-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_11/scaffold_11_10932173-11316979

-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_11-snap.2427-T1
Valid prediction for snap_scaffold_11-snap.2420-T1
Valid prediction for Augustus_model.g18462.t1
Valid prediction for pasa_asmbl_5963.p1
Valid prediction for snap_scaffold_11-snap.2422-T1
Valid prediction for GlimmerHMM_glimmerT_27879-T1
Valid prediction for GlimmerHMM_glimmerT_27865-T1
Valid prediction for snap_scaffold_11-snap.2432-T1
Valid prediction for Augustus_model.g18468.t1
Couldn't classify 154854, 154935
Couldn't classify 158336, 158389
Sorry, prediction pasa_asmbl_5959.p1 fails validation.
(ATC)	 AG	154854-154935	GT	AGG
(AAC)	 AG	155116-155636	GT	AGG
(AAA)	 AG	158336-158389	GT	GGG
-recovered pasa_asmbl_5959.p1, internal, 154854, 154935
-recovered pasa_asmbl_5959.p1, internal, 155116, 155636
-recovered pasa_asmbl_5959.p1, internal, 158336, 158389
Valid prediction for HiQ_model.g18466.t1
Valid prediction for snap_scaffold_11-snap.2428-T1
Valid prediction for GlimmerHMM_glimmerT_27882-T1
Valid prediction for snap_scaffold_11-snap.2423-T1
Valid prediction for CodingQuarry_transcript_8244-T1
Valid prediction for snap_scaffold_11-snap.2417-T1
Valid prediction for GlimmerHMM_glimmerT_27873-T1
Valid prediction for snap_scaffold_11-snap.2435-T1
Valid prediction for snap_scaffold_11-snap.2421-T1
Valid prediction for GlimmerHMM_glimmerT_27881-T1
Valid prediction for snap_scaffold_11-snap.2425-T1
Valid prediction for GlimmerHMM_glimmerT_27891-T1
Valid prediction for Augustus_model.g18469.t1
Valid prediction for GlimmerHMM_glimmerT_27885-T1
Valid prediction for snap_scaffold_11-snap.2439-T1
Valid prediction for snap_scaffold_11-snap.2440-T1
Valid prediction for GlimmerHMM_glimmerT_27868-T1
Valid prediction for GlimmerHMM_glimmerT_27884-T1
Valid prediction for Augustus_model.g18464.t1
Valid prediction for snap_scaffold_11-snap.2441-T1
Couldn't classify 120448, 120582
Couldn't classify 123089, 123252
Sorry, prediction pasa_asmbl_6362.p2 fails validation.
(AGC)	 TC	120448-120582	GT	AGG
(GTG)	 AG	121721-121784	GT	AGG
(AGT)	 AG	122017-122079	GT	AGG
(GTC)	 AG	123089-123252	GG	ACG
-recovered pasa_asmbl_6362.p2, internal, 121721, 121784
-recovered pasa_asmbl_6362.p2, internal, 122017, 122079
Valid prediction for GlimmerHMM_glimmerT_27887-T1
Valid prediction for GlimmerHMM_glimmerT_27878-T1
Valid prediction for snap_scaffold_11-snap.2414-T1
Valid prediction for snap_scaffold_11-snap.2429-T1
Valid prediction for Augustus_model.g18454.t1
Valid prediction for GlimmerHMM_glimmerT_27890-T1
Valid prediction for Augustus_model.g18456.t1
Valid prediction for snap_scaffold_11-snap.2433-T1
Valid prediction for Augustus_model.g18463.t1
Valid prediction for snap_scaffold_11-snap.2438-T1
Valid prediction for snap_scaffold_11-snap.2411-T1
Valid prediction for snap_scaffold_11-snap.2436-T1
Valid prediction for GlimmerHMM_glimmerT_27874-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_11-snap.2426-T1
Valid prediction for snap_scaffold_11-snap.2415-T1
Valid prediction for Augustus_model.g18470.t1
Valid prediction for snap_scaffold_11-snap.2442-T1
Valid prediction for GlimmerHMM_glimmerT_27866-T1
Valid prediction for GlimmerHMM_glimmerT_27893-T1
Valid prediction for Augustus_model.g18453.t1
Valid prediction for snap_scaffold_11-snap.2434-T1
Valid prediction for snap_scaffold_11-snap.2410-T1
Valid prediction for HiQ_model.g18461.t1
Valid prediction for snap_scaffold_11-snap.2430-T1
Valid prediction for HiQ_model.g18465.t1
Valid prediction for GlimmerHMM_glimmerT_27877-T1
Valid prediction for GlimmerHMM_glimmerT_27892-T1
Valid prediction for GlimmerHMM_glimmerT_27876-T1
Valid prediction for Augustus_model.g18455.t1
Valid prediction for GlimmerHMM_glimmerT_27883-T1
Valid prediction for snap_scaffold_11-snap.2409-T1
Valid prediction for snap_scaffold_11-snap.2437-T1
Couldn't classify 338254, 338583
Sorry, prediction pasa_asmbl_7005.p1 fails validation.
(ATA)	 AT	338254-338583	GT	AGG
(TTA)	 AG	338893-339000	GT	GGG
(GAG)	 AG	340617-341225	GC	GAG
-recovered pasa_asmbl_7005.p1, terminal, 340617, 341225
-recovered pasa_asmbl_7005.p1, internal, 338893, 339000
-recovered pasa_asmbl_7005.p1, internal, 340617, 341225
Valid prediction for GlimmerHMM_glimmerT_27875-T1
Couldn't classify 317798, 317896
Sorry, prediction pasa_asmbl_7350.p1 fails validation.
(GCC)	 GT	317798-317896	GT	AGG
(GTG)	 AG	320185-320255	GT	ATG
(GGG)	 AG	320566-320648	GT	CGG
(TGG)	 AG	320778-320931	GT	AAG
(AGC)	 AG	321952-322015	GA	AGG
add_exon() Sorry, pasa_asmbl_7350.p1 320778-320931-terminal-3 is invalid.
-recovered pasa_asmbl_7350.p1, terminal, 320778, 320931
-recovered pasa_asmbl_7350.p1, terminal, 321952, 322015
-recovered pasa_asmbl_7350.p1, internal, 320185, 320255
-recovered pasa_asmbl_7350.p1, internal, 320566, 320648
-recovered pasa_asmbl_7350.p1, internal, 320778, 320931
Valid prediction for GlimmerHMM_glimmerT_27867-T1
Valid prediction for GlimmerHMM_glimmerT_27889-T1
Valid prediction for Augustus_model.g18457.t1
Valid prediction for snap_scaffold_11-snap.2424-T1
Valid prediction for GlimmerHMM_glimmerT_27880-T1
Valid prediction for Augustus_model.g18459.t1
Valid prediction for GlimmerHMM_glimmerT_27872-T1
Valid prediction for Augustus_model.g18467.t1
Valid prediction for GlimmerHMM_glimmerT_27870-T1
Valid prediction for snap_scaffold_11-snap.2443-T1
Valid prediction for GlimmerHMM_glimmerT_27886-T1
Valid prediction for snap_scaffold_11-snap.2412-T1
Couldn't classify 212962, 213102
Sorry, prediction pasa_asmbl_7018.p1 fails validation.
(AGG)	 AG	212962-213102	GT	AGG
(GGT)	 AG	213236-213446	GT	GGG
(CTG)	 AG	213586-213714	GT	AGG
(GAG)	 AG	213876-213936	GT	AGG
(ACT)	 AG	214079-214218	GT	AGG
(TTT)	 AG	214422-214582	GT	TGG
(GTG)	 AG	214834-214903	GT	AGG
(ACT)	 AG	214998-215187	GT	AGG
(TTT)	 AG	215466-215571	GT	GGG
(AAG)	 AG	215867-216113	GT	AGG
(GGA)	 AG	216487-216582	GT	AGG
(AGG)	 AG	216715-216791	GT	GAG
(CCT)	 AG	217029-217098	GT	AGG
(GTC)	 AG	218553-218602	AA	AGA
-recovered pasa_asmbl_7018.p1, terminal, 218553, 218602
-recovered pasa_asmbl_7018.p1, internal, 212962, 213102
-recovered pasa_asmbl_7018.p1, internal, 213236, 213446
-recovered pasa_asmbl_7018.p1, internal, 213586, 213714
-recovered pasa_asmbl_7018.p1, internal, 213876, 213936
-recovered pasa_asmbl_7018.p1, internal, 214079, 214218
-recovered pasa_asmbl_7018.p1, internal, 214422, 214582
-recovered pasa_asmbl_7018.p1, internal, 214834, 214903
-recovered pasa_asmbl_7018.p1, internal, 214998, 215187
-recovered pasa_asmbl_7018.p1, internal, 215466, 215571
-recovered pasa_asmbl_7018.p1, internal, 215867, 216113
-recovered pasa_asmbl_7018.p1, internal, 216487, 216582
-recovered pasa_asmbl_7018.p1, internal, 216715, 216791
-recovered pasa_asmbl_7018.p1, internal, 217029, 217098
Valid prediction for Augustus_model.g18460.t1
Valid prediction for snap_scaffold_11-snap.2418-T1
Valid prediction for snap_scaffold_11-snap.2408-T1
Couldn't classify 320254, 320255
Sorry, prediction CodingQuarry_transcript_8243-T1 fails validation.
(ATG)	 GA	320254-320255	GT	ATG
(GGG)	 AG	320566-320648	GT	CGG
(TGG)	 AG	320778-320931	GT	AAG
(AGC)	 AG	321952-322015	GA	AGG
add_exon() Sorry, CodingQuarry_transcript_8243-T1 320778-320931-terminal-3 is invalid.
-recovered CodingQuarry_transcript_8243-T1, terminal, 320778, 320931
-recovered CodingQuarry_transcript_8243-T1, terminal, 321952, 322015
-recovered CodingQuarry_transcript_8243-T1, internal, 320566, 320648
-recovered CodingQuarry_transcript_8243-T1, internal, 320778, 320931
Couldn't classify 212287, 212751
Sorry, prediction pasa_asmbl_7019.p1 fails validation.
(ATG)	 GT	212287-212751	GG	GGG
Valid prediction for GlimmerHMM_glimmerT_27888-T1
Valid prediction for GlimmerHMM_glimmerT_27869-T1
Valid prediction for snap_scaffold_11-snap.2431-T1
Valid prediction for snap_scaffold_11-snap.2419-T1
Valid prediction for GlimmerHMM_glimmerT_27871-T1
Valid prediction for Augustus_model.g18458.t1
Valid prediction for snap_scaffold_11-snap.2416-T1
Valid prediction for snap_scaffold_11-snap.2413-T1
Valid prediction for Augustus_model.g18471.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 32046, rend_intergenic: 31035  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34463, rend_intergenic: 32613  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68252, rend_intergenic: 63873  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162685, rend_intergenic: 154699  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 384807
-exon list size: 277


building trellis

0.4    
0.7    
1.1    
1.4    
1.8    
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2.9    
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3.9    
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5.7    
6.1    
6.5    
6.8    
7.2    
7.5    
7.9    
8.2    
8.6    
9.0    
9.3    
9.7    
10.0    
10.4    
10.8    
11.1    
11.5    
11.8    
12.2    
12.5    
12.9    
13.3    
13.6    
14.0    
14.3    
14.7    
15.1    
15.4    
15.8    
16.1    
16.5    
16.8    
17.2    
17.6    
17.9    
18.3    
18.6    
19.0    
19.4    
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20.1    
20.4    
20.8    
21.1    
21.5    
21.9    
22.2    
22.6    
22.9    
23.3    
23.7    
24.0    
24.4    
24.7    
25.1    
25.4    
25.8    
26.2    
26.5    
26.9    
27.2    
27.6    
28.0    
28.3    
28.7    
29.0    
29.4    
29.7    
30.1    
30.5    
30.8    
31.2    
31.5    
31.9    
32.3    
32.6    
33.0    
33.3    
33.7    
34.1    
34.4    
34.8    
35.1    
35.5    
35.8    
36.2    
36.6    
36.9    
37.3    
37.6    
38.0    
38.4    
38.7    
39.1    
39.4    
39.8    
40.1    
40.5    
40.9    
41.2    
41.6    
41.9    
42.3    
42.7    
43.0    
43.4    
43.7    
44.1    
44.4    
44.8    
45.2    
45.5    
45.9    
46.2    
46.6    
47.0    
47.3    
47.7    
48.0    
48.4    
48.7    
49.1    
49.5    
49.8    
50.2    
50.5    
50.9    
51.3    
51.6    
52.0    
52.3    
52.7    
53.0    
53.4    
53.8    
54.1    
54.5    
54.8    
55.2    
55.6    
55.9    
56.3    
56.6    
57.0    
57.3    
57.7    
58.1    
58.4    
58.8    
59.1    
59.5    
59.9    
60.2    
60.6    
60.9    
61.3    
61.6    
62.0    
62.4    
62.7    
63.1    
63.4    
63.8    
64.2    
64.5    
64.9    
65.2    
65.6    
65.9    
66.3    
66.7    
67.0    
67.4    
67.7    
68.1    
68.5    
68.8    
69.2    
69.5    
69.9    
70.3    
70.6    
71.0    
71.3    
71.7    
72.0    
72.4    
72.8    
73.1    
73.5    
73.8    
74.2    
74.6    
74.9    
75.3    
75.6    
76.0    
76.3    
76.7    
77.1    
77.4    
77.8    
78.1    
78.5    
78.9    
79.2    
79.6    
79.9    
80.3    
80.6    
81.0    
81.4    
81.7    
82.1    
82.4    
82.8    
83.2    
83.5    
83.9    
84.2    
84.6    
84.9    
85.3    
85.7    
86.0    
86.4    
86.7    
87.1    
87.5    
87.8    
88.2    
88.5    
88.9    
89.2    
89.6    
90.0    
90.3    
90.7    
91.0    
91.4    
91.8    
92.1    
92.5    
92.8    
93.2    
93.5    
93.9    
94.3    
94.6    
95.0    
95.3    
95.7    
96.1    
96.4    
96.8    
97.1    
97.5    
97.8    
98.2    
98.6    
98.9    
99.3    
99.6    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 32046, rend_intergenic: 31035  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34463, rend_intergenic: 32613  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68252, rend_intergenic: 63873  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162685, rend_intergenic: 154699  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

-building DP trellis

-building trellis in range 1 - 21256
-exon list size: 9


building trellis

9.1    
18.2    
27.3    
36.4    
45.5    
54.5    
63.6    
72.7    
81.8    
90.9    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 20673
-exon list size: 8


building trellis

10.0    
20.0    
30.0    
40.0    
50.0    
60.0    
70.0    
80.0    
90.0    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 20010
-exon list size: 7


building trellis

11.1    
22.2    
33.3    
44.4    
55.6    
66.7    
77.8    
88.9    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 9460 - 20010
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support