-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_13/scaffold_13_13544446-13775053

-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_13-snap.2615-T1
Valid prediction for GlimmerHMM_glimmerT_32679-T1
Valid prediction for snap_scaffold_13-snap.2618-T1
Valid prediction for GlimmerHMM_glimmerT_32681-T1
Valid prediction for snap_scaffold_13-snap.2578-T1
Valid prediction for Augustus_model.g21796.t1
Valid prediction for Augustus_model.g21801.t1
Valid prediction for snap_scaffold_13-snap.2614-T1
Valid prediction for GlimmerHMM_glimmerT_32669-T1
Valid prediction for GlimmerHMM_glimmerT_32663-T1
Valid prediction for snap_scaffold_13-snap.2609-T1
Valid prediction for Augustus_model.g21805.t1
Valid prediction for GlimmerHMM_glimmerT_32668-T1
Valid prediction for Augustus_model.g21812.t1
Valid prediction for GlimmerHMM_glimmerT_32686-T1
Valid prediction for GlimmerHMM_glimmerT_32664-T1
Valid prediction for snap_scaffold_13-snap.2581-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_32671-T1
Valid prediction for snap_scaffold_13-snap.2621-T1
Valid prediction for GlimmerHMM_glimmerT_32661-T1
Valid prediction for snap_scaffold_13-snap.2591-T1
Valid prediction for Augustus_model.g21798.t1
Valid prediction for GlimmerHMM_glimmerT_32678-T1
Valid prediction for Augustus_model.g21804.t1
Valid prediction for snap_scaffold_13-snap.2612-T1
Valid prediction for snap_scaffold_13-snap.2594-T1
Valid prediction for Augustus_model.g21797.t1
Valid prediction for snap_scaffold_13-snap.2597-T1
Valid prediction for GlimmerHMM_glimmerT_32665-T1
Couldn't classify 209767, 209778
Couldn't classify 221465, 221671
Sorry, prediction pasa_asmbl_11402.p1 fails validation.
(CAC)	 CG	209767-209778	GT	AGG
(CTG)	 AG	209983-210150	GT	AGG
(GTG)	 AG	212396-212538	GT	AGG
(CCA)	 AG	214229-214392	GT	GGG
(TGG)	 AG	214870-215083	GT	AGG
(AGA)	 AG	216156-216255	GT	TGG
(CTG)	 AG	217184-217279	GT	AGG
(GTC)	 AG	218220-218267	GT	AGG
(AAG)	 AG	218536-218625	GT	AGG
(GAG)	 AG	220618-220755	GT	AGG
(CTG)	 AG	221465-221671	CA	ACC
-recovered pasa_asmbl_11402.p1, internal, 209983, 210150
-recovered pasa_asmbl_11402.p1, internal, 212396, 212538
-recovered pasa_asmbl_11402.p1, internal, 214229, 214392
-recovered pasa_asmbl_11402.p1, internal, 214870, 215083
-recovered pasa_asmbl_11402.p1, internal, 216156, 216255
-recovered pasa_asmbl_11402.p1, internal, 217184, 217279
-recovered pasa_asmbl_11402.p1, internal, 218220, 218267
-recovered pasa_asmbl_11402.p1, internal, 218536, 218625
-recovered pasa_asmbl_11402.p1, internal, 220618, 220755
Couldn't classify 222428, 223018
Sorry, prediction pasa_asmbl_11404.p1 fails validation.
(TCC)	 TC	222428-223018	GT	AGG
(GGA)	 AG	223152-223196	CA	GAC
-recovered pasa_asmbl_11404.p1, terminal, 223152, 223196
Valid prediction for GlimmerHMM_glimmerT_32666-T1
Valid prediction for GlimmerHMM_glimmerT_32684-T1
Valid prediction for Augustus_model.g21802.t1
Couldn't classify 112342, 113070
Sorry, prediction pasa_asmbl_11399.p1 fails validation.
(TTC)	 TG	112342-113070	AT	GAA
Valid prediction for snap_scaffold_13-snap.2607-T1
Valid prediction for snap_scaffold_13-snap.2602-T1
Valid prediction for GlimmerHMM_glimmerT_32670-T1
Couldn't classify 108875, 109060
Couldn't classify 109384, 109599
Sorry, prediction pasa_asmbl_11398.p1 fails validation.
(GAG)	 AG	108875-109060	GT	AGG
(GGC)	 AG	109384-109599	AA	GAA
-recovered pasa_asmbl_11398.p1, internal, 108875, 109060
Valid prediction for snap_scaffold_13-snap.2604-T1
Valid prediction for GlimmerHMM_glimmerT_32677-T1
Valid prediction for CodingQuarry_transcript_13283-T1
Valid prediction for snap_scaffold_13-snap.2586-T1
Couldn't classify 87368, 87418
Couldn't classify 88431, 88508
Sorry, prediction pasa_asmbl_11616.p1 fails validation.
(GAC)	 CC	87368-87418	GT	AGG
(GCC)	 AG	87858-88025	GT	GGG
(GTT)	 AG	88431-88508	GA	ACG
-recovered pasa_asmbl_11616.p1, internal, 87858, 88025
Valid prediction for Augustus_model.g21803.t1
Valid prediction for Augustus_model.g21800.t1
Valid prediction for snap_scaffold_13-snap.2610-T1
Couldn't classify 208651, 208710
Couldn't classify 209662, 209730
Sorry, prediction pasa_asmbl_11697.p1 fails validation.
(GAA)	 TG	208651-208710	GT	AGG
(CTG)	 AG	209021-209134	GT	AGG
(GAG)	 AG	209298-209375	GT	AGG
(GTG)	 AG	209662-209730	GA	AGG
-recovered pasa_asmbl_11697.p1, internal, 209021, 209134
-recovered pasa_asmbl_11697.p1, internal, 209298, 209375
Valid prediction for Augustus_model.g21799.t1
Valid prediction for GlimmerHMM_glimmerT_32667-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_13-snap.2608-T1
Valid prediction for snap_scaffold_13-snap.2600-T1
Valid prediction for snap_scaffold_13-snap.2579-T1
Valid prediction for snap_scaffold_13-snap.2603-T1
Valid prediction for snap_scaffold_13-snap.2605-T1
Valid prediction for snap_scaffold_13-snap.2577-T1
Valid prediction for snap_scaffold_13-snap.2617-T1
Valid prediction for CodingQuarry_transcript_13287-T1
Valid prediction for snap_scaffold_13-snap.2598-T1
Valid prediction for GlimmerHMM_glimmerT_32685-T1
Valid prediction for Augustus_model.g21807.t1
Valid prediction for snap_scaffold_13-snap.2580-T1
Valid prediction for snap_scaffold_13-snap.2613-T1
Valid prediction for snap_scaffold_13-snap.2596-T1
Valid prediction for snap_scaffold_13-snap.2616-T1
Valid prediction for GlimmerHMM_glimmerT_32682-T1
Valid prediction for snap_scaffold_13-snap.2592-T1
Valid prediction for pasa_asmbl_10157.p1
Valid prediction for pasa_asmbl_10154.p1
Valid prediction for CodingQuarry_transcript_13284-T1
Valid prediction for snap_scaffold_13-snap.2589-T1
Valid prediction for snap_scaffold_13-snap.2593-T1
Valid prediction for snap_scaffold_13-snap.2619-T1
Valid prediction for GlimmerHMM_glimmerT_32683-T1
Valid prediction for Augustus_model.g21808.t1
Valid prediction for GlimmerHMM_glimmerT_32676-T1
Valid prediction for snap_scaffold_13-snap.2595-T1
Valid prediction for snap_scaffold_13-snap.2601-T1
Valid prediction for GlimmerHMM_glimmerT_32672-T1
Valid prediction for GlimmerHMM_glimmerT_32675-T1
Valid prediction for snap_scaffold_13-snap.2583-T1
Valid prediction for snap_scaffold_13-snap.2620-T1
Valid prediction for snap_scaffold_13-snap.2611-T1
Valid prediction for GlimmerHMM_glimmerT_32662-T1
Valid prediction for snap_scaffold_13-snap.2587-T1
Valid prediction for snap_scaffold_13-snap.2606-T1
Valid prediction for snap_scaffold_13-snap.2599-T1
Valid prediction for HiQ_model.g21810.t1
Valid prediction for GlimmerHMM_glimmerT_32680-T1
Valid prediction for GlimmerHMM_glimmerT_32660-T1
Couldn't classify 90260, 90338
Couldn't classify 92840, 93148
Sorry, prediction pasa_asmbl_10443.p2 fails validation.
(GGA)	 CA	90260-90338	GT	AGG
(CTG)	 AG	92324-92395	GT	AGG
(AAC)	 AG	92583-92668	GT	AGG
(GTG)	 AG	92840-93148	GT	TGG
-recovered pasa_asmbl_10443.p2, internal, 92324, 92395
-recovered pasa_asmbl_10443.p2, internal, 92583, 92668
-recovered pasa_asmbl_10443.p2, internal, 92840, 93148
Valid prediction for snap_scaffold_13-snap.2585-T1
Valid prediction for snap_scaffold_13-snap.2584-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for Augustus_model.g21806.t1
Valid prediction for GlimmerHMM_glimmerT_32674-T1
Valid prediction for Augustus_model.g21811.t1
Valid prediction for pasa_asmbl_10158.p1
Valid prediction for GlimmerHMM_glimmerT_32673-T1
Valid prediction for snap_scaffold_13-snap.2590-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_13-snap.2588-T1
Valid prediction for HiQ_model.g21809.t1
Valid prediction for CodingQuarry_transcript_13286-T1
Valid prediction for snap_scaffold_13-snap.2582-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 5950, rend_intergenic: 4755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26295, rend_intergenic: 6000  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58576, rend_intergenic: 33100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68453, rend_intergenic: 61213  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91161, rend_intergenic: 69155  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100037, rend_intergenic: 93907  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101457, rend_intergenic: 100037  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107022, rend_intergenic: 101965  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116044, rend_intergenic: 109796  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141115, rend_intergenic: 135106  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156703, rend_intergenic: 150835  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174636, rend_intergenic: 173430  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184750, rend_intergenic: 174719  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186167, rend_intergenic: 185385  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198163, rend_intergenic: 188466  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 210914, rend_intergenic: 203617  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211702, rend_intergenic: 211236  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 219767, rend_intergenic: 211916  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 225092, rend_intergenic: 219810  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 230608
-exon list size: 405


building trellis

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2.9    
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19.9    
20.1    
20.4    
20.6    
20.9    
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21.4    
21.6    
21.9    
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22.4    
22.6    
22.9    
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23.3    
23.6    
23.8    
24.1    
24.3    
24.6    
24.8    
25.1    
25.3    
25.6    
25.8    
26.0    
26.3    
26.5    
26.8    
27.0    
27.3    
27.5    
27.8    
28.0    
28.3    
28.5    
28.7    
29.0    
29.2    
29.5    
29.7    
30.0    
30.2    
30.5    
30.7    
31.0    
31.2    
31.4    
31.7    
31.9    
32.2    
32.4    
32.7    
32.9    
33.2    
33.4    
33.7    
33.9    
34.2    
34.4    
34.6    
34.9    
35.1    
35.4    
35.6    
35.9    
36.1    
36.4    
36.6    
36.9    
37.1    
37.3    
37.6    
37.8    
38.1    
38.3    
38.6    
38.8    
39.1    
39.3    
39.6    
39.8    
40.0    
40.3    
40.5    
40.8    
41.0    
41.3    
41.5    
41.8    
42.0    
42.3    
42.5    
42.8    
43.0    
43.2    
43.5    
43.7    
44.0    
44.2    
44.5    
44.7    
45.0    
45.2    
45.5    
45.7    
45.9    
46.2    
46.4    
46.7    
46.9    
47.2    
47.4    
47.7    
47.9    
48.2    
48.4    
48.6    
48.9    
49.1    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.9    
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51.4    
51.6    
51.8    
52.1    
52.3    
52.6    
52.8    
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53.3    
53.6    
53.8    
54.1    
54.3    
54.5    
54.8    
55.0    
55.3    
55.5    
55.8    
56.0    
56.3    
56.5    
56.8    
57.0    
57.2    
57.5    
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58.0    
58.2    
58.5    
58.7    
59.0    
59.2    
59.5    
59.7    
60.0    
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60.4    
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60.9    
61.2    
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63.6    
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67.6    
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68.1    
68.3    
68.6    
68.8    
69.0    
69.3    
69.5    
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70.0    
70.3    
70.5    
70.8    
71.0    
71.3    
71.5    
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72.0    
72.2    
72.5    
72.7    
73.0    
73.2    
73.5    
73.7    
74.0    
74.2    
74.4    
74.7    
74.9    
75.2    
75.4    
75.7    
75.9    
76.2    
76.4    
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77.6    
77.9    
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78.4    
78.6    
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79.6    
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80.1    
80.3    
80.6    
80.8    
81.1    
81.3    
81.6    
81.8    
82.1    
82.3    
82.6    
82.8    
83.0    
83.3    
83.5    
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84.3    
84.5    
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86.0    
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86.5    
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87.0    
87.2    
87.5    
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88.0    
88.2    
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89.2    
89.4    
89.7    
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90.2    
90.4    
90.7    
90.9    
91.2    
91.4    
91.6    
91.9    
92.1    
92.4    
92.6    
92.9    
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93.6    
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95.8    
96.1    
96.3    
96.6    
96.8    
97.1    
97.3    
97.5    
97.8    
98.0    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 5950, rend_intergenic: 4755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26295, rend_intergenic: 6000  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58576, rend_intergenic: 33100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68453, rend_intergenic: 61213  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91161, rend_intergenic: 69155  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100037, rend_intergenic: 93907  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101457, rend_intergenic: 100037  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107022, rend_intergenic: 101965  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116044, rend_intergenic: 109796  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141115, rend_intergenic: 135106  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156703, rend_intergenic: 150835  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174636, rend_intergenic: 173430  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184750, rend_intergenic: 174719  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186167, rend_intergenic: 185385  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198163, rend_intergenic: 188466  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 210914, rend_intergenic: 203617  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211702, rend_intergenic: 211236  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 219767, rend_intergenic: 211916  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 225092, rend_intergenic: 219810  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support