-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_4/scaffold_4_4089035-4239951

-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 snap_scaffold_4-snap.963-T1
Valid prediction for GlimmerHMM_glimmerT_9190-T1
Valid prediction for pasa_asmbl_41219.p1
Couldn't classify 43834, 43987
Couldn't classify 44143, 44300
Sorry, prediction pasa_asmbl_42269.p1 fails validation.
(CAG)	 GC	43834-43987	GT	AGG
(ACT)	 AG	44143-44300	TC	CCT
Valid prediction for CodingQuarry_transcript_48932-T1
Valid prediction for snap_scaffold_4-snap.956-T1
Valid prediction for Augustus_model.g5920.t1
Valid prediction for GlimmerHMM_glimmerT_9202-T1
Valid prediction for GlimmerHMM_glimmerT_9198-T1
Valid prediction for Augustus_model.g5910.t1
Valid prediction for snap_scaffold_4-snap.961-T1
Valid prediction for snap_scaffold_4-snap.957-T1
Valid prediction for CodingQuarry_transcript_48934-T1
Valid prediction for GlimmerHMM_glimmerT_9197-T1
Couldn't classify 26738, 26766
Couldn't classify 28788, 28798
Sorry, prediction pasa_asmbl_41233.p1 fails validation.
(GGA)	 GA	26738-26766	GT	AAG
(GTA)	 AG	26850-27001	GT	AAG
(AGT)	 AG	27095-27210	GT	TGG
(GGC)	 AG	28017-28102	GT	AGG
(CGA)	 AG	28490-28623	GT	TGG
(CAA)	 AG	28788-28798	AC	GGA
-recovered pasa_asmbl_41233.p1, internal, 26850, 27001
-recovered pasa_asmbl_41233.p1, internal, 27095, 27210
-recovered pasa_asmbl_41233.p1, internal, 28017, 28102
-recovered pasa_asmbl_41233.p1, internal, 28490, 28623
Valid prediction for snap_scaffold_4-snap.958-T1
Valid prediction for GlimmerHMM_glimmerT_9211-T1
Valid prediction for Augustus_model.g5913.t1
Valid prediction for GlimmerHMM_glimmerT_9200-T1
Valid prediction for snap_scaffold_4-snap.965-T1
Valid prediction for CodingQuarry_transcript_48930-T1
Valid prediction for snap_scaffold_4-snap.946-T1
Valid prediction for GlimmerHMM_glimmerT_9208-T1
Valid prediction for Augustus_model.g5911.t1
Valid prediction for snap_scaffold_4-snap.948-T1
Valid prediction for GlimmerHMM_glimmerT_9210-T1
Valid prediction for Augustus_model.g5923.t1
Valid prediction for CodingQuarry_transcript_48931-T1
Valid prediction for snap_scaffold_4-snap.939-T1
Valid prediction for HiQ_model.g5908.t1
Valid prediction for snap_scaffold_4-snap.943-T1
Couldn't classify 66396, 66600
Sorry, prediction pasa_asmbl_42202.p1 fails validation.
(GTG)	 CG	66396-66600	GT	AGG
(GAA)	 AG	66890-67293	CA	AAC
-recovered pasa_asmbl_42202.p1, terminal, 66890, 67293
Couldn't classify 38191, 38269
Couldn't classify 38504, 38802
Sorry, prediction pasa_asmbl_42219.p1 fails validation.
(GGG)	 AG	38191-38269	GT	AGG
(GTG)	 AG	38504-38802	GC	GGG
-recovered pasa_asmbl_42219.p1, internal, 38191, 38269
-recovered pasa_asmbl_42219.p1, internal, 38504, 38802
Valid prediction for GlimmerHMM_glimmerT_9193-T1
Valid prediction for snap_scaffold_4-snap.953-T1
Valid prediction for snap_scaffold_4-snap.967-T1
Valid prediction for GlimmerHMM_glimmerT_9204-T1
Valid prediction for GlimmerHMM_glimmerT_9209-T1
Valid prediction for snap_scaffold_4-snap.950-T1
Valid prediction for snap_scaffold_4-snap.962-T1
Valid prediction for snap_scaffold_4-snap.940-T1
Valid prediction for GlimmerHMM_glimmerT_9206-T1
Valid prediction for CodingQuarry_transcript_48941-T1
Valid prediction for GlimmerHMM_glimmerT_9192-T1
Valid prediction for GlimmerHMM_glimmerT_9191-T1
Couldn't classify 41905, 42082
Couldn't classify 42178, 42335
Sorry, prediction pasa_asmbl_42258.p1 fails validation.
(CTC)	 GT	41905-42082	GT	AGG
(AAG)	 AG	42178-42335	GA	TCG
Valid prediction for Augustus_model.g5909.t1
Valid prediction for Augustus_model.g5916.t1
Valid prediction for pasa_asmbl_41232.p1
Valid prediction for GlimmerHMM_glimmerT_9194-T1
Valid prediction for snap_scaffold_4-snap.960-T1
Valid prediction for snap_scaffold_4-snap.941-T1
Valid prediction for Augustus_model.g5922.t1
Valid prediction for CodingQuarry_transcript_48938-T1
Valid prediction for snap_scaffold_4-snap.938-T1
Couldn't classify 52834, 54965
Sorry, prediction pasa_asmbl_41238.p1 fails validation.
(TTG)	 AC	52834-54965	GT	AGG
(GCC)	 AG	55303-55409	GT	AGG
(GTG)	 AG	55552-55692	GT	GGG
(TGG)	 AG	55947-56199	GT	AGG
(AAA)	 AG	56387-56494	GT	AGG
(ACG)	 AG	56666-56749	GT	AGG
(GTC)	 AG	56982-57111	GT	AGG
(GGC)	 AG	57276-57551	GG	AGG
add_exon() Sorry, pasa_asmbl_41238.p1 56666-56749-terminal-1 is invalid.
-recovered pasa_asmbl_41238.p1, terminal, 56666, 56749
-recovered pasa_asmbl_41238.p1, terminal, 57276, 57551
-recovered pasa_asmbl_41238.p1, internal, 55303, 55409
-recovered pasa_asmbl_41238.p1, internal, 55552, 55692
-recovered pasa_asmbl_41238.p1, internal, 55947, 56199
-recovered pasa_asmbl_41238.p1, internal, 56387, 56494
-recovered pasa_asmbl_41238.p1, internal, 56666, 56749
-recovered pasa_asmbl_41238.p1, internal, 56982, 57111
Valid prediction for snap_scaffold_4-snap.947-T1
Valid prediction for pasa_asmbl_41235.p1
Valid prediction for Augustus_model.g5918.t1
Valid prediction for CodingQuarry_transcript_48933-T1
Couldn't classify 52042, 52647
Sorry, prediction pasa_asmbl_41237.p1 fails validation.
(TCA)	 CC	52042-52647	AC	GCA

-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 61635, 61833
Couldn't classify 63332, 63361
Sorry, prediction pasa_asmbl_42506.p1 fails validation.
(GTG)	 AG	61635-61833	GT	CTG
(TGC)	 AG	62537-62664	GT	GGG
(ATC)	 AG	63063-63137	GT	AGG
(CAC)	 AG	63332-63361	GA	AGG
-recovered pasa_asmbl_42506.p1, internal, 61635, 61833
-recovered pasa_asmbl_42506.p1, internal, 62537, 62664
-recovered pasa_asmbl_42506.p1, internal, 63063, 63137
Valid prediction for snap_scaffold_4-snap.964-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_4-snap.949-T1
Valid prediction for snap_scaffold_4-snap.945-T1
Valid prediction for pasa_asmbl_43588.p1
Valid prediction for snap_scaffold_4-snap.959-T1
Valid prediction for Augustus_model.g5924.t1
Valid prediction for GlimmerHMM_glimmerT_9195-T1
Valid prediction for GlimmerHMM_glimmerT_9201-T1
Valid prediction for GlimmerHMM_glimmerT_9199-T1
Valid prediction for GlimmerHMM_glimmerT_9196-T1
Valid prediction for pasa_asmbl_42480.p1
Valid prediction for snap_scaffold_4-snap.954-T1
Valid prediction for HiQ_model.g5914.t1
Valid prediction for GlimmerHMM_glimmerT_9205-T1
Valid prediction for HiQ_model.g5917.t1
Valid prediction for Augustus_model.g5921.t1
Valid prediction for snap_scaffold_4-snap.942-T1
Valid prediction for HiQ_model.g5912.t1
Valid prediction for snap_scaffold_4-snap.966-T1
Valid prediction for CodingQuarry_transcript_48939-T1
Valid prediction for Augustus_model.g5919.t1
Valid prediction for CodingQuarry_transcript_48940-T1
Couldn't classify 63446, 63490
Sorry, prediction pasa_asmbl_42505.p1 fails validation.
(GCC)	 TG	63446-63490	GT	AGG
(CCT)	 AG	63987-64115	GT	AGG
(GTG)	 AG	64697-64796	GT	CCG
(AGG)	 AG	65133-65300	GT	CGG
(ATC)	 AG	65529-65552	GT	AGG
(CAT)	 AG	65671-65738	GT	AGG
(ATA)	 AG	65952-66017	GT	TGG
(CAA)	 AG	66220-66363	GT	AGG
(CAG)	 AG	66518-66619	GG	GAG
-recovered pasa_asmbl_42505.p1, terminal, 66518, 66619
-recovered pasa_asmbl_42505.p1, internal, 63987, 64115
-recovered pasa_asmbl_42505.p1, internal, 64697, 64796
-recovered pasa_asmbl_42505.p1, internal, 65133, 65300
-recovered pasa_asmbl_42505.p1, internal, 65529, 65552
-recovered pasa_asmbl_42505.p1, internal, 65671, 65738
-recovered pasa_asmbl_42505.p1, internal, 65952, 66017
-recovered pasa_asmbl_42505.p1, internal, 66220, 66363
Valid prediction for snap_scaffold_4-snap.951-T1
Valid prediction for GlimmerHMM_glimmerT_9207-T1
Valid prediction for HiQ_model.g5915.t1
Valid prediction for GlimmerHMM_glimmerT_9212-T1
Valid prediction for CodingQuarry_transcript_48942-T1
Valid prediction for snap_scaffold_4-snap.952-T1
Valid prediction for snap_scaffold_4-snap.955-T1
Valid prediction for pasa_asmbl_42496.p1
Valid prediction for GlimmerHMM_glimmerT_9203-T1
Valid prediction for snap_scaffold_4-snap.944-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 108512, rend_intergenic: 106728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126066, rend_intergenic: 125811  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128905, rend_intergenic: 126350  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146092, rend_intergenic: 143068  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 150917
-exon list size: 356


building trellis

0.3    
0.6    
0.8    
1.1    
1.4    
1.7    
2.0    
2.2    
2.5    
2.8    
3.1    
3.4    
3.6    
3.9    
4.2    
4.5    
4.7    
5.0    
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5.6    
5.9    
6.1    
6.4    
6.7    
7.0    
7.3    
7.5    
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8.1    
8.4    
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10.1    
10.3    
10.6    
10.9    
11.2    
11.5    
11.7    
12.0    
12.3    
12.6    
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13.1    
13.4    
13.7    
14.0    
14.2    
14.5    
14.8    
15.1    
15.4    
15.6    
15.9    
16.2    
16.5    
16.8    
17.0    
17.3    
17.6    
17.9    
18.2    
18.4    
18.7    
19.0    
19.3    
19.6    
19.8    
20.1    
20.4    
20.7    
20.9    
21.2    
21.5    
21.8    
22.1    
22.3    
22.6    
22.9    
23.2    
23.5    
23.7    
24.0    
24.3    
24.6    
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25.1    
25.4    
25.7    
26.0    
26.3    
26.5    
26.8    
27.1    
27.4    
27.7    
27.9    
28.2    
28.5    
28.8    
29.1    
29.3    
29.6    
29.9    
30.2    
30.4    
30.7    
31.0    
31.3    
31.6    
31.8    
32.1    
32.4    
32.7    
33.0    
33.2    
33.5    
33.8    
34.1    
34.4    
34.6    
34.9    
35.2    
35.5    
35.8    
36.0    
36.3    
36.6    
36.9    
37.2    
37.4    
37.7    
38.0    
38.3    
38.5    
38.8    
39.1    
39.4    
39.7    
39.9    
40.2    
40.5    
40.8    
41.1    
41.3    
41.6    
41.9    
42.2    
42.5    
42.7    
43.0    
43.3    
43.6    
43.9    
44.1    
44.4    
44.7    
45.0    
45.3    
45.5    
45.8    
46.1    
46.4    
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    
53.6    
53.9    
54.2    
54.5    
54.7    
55.0    
55.3    
55.6    
55.9    
56.1    
56.4    
56.7    
57.0    
57.3    
57.5    
57.8    
58.1    
58.4    
58.7    
58.9    
59.2    
59.5    
59.8    
60.1    
60.3    
60.6    
60.9    
61.2    
61.5    
61.7    
62.0    
62.3    
62.6    
62.8    
63.1    
63.4    
63.7    
64.0    
64.2    
64.5    
64.8    
65.1    
65.4    
65.6    
65.9    
66.2    
66.5    
66.8    
67.0    
67.3    
67.6    
67.9    
68.2    
68.4    
68.7    
69.0    
69.3    
69.6    
69.8    
70.1    
70.4    
70.7    
70.9    
71.2    
71.5    
71.8    
72.1    
72.3    
72.6    
72.9    
73.2    
73.5    
73.7    
74.0    
74.3    
74.6    
74.9    
75.1    
75.4    
75.7    
76.0    
76.3    
76.5    
76.8    
77.1    
77.4    
77.7    
77.9    
78.2    
78.5    
78.8    
79.1    
79.3    
79.6    
79.9    
80.2    
80.4    
80.7    
81.0    
81.3    
81.6    
81.8    
82.1    
82.4    
82.7    
83.0    
83.2    
83.5    
83.8    
84.1    
84.4    
84.6    
84.9    
85.2    
85.5    
85.8    
86.0    
86.3    
86.6    
86.9    
87.2    
87.4    
87.7    
88.0    
88.3    
88.5    
88.8    
89.1    
89.4    
89.7    
89.9    
90.2    
90.5    
90.8    
91.1    
91.3    
91.6    
91.9    
92.2    
92.5    
92.7    
93.0    
93.3    
93.6    
93.9    
94.1    
94.4    
94.7    
95.0    
95.3    
95.5    
95.8    
96.1    
96.4    
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 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 108512, rend_intergenic: 106728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126066, rend_intergenic: 125811  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128905, rend_intergenic: 126350  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146092, rend_intergenic: 143068  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