-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_6674357-6928962

-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_3996-T1
Valid prediction for Augustus_model.g2666.t1
Valid prediction for snap_scaffold_2-snap.1466-T1
Valid prediction for GlimmerHMM_glimmerT_3980-T1
Valid prediction for snap_scaffold_2-snap.1454-T1
Couldn't classify 208936, 209238
Sorry, prediction pasa_asmbl_24501.p2 fails validation.
(AAA)	 AC	208936-209238	CT	GAC
Valid prediction for pasa_asmbl_24490.p1
Valid prediction for Augustus_model.g2675.t1
Valid prediction for snap_scaffold_2-snap.1483-T1
Valid prediction for snap_scaffold_2-snap.1455-T1
Valid prediction for GlimmerHMM_glimmerT_4003-T1
Valid prediction for Augustus_model.g2673.t1
Valid prediction for snap_scaffold_2-snap.1489-T1
Valid prediction for GlimmerHMM_glimmerT_3998-T1
Valid prediction for Augustus_model.g2652.t1
Valid prediction for pasa_asmbl_24517.p1
Couldn't classify 224727, 224810
Couldn't classify 229369, 229403
Sorry, prediction pasa_asmbl_24513.p1 fails validation.
(GCG)	 TA	224727-224810	GT	AGG
(GAC)	 AG	225936-226007	GT	AGG
(AAG)	 AG	226326-226403	GT	GGG
(GCT)	 AG	227195-227269	GT	TGG
(ATA)	 AG	227475-227676	GT	AGG
(AGG)	 AG	227753-227864	GT	AGG
(GTT)	 AG	228036-228093	GT	AGG
(TGT)	 AG	228668-228768	GT	CCG
(CAA)	 AG	228858-229000	GT	GCG
(ATT)	 AG	229369-229403	AT	TGA
add_exon() Sorry, pasa_asmbl_24513.p1 227475-227676-terminal-3 is invalid.
-recovered pasa_asmbl_24513.p1, terminal, 227475, 227676
-recovered pasa_asmbl_24513.p1, internal, 225936, 226007
-recovered pasa_asmbl_24513.p1, internal, 226326, 226403
-recovered pasa_asmbl_24513.p1, internal, 227195, 227269
-recovered pasa_asmbl_24513.p1, internal, 227475, 227676
-recovered pasa_asmbl_24513.p1, internal, 227753, 227864
-recovered pasa_asmbl_24513.p1, internal, 228036, 228093
-recovered pasa_asmbl_24513.p1, internal, 228668, 228768
-recovered pasa_asmbl_24513.p1, internal, 228858, 229000
Valid prediction for CodingQuarry_transcript_28592-T1
Valid prediction for GlimmerHMM_glimmerT_3995-T1
Valid prediction for snap_scaffold_2-snap.1487-T1
Valid prediction for snap_scaffold_2-snap.1492-T1
Valid prediction for GlimmerHMM_glimmerT_3987-T1
Valid prediction for GlimmerHMM_glimmerT_3992-T1
Couldn't classify 195850, 196203
Sorry, prediction pasa_asmbl_24500.p1 fails validation.
(ATG)	 AG	193965-194069	GT	AAG
(CTC)	 AG	195850-196203	GT	ATG
-recovered pasa_asmbl_24500.p1, initial, 193965, 194069
-recovered pasa_asmbl_24500.p1, internal, 193965, 194069
-recovered pasa_asmbl_24500.p1, internal, 195850, 196203
Valid prediction for GlimmerHMM_glimmerT_3984-T1
Valid prediction for snap_scaffold_2-snap.1473-T1
Valid prediction for GlimmerHMM_glimmerT_3973-T1
Valid prediction for snap_scaffold_2-snap.1451-T1
Valid prediction for CodingQuarry_transcript_28590-T1
Valid prediction for snap_scaffold_2-snap.1458-T1
Valid prediction for HiQ_model.g2670.t1
Valid prediction for Augustus_model.g2672.t1
Valid prediction for GlimmerHMM_glimmerT_3979-T1
Valid prediction for HiQ_model.g2662.t1
Valid prediction for GlimmerHMM_glimmerT_3983-T1
Valid prediction for snap_scaffold_2-snap.1456-T1
Valid prediction for snap_scaffold_2-snap.1464-T1
Valid prediction for snap_scaffold_2-snap.1480-T1
Valid prediction for GlimmerHMM_glimmerT_3988-T1
Valid prediction for snap_scaffold_2-snap.1484-T1
Valid prediction for Augustus_model.g2671.t1
Valid prediction for Augustus_model.g2656.t1
Valid prediction for Augustus_model.g2677.t1
Valid prediction for Augustus_model.g2674.t1
Valid prediction for snap_scaffold_2-snap.1485-T1
Valid prediction for snap_scaffold_2-snap.1476-T1
Valid prediction for GlimmerHMM_glimmerT_3999-T1
Valid prediction for GlimmerHMM_glimmerT_4002-T1
Valid prediction for GlimmerHMM_glimmerT_3991-T1
Valid prediction for snap_scaffold_2-snap.1471-T1
Valid prediction for Augustus_model.g2669.t1
Valid prediction for snap_scaffold_2-snap.1452-T1
Valid prediction for snap_scaffold_2-snap.1463-T1
Valid prediction for Augustus_model.g2665.t1
Valid prediction for Augustus_model.g2655.t1
Valid prediction for snap_scaffold_2-snap.1486-T1
Valid prediction for GlimmerHMM_glimmerT_3978-T1
Valid prediction for GlimmerHMM_glimmerT_3990-T1
Valid prediction for GlimmerHMM_glimmerT_3975-T1
Valid prediction for Augustus_model.g2654.t1
Valid prediction for snap_scaffold_2-snap.1477-T1
Valid prediction for Augustus_model.g2663.t1
Valid prediction for Augustus_model.g2676.t1
Valid prediction for GlimmerHMM_glimmerT_3997-T1
Valid prediction for snap_scaffold_2-snap.1467-T1
Valid prediction for Augustus_model.g2667.t1
Valid prediction for snap_scaffold_2-snap.1457-T1
Valid prediction for snap_scaffold_2-snap.1478-T1
Valid prediction for GlimmerHMM_glimmerT_3986-T1
Valid prediction for snap_scaffold_2-snap.1472-T1
Valid prediction for GlimmerHMM_glimmerT_3977-T1
Couldn't classify 201414, 201509
Couldn't classify 205146, 205201
Sorry, prediction pasa_asmbl_25343.p1 fails validation.
(AGG)	 GC	201414-201509	GT	AAG
(GTG)	 AG	201713-201864	GT	CTG
(GTT)	 AG	203004-203058	GT	TTG
(GTT)	 AG	204612-204663	GT	GGG
(GCA)	 AG	205146-205201	GT	ATG
-recovered pasa_asmbl_25343.p1, internal, 201713, 201864
-recovered pasa_asmbl_25343.p1, internal, 203004, 203058
-recovered pasa_asmbl_25343.p1, internal, 204612, 204663
-recovered pasa_asmbl_25343.p1, internal, 205146, 205201
Valid prediction for Augustus_model.g2668.t1
Valid prediction for snap_scaffold_2-snap.1465-T1
Valid prediction for GlimmerHMM_glimmerT_3994-T1
Valid prediction for Augustus_model.g2679.t1
Valid prediction for Augustus_model.g2680.t1
Valid prediction for snap_scaffold_2-snap.1470-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.1491-T1
Valid prediction for snap_scaffold_2-snap.1490-T1
Valid prediction for snap_scaffold_2-snap.1488-T1
Valid prediction for snap_scaffold_2-snap.1481-T1
Valid prediction for snap_scaffold_2-snap.1482-T1
Valid prediction for Augustus_model.g2658.t1
Valid prediction for Augustus_model.g2657.t1
Valid prediction for snap_scaffold_2-snap.1462-T1
Valid prediction for snap_scaffold_2-snap.1453-T1
Valid prediction for GlimmerHMM_glimmerT_4001-T1
Valid prediction for snap_scaffold_2-snap.1474-T1
Valid prediction for CodingQuarry_transcript_28589-T1
Valid prediction for snap_scaffold_2-snap.1460-T1
Valid prediction for snap_scaffold_2-snap.1479-T1
Valid prediction for GlimmerHMM_glimmerT_3972-T1
Valid prediction for GlimmerHMM_glimmerT_3981-T1
Valid prediction for snap_scaffold_2-snap.1449-T1
Valid prediction for GlimmerHMM_glimmerT_4000-T1
Valid prediction for snap_scaffold_2-snap.1459-T1
Valid prediction for Augustus_model.g2659.t1
Valid prediction for snap_scaffold_2-snap.1450-T1
Valid prediction for Augustus_model.g2660.t1
Valid prediction for GlimmerHMM_glimmerT_3993-T1
Valid prediction for snap_scaffold_2-snap.1461-T1
Valid prediction for GlimmerHMM_glimmerT_3989-T1
Valid prediction for Augustus_model.g2678.t1
Valid prediction for Augustus_model.g2653.t1
Valid prediction for GlimmerHMM_glimmerT_3982-T1
Valid prediction for GlimmerHMM_glimmerT_3974-T1
Valid prediction for GlimmerHMM_glimmerT_3985-T1
Valid prediction for snap_scaffold_2-snap.1468-T1
Valid prediction for GlimmerHMM_glimmerT_3976-T1
Valid prediction for snap_scaffold_2-snap.1469-T1
Valid prediction for snap_scaffold_2-snap.1475-T1
Valid prediction for Augustus_model.g2664.t1
Valid prediction for HiQ_model.g2661.t1
Valid prediction for CodingQuarry_transcript_28588-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 35525, rend_intergenic: 33522  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108743, rend_intergenic: 105458  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138159, rend_intergenic: 135770  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154904, rend_intergenic: 151766  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177433, rend_intergenic: 174568  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 254606
-exon list size: 329


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.8    
2.1    
2.4    
2.7    
3.0    
3.3    
3.6    
3.9    
4.2    
4.5    
4.8    
5.1    
5.4    
5.7    
6.0    
6.3    
6.6    
6.9    
7.3    
7.6    
7.9    
8.2    
8.5    
8.8    
9.1    
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9.7    
10.0    
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10.6    
10.9    
11.2    
11.5    
11.8    
12.1    
12.4    
12.7    
13.0    
13.3    
13.6    
13.9    
14.2    
14.5    
14.8    
15.1    
15.4    
15.7    
16.0    
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16.6    
16.9    
17.2    
17.5    
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    
22.4    
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    
40.2    
40.5    
40.8    
41.1    
41.4    
41.7    
42.0    
42.3    
42.6    
42.9    
43.2    
43.5    
43.8    
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    
56.8    
57.1    
57.4    
57.7    
58.0    
58.3    
58.6    
58.9    
59.2    
59.5    
59.8    
60.1    
60.4    
60.7    
61.0    
61.3    
61.6    
61.9    
62.2    
62.5    
62.8    
63.1    
63.4    
63.7    
64.0    
64.4    
64.7    
65.0    
65.3    
65.6    
65.9    
66.2    
66.5    
66.8    
67.1    
67.4    
67.7    
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    
72.5    
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73.1    
73.4    
73.7    
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74.3    
74.6    
74.9    
75.2    
75.5    
75.8    
76.1    
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77.3    
77.6    
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78.5    
78.9    
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80.1    
80.4    
80.7    
81.0    
81.3    
81.6    
81.9    
82.2    
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82.8    
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 43 predictions from path traversal
Error with prediction: snap lend_intergenic: 35525, rend_intergenic: 33522  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108743, rend_intergenic: 105458  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138159, rend_intergenic: 135770  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154904, rend_intergenic: 151766  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177433, rend_intergenic: 174568  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 41 predictions persist after filtering for low support