-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_649526-796725

-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 Augustus_model.g2096.t1
Valid prediction for snap_scaffold_2-snap.173-T1
Valid prediction for Augustus_model.g2108.t1
Valid prediction for GlimmerHMM_glimmerT_3109-T1
Valid prediction for CodingQuarry_transcript_28429-T1
Valid prediction for GlimmerHMM_glimmerT_3091-T1
Valid prediction for snap_scaffold_2-snap.164-T1
Valid prediction for snap_scaffold_2-snap.155-T1
Valid prediction for GlimmerHMM_glimmerT_3103-T1
Valid prediction for snap_scaffold_2-snap.161-T1
Valid prediction for snap_scaffold_2-snap.175-T1
Valid prediction for snap_scaffold_2-snap.180-T1
Valid prediction for snap_scaffold_2-snap.163-T1
Valid prediction for snap_scaffold_2-snap.157-T1
Couldn't classify 137269, 137643
Sorry, prediction pasa_asmbl_24103.p1 fails validation.
(TTC)	 GC	137269-137643	TG	GAT
Valid prediction for GlimmerHMM_glimmerT_3106-T1
Couldn't classify 27729, 28043
Sorry, prediction pasa_asmbl_24093.p1 fails validation.
(CAC)	 CC	27729-28043	GT	CCG
Valid prediction for Augustus_model.g2103.t1
Valid prediction for Augustus_model.g2106.t1
Couldn't classify 38763, 39137
Sorry, prediction pasa_asmbl_24097.p2 fails validation.
(CCG)	 GG	38763-39137	CA	GAC
Valid prediction for snap_scaffold_2-snap.159-T1
Valid prediction for Augustus_model.g2099.t1
Valid prediction for snap_scaffold_2-snap.166-T1
Couldn't classify 124836, 125199
Sorry, prediction pasa_asmbl_24100.p1 fails validation.
(TCC)	 CC	124836-125199	GT	GGG
(GCA)	 AG	125335-125474	GT	GAG
-recovered pasa_asmbl_24100.p1, terminal, 125335, 125474
-recovered pasa_asmbl_24100.p1, internal, 125335, 125474
Valid prediction for Augustus_model.g2097.t1
Valid prediction for snap_scaffold_2-snap.171-T1
Valid prediction for HiQ_model.g2098.t1
Couldn't classify 25671, 25820
Couldn't classify 27351, 27584
Sorry, prediction pasa_asmbl_24092.p1 fails validation.
(ATC)	 AC	25671-25820	GT	ATG
(GGA)	 AG	26665-26837	GT	AGG
(GTT)	 AG	26950-27016	GT	AGG
(AAT)	 AG	27351-27584	CG	AGC
-recovered pasa_asmbl_24092.p1, internal, 26665, 26837
-recovered pasa_asmbl_24092.p1, internal, 26950, 27016
Valid prediction for GlimmerHMM_glimmerT_3107-T1
Valid prediction for Augustus_model.g2104.t1
Valid prediction for GlimmerHMM_glimmerT_3102-T1
Valid prediction for snap_scaffold_2-snap.177-T1
Couldn't classify 28434, 28888
Couldn't classify 31466, 31542
Sorry, prediction pasa_asmbl_25417.p1 fails validation.
(CAG)	 CT	28434-28888	GT	AGG
(GAG)	 AG	29082-29168	GT	AGG
(GTT)	 AG	29500-29685	GT	GAG
(CGA)	 AG	30052-30132	GT	AGG
(ACG)	 AG	30265-30365	GT	AGG
(GTG)	 AG	30855-30965	GT	CGG
(CCT)	 AG	31107-31295	GT	CGG
(GTC)	 AG	31466-31542	TC	TGT
-recovered pasa_asmbl_25417.p1, internal, 29082, 29168
-recovered pasa_asmbl_25417.p1, internal, 29500, 29685
-recovered pasa_asmbl_25417.p1, internal, 30052, 30132
-recovered pasa_asmbl_25417.p1, internal, 30265, 30365
-recovered pasa_asmbl_25417.p1, internal, 30855, 30965
-recovered pasa_asmbl_25417.p1, internal, 31107, 31295
Valid prediction for Augustus_model.g2107.t1
Valid prediction for snap_scaffold_2-snap.154-T1
Valid prediction for GlimmerHMM_glimmerT_3094-T1
Valid prediction for Augustus_model.g2095.t1
Valid prediction for GlimmerHMM_glimmerT_3092-T1
Valid prediction for snap_scaffold_2-snap.182-T1
Valid prediction for GlimmerHMM_glimmerT_3100-T1
Valid prediction for GlimmerHMM_glimmerT_3090-T1
Couldn't classify 120802, 120858
Couldn't classify 124071, 124187
Sorry, prediction pasa_asmbl_24099.p1 fails validation.
(CCA)	 AC	120802-120858	GT	AGG
(ATA)	 AG	121282-121357	GT	AGG
(CTA)	 AG	123708-123811	GT	CGG
(AAA)	 AG	124071-124187	GA	TGG
-recovered pasa_asmbl_24099.p1, internal, 121282, 121357
-recovered pasa_asmbl_24099.p1, internal, 123708, 123811
Valid prediction for GlimmerHMM_glimmerT_3087-T1
Valid prediction for snap_scaffold_2-snap.181-T1
Couldn't classify 37289, 37464
Sorry, prediction pasa_asmbl_24094.p1 fails validation.
(ATG)	 AG	34729-34868	GT	GTG
(GTT)	 AG	35649-35756	GT	GGG
(GCC)	 AG	36161-36360	GT	TGG
(ACC)	 AG	36919-37047	GT	CGG
(GTG)	 AG	37289-37464	AG	CCA
-recovered pasa_asmbl_24094.p1, initial, 34729, 34868
-recovered pasa_asmbl_24094.p1, internal, 34729, 34868
-recovered pasa_asmbl_24094.p1, internal, 35649, 35756
-recovered pasa_asmbl_24094.p1, internal, 36161, 36360
-recovered pasa_asmbl_24094.p1, internal, 36919, 37047
Valid prediction for GlimmerHMM_glimmerT_3088-T1
Valid prediction for snap_scaffold_2-snap.174-T1
Valid prediction for GlimmerHMM_glimmerT_3089-T1
Valid prediction for snap_scaffold_2-snap.170-T1
Valid prediction for GlimmerHMM_glimmerT_3093-T1
Valid prediction for snap_scaffold_2-snap.160-T1
Valid prediction for CodingQuarry_transcript_28430-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.183-T1
Valid prediction for snap_scaffold_2-snap.179-T1
Valid prediction for snap_scaffold_2-snap.156-T1
Valid prediction for GlimmerHMM_glimmerT_3105-T1
Valid prediction for Augustus_model.g2102.t1
Valid prediction for Augustus_model.g2100.t1
Couldn't classify 1545, 1784
Couldn't classify 3386, 3459
Sorry, prediction pasa_asmbl_22821.p1 fails validation.
(ACA)	 TG	1545-1784	GT	AGG
(GTG)	 AG	2911-3118	GT	AGG
(GTG)	 AG	3386-3459	CG	GGC
-recovered pasa_asmbl_22821.p1, internal, 2911, 3118
Valid prediction for GlimmerHMM_glimmerT_3099-T1
Valid prediction for GlimmerHMM_glimmerT_3110-T1
Valid prediction for snap_scaffold_2-snap.176-T1
Valid prediction for HiQ_model.g2094.t1
Valid prediction for Augustus_model.g2101.t1
Valid prediction for snap_scaffold_2-snap.168-T1
Valid prediction for GlimmerHMM_glimmerT_3086-T1
Valid prediction for Augustus_model.g2109.t1
Valid prediction for snap_scaffold_2-snap.169-T1
Valid prediction for CodingQuarry_transcript_28431-T1
Valid prediction for GlimmerHMM_glimmerT_3101-T1
Valid prediction for Augustus_model.g2105.t1
Valid prediction for GlimmerHMM_glimmerT_3108-T1
Valid prediction for GlimmerHMM_glimmerT_3097-T1
Valid prediction for snap_scaffold_2-snap.178-T1
Valid prediction for pasa_asmbl_22812.p1
Valid prediction for GlimmerHMM_glimmerT_3098-T1
Valid prediction for snap_scaffold_2-snap.165-T1
Valid prediction for snap_scaffold_2-snap.158-T1
Valid prediction for GlimmerHMM_glimmerT_3096-T1
Valid prediction for snap_scaffold_2-snap.162-T1
Valid prediction for snap_scaffold_2-snap.172-T1
Valid prediction for snap_scaffold_2-snap.167-T1
Valid prediction for snap_scaffold_2-snap.153-T1
Valid prediction for GlimmerHMM_glimmerT_3104-T1
Valid prediction for GlimmerHMM_glimmerT_3095-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 18171, rend_intergenic: 10674  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26492, rend_intergenic: 24186  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68557, rend_intergenic: 55077  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84952, rend_intergenic: 83461  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99566, rend_intergenic: 92005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125474, rend_intergenic: 110166  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145118, rend_intergenic: 143376  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 147200
-exon list size: 329


building trellis

0.3    
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1.2    
1.5    
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2.4    
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3.6    
3.9    
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5.1    
5.4    
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6.0    
6.3    
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6.9    
7.3    
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9.1    
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10.9    
11.2    
11.5    
11.8    
12.1    
12.4    
12.7    
13.0    
13.3    
13.6    
13.9    
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17.8    
18.1    
18.4    
18.7    
19.0    
19.3    
19.6    
19.9    
20.2    
20.5    
20.8    
21.1    
21.5    
21.8    
22.1    
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22.7    
23.0    
23.3    
23.6    
23.9    
24.2    
24.5    
24.8    
25.1    
25.4    
25.7    
26.0    
26.3    
26.6    
26.9    
27.2    
27.5    
27.8    
28.1    
28.4    
28.7    
29.0    
29.3    
29.6    
29.9    
30.2    
30.5    
30.8    
31.1    
31.4    
31.7    
32.0    
32.3    
32.6    
32.9    
33.2    
33.5    
33.8    
34.1    
34.4    
34.7    
35.0    
35.3    
35.6    
36.0    
36.3    
36.6    
36.9    
37.2    
37.5    
37.8    
38.1    
38.4    
38.7    
39.0    
39.3    
39.6    
39.9    
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40.5    
40.8    
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41.4    
41.7    
42.0    
42.3    
42.6    
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43.2    
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44.1    
44.4    
44.7    
45.0    
45.3    
45.6    
45.9    
46.2    
46.5    
46.8    
47.1    
47.4    
47.7    
48.0    
48.3    
48.6    
48.9    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.1    
51.4    
51.7    
52.0    
52.3    
52.6    
52.9    
53.2    
53.5    
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54.1    
54.4    
54.7    
55.0    
55.3    
55.6    
55.9    
56.2    
56.5    
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57.1    
57.4    
57.7    
58.0    
58.3    
58.6    
58.9    
59.2    
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60.1    
60.4    
60.7    
61.0    
61.3    
61.6    
61.9    
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63.1    
63.4    
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64.0    
64.4    
64.7    
65.0    
65.3    
65.6    
65.9    
66.2    
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66.8    
67.1    
67.4    
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68.0    
68.3    
68.6    
68.9    
69.2    
69.5    
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70.1    
70.4    
70.7    
71.0    
71.3    
71.6    
71.9    
72.2    
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72.8    
73.1    
73.4    
73.7    
74.0    
74.3    
74.6    
74.9    
75.2    
75.5    
75.8    
76.1    
76.4    
76.7    
77.0    
77.3    
77.6    
77.9    
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78.5    
78.9    
79.2    
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80.1    
80.4    
80.7    
81.0    
81.3    
81.6    
81.9    
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83.1    
83.4    
83.7    
84.0    
84.3    
84.6    
84.9    
85.2    
85.5    
85.8    
86.1    
86.4    
86.7    
87.0    
87.3    
87.6    
87.9    
88.2    
88.5    
88.8    
89.1    
89.4    
89.7    
90.0    
90.3    
90.6    
90.9    
91.2    
91.5    
91.8    
92.1    
92.4    
92.7    
93.1    
93.4    
93.7    
94.0    
94.3    
94.6    
94.9    
95.2    
95.5    
95.8    
96.1    
96.4    
96.7    
97.0    
97.3    
97.6    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 18171, rend_intergenic: 10674  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26492, rend_intergenic: 24186  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68557, rend_intergenic: 55077  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84952, rend_intergenic: 83461  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99566, rend_intergenic: 92005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125474, rend_intergenic: 110166  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145118, rend_intergenic: 143376  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