-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_11/scaffold_11_2127383-2273628

-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_26631-T1
Valid prediction for GlimmerHMM_glimmerT_26644-T1
Valid prediction for snap_scaffold_11-snap.568-T1
Valid prediction for GlimmerHMM_glimmerT_26637-T1
Valid prediction for CodingQuarry_transcript_7992-T1
Valid prediction for snap_scaffold_11-snap.538-T1
Couldn't classify 16389, 16558
Sorry, prediction pasa_asmbl_5366.p1 fails validation.
(AGG)	 AC	16389-16558	GT	AGG
(GGA)	 AG	16650-16749	GT	AGG
(AGA)	 AG	16866-17032	GT	AGG
(GGA)	 AG	17290-17365	AA	AGA
-recovered pasa_asmbl_5366.p1, terminal, 17290, 17365
-recovered pasa_asmbl_5366.p1, internal, 16650, 16749
-recovered pasa_asmbl_5366.p1, internal, 16866, 17032
Valid prediction for Augustus_model.g17645.t1
Valid prediction for Augustus_model.g17646.t1
Valid prediction for GlimmerHMM_glimmerT_26650-T1
Valid prediction for GlimmerHMM_glimmerT_26645-T1
Valid prediction for snap_scaffold_11-snap.555-T1
Valid prediction for snap_scaffold_11-snap.556-T1
Valid prediction for GlimmerHMM_glimmerT_26630-T1
Valid prediction for GlimmerHMM_glimmerT_26634-T1
Valid prediction for snap_scaffold_11-snap.533-T1
Valid prediction for snap_scaffold_11-snap.558-T1
Valid prediction for Augustus_model.g17635.t1
Valid prediction for GlimmerHMM_glimmerT_26651-T1
Valid prediction for snap_scaffold_11-snap.550-T1
Valid prediction for snap_scaffold_11-snap.535-T1
Valid prediction for snap_scaffold_11-snap.557-T1
Valid prediction for GlimmerHMM_glimmerT_26642-T1
Valid prediction for Augustus_model.g17639.t1
Valid prediction for snap_scaffold_11-snap.561-T1
Valid prediction for GlimmerHMM_glimmerT_26643-T1
Valid prediction for GlimmerHMM_glimmerT_26646-T1
Valid prediction for snap_scaffold_11-snap.541-T1
Valid prediction for snap_scaffold_11-snap.565-T1
Valid prediction for snap_scaffold_11-snap.542-T1
Valid prediction for snap_scaffold_11-snap.539-T1
Valid prediction for snap_scaffold_11-snap.534-T1
Valid prediction for snap_scaffold_11-snap.531-T1
Valid prediction for GlimmerHMM_glimmerT_26638-T1
Valid prediction for snap_scaffold_11-snap.547-T1
Valid prediction for snap_scaffold_11-snap.540-T1
Valid prediction for GlimmerHMM_glimmerT_26647-T1
Valid prediction for snap_scaffold_11-snap.553-T1
Valid prediction for snap_scaffold_11-snap.537-T1
Valid prediction for Augustus_model.g17640.t1
Valid prediction for GlimmerHMM_glimmerT_26641-T1
Valid prediction for snap_scaffold_11-snap.548-T1
Valid prediction for snap_scaffold_11-snap.560-T1
Valid prediction for GlimmerHMM_glimmerT_26636-T1
Valid prediction for snap_scaffold_11-snap.546-T1
Valid prediction for HiQ_model.g17636.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 GlimmerHMM_glimmerT_26648-T1
Valid prediction for CodingQuarry_transcript_7994-T1
Valid prediction for snap_scaffold_11-snap.529-T1
Valid prediction for CodingQuarry_transcript_7990-T1
Valid prediction for CodingQuarry_transcript_7993-T1
Valid prediction for snap_scaffold_11-snap.563-T1
Couldn't classify 134239, 134261
Couldn't classify 136012, 136139
Sorry, prediction CodingQuarry_transcript_7991-T1 fails validation.
(ATG)	 AG	134239-134261	AG	GCA
(GGT)	 TA	136012-136139	GT	AGG
(ATA)	 AG	137656-137786	GT	TGG
(GTG)	 AG	137898-138005	GT	AGG
(CCC)	 AG	138701-138763	GT	CGG
(TTG)	 AG	139132-139239	GT	TCG
(TGG)	 AG	139884-140086	GT	GGG
(CGA)	 AG	140388-140503	GT	AGG
(GAG)	 AG	140903-141069	GT	AAG
(GAA)	 AG	141763-141792	TT	GAT
add_exon() Sorry, CodingQuarry_transcript_7991-T1 140388-140503-terminal-2 is invalid.
-recovered CodingQuarry_transcript_7991-T1, terminal, 140388, 140503
-recovered CodingQuarry_transcript_7991-T1, terminal, 141763, 141792
-recovered CodingQuarry_transcript_7991-T1, internal, 137656, 137786
-recovered CodingQuarry_transcript_7991-T1, internal, 137898, 138005
-recovered CodingQuarry_transcript_7991-T1, internal, 138701, 138763
-recovered CodingQuarry_transcript_7991-T1, internal, 139132, 139239
-recovered CodingQuarry_transcript_7991-T1, internal, 139884, 140086
-recovered CodingQuarry_transcript_7991-T1, internal, 140388, 140503
-recovered CodingQuarry_transcript_7991-T1, internal, 140903, 141069
Valid prediction for snap_scaffold_11-snap.567-T1
Valid prediction for GlimmerHMM_glimmerT_26649-T1
Valid prediction for GlimmerHMM_glimmerT_26633-T1
Valid prediction for snap_scaffold_11-snap.545-T1
Valid prediction for snap_scaffold_11-snap.559-T1
Valid prediction for snap_scaffold_11-snap.530-T1
Valid prediction for GlimmerHMM_glimmerT_26635-T1
Valid prediction for snap_scaffold_11-snap.566-T1
Valid prediction for snap_scaffold_11-snap.551-T1
Valid prediction for snap_scaffold_11-snap.536-T1
Valid prediction for pasa_asmbl_6480.p1
Valid prediction for HiQ_model.g17641.t1
Valid prediction for snap_scaffold_11-snap.554-T1
Valid prediction for snap_scaffold_11-snap.544-T1
Valid prediction for GlimmerHMM_glimmerT_26640-T1
Valid prediction for snap_scaffold_11-snap.549-T1
Valid prediction for snap_scaffold_11-snap.564-T1
Valid prediction for snap_scaffold_11-snap.552-T1
Valid prediction for GlimmerHMM_glimmerT_26639-T1
Valid prediction for pasa_asmbl_6483.p1
Valid prediction for snap_scaffold_11-snap.562-T1
Valid prediction for Augustus_model.g17637.t1
Valid prediction for HiQ_model.g17634.t1
Valid prediction for Augustus_model.g17644.t1
Valid prediction for snap_scaffold_11-snap.543-T1
Valid prediction for Augustus_model.g17638.t1
Valid prediction for Augustus_model.g17643.t1
Valid prediction for GlimmerHMM_glimmerT_26629-T1
Valid prediction for HiQ_model.g17642.t1
Valid prediction for snap_scaffold_11-snap.532-T1
Valid prediction for GlimmerHMM_glimmerT_26632-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 25400, rend_intergenic: 20976  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34038, rend_intergenic: 33748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57229, rend_intergenic: 34303  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63873, rend_intergenic: 61820  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85010, rend_intergenic: 84028  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87040, rend_intergenic: 85885  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95206, rend_intergenic: 87428  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121438, rend_intergenic: 119622  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136299, rend_intergenic: 132704  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144008, rend_intergenic: 142171  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 146246
-exon list size: 270


building trellis

0.4    
0.7    
1.1    
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1.8    
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2.6    
2.9    
3.3    
3.7    
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5.5    
5.9    
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6.6    
7.0    
7.4    
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8.8    
9.2    
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10.3    
10.7    
11.0    
11.4    
11.8    
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12.5    
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13.2    
13.6    
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14.3    
14.7    
15.1    
15.4    
15.8    
16.2    
16.5    
16.9    
17.3    
17.6    
18.0    
18.4    
18.8    
19.1    
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20.6    
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21.3    
21.7    
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22.8    
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24.3    
24.6    
25.0    
25.4    
25.7    
26.1    
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27.9    
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29.0    
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29.8    
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30.5    
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31.2    
31.6    
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32.4    
32.7    
33.1    
33.5    
33.8    
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34.6    
34.9    
35.3    
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36.0    
36.4    
36.8    
37.1    
37.5    
37.9    
38.2    
38.6    
39.0    
39.3    
39.7    
40.1    
40.4    
40.8    
41.2    
41.5    
41.9    
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43.0    
43.4    
43.8    
44.1    
44.5    
44.9    
45.2    
45.6    
46.0    
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46.7    
47.1    
47.4    
47.8    
48.2    
48.5    
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49.3    
49.6    
50.0    
50.4    
50.7    
51.1    
51.5    
51.8    
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52.6    
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53.7    
54.0    
54.4    
54.8    
55.1    
55.5    
55.9    
56.2    
56.6    
57.0    
57.4    
57.7    
58.1    
58.5    
58.8    
59.2    
59.6    
59.9    
60.3    
60.7    
61.0    
61.4    
61.8    
62.1    
62.5    
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63.2    
63.6    
64.0    
64.3    
64.7    
65.1    
65.4    
65.8    
66.2    
66.5    
66.9    
67.3    
67.6    
68.0    
68.4    
68.8    
69.1    
69.5    
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70.2    
70.6    
71.0    
71.3    
71.7    
72.1    
72.4    
72.8    
73.2    
73.5    
73.9    
74.3    
74.6    
75.0    
75.4    
75.7    
76.1    
76.5    
76.8    
77.2    
77.6    
77.9    
78.3    
78.7    
79.0    
79.4    
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80.1    
80.5    
80.9    
81.2    
81.6    
82.0    
82.4    
82.7    
83.1    
83.5    
83.8    
84.2    
84.6    
84.9    
85.3    
85.7    
86.0    
86.4    
86.8    
87.1    
87.5    
87.9    
88.2    
88.6    
89.0    
89.3    
89.7    
90.1    
90.4    
90.8    
91.2    
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91.9    
92.3    
92.6    
93.0    
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95.2    
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96.0    
96.3    
96.7    
97.1    
97.4    
97.8    
98.2    
98.5    
98.9    
99.3    
99.6    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 25400, rend_intergenic: 20976  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34038, rend_intergenic: 33748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57229, rend_intergenic: 34303  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63873, rend_intergenic: 61820  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85010, rend_intergenic: 84028  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87040, rend_intergenic: 85885  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95206, rend_intergenic: 87428  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121438, rend_intergenic: 119622  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136299, rend_intergenic: 132704  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144008, rend_intergenic: 142171  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support