-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_6/scaffold_6_4501866-4658544

-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_14537-T1
Valid prediction for Augustus_model.g9604.t1
Valid prediction for snap_scaffold_6-snap.1076-T1
Valid prediction for snap_scaffold_6-snap.1087-T1
Valid prediction for Augustus_model.g9614.t1
Valid prediction for GlimmerHMM_glimmerT_14519-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_14538-T1
Valid prediction for snap_scaffold_6-snap.1088-T1
Valid prediction for GlimmerHMM_glimmerT_14524-T1
Valid prediction for Augustus_model.g9606.t1
Valid prediction for snap_scaffold_6-snap.1077-T1
Valid prediction for snap_scaffold_6-snap.1074-T1
Valid prediction for GlimmerHMM_glimmerT_14534-T1
Valid prediction for snap_scaffold_6-snap.1089-T1
Valid prediction for GlimmerHMM_glimmerT_14529-T1
Valid prediction for snap_scaffold_6-snap.1071-T1
Valid prediction for snap_scaffold_6-snap.1065-T1
Valid prediction for snap_scaffold_6-snap.1094-T1
Valid prediction for snap_scaffold_6-snap.1079-T1
Couldn't classify 95580, 95615
Sorry, prediction pasa_asmbl_46890.p1 fails validation.
(GTG)	 AC	95580-95615	GT	GGG
(TCT)	 AG	95718-95792	GT	AGG
(GGT)	 AG	96284-96378	GT	AGG
(AAC)	 AG	96526-96594	GT	AGG
(TAC)	 AG	96691-96786	GT	AGG
(TGA)	 AG	97122-97248	GT	AGG
(TTG)	 AG	97500-97574	GT	CGG
(CAG)	 AG	98645-98775	GT	AGG
(AAT)	 AG	98900-98960	GT	GGG
(AAC)	 AG	99059-99103	GT	AGG
(ATC)	 AG	99247-99303	GT	TGG
(AGC)	 AG	99398-99610	GT	GGG
(ACT)	 AG	99749-99856	TG	GAT
-recovered pasa_asmbl_46890.p1, terminal, 99749, 99856
-recovered pasa_asmbl_46890.p1, internal, 95718, 95792
-recovered pasa_asmbl_46890.p1, internal, 96284, 96378
-recovered pasa_asmbl_46890.p1, internal, 96526, 96594
-recovered pasa_asmbl_46890.p1, internal, 96691, 96786
-recovered pasa_asmbl_46890.p1, internal, 97122, 97248
-recovered pasa_asmbl_46890.p1, internal, 97500, 97574
-recovered pasa_asmbl_46890.p1, internal, 98645, 98775
-recovered pasa_asmbl_46890.p1, internal, 98900, 98960
-recovered pasa_asmbl_46890.p1, internal, 99059, 99103
-recovered pasa_asmbl_46890.p1, internal, 99247, 99303
-recovered pasa_asmbl_46890.p1, internal, 99398, 99610
Valid prediction for snap_scaffold_6-snap.1096-T1
Valid prediction for snap_scaffold_6-snap.1081-T1
Valid prediction for Augustus_model.g9620.t1
Valid prediction for GlimmerHMM_glimmerT_14530-T1
Valid prediction for GlimmerHMM_glimmerT_14532-T1
Valid prediction for Augustus_model.g9619.t1
Valid prediction for Augustus_model.g9615.t1
Valid prediction for Augustus_model.g9622.t1
Valid prediction for GlimmerHMM_glimmerT_14510-T1
Valid prediction for GlimmerHMM_glimmerT_14521-T1
Valid prediction for snap_scaffold_6-snap.1085-T1
Valid prediction for snap_scaffold_6-snap.1082-T1
Valid prediction for GlimmerHMM_glimmerT_14533-T1
Valid prediction for snap_scaffold_6-snap.1066-T1
Valid prediction for GlimmerHMM_glimmerT_14512-T1
Valid prediction for snap_scaffold_6-snap.1091-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 Augustus_model.g9617.t1
Valid prediction for snap_scaffold_6-snap.1072-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_14514-T1
Valid prediction for Augustus_model.g9609.t1
Couldn't classify 133451, 133461
Sorry, prediction pasa_asmbl_48331.p1 fails validation.
(CCT)	 AG	133451-133461	GT	AGG
(TCA)	 AG	133725-133887	GT	AGG
(GGT)	 AG	134033-134123	GT	TGG
(GTT)	 AG	134282-134445	GT	TGG
(GAT)	 AG	134593-134811	AA	GAA
-recovered pasa_asmbl_48331.p1, terminal, 134593, 134811
-recovered pasa_asmbl_48331.p1, internal, 133451, 133461
-recovered pasa_asmbl_48331.p1, internal, 133725, 133887
-recovered pasa_asmbl_48331.p1, internal, 134033, 134123
-recovered pasa_asmbl_48331.p1, internal, 134282, 134445
Valid prediction for GlimmerHMM_glimmerT_14516-T1
Valid prediction for Augustus_model.g9608.t1
Valid prediction for Augustus_model.g9621.t1
Valid prediction for GlimmerHMM_glimmerT_14517-T1
Valid prediction for CodingQuarry_transcript_55019-T1
Valid prediction for snap_scaffold_6-snap.1092-T1
Valid prediction for Augustus_model.g9605.t1
Couldn't classify 120089, 120172
Sorry, prediction pasa_asmbl_48336.p1 fails validation.
(ATA)	 AG	120089-120172	GT	AGG
(TGG)	 AG	120337-120412	GT	AGG
(CCG)	 AG	121947-122126	GT	TGG
(ATC)	 AG	122996-123168	TA	GAT
-recovered pasa_asmbl_48336.p1, terminal, 122996, 123168
-recovered pasa_asmbl_48336.p1, internal, 120089, 120172
-recovered pasa_asmbl_48336.p1, internal, 120337, 120412
-recovered pasa_asmbl_48336.p1, internal, 121947, 122126
Valid prediction for snap_scaffold_6-snap.1073-T1
Valid prediction for GlimmerHMM_glimmerT_14525-T1
Valid prediction for GlimmerHMM_glimmerT_14518-T1
Valid prediction for snap_scaffold_6-snap.1084-T1
Valid prediction for snap_scaffold_6-snap.1064-T1
Valid prediction for GlimmerHMM_glimmerT_14511-T1
Valid prediction for GlimmerHMM_glimmerT_14523-T1
Couldn't classify 77288, 77608
Sorry, prediction pasa_asmbl_48340.p1 fails validation.
(ATG)	 TC	77288-77608	CT	CCC
Valid prediction for GlimmerHMM_glimmerT_14515-T1
Valid prediction for snap_scaffold_6-snap.1075-T1
Valid prediction for Augustus_model.g9616.t1
Valid prediction for Augustus_model.g9611.t1
Valid prediction for Augustus_model.g9618.t1
Valid prediction for pasa_asmbl_48328.p1
Valid prediction for snap_scaffold_6-snap.1083-T1
Couldn't classify 67233, 68432
Sorry, prediction pasa_asmbl_48345.p1 fails validation.
(ATG)	 GA	67233-68432	CG	CCC
Valid prediction for GlimmerHMM_glimmerT_14520-T1
Valid prediction for GlimmerHMM_glimmerT_14526-T1
Valid prediction for GlimmerHMM_glimmerT_14527-T1
Valid prediction for CodingQuarry_transcript_55017-T1
Valid prediction for CodingQuarry_transcript_55020-T1
Valid prediction for GlimmerHMM_glimmerT_14522-T1
Valid prediction for snap_scaffold_6-snap.1078-T1
Valid prediction for snap_scaffold_6-snap.1067-T1
Couldn't classify 20556, 20585
Sorry, prediction pasa_asmbl_48346.p1 fails validation.
(CCA)	 TC	20556-20585	GT	GGG
(GAG)	 AG	21161-21214	GT	AGG
(CAG)	 AG	21560-21823	AC	AAA
-recovered pasa_asmbl_48346.p1, terminal, 21560, 21823
-recovered pasa_asmbl_48346.p1, internal, 21161, 21214
Valid prediction for snap_scaffold_6-snap.1090-T1
Valid prediction for snap_scaffold_6-snap.1097-T1
Valid prediction for snap_scaffold_6-snap.1080-T1
Valid prediction for GlimmerHMM_glimmerT_14535-T1
Valid prediction for GlimmerHMM_glimmerT_14528-T1
Valid prediction for Augustus_model.g9612.t1
Valid prediction for snap_scaffold_6-snap.1069-T1
Valid prediction for Augustus_model.g9613.t1
Valid prediction for HiQ_model.g9607.t1
Valid prediction for snap_scaffold_6-snap.1070-T1
Valid prediction for snap_scaffold_6-snap.1086-T1
Valid prediction for GlimmerHMM_glimmerT_14513-T1
Valid prediction for GlimmerHMM_glimmerT_14531-T1
Couldn't classify 70713, 70756
Sorry, prediction pasa_asmbl_48342.p1 fails validation.
(CGG)	 AG	70713-70756	GT	AAG
(GTT)	 AG	70869-71008	GT	TGG
(GTG)	 AG	71144-71314	GT	AGG
(GAG)	 AG	71439-71628	GT	AGG
(CGG)	 AG	71748-71804	GT	AGG
(TCG)	 AG	71947-72048	GT	GGG
(GTG)	 AG	72172-72249	GT	AGG
(CCG)	 AG	72537-72653	GT	TTG
(TCT)	 AG	72895-73026	GT	GAG
(TCT)	 AG	73124-73347	GT	AGG
(GGC)	 AG	73486-73946	GG	AGG
-recovered pasa_asmbl_48342.p1, terminal, 73486, 73946
-recovered pasa_asmbl_48342.p1, internal, 70713, 70756
-recovered pasa_asmbl_48342.p1, internal, 70869, 71008
-recovered pasa_asmbl_48342.p1, internal, 71144, 71314
-recovered pasa_asmbl_48342.p1, internal, 71439, 71628
-recovered pasa_asmbl_48342.p1, internal, 71748, 71804
-recovered pasa_asmbl_48342.p1, internal, 71947, 72048
-recovered pasa_asmbl_48342.p1, internal, 72172, 72249
-recovered pasa_asmbl_48342.p1, internal, 72537, 72653
-recovered pasa_asmbl_48342.p1, internal, 72895, 73026
-recovered pasa_asmbl_48342.p1, internal, 73124, 73347
Valid prediction for GlimmerHMM_glimmerT_14536-T1
Valid prediction for HiQ_model.g9610.t1
Valid prediction for snap_scaffold_6-snap.1095-T1
Valid prediction for CodingQuarry_transcript_55018-T1
Valid prediction for snap_scaffold_6-snap.1068-T1
Valid prediction for snap_scaffold_6-snap.1098-T1
Valid prediction for snap_scaffold_6-snap.1093-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 20784, rend_intergenic: 17822  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46638, rend_intergenic: 33512  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47584, rend_intergenic: 47316  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50427, rend_intergenic: 47917  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54907, rend_intergenic: 51397  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65425, rend_intergenic: 63030  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66663, rend_intergenic: 65572  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74102, rend_intergenic: 66780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79836, rend_intergenic: 76979  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87134, rend_intergenic: 82090  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116640, rend_intergenic: 113061  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123969, rend_intergenic: 118230  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131986, rend_intergenic: 125981  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152308, rend_intergenic: 142653  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 156679
-exon list size: 379


building trellis

0.3    
0.5    
0.8    
1.0    
1.3    
1.6    
1.8    
2.1    
2.4    
2.6    
2.9    
3.1    
3.4    
3.7    
3.9    
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4.5    
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5.0    
5.2    
5.5    
5.8    
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6.3    
6.6    
6.8    
7.1    
7.3    
7.6    
7.9    
8.1    
8.4    
8.7    
8.9    
9.2    
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9.7    
10.0    
10.2    
10.5    
10.8    
11.0    
11.3    
11.5    
11.8    
12.1    
12.3    
12.6    
12.9    
13.1    
13.4    
13.6    
13.9    
14.2    
14.4    
14.7    
15.0    
15.2    
15.5    
15.7    
16.0    
16.3    
16.5    
16.8    
17.1    
17.3    
17.6    
17.8    
18.1    
18.4    
18.6    
18.9    
19.2    
19.4    
19.7    
19.9    
20.2    
20.5    
20.7    
21.0    
21.3    
21.5    
21.8    
22.0    
22.3    
22.6    
22.8    
23.1    
23.4    
23.6    
23.9    
24.1    
24.4    
24.7    
24.9    
25.2    
25.5    
25.7    
26.0    
26.2    
26.5    
26.8    
27.0    
27.3    
27.6    
27.8    
28.1    
28.3    
28.6    
28.9    
29.1    
29.4    
29.7    
29.9    
30.2    
30.4    
30.7    
31.0    
31.2    
31.5    
31.8    
32.0    
32.3    
32.5    
32.8    
33.1    
33.3    
33.6    
33.9    
34.1    
34.4    
34.6    
34.9    
35.2    
35.4    
35.7    
36.0    
36.2    
36.5    
36.7    
37.0    
37.3    
37.5    
37.8    
38.1    
38.3    
38.6    
38.8    
39.1    
39.4    
39.6    
39.9    
40.2    
40.4    
40.7    
40.9    
41.2    
41.5    
41.7    
42.0    
42.3    
42.5    
42.8    
43.0    
43.3    
43.6    
43.8    
44.1    
44.4    
44.6    
44.9    
45.1    
45.4    
45.7    
45.9    
46.2    
46.5    
46.7    
47.0    
47.2    
47.5    
47.8    
48.0    
48.3    
48.6    
48.8    
49.1    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
50.9    
51.2    
51.4    
51.7    
52.0    
52.2    
52.5    
52.8    
53.0    
53.3    
53.5    
53.8    
54.1    
54.3    
54.6    
54.9    
55.1    
55.4    
55.6    
55.9    
56.2    
56.4    
56.7    
57.0    
57.2    
57.5    
57.7    
58.0    
58.3    
58.5    
58.8    
59.1    
59.3    
59.6    
59.8    
60.1    
60.4    
60.6    
60.9    
61.2    
61.4    
61.7    
61.9    
62.2    
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63.0    
63.3    
63.5    
63.8    
64.0    
64.3    
64.6    
64.8    
65.1    
65.4    
65.6    
65.9    
66.1    
66.4    
66.7    
66.9    
67.2    
67.5    
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68.0    
68.2    
68.5    
68.8    
69.0    
69.3    
69.6    
69.8    
70.1    
70.3    
70.6    
70.9    
71.1    
71.4    
71.7    
71.9    
72.2    
72.4    
72.7    
73.0    
73.2    
73.5    
73.8    
74.0    
74.3    
74.5    
74.8    
75.1    
75.3    
75.6    
75.9    
76.1    
76.4    
76.6    
76.9    
77.2    
77.4    
77.7    
78.0    
78.2    
78.5    
78.7    
79.0    
79.3    
79.5    
79.8    
80.1    
80.3    
80.6    
80.8    
81.1    
81.4    
81.6    
81.9    
82.2    
82.4    
82.7    
82.9    
83.2    
83.5    
83.7    
84.0    
84.3    
84.5    
84.8    
85.0    
85.3    
85.6    
85.8    
86.1    
86.4    
86.6    
86.9    
87.1    
87.4    
87.7    
87.9    
88.2    
88.5    
88.7    
89.0    
89.2    
89.5    
89.8    
90.0    
90.3    
90.6    
90.8    
91.1    
91.3    
91.6    
91.9    
92.1    
92.4    
92.7    
92.9    
93.2    
93.4    
93.7    
94.0    
94.2    
94.5    
94.8    
95.0    
95.3    
95.5    
95.8    
96.1    
96.3    
96.6    
96.9    
97.1    
97.4    
97.6    
97.9    
98.2    
98.4    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 20784, rend_intergenic: 17822  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46638, rend_intergenic: 33512  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47584, rend_intergenic: 47316  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50427, rend_intergenic: 47917  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54907, rend_intergenic: 51397  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65425, rend_intergenic: 63030  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66663, rend_intergenic: 65572  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74102, rend_intergenic: 66780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79836, rend_intergenic: 76979  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87134, rend_intergenic: 82090  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116640, rend_intergenic: 113061  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123969, rend_intergenic: 118230  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131986, rend_intergenic: 125981  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152308, rend_intergenic: 142653  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support