-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_3/scaffold_3_12716275-12972708

-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.g4905.t1
Valid prediction for snap_scaffold_3-snap.2509-T1
Valid prediction for snap_scaffold_3-snap.2485-T1
Valid prediction for snap_scaffold_3-snap.2476-T1
Valid prediction for GlimmerHMM_glimmerT_7498-T1
Valid prediction for snap_scaffold_3-snap.2478-T1
Valid prediction for Augustus_model.g4890.t1
Valid prediction for GlimmerHMM_glimmerT_7507-T1
Valid prediction for snap_scaffold_3-snap.2492-T1
Valid prediction for GlimmerHMM_glimmerT_7493-T1
Couldn't classify 121083, 121121
Sorry, prediction pasa_asmbl_40417.p1 fails validation.
(ACC)	 CC	121083-121121	GT	AGG
(GGC)	 AG	123387-123448	GT	AGG
(GGT)	 AG	123835-123892	GT	AGG
(ATC)	 AG	124335-124409	GT	AGG
(ATA)	 AG	125648-125822	GT	AGG
(AGC)	 AG	126116-126239	GT	TGG
(TGC)	 AG	127759-128011	AC	AGA
-recovered pasa_asmbl_40417.p1, terminal, 127759, 128011
-recovered pasa_asmbl_40417.p1, internal, 123387, 123448
-recovered pasa_asmbl_40417.p1, internal, 123835, 123892
-recovered pasa_asmbl_40417.p1, internal, 124335, 124409
-recovered pasa_asmbl_40417.p1, internal, 125648, 125822
-recovered pasa_asmbl_40417.p1, internal, 126116, 126239
Valid prediction for snap_scaffold_3-snap.2495-T1
Valid prediction for snap_scaffold_3-snap.2469-T1
Valid prediction for snap_scaffold_3-snap.2487-T1
Valid prediction for snap_scaffold_3-snap.2481-T1
Valid prediction for CodingQuarry_transcript_46305-T1
Couldn't classify 114120, 114169
Couldn't classify 115821, 115857
Sorry, prediction pasa_asmbl_40787.p1 fails validation.
(ATC)	 TG	114120-114169	GT	AGG
(GCC)	 AG	114311-114450	GT	AGG
(CCT)	 AG	114977-115113	GT	AGG
(ACC)	 AG	115253-115333	GT	CGG
(GAT)	 AG	115509-115636	GT	AGG
(GAT)	 AG	115821-115857	AG	AGA
-recovered pasa_asmbl_40787.p1, internal, 114311, 114450
-recovered pasa_asmbl_40787.p1, internal, 114977, 115113
-recovered pasa_asmbl_40787.p1, internal, 115253, 115333
-recovered pasa_asmbl_40787.p1, internal, 115509, 115636
Valid prediction for Augustus_model.g4900.t1
Valid prediction for CodingQuarry_transcript_46306-T1
Valid prediction for Augustus_model.g4895.t1
Valid prediction for GlimmerHMM_glimmerT_7500-T1
Valid prediction for GlimmerHMM_glimmerT_7511-T1
Valid prediction for snap_scaffold_3-snap.2482-T1
Valid prediction for snap_scaffold_3-snap.2472-T1
Valid prediction for snap_scaffold_3-snap.2477-T1
Valid prediction for Augustus_model.g4893.t1
Valid prediction for CodingQuarry_transcript_46307-T1
Valid prediction for GlimmerHMM_glimmerT_7515-T1
Valid prediction for GlimmerHMM_glimmerT_7496-T1
Valid prediction for GlimmerHMM_glimmerT_7497-T1
Valid prediction for snap_scaffold_3-snap.2503-T1
Valid prediction for snap_scaffold_3-snap.2484-T1
Valid prediction for GlimmerHMM_glimmerT_7514-T1
Valid prediction for GlimmerHMM_glimmerT_7506-T1
Valid prediction for snap_scaffold_3-snap.2483-T1
Valid prediction for GlimmerHMM_glimmerT_7490-T1
Valid prediction for Augustus_model.g4891.t1
Valid prediction for Augustus_model.g4902.t1
Valid prediction for GlimmerHMM_glimmerT_7502-T1
Valid prediction for snap_scaffold_3-snap.2465-T1
Valid prediction for snap_scaffold_3-snap.2480-T1
Valid prediction for GlimmerHMM_glimmerT_7494-T1
Valid prediction for pasa_asmbl_40414.p1
Valid prediction for snap_scaffold_3-snap.2471-T1
Valid prediction for snap_scaffold_3-snap.2507-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_7508-T1
Valid prediction for Augustus_model.g4892.t1
Valid prediction for Augustus_model.g4906.t1
Valid prediction for GlimmerHMM_glimmerT_7492-T1
Valid prediction for snap_scaffold_3-snap.2486-T1
Valid prediction for snap_scaffold_3-snap.2464-T1
Valid prediction for GlimmerHMM_glimmerT_7516-T1
Valid prediction for GlimmerHMM_glimmerT_7491-T1
Valid prediction for snap_scaffold_3-snap.2497-T1
Valid prediction for snap_scaffold_3-snap.2504-T1
Valid prediction for CodingQuarry_transcript_46308-T1
Valid prediction for snap_scaffold_3-snap.2474-T1
Valid prediction for snap_scaffold_3-snap.2508-T1
Valid prediction for pasa_asmbl_39237.p1
Valid prediction for snap_scaffold_3-snap.2490-T1
Valid prediction for GlimmerHMM_glimmerT_7517-T1
Valid prediction for Augustus_model.g4896.t1
Valid prediction for CodingQuarry_transcript_46309-T1
Valid prediction for snap_scaffold_3-snap.2475-T1
Valid prediction for snap_scaffold_3-snap.2470-T1
Valid prediction for snap_scaffold_3-snap.2510-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for pasa_asmbl_39240.p1
Valid prediction for snap_scaffold_3-snap.2505-T1
Valid prediction for Augustus_model.g4904.t1
Valid prediction for snap_scaffold_3-snap.2489-T1
Valid prediction for snap_scaffold_3-snap.2500-T1
Valid prediction for Augustus_model.g4894.t1
Valid prediction for snap_scaffold_3-snap.2502-T1
Valid prediction for snap_scaffold_3-snap.2496-T1
Valid prediction for GlimmerHMM_glimmerT_7510-T1
Valid prediction for Augustus_model.g4897.t1
Valid prediction for snap_scaffold_3-snap.2494-T1
Valid prediction for GlimmerHMM_glimmerT_7513-T1
Valid prediction for snap_scaffold_3-snap.2466-T1
Valid prediction for Augustus_model.g4899.t1
Valid prediction for GlimmerHMM_glimmerT_7499-T1
Valid prediction for snap_scaffold_3-snap.2488-T1
Valid prediction for CodingQuarry_transcript_46310-T1
Valid prediction for Augustus_model.g4888.t1
Valid prediction for Augustus_model.g4907.t1
Valid prediction for snap_scaffold_3-snap.2493-T1
Valid prediction for GlimmerHMM_glimmerT_7505-T1
Valid prediction for snap_scaffold_3-snap.2479-T1
Valid prediction for Augustus_model.g4889.t1
Valid prediction for snap_scaffold_3-snap.2467-T1
Valid prediction for HiQ_model.g4901.t1
Valid prediction for snap_scaffold_3-snap.2473-T1
Valid prediction for GlimmerHMM_glimmerT_7495-T1
Valid prediction for snap_scaffold_3-snap.2468-T1
Valid prediction for CodingQuarry_transcript_46311-T1
Valid prediction for GlimmerHMM_glimmerT_7509-T1
Valid prediction for GlimmerHMM_glimmerT_7503-T1
Valid prediction for Augustus_model.g4898.t1
Couldn't classify 224038, 224101
Couldn't classify 226675, 227162
Sorry, prediction pasa_asmbl_39749.p1 fails validation.
(GCA)	 CG	224038-224101	GC	GGG
(ATG)	 AG	226675-227162	GC	GCG
add_exon() Sorry, pasa_asmbl_39749.p1 226675-227162-initial-1 is invalid.
-recovered pasa_asmbl_39749.p1, initial, 226675, 227162
-recovered pasa_asmbl_39749.p1, internal, 226675, 227162
Valid prediction for GlimmerHMM_glimmerT_7504-T1
Valid prediction for snap_scaffold_3-snap.2501-T1
Valid prediction for Augustus_model.g4903.t1
Valid prediction for snap_scaffold_3-snap.2491-T1
Valid prediction for GlimmerHMM_glimmerT_7489-T1
Valid prediction for snap_scaffold_3-snap.2506-T1
Valid prediction for snap_scaffold_3-snap.2498-T1
Valid prediction for GlimmerHMM_glimmerT_7501-T1
Valid prediction for snap_scaffold_3-snap.2499-T1
Valid prediction for GlimmerHMM_glimmerT_7512-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 19584, rend_intergenic: 10741  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45789, rend_intergenic: 38035  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85520, rend_intergenic: 66416  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92481, rend_intergenic: 85983  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108479, rend_intergenic: 108407  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118660, rend_intergenic: 108483  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 256434
-exon list size: 408


building trellis

0.2    
0.5    
0.7    
1.0    
1.2    
1.5    
1.7    
2.0    
2.2    
2.4    
2.7    
2.9    
3.2    
3.4    
3.7    
3.9    
4.1    
4.4    
4.6    
4.9    
5.1    
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5.6    
5.9    
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6.8    
7.1    
7.3    
7.6    
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8.3    
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9.0    
9.3    
9.5    
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10.5    
10.7    
11.0    
11.2    
11.5    
11.7    
12.0    
12.2    
12.4    
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12.9    
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13.9    
14.1    
14.4    
14.6    
14.9    
15.1    
15.4    
15.6    
15.9    
16.1    
16.3    
16.6    
16.8    
17.1    
17.3    
17.6    
17.8    
18.0    
18.3    
18.5    
18.8    
19.0    
19.3    
19.5    
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20.2    
20.5    
20.7    
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21.5    
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22.0    
22.2    
22.4    
22.7    
22.9    
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23.4    
23.7    
23.9    
24.1    
24.4    
24.6    
24.9    
25.1    
25.4    
25.6    
25.9    
26.1    
26.3    
26.6    
26.8    
27.1    
27.3    
27.6    
27.8    
28.0    
28.3    
28.5    
28.8    
29.0    
29.3    
29.5    
29.8    
30.0    
30.2    
30.5    
30.7    
31.0    
31.2    
31.5    
31.7    
32.0    
32.2    
32.4    
32.7    
32.9    
33.2    
33.4    
33.7    
33.9    
34.1    
34.4    
34.6    
34.9    
35.1    
35.4    
35.6    
35.9    
36.1    
36.3    
36.6    
36.8    
37.1    
37.3    
37.6    
37.8    
38.0    
38.3    
38.5    
38.8    
39.0    
39.3    
39.5    
39.8    
40.0    
40.2    
40.5    
40.7    
41.0    
41.2    
41.5    
41.7    
42.0    
42.2    
42.4    
42.7    
42.9    
43.2    
43.4    
43.7    
43.9    
44.1    
44.4    
44.6    
44.9    
45.1    
45.4    
45.6    
45.9    
46.1    
46.3    
46.6    
46.8    
47.1    
47.3    
47.6    
47.8    
48.0    
48.3    
48.5    
48.8    
49.0    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
50.7    
51.0    
51.2    
51.5    
51.7    
52.0    
52.2    
52.4    
52.7    
52.9    
53.2    
53.4    
53.7    
53.9    
54.1    
54.4    
54.6    
54.9    
55.1    
55.4    
55.6    
55.9    
56.1    
56.3    
56.6    
56.8    
57.1    
57.3    
57.6    
57.8    
58.0    
58.3    
58.5    
58.8    
59.0    
59.3    
59.5    
59.8    
60.0    
60.2    
60.5    
60.7    
61.0    
61.2    
61.5    
61.7    
62.0    
62.2    
62.4    
62.7    
62.9    
63.2    
63.4    
63.7    
63.9    
64.1    
64.4    
64.6    
64.9    
65.1    
65.4    
65.6    
65.9    
66.1    
66.3    
66.6    
66.8    
67.1    
67.3    
67.6    
67.8    
68.0    
68.3    
68.5    
68.8    
69.0    
69.3    
69.5    
69.8    
70.0    
70.2    
70.5    
70.7    
71.0    
71.2    
71.5    
71.7    
72.0    
72.2    
72.4    
72.7    
72.9    
73.2    
73.4    
73.7    
73.9    
74.1    
74.4    
74.6    
74.9    
75.1    
75.4    
75.6    
75.9    
76.1    
76.3    
76.6    
76.8    
77.1    
77.3    
77.6    
77.8    
78.0    
78.3    
78.5    
78.8    
79.0    
79.3    
79.5    
79.8    
80.0    
80.2    
80.5    
80.7    
81.0    
81.2    
81.5    
81.7    
82.0    
82.2    
82.4    
82.7    
82.9    
83.2    
83.4    
83.7    
83.9    
84.1    
84.4    
84.6    
84.9    
85.1    
85.4    
85.6    
85.9    
86.1    
86.3    
86.6    
86.8    
87.1    
87.3    
87.6    
87.8    
88.0    
88.3    
88.5    
88.8    
89.0    
89.3    
89.5    
89.8    
90.0    
90.2    
90.5    
90.7    
91.0    
91.2    
91.5    
91.7    
92.0    
92.2    
92.4    
92.7    
92.9    
93.2    
93.4    
93.7    
93.9    
94.1    
94.4    
94.6    
94.9    
95.1    
95.4    
95.6    
95.9    
96.1    
96.3    
96.6    
96.8    
97.1    
97.3    
97.6    
97.8    
98.0    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 19584, rend_intergenic: 10741  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45789, rend_intergenic: 38035  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85520, rend_intergenic: 66416  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92481, rend_intergenic: 85983  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108479, rend_intergenic: 108407  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118660, rend_intergenic: 108483  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support