snap.2655-T1
Couldn't classify 76110, 76229
Couldn't classify 76268, 76285
Sorry, prediction CodingQuarry_transcript_59899-T1 fails validation.
(ATG)	 GC	74379-74398	GT	GGG
(TTG)	 AG	74626-74760	GT	AGG
(GTG)	 AG	74972-75101	GT	AGG
(CAA)	 AG	75347-75454	GT	AGG
(CTT)	 AG	75572-75712	GT	AGG
(GCT)	 AG	76110-76229	CC	ACC
(CCC)	 AT	76268-76285	AC	AAA
-recovered CodingQuarry_transcript_59899-T1, initial, 74379, 74398
-recovered CodingQuarry_transcript_59899-T1, internal, 74626, 74760
-recovered CodingQuarry_transcript_59899-T1, internal, 74972, 75101
-recovered CodingQuarry_transcript_59899-T1, internal, 75347, 75454
-recovered CodingQuarry_transcript_59899-T1, internal, 75572, 75712
Valid prediction for snap_scaffold_8-snap.2689-T1
Valid prediction for Augustus_model.g13894.t1
Valid prediction for snap_scaffold_8-snap.2690-T1
Valid prediction for snap_scaffold_8-snap.2643-T1
Valid prediction for GlimmerHMM_glimmerT_20873-T1
Valid prediction for Augustus_model.g13896.t1
Valid prediction for snap_scaffold_8-snap.2686-T1
Valid prediction for CodingQuarry_transcript_59898-T1
Valid prediction for Augustus_model.g13897.t1
Valid prediction for snap_scaffold_8-snap.2644-T1
Valid prediction for GlimmerHMM_glimmerT_20856-T1
Valid prediction for GlimmerHMM_glimmerT_20853-T1
Valid prediction for GlimmerHMM_glimmerT_20860-T1
Valid prediction for GlimmerHMM_glimmerT_20855-T1
Couldn't classify 42088, 42195
Couldn't classify 50728, 50925
Sorry, prediction pasa_asmbl_53377.p1 fails validation.
(GTG)	 AG	42088-42195	GT	AGG
(ATT)	 AG	42504-42584	GT	AGG
(GTG)	 AG	44994-45109	GT	AGG
(TTC)	 AG	47404-47467	GT	AGG
(GGC)	 AG	50087-50182	GT	ACG
(AAC)	 AG	50728-50925	GT	AGG
-recovered pasa_asmbl_53377.p1, internal, 42088, 42195
-recovered pasa_asmbl_53377.p1, internal, 42504, 42584
-recovered pasa_asmbl_53377.p1, internal, 44994, 45109
-recovered pasa_asmbl_53377.p1, internal, 47404, 47467
-recovered pasa_asmbl_53377.p1, internal, 50087, 50182
-recovered pasa_asmbl_53377.p1, internal, 50728, 50925
Valid prediction for Augustus_model.g13899.t1
Valid prediction for GlimmerHMM_glimmerT_20858-T1
Valid prediction for GlimmerHMM_glimmerT_20870-T1
Valid prediction for GlimmerHMM_glimmerT_20847-T1
Valid prediction for snap_scaffold_8-snap.2641-T1
Couldn't classify 32235, 32310
Couldn't classify 38818, 38920
Sorry, prediction pasa_asmbl_53375.p1 fails validation.
(TTC)	 AG	32235-32310	GT	AGG
(GCT)	 AG	33986-34072	GT	TGG
(TGA)	 AG	36815-36953	GT	AGG
(GCG)	 AG	38818-38920	AG	TGA
-recovered pasa_asmbl_53375.p1, internal, 32235, 32310
-recovered pasa_asmbl_53375.p1, internal, 33986, 34072
-recovered pasa_asmbl_53375.p1, internal, 36815, 36953
Valid prediction for snap_scaffold_8-snap.2683-T1
Valid prediction for snap_scaffold_8-snap.2664-T1
Valid prediction for snap_scaffold_8-snap.2657-T1
Valid prediction for GlimmerHMM_glimmerT_20861-T1
Valid prediction for snap_scaffold_8-snap.2663-T1
Valid prediction for snap_scaffold_8-snap.2682-T1
Valid prediction for snap_scaffold_8-snap.2670-T1
Valid prediction for GlimmerHMM_glimmerT_20846-T1
Valid prediction for GlimmerHMM_glimmerT_20857-T1
Couldn't classify 63233, 63291
Sorry, prediction pasa_asmbl_53625.p1 fails validation.
(CAG)	 TC	63233-63291	GT	AGG
(ACT)	 AG	63920-64190	CA	AAC
-recovered pasa_asmbl_53625.p1, terminal, 63920, 64190
Valid prediction for snap_scaffold_8-snap.2684-T1
Valid prediction for snap_scaffold_8-snap.2666-T1
Valid prediction for GlimmerHMM_glimmerT_20854-T1
Valid prediction for snap_scaffold_8-snap.2649-T1
Valid prediction for Augustus_model.g13900.t1
Couldn't classify 67321, 67404
Sorry, prediction pasa_asmbl_53380.p1 fails validation.
(GCG)	 AG	67321-67404	GT	AGG
(ATC)	 AG	68293-68397	GT	AGG
(AAT)	 AG	68618-68700	GT	AAG
(AGG)	 AG	69258-69348	GT	AGG
(ACG)	 AG	70478-70536	GT	GAG
(GAT)	 AG	70765-70927	GT	ACG
(GAG)	 AG	71038-71119	GT	TGG
(AAA)	 AG	71287-71344	GT	TGG
(GAT)	 AG	71564-71654	GT	AGG
(GTG)	 AG	74193-74398	GT	GGG
(TTG)	 AG	74626-74760	GT	AGG
(GTG)	 AG	74972-75101	GT	AGG
(CAA)	 AG	75347-75454	GT	AGG
(CTT)	 AG	75572-75712	GT	AGG
(GCT)	 AG	76110-76247	AC	AAA
-recovered pasa_asmbl_53380.p1, terminal, 70478, 70536
-recovered pasa_asmbl_53380.p1, terminal, 76110, 76247
-recovered pasa_asmbl_53380.p1, internal, 67321, 67404
-recovered pasa_asmbl_53380.p1, internal, 68293, 68397
-recovered pasa_asmbl_53380.p1, internal, 68618, 68700
-recovered pasa_asmbl_53380.p1, internal, 69258, 69348
-recovered pasa_asmbl_53380.p1, internal, 70478, 70536
-recovered pasa_asmbl_53380.p1, internal, 70765, 70927
-recovered pasa_asmbl_53380.p1, internal, 71038, 71119
-recovered pasa_asmbl_53380.p1, internal, 71287, 71344
-recovered pasa_asmbl_53380.p1, internal, 71564, 71654
-recovered pasa_asmbl_53380.p1, internal, 74193, 74398
-recovered pasa_asmbl_53380.p1, internal, 74626, 74760
-recovered pasa_asmbl_53380.p1, internal, 74972, 75101
-recovered pasa_asmbl_53380.p1, internal, 75347, 75454
-recovered pasa_asmbl_53380.p1, internal, 75572, 75712
Valid prediction for snap_scaffold_8-snap.2665-T1
Valid prediction for snap_scaffold_8-snap.2668-T1
Valid prediction for snap_scaffold_8-snap.2672-T1
Couldn't classify 54277, 54334
Couldn't classify 55613, 55707
Sorry, prediction pasa_asmbl_53664.p1 fails validation.
(CTT)	 AG	54277-54334	GT	TGG
(GTG)	 AG	54454-54531	GT	GGG
(GCC)	 AG	55274-55432	GT	AGG
(TCG)	 AG	55613-55707	GT	AGG
add_exon() Sorry, pasa_asmbl_53664.p1 55274-55432-terminal-1 is invalid.
-recovered pasa_asmbl_53664.p1, terminal, 55274, 55432
-recovered pasa_asmbl_53664.p1, internal, 54277, 54334
-recovered pasa_asmbl_53664.p1, internal, 54454, 54531
-recovered pasa_asmbl_53664.p1, internal, 55274, 55432
-recovered pasa_asmbl_53664.p1, internal, 55613, 55707
Valid prediction for Augustus_model.g13893.t1
Valid prediction for snap_scaffold_8-snap.2650-T1
Valid prediction for snap_scaffold_8-snap.2678-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_8-snap.2685-T1
Valid prediction for GlimmerHMM_glimmerT_20868-T1
Valid prediction for Augustus_model.g13901.t1
Valid prediction for snap_scaffold_8-snap.2642-T1
Valid prediction for GlimmerHMM_glimmerT_20871-T1
Valid prediction for snap_scaffold_8-snap.2673-T1
Valid prediction for snap_scaffold_8-snap.2680-T1
Valid prediction for snap_scaffold_8-snap.2675-T1
Valid prediction for snap_scaffold_8-snap.2646-T1
Valid prediction for GlimmerHMM_glimmerT_20859-T1
Valid prediction for snap_scaffold_8-snap.2656-T1
Valid prediction for snap_scaffold_8-snap.2640-T1
Valid prediction for GlimmerHMM_glimmerT_20848-T1
Valid prediction for snap_scaffold_8-snap.2671-T1
Valid prediction for snap_scaffold_8-snap.2681-T1
Valid prediction for snap_scaffold_8-snap.2669-T1
Valid prediction for snap_scaffold_8-snap.2661-T1
Valid prediction for GlimmerHMM_glimmerT_20866-T1
Valid prediction for GlimmerHMM_glimmerT_20864-T1
Valid prediction for snap_scaffold_8-snap.2676-T1
Valid prediction for snap_scaffold_8-snap.2654-T1
Valid prediction for GlimmerHMM_glimmerT_20867-T1
Valid prediction for snap_scaffold_8-snap.2688-T1
Valid prediction for GlimmerHMM_glimmerT_20849-T1
Valid prediction for GlimmerHMM_glimmerT_20845-T1
Valid prediction for snap_scaffold_8-snap.2653-T1
Valid prediction for snap_scaffold_8-snap.2652-T1
Valid prediction for snap_scaffold_8-snap.2667-T1
Valid prediction for Augustus_model.g13891.t1
Valid prediction for HiQ_model.g13892.t1
Valid prediction for snap_scaffold_8-snap.2687-T1
Valid prediction for snap_scaffold_8-snap.2651-T1
Valid prediction for snap_scaffold_8-snap.2658-T1
Valid prediction for snap_scaffold_8-snap.2660-T1
Valid prediction for snap_scaffold_8-snap.2645-T1
Valid prediction for snap_scaffold_8-snap.2662-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 4261, rend_intergenic: 4088  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12699, rend_intergenic: 4282  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19690, rend_intergenic: 14158  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25013, rend_intergenic: 23458  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69372, rend_intergenic: 48789  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76247, rend_intergenic: 74270  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78933, rend_intergenic: 78266  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81429, rend_intergenic: 80495  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93251, rend_intergenic: 84348  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103786, rend_intergenic: 101713  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113069, rend_intergenic: 110076  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114463, rend_intergenic: 114105  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119254, rend_intergenic: 114779  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120847, rend_intergenic: 120754  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125347, rend_intergenic: 121039  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131001, rend_intergenic: 128743  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136759, rend_intergenic: 131792  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144639, rend_intergenic: 137147  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158127, rend_intergenic: 153016  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 280657
-exon list size: 385


building trellis

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11.9    
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17.3    
17.6    
17.8    
18.1    
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18.6    
18.9    
19.1    
19.4    
19.6    
19.9    
20.2    
20.4    
20.7    
20.9    
21.2    
21.4    
21.7    
22.0    
22.2    
22.5    
22.7    
23.0    
23.3    
23.5    
23.8    
24.0    
24.3    
24.5    
24.8    
25.1    
25.3    
25.6    
25.8    
26.1    
26.4    
26.6    
26.9    
27.1    
27.4    
27.6    
27.9    
28.2    
28.4    
28.7    
28.9    
29.2    
29.5    
29.7    
30.0    
30.2    
30.5    
30.7    
31.0    
31.3    
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    
35.1    
35.4    
35.7    
35.9    
36.2    
36.4    
36.7    
37.0    
37.2    
37.5    
37.7    
38.0    
38.2    
38.5    
38.8    
39.0    
39.3    
39.5    
39.8    
40.1    
40.3    
40.6    
40.8    
41.1    
41.3    
41.6    
41.9    
42.1    
42.4    
42.6    
42.9    
43.2    
43.4    
43.7    
43.9    
44.2    
44.4    
44.7    
45.0    
45.2    
45.5    
45.7    
46.0    
46.3    
46.5    
46.8    
47.0    
47.3    
47.5    
47.8    
48.1    
48.3    
48.6    
48.8    
49.1    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.9    
51.2    
51.4    
51.7    
51.9    
52.2    
52.5    
52.7    
53.0    
53.2    
53.5    
53.7    
54.0    
54.3    
54.5    
54.8    
55.0    
55.3    
55.6    
55.8    
56.1    
56.3    
56.6    
56.8    
57.1    
57.4    
57.6    
57.9    
58.1    
58.4    
58.7    
58.9    
59.2    
59.4    
59.7    
59.9    
60.2    
60.5    
60.7    
61.0    
61.2    
61.5    
61.8    
62.0    
62.3    
62.5    
62.8    
63.0    
63.3    
63.6    
63.8    
64.1    
64.3    
64.6    
64.9    
65.1    
65.4    
65.6    
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66.1    
66.4    
66.7    
66.9    
67.2    
67.4    
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68.0    
68.2    
68.5    
68.7    
69.0    
69.3    
69.5    
69.8    
70.0    
70.3    
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71.1    
71.3    
71.6    
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72.1    
72.4    
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73.1    
73.4    
73.6    
73.9    
74.2    
74.4    
74.7    
74.9    
75.2    
75.5    
75.7    
76.0    
76.2    
76.5    
76.7    
77.0    
77.3    
77.5    
77.8    
78.0    
78.3    
78.6    
78.8    
79.1    
79.3    
79.6    
79.8    
80.1    
80.4    
80.6    
80.9    
81.1    
81.4    
81.7    
81.9    
82.2    
82.4    
82.7    
82.9    
83.2    
83.5    
83.7    
84.0    
84.2    
84.5    
84.8    
85.0    
85.3    
85.5    
85.8    
86.0    
86.3    
86.6    
86.8    
87.1    
87.3    
87.6    
87.9    
88.1    
88.4    
88.6    
88.9    
89.1    
89.4    
89.7    
89.9    
90.2    
90.4    
90.7    
91.0    
91.2    
91.5    
91.7    
92.0    
92.2    
92.5    
92.8    
93.0    
93.3    
93.5    
93.8    
94.1    
94.3    
94.6    
94.8    
95.1    
95.3    
95.6    
95.9    
96.1    
96.4    
96.6    
96.9    
97.2    
97.4    
97.7    
97.9    
98.2    
98.4    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 4261, rend_intergenic: 4088  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12699, rend_intergenic: 4282  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19690, rend_intergenic: 14158  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25013, rend_intergenic: 23458  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69372, rend_intergenic: 48789  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76247, rend_intergenic: 74270  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78933, rend_intergenic: 78266  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81429, rend_intergenic: 80495  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93251, rend_intergenic: 84348  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103786, rend_intergenic: 101713  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113069, rend_intergenic: 110076  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114463, rend_intergenic: 114105  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119254, rend_intergenic: 114779  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120847, rend_intergenic: 120754  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125347, rend_intergenic: 121039  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131001, rend_intergenic: 128743  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136759, rend_intergenic: 131792  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144639, rend_intergenic: 137147  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158127, rend_intergenic: 153016  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