-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_347231-564374

-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: +)Couldn't classify 53269, 53367
Sorry, prediction pasa_asmbl_46659.p1 fails validation.
(ATG)	 CT	49976-50068	GT	AGG
(GTG)	 AG	50739-50884	GT	AGG
(GTA)	 AG	51743-51858	GT	AGG
(GTT)	 AG	52893-53053	GT	AGG
(GTG)	 AG	53269-53367	AT	ACA
-recovered pasa_asmbl_46659.p1, initial, 49976, 50068
-recovered pasa_asmbl_46659.p1, internal, 50739, 50884
-recovered pasa_asmbl_46659.p1, internal, 51743, 51858
-recovered pasa_asmbl_46659.p1, internal, 52893, 53053
Valid prediction for snap_scaffold_6-snap.79-T1
Valid prediction for snap_scaffold_6-snap.116-T1
Couldn't classify 98006, 98085
Sorry, prediction pasa_asmbl_46662.p1 fails validation.
(TCC)	 TC	98006-98085	GT	CGG
(GTT)	 AG	98321-98404	GT	AGG
(GCT)	 AG	99430-99601	GT	AGG
(GTC)	 AG	100388-100492	GT	TGG
(TTG)	 AG	101043-101234	GT	AGG
(ATC)	 AG	101791-101886	GT	AAG
(GTT)	 AG	102310-102399	GT	AGG
(GCT)	 AG	102849-102988	GT	CGG
(GTA)	 AG	103464-103707	GT	AGG
(GTG)	 AG	104136-104290	GT	AGG
(GAC)	 AG	104378-104438	GT	AGG
(GTT)	 AG	104582-104710	GT	AGG
(GTG)	 AG	105086-105192	GT	AGG
(GTG)	 AG	105550-105655	GT	AGG
(GTT)	 AG	105801-105866	GT	AGG
(GTG)	 AG	106201-106335	AC	AGA
-recovered pasa_asmbl_46662.p1, terminal, 106201, 106335
-recovered pasa_asmbl_46662.p1, internal, 98321, 98404
-recovered pasa_asmbl_46662.p1, internal, 99430, 99601
-recovered pasa_asmbl_46662.p1, internal, 100388, 100492
-recovered pasa_asmbl_46662.p1, internal, 101043, 101234
-recovered pasa_asmbl_46662.p1, internal, 101791, 101886
-recovered pasa_asmbl_46662.p1, internal, 102310, 102399
-recovered pasa_asmbl_46662.p1, internal, 102849, 102988
-recovered pasa_asmbl_46662.p1, internal, 103464, 103707
-recovered pasa_asmbl_46662.p1, internal, 104136, 104290
-recovered pasa_asmbl_46662.p1, internal, 104378, 104438
-recovered pasa_asmbl_46662.p1, internal, 104582, 104710
-recovered pasa_asmbl_46662.p1, internal, 105086, 105192
-recovered pasa_asmbl_46662.p1, internal, 105550, 105655
-recovered pasa_asmbl_46662.p1, internal, 105801, 105866
Valid prediction for HiQ_model.g9250.t1
Valid prediction for snap_scaffold_6-snap.87-T1
Valid prediction for Augustus_model.g9257.t1
Valid prediction for snap_scaffold_6-snap.90-T1
Valid prediction for snap_scaffold_6-snap.119-T1
Sorry, intron length (3) is less than minimum required (10)
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_6-snap.81-T1
Valid prediction for snap_scaffold_6-snap.96-T1
Couldn't classify 60330, 60453
Sorry, prediction pasa_asmbl_46660.p1 fails validation.
(GGG)	 CA	60330-60453	GT	CGG
(GAG)	 AG	60675-60791	GT	AGG
(GTG)	 AG	61056-61166	GT	AGG
(GCA)	 AG	61296-61468	AG	AGA
-recovered pasa_asmbl_46660.p1, terminal, 61296, 61468
-recovered pasa_asmbl_46660.p1, internal, 60675, 60791
-recovered pasa_asmbl_46660.p1, internal, 61056, 61166
Valid prediction for HiQ_model.g9247.t1
Valid prediction for GlimmerHMM_glimmerT_13920-T1
Valid prediction for snap_scaffold_6-snap.114-T1
Valid prediction for snap_scaffold_6-snap.105-T1
Valid prediction for snap_scaffold_6-snap.121-T1
Valid prediction for snap_scaffold_6-snap.109-T1
Valid prediction for Augustus_model.g9245.t1
Valid prediction for snap_scaffold_6-snap.122-T1
Valid prediction for snap_scaffold_6-snap.115-T1
Valid prediction for snap_scaffold_6-snap.86-T1
Valid prediction for Augustus_model.g9253.t1
Valid prediction for CodingQuarry_transcript_54899-T1
Valid prediction for GlimmerHMM_glimmerT_13914-T1
Valid prediction for CodingQuarry_transcript_54895-T1
Valid prediction for snap_scaffold_6-snap.93-T1
Valid prediction for GlimmerHMM_glimmerT_13913-T1
Valid prediction for Augustus_model.g9251.t1
Valid prediction for snap_scaffold_6-snap.111-T1
Valid prediction for snap_scaffold_6-snap.104-T1
Valid prediction for snap_scaffold_6-snap.83-T1
Valid prediction for GlimmerHMM_glimmerT_13916-T1
Valid prediction for GlimmerHMM_glimmerT_13917-T1
Couldn't classify 84230, 84449
Sorry, prediction pasa_asmbl_46661.p1 fails validation.
(CCC)	 CC	84230-84449	GT	AGG
(GGT)	 AG	84696-84850	GC	GAG
-recovered pasa_asmbl_46661.p1, terminal, 84696, 84850
-recovered pasa_asmbl_46661.p1, internal, 84696, 84850
Valid prediction for GlimmerHMM_glimmerT_13907-T1
Valid prediction for CodingQuarry_transcript_54901-T1
Valid prediction for CodingQuarry_transcript_54898-T1
Valid prediction for Augustus_model.g9254.t1
Valid prediction for snap_scaffold_6-snap.100-T1
Valid prediction for snap_scaffold_6-snap.108-T1
Valid prediction for snap_scaffold_6-snap.84-T1
Valid prediction for GlimmerHMM_glimmerT_13921-T1
Valid prediction for GlimmerHMM_glimmerT_13910-T1
Valid prediction for pasa_asmbl_46657.p1
Valid prediction for CodingQuarry_transcript_54900-T1
Valid prediction for snap_scaffold_6-snap.110-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 GlimmerHMM_glimmerT_13923-T1
Valid prediction for snap_scaffold_6-snap.97-T1
Valid prediction for Augustus_model.g9260.t1
Couldn't classify 150818, 151303
Sorry, prediction pasa_asmbl_48037.p1 fails validation.
(AAC)	 CC	150818-151303	GG	GGG
Valid prediction for snap_scaffold_6-snap.94-T1
Valid prediction for snap_scaffold_6-snap.89-T1
Valid prediction for snap_scaffold_6-snap.120-T1
Valid prediction for CodingQuarry_transcript_54896-T1
Valid prediction for snap_scaffold_6-snap.85-T1
Valid prediction for GlimmerHMM_glimmerT_13926-T1
Valid prediction for GlimmerHMM_glimmerT_13922-T1
Valid prediction for GlimmerHMM_glimmerT_13912-T1
Valid prediction for snap_scaffold_6-snap.88-T1
Valid prediction for HiQ_model.g9249.t1
Valid prediction for snap_scaffold_6-snap.92-T1
Valid prediction for CodingQuarry_transcript_54897-T1
Couldn't classify 151580, 151936
Sorry, prediction pasa_asmbl_48036.p1 fails validation.
(CAA)	 AC	151580-151936	GC	TGG
Valid prediction for Augustus_model.g9259.t1
Valid prediction for GlimmerHMM_glimmerT_13925-T1
Valid prediction for GlimmerHMM_glimmerT_13909-T1
Valid prediction for snap_scaffold_6-snap.103-T1
Valid prediction for GlimmerHMM_glimmerT_13919-T1
Valid prediction for snap_scaffold_6-snap.102-T1
Valid prediction for Augustus_model.g9255.t1
Valid prediction for Augustus_model.g9246.t1
Valid prediction for snap_scaffold_6-snap.99-T1
Valid prediction for snap_scaffold_6-snap.112-T1
Valid prediction for GlimmerHMM_glimmerT_13908-T1
Valid prediction for snap_scaffold_6-snap.106-T1
Valid prediction for snap_scaffold_6-snap.107-T1
Valid prediction for Augustus_model.g9256.t1
Valid prediction for Augustus_model.g9252.t1
Valid prediction for snap_scaffold_6-snap.80-T1
Valid prediction for GlimmerHMM_glimmerT_13927-T1
Valid prediction for snap_scaffold_6-snap.82-T1
Valid prediction for GlimmerHMM_glimmerT_13911-T1
Valid prediction for snap_scaffold_6-snap.113-T1
Valid prediction for GlimmerHMM_glimmerT_13918-T1
Valid prediction for snap_scaffold_6-snap.95-T1
Valid prediction for Augustus_model.g9248.t1
Valid prediction for snap_scaffold_6-snap.118-T1
Valid prediction for Augustus_model.g9258.t1
Valid prediction for snap_scaffold_6-snap.78-T1
Valid prediction for snap_scaffold_6-snap.98-T1
Valid prediction for snap_scaffold_6-snap.91-T1
Valid prediction for pasa_asmbl_48033.p1
Valid prediction for snap_scaffold_6-snap.117-T1
Valid prediction for GlimmerHMM_glimmerT_13924-T1
Valid prediction for GlimmerHMM_glimmerT_13915-T1
Valid prediction for snap_scaffold_6-snap.101-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 5163, rend_intergenic: 1921  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19302, rend_intergenic: 17578  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29454, rend_intergenic: 19897  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36358, rend_intergenic: 30227  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41432, rend_intergenic: 39335  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47421, rend_intergenic: 45687  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54285, rend_intergenic: 50036  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61468, rend_intergenic: 54910  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84850, rend_intergenic: 68916  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106335, rend_intergenic: 87435  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112828, rend_intergenic: 111663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143658, rend_intergenic: 122878  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154555, rend_intergenic: 143989  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174328, rend_intergenic: 155425  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189787, rend_intergenic: 174503  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197884, rend_intergenic: 191510  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200172, rend_intergenic: 198465  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202600, rend_intergenic: 201320  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 214354, rend_intergenic: 206833  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 217144
-exon list size: 466


building trellis

0.2    
0.4    
0.6    
0.9    
1.1    
1.3    
1.5    
1.7    
1.9    
2.1    
2.4    
2.6    
2.8    
3.0    
3.2    
3.4    
3.6    
3.8    
4.1    
4.3    
4.5    
4.7    
4.9    
5.1    
5.3    
5.6    
5.8    
6.0    
6.2    
6.4    
6.6    
6.8    
7.1    
7.3    
7.5    
7.7    
7.9    
8.1    
8.3    
8.5    
8.8    
9.0    
9.2    
9.4    
9.6    
9.8    
10.0    
10.3    
10.5    
10.7    
10.9    
11.1    
11.3    
11.5    
11.8    
12.0    
12.2    
12.4    
12.6    
12.8    
13.0    
13.2    
13.5    
13.7    
13.9    
14.1    
14.3    
14.5    
14.7    
15.0    
15.2    
15.4    
15.6    
15.8    
16.0    
16.2    
16.5    
16.7    
16.9    
17.1    
17.3    
17.5    
17.7    
17.9    
18.2    
18.4    
18.6    
18.8    
19.0    
19.2    
19.4    
19.7    
19.9    
20.1    
20.3    
20.5    
20.7    
20.9    
21.2    
21.4    
21.6    
21.8    
22.0    
22.2    
22.4    
22.6    
22.9    
23.1    
23.3    
23.5    
23.7    
23.9    
24.1    
24.4    
24.6    
24.8    
25.0    
25.2    
25.4    
25.6    
25.9    
26.1    
26.3    
26.5    
26.7    
26.9    
27.1    
27.4    
27.6    
27.8    
28.0    
28.2    
28.4    
28.6    
28.8    
29.1    
29.3    
29.5    
29.7    
29.9    
30.1    
30.3    
30.6    
30.8    
31.0    
31.2    
31.4    
31.6    
31.8    
32.1    
32.3    
32.5    
32.7    
32.9    
33.1    
33.3    
33.5    
33.8    
34.0    
34.2    
34.4    
34.6    
34.8    
35.0    
35.3    
35.5    
35.7    
35.9    
36.1    
36.3    
36.5    
36.8    
37.0    
37.2    
37.4    
37.6    
37.8    
38.0    
38.2    
38.5    
38.7    
38.9    
39.1    
39.3    
39.5    
39.7    
40.0    
40.2    
40.4    
40.6    
40.8    
41.0    
41.2    
41.5    
41.7    
41.9    
42.1    
42.3    
42.5    
42.7    
42.9    
43.2    
43.4    
43.6    
43.8    
44.0    
44.2    
44.4    
44.7    
44.9    
45.1    
45.3    
45.5    
45.7    
45.9    
46.2    
46.4    
46.6    
46.8    
47.0    
47.2    
47.4    
47.6    
47.9    
48.1    
48.3    
48.5    
48.7    
48.9    
49.1    
49.4    
49.6    
49.8    
50.0    
50.2    
50.4    
50.6    
50.9    
51.1    
51.3    
51.5    
51.7    
51.9    
52.1    
52.4    
52.6    
52.8    
53.0    
53.2    
53.4    
53.6    
53.8    
54.1    
54.3    
54.5    
54.7    
54.9    
55.1    
55.3    
55.6    
55.8    
56.0    
56.2    
56.4    
56.6    
56.8    
57.1    
57.3    
57.5    
57.7    
57.9    
58.1    
58.3    
58.5    
58.8    
59.0    
59.2    
59.4    
59.6    
59.8    
60.0    
60.3    
60.5    
60.7    
60.9    
61.1    
61.3    
61.5    
61.8    
62.0    
62.2    
62.4    
62.6    
62.8    
63.0    
63.2    
63.5    
63.7    
63.9    
64.1    
64.3    
64.5    
64.7    
65.0    
65.2    
65.4    
65.6    
65.8    
66.0    
66.2    
66.5    
66.7    
66.9    
67.1    
67.3    
67.5    
67.7    
67.9    
68.2    
68.4    
68.6    
68.8    
69.0    
69.2    
69.4    
69.7    
69.9    
70.1    
70.3    
70.5    
70.7    
70.9    
71.2    
71.4    
71.6    
71.8    
72.0    
72.2    
72.4    
72.6    
72.9    
73.1    
73.3    
73.5    
73.7    
73.9    
74.1    
74.4    
74.6    
74.8    
75.0    
75.2    
75.4    
75.6    
75.9    
76.1    
76.3    
76.5    
76.7    
76.9    
77.1    
77.4    
77.6    
77.8    
78.0    
78.2    
78.4    
78.6    
78.8    
79.1    
79.3    
79.5    
79.7    
79.9    
80.1    
80.3    
80.6    
80.8    
81.0    
81.2    
81.4    
81.6    
81.8    
82.1    
82.3    
82.5    
82.7    
82.9    
83.1    
83.3    
83.5    
83.8    
84.0    
84.2    
84.4    
84.6    
84.8    
85.0    
85.3    
85.5    
85.7    
85.9    
86.1    
86.3    
86.5    
86.8    
87.0    
87.2    
87.4    
87.6    
87.8    
88.0    
88.2    
88.5    
88.7    
88.9    
89.1    
89.3    
89.5    
89.7    
90.0    
90.2    
90.4    
90.6    
90.8    
91.0    
91.2    
91.5    
91.7    
91.9    
92.1    
92.3    
92.5    
92.7    
92.9    
93.2    
93.4    
93.6    
93.8    
94.0    
94.2    
94.4    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.9    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.4    
99.6    
99.8    
-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 5163, rend_intergenic: 1921  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19302, rend_intergenic: 17578  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29454, rend_intergenic: 19897  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36358, rend_intergenic: 30227  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41432, rend_intergenic: 39335  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47421, rend_intergenic: 45687  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54285, rend_intergenic: 50036  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61468, rend_intergenic: 54910  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84850, rend_intergenic: 68916  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106335, rend_intergenic: 87435  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112828, rend_intergenic: 111663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143658, rend_intergenic: 122878  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154555, rend_intergenic: 143989  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174328, rend_intergenic: 155425  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189787, rend_intergenic: 174503  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197884, rend_intergenic: 191510  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200172, rend_intergenic: 198465  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202600, rend_intergenic: 201320  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 214354, rend_intergenic: 206833  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support