-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_25/scaffold_25_1-187314

-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.g35525.t1
Valid prediction for snap_scaffold_25-snap.6-T1
Valid prediction for CodingQuarry_transcript_38611-T1
Valid prediction for GlimmerHMM_glimmerT_53414-T1
Valid prediction for snap_scaffold_25-snap.21-T1
Valid prediction for snap_scaffold_25-snap.24-T1
Valid prediction for GlimmerHMM_glimmerT_53417-T1
Valid prediction for GlimmerHMM_glimmerT_53416-T1
Couldn't classify 149548, 149772
Couldn't classify 150927, 151088
Sorry, prediction pasa_asmbl_33317.p1 fails validation.
(ACC)	 GC	149548-149772	GT	CTG
(GGG)	 AG	150353-150475	GT	AGG
(GAC)	 AG	150666-150788	GT	AGG
(GTG)	 AG	150927-151088	AC	AGA
-recovered pasa_asmbl_33317.p1, internal, 150353, 150475
-recovered pasa_asmbl_33317.p1, internal, 150666, 150788
Valid prediction for snap_scaffold_25-snap.20-T1
Valid prediction for snap_scaffold_25-snap.17-T1
Valid prediction for pasa_asmbl_33314.p1
Valid prediction for Augustus_model.g35522.t1
Valid prediction for Augustus_model.g35529.t1
Valid prediction for GlimmerHMM_glimmerT_53423-T1
Valid prediction for GlimmerHMM_glimmerT_53413-T1
Valid prediction for Augustus_model.g35537.t1
Valid prediction for GlimmerHMM_glimmerT_53420-T1
Valid prediction for Augustus_model.g35521.t1
Valid prediction for snap_scaffold_25-snap.25-T1
Valid prediction for snap_scaffold_25-snap.19-T1
Valid prediction for GlimmerHMM_glimmerT_53439-T1
Valid prediction for GlimmerHMM_glimmerT_53412-T1
Valid prediction for snap_scaffold_25-snap.4-T1
Valid prediction for snap_scaffold_25-snap.30-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_53432-T1
Valid prediction for Augustus_model.g35527.t1
Valid prediction for snap_scaffold_25-snap.12-T1
Valid prediction for snap_scaffold_25-snap.27-T1
Valid prediction for HiQ_model.g35530.t1
Valid prediction for snap_scaffold_25-snap.3-T1
Valid prediction for snap_scaffold_25-snap.1-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_53425-T1
Valid prediction for GlimmerHMM_glimmerT_53411-T1
Valid prediction for snap_scaffold_25-snap.14-T1
Valid prediction for snap_scaffold_25-snap.16-T1
Valid prediction for Augustus_model.g35523.t1
Valid prediction for Augustus_model.g35520.t1
Valid prediction for GlimmerHMM_glimmerT_53434-T1
Valid prediction for snap_scaffold_25-snap.8-T1
Valid prediction for snap_scaffold_25-snap.38-T1
Valid prediction for GlimmerHMM_glimmerT_53438-T1
Valid prediction for snap_scaffold_25-snap.36-T1
Valid prediction for Augustus_model.g35535.t1
Valid prediction for snap_scaffold_25-snap.9-T1
Couldn't classify 138577, 139098
Sorry, prediction pasa_asmbl_33926.p1 fails validation.
(TCT)	 GC	138577-139098	GC	GGG
Valid prediction for CodingQuarry_transcript_38614-T1
Valid prediction for snap_scaffold_25-snap.10-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: -)Couldn't classify 178940, 179072
Sorry, prediction snap_scaffold_25-snap.2-T1 fails validation.
(ATG)	 GG	173245-173280	GT	GGG
(ATT)	 AG	173729-173831	GT	AGG
(GGC)	 AG	176452-176611	GT	GGG
(ATT)	 AG	178940-179072	GT	GGG
-recovered snap_scaffold_25-snap.2-T1, initial, 173245, 173280
-recovered snap_scaffold_25-snap.2-T1, internal, 173729, 173831
-recovered snap_scaffold_25-snap.2-T1, internal, 176452, 176611
-recovered snap_scaffold_25-snap.2-T1, internal, 178940, 179072
Valid prediction for GlimmerHMM_glimmerT_53418-T1
Couldn't classify 79855, 80089
Sorry, prediction CodingQuarry_transcript_38612-T1 fails validation.
(ATG)	 GC	77856-77875	GT	AGG
(GAA)	 AG	79519-79766	GT	GGG
(TCA)	 AG	79855-80089	TG	GGT
(GAA)	 AG	81425-81629	AG	AGA
-recovered CodingQuarry_transcript_38612-T1, initial, 77856, 77875
-recovered CodingQuarry_transcript_38612-T1, terminal, 81425, 81629
-recovered CodingQuarry_transcript_38612-T1, internal, 79519, 79766
Valid prediction for snap_scaffold_25-snap.7-T1
Valid prediction for GlimmerHMM_glimmerT_53424-T1
Valid prediction for snap_scaffold_25-snap.26-T1
Valid prediction for Augustus_model.g35526.t1
Valid prediction for snap_scaffold_25-snap.31-T1
Valid prediction for snap_scaffold_25-snap.11-T1
Valid prediction for GlimmerHMM_glimmerT_53415-T1
Valid prediction for GlimmerHMM_glimmerT_53435-T1
Valid prediction for Augustus_model.g35539.t1
Valid prediction for Augustus_model.g35533.t1
Valid prediction for Augustus_model.g35536.t1
Couldn't classify 90522, 90702
Sorry, prediction pasa_asmbl_34549.p1 fails validation.
(TTC)	 CT	90522-90702	GT	AGG
(AGT)	 AG	91253-91383	GT	AGG
(GTA)	 AG	91610-91813	GT	AGG
(GTG)	 AG	92020-92113	GT	GGG
(CTA)	 AG	92899-93064	GT	AGG
(GGA)	 AG	93214-93397	GG	GAG
-recovered pasa_asmbl_34549.p1, terminal, 93214, 93397
-recovered pasa_asmbl_34549.p1, internal, 91253, 91383
-recovered pasa_asmbl_34549.p1, internal, 91610, 91813
-recovered pasa_asmbl_34549.p1, internal, 92020, 92113
-recovered pasa_asmbl_34549.p1, internal, 92899, 93064
Valid prediction for GlimmerHMM_glimmerT_53426-T1
Valid prediction for snap_scaffold_25-snap.5-T1
Valid prediction for snap_scaffold_25-snap.37-T1
Valid prediction for GlimmerHMM_glimmerT_53421-T1
Valid prediction for snap_scaffold_25-snap.33-T1
Valid prediction for snap_scaffold_25-snap.18-T1
Valid prediction for Augustus_model.g35524.t1
Valid prediction for snap_scaffold_25-snap.23-T1
Valid prediction for GlimmerHMM_glimmerT_53430-T1
Valid prediction for GlimmerHMM_glimmerT_53433-T1
Valid prediction for Augustus_model.g35532.t1
Valid prediction for snap_scaffold_25-snap.35-T1
Valid prediction for GlimmerHMM_glimmerT_53419-T1
Couldn't classify 2050, 2237
Sorry, prediction pasa_asmbl_33955.p1 fails validation.
(ATG)	 TC	879-1527	GT	ACG
(AGC)	 AG	2050-2237	GG	AGG
-recovered pasa_asmbl_33955.p1, initial, 879, 1527
Valid prediction for snap_scaffold_25-snap.13-T1
Valid prediction for GlimmerHMM_glimmerT_53440-T1
Valid prediction for snap_scaffold_25-snap.39-T1
Valid prediction for Augustus_model.g35531.t1
Valid prediction for GlimmerHMM_glimmerT_53422-T1
Valid prediction for snap_scaffold_25-snap.34-T1
Valid prediction for GlimmerHMM_glimmerT_53427-T1
Valid prediction for snap_scaffold_25-snap.15-T1
Valid prediction for Augustus_model.g35534.t1
Valid prediction for GlimmerHMM_glimmerT_53429-T1
Valid prediction for snap_scaffold_25-snap.40-T1
Couldn't classify 75149, 75388
Couldn't classify 76035, 76172
Sorry, prediction pasa_asmbl_33953.p1 fails validation.
(GCA)	 AA	75149-75388	GT	CGG
(GGA)	 AG	76035-76172	AT	TCA
Valid prediction for snap_scaffold_25-snap.28-T1
Valid prediction for GlimmerHMM_glimmerT_53431-T1
Valid prediction for snap_scaffold_25-snap.32-T1
Valid prediction for snap_scaffold_25-snap.29-T1
Valid prediction for Augustus_model.g35538.t1
Valid prediction for snap_scaffold_25-snap.22-T1
Valid prediction for GlimmerHMM_glimmerT_53436-T1
Couldn't classify 4686, 4692
Couldn't classify 5715, 5953
Sorry, prediction CodingQuarry_transcript_38615-T1 fails validation.
(ATG)	 GC	4686-4692	CT	ACC
(CTG)	 AC	5715-5953	TG	GAT
Valid prediction for GlimmerHMM_glimmerT_53437-T1
Valid prediction for GlimmerHMM_glimmerT_53428-T1
Valid prediction for Augustus_model.g35528.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14070, rend_intergenic: 9034  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24826, rend_intergenic: 15875  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38667, rend_intergenic: 28590  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42589, rend_intergenic: 38928  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54143, rend_intergenic: 46585  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55213, rend_intergenic: 54362  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70438, rend_intergenic: 69621  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88687, rend_intergenic: 70974  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98159, rend_intergenic: 91823  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109459, rend_intergenic: 106527  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114774, rend_intergenic: 111128  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119225, rend_intergenic: 115833  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131556, rend_intergenic: 120990  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134404, rend_intergenic: 134153  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161753, rend_intergenic: 134534  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165865, rend_intergenic: 163854  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175841, rend_intergenic: 169275  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 187314
-exon list size: 354


building trellis

0.3    
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1.4    
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2.0    
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3.7    
3.9    
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10.7    
11.0    
11.2    
11.5    
11.8    
12.1    
12.4    
12.6    
12.9    
13.2    
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13.8    
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14.3    
14.6    
14.9    
15.2    
15.4    
15.7    
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16.3    
16.6    
16.9    
17.1    
17.4    
17.7    
18.0    
18.3    
18.5    
18.8    
19.1    
19.4    
19.7    
19.9    
20.2    
20.5    
20.8    
21.1    
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21.6    
21.9    
22.2    
22.5    
22.8    
23.0    
23.3    
23.6    
23.9    
24.2    
24.4    
24.7    
25.0    
25.3    
25.6    
25.8    
26.1    
26.4    
26.7    
27.0    
27.2    
27.5    
27.8    
28.1    
28.4    
28.7    
28.9    
29.2    
29.5    
29.8    
30.1    
30.3    
30.6    
30.9    
31.2    
31.5    
31.7    
32.0    
32.3    
32.6    
32.9    
33.1    
33.4    
33.7    
34.0    
34.3    
34.6    
34.8    
35.1    
35.4    
35.7    
36.0    
36.2    
36.5    
36.8    
37.1    
37.4    
37.6    
37.9    
38.2    
38.5    
38.8    
39.0    
39.3    
39.6    
39.9    
40.2    
40.4    
40.7    
41.0    
41.3    
41.6    
41.9    
42.1    
42.4    
42.7    
43.0    
43.3    
43.5    
43.8    
44.1    
44.4    
44.7    
44.9    
45.2    
45.5    
45.8    
46.1    
46.3    
46.6    
46.9    
47.2    
47.5    
47.8    
48.0    
48.3    
48.6    
48.9    
49.2    
49.4    
49.7    
50.0    
50.3    
50.6    
50.8    
51.1    
51.4    
51.7    
52.0    
52.2    
52.5    
52.8    
53.1    
53.4    
53.7    
53.9    
54.2    
54.5    
54.8    
55.1    
55.3    
55.6    
55.9    
56.2    
56.5    
56.7    
57.0    
57.3    
57.6    
57.9    
58.1    
58.4    
58.7    
59.0    
59.3    
59.6    
59.8    
60.1    
60.4    
60.7    
61.0    
61.2    
61.5    
61.8    
62.1    
62.4    
62.6    
62.9    
63.2    
63.5    
63.8    
64.0    
64.3    
64.6    
64.9    
65.2    
65.4    
65.7    
66.0    
66.3    
66.6    
66.9    
67.1    
67.4    
67.7    
68.0    
68.3    
68.5    
68.8    
69.1    
69.4    
69.7    
69.9    
70.2    
70.5    
70.8    
71.1    
71.3    
71.6    
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72.2    
72.5    
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73.0    
73.3    
73.6    
73.9    
74.2    
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74.7    
75.0    
75.3    
75.6    
75.8    
76.1    
76.4    
76.7    
77.0    
77.2    
77.5    
77.8    
78.1    
78.4    
78.7    
78.9    
79.2    
79.5    
79.8    
80.1    
80.3    
80.6    
80.9    
81.2    
81.5    
81.7    
82.0    
82.3    
82.6    
82.9    
83.1    
83.4    
83.7    
84.0    
84.3    
84.6    
84.8    
85.1    
85.4    
85.7    
86.0    
86.2    
86.5    
86.8    
87.1    
87.4    
87.6    
87.9    
88.2    
88.5    
88.8    
89.0    
89.3    
89.6    
89.9    
90.2    
90.4    
90.7    
91.0    
91.3    
91.6    
91.9    
92.1    
92.4    
92.7    
93.0    
93.3    
93.5    
93.8    
94.1    
94.4    
94.7    
94.9    
95.2    
95.5    
95.8    
96.1    
96.3    
96.6    
96.9    
97.2    
97.5    
97.8    
98.0    
98.3    
98.6    
98.9    
99.2    
99.4    
99.7    
-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 14070, rend_intergenic: 9034  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24826, rend_intergenic: 15875  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38667, rend_intergenic: 28590  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42589, rend_intergenic: 38928  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54143, rend_intergenic: 46585  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55213, rend_intergenic: 54362  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70438, rend_intergenic: 69621  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88687, rend_intergenic: 70974  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98159, rend_intergenic: 91823  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109459, rend_intergenic: 106527  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114774, rend_intergenic: 111128  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119225, rend_intergenic: 115833  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131556, rend_intergenic: 120990  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134404, rend_intergenic: 134153  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161753, rend_intergenic: 134534  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165865, rend_intergenic: 163854  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175841, rend_intergenic: 169275  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support