-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_28/scaffold_28_5672275-5851303

-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_60282-T1
Valid prediction for GlimmerHMM_glimmerT_60272-T1
Valid prediction for GeneMark_model.104966_t
Valid prediction for snap_scaffold_28-snap.1309-T1
Couldn't classify 150205, 150300
Sorry, prediction pasa_asmbl_38302.p1 fails validation.
(TCC)	 CT	150205-150300	GT	AGG
(GCT)	 AG	150518-150621	GT	GAG
(TAT)	 AG	150833-150930	GT	ATG
(TCG)	 AG	151127-151265	GT	AGG
(CCT)	 AG	151358-151650	GT	AGG
(AGA)	 AG	151737-151802	GT	GGG
(CTG)	 AG	152030-152103	AT	AAA
-recovered pasa_asmbl_38302.p1, terminal, 152030, 152103
-recovered pasa_asmbl_38302.p1, internal, 150518, 150621
-recovered pasa_asmbl_38302.p1, internal, 150833, 150930
-recovered pasa_asmbl_38302.p1, internal, 151127, 151265
-recovered pasa_asmbl_38302.p1, internal, 151358, 151650
-recovered pasa_asmbl_38302.p1, internal, 151737, 151802
Valid prediction for GlimmerHMM_glimmerT_60270-T1
Valid prediction for GlimmerHMM_glimmerT_60291-T1
Couldn't classify 143523, 143735
Couldn't classify 144182, 144379
Sorry, prediction pasa_asmbl_38544.p1 fails validation.
(TTG)	 AG	143523-143735	GT	TGG
(ATG)	 AG	143857-144009	GT	ACG
(ATC)	 AG	144182-144379	GA	GAG
-recovered pasa_asmbl_38544.p1, initial, 143857, 144009
-recovered pasa_asmbl_38544.p1, internal, 143523, 143735
-recovered pasa_asmbl_38544.p1, internal, 143857, 144009
Valid prediction for snap_scaffold_28-snap.1312-T1
Valid prediction for snap_scaffold_28-snap.1306-T1
Valid prediction for snap_scaffold_28-snap.1288-T1
Valid prediction for Augustus_model.g40142.t1
Valid prediction for snap_scaffold_28-snap.1299-T1
Valid prediction for Augustus_model.g40154.t1
Valid prediction for GlimmerHMM_glimmerT_60280-T1
Valid prediction for GeneMark_model.104958_t
Valid prediction for snap_scaffold_28-snap.1290-T1
Valid prediction for Augustus_model.g40147.t1
Valid prediction for GeneMark_model.104951_t
Valid prediction for snap_scaffold_28-snap.1293-T1
Valid prediction for Augustus_model.g40155.t1
Valid prediction for snap_scaffold_28-snap.1314-T1
Valid prediction for snap_scaffold_28-snap.1302-T1
Valid prediction for snap_scaffold_28-snap.1316-T1
Valid prediction for CodingQuarry_transcript_43588-T1
Valid prediction for Augustus_model.g40153.t1
Valid prediction for GlimmerHMM_glimmerT_60278-T1
Valid prediction for GeneMark_model.104967_t
Valid prediction for GeneMark_model.104952_t
Valid prediction for GeneMark_model.104969_t
Valid prediction for Augustus_model.g40148.t1
Valid prediction for GlimmerHMM_glimmerT_60292-T1
Valid prediction for GlimmerHMM_glimmerT_60266-T1
Valid prediction for GlimmerHMM_glimmerT_60267-T1
Valid prediction for CodingQuarry_transcript_43586-T1
Valid prediction for snap_scaffold_28-snap.1298-T1
Valid prediction for snap_scaffold_28-snap.1292-T1
Valid prediction for GeneMark_model.104961_t
Valid prediction for pasa_asmbl_38300.p1
Valid prediction for pasa_asmbl_38298.p1
Valid prediction for snap_scaffold_28-snap.1315-T1
Valid prediction for Augustus_model.g40156.t1
Valid prediction for GlimmerHMM_glimmerT_60285-T1
Valid prediction for GeneMark_model.104960_t
Valid prediction for Augustus_model.g40133.t1
Valid prediction for GlimmerHMM_glimmerT_60276-T1
Valid prediction for GeneMark_model.104954_t
Valid prediction for Augustus_model.g40137.t1
Valid prediction for GeneMark_model.104956_t
Valid prediction for GlimmerHMM_glimmerT_60268-T1
Valid prediction for Augustus_model.g40138.t1
Valid prediction for GlimmerHMM_glimmerT_60293-T1
Valid prediction for CodingQuarry_transcript_43587-T1
Valid prediction for GeneMark_model.104965_t
Couldn't classify 175341, 175430
Sorry, prediction pasa_asmbl_38303.p1 fails validation.
(ATG)	 AG	173367-173510	GT	AAG
(TTT)	 AG	173681-173766	GT	ACG
(GCT)	 AG	174060-174216	GT	TTG
(AAC)	 AG	174411-174451	GT	CGG
(ATA)	 AG	174569-174659	GT	AGG
(TGG)	 AG	174830-174949	GT	AAG
(ATG)	 AG	175341-175430	GT	TGG
-recovered pasa_asmbl_38303.p1, initial, 173367, 173510
-recovered pasa_asmbl_38303.p1, initial, 175341, 175430
-recovered pasa_asmbl_38303.p1, internal, 173367, 173510
-recovered pasa_asmbl_38303.p1, internal, 173681, 173766
-recovered pasa_asmbl_38303.p1, internal, 174060, 174216
-recovered pasa_asmbl_38303.p1, internal, 174411, 174451
-recovered pasa_asmbl_38303.p1, internal, 174569, 174659
-recovered pasa_asmbl_38303.p1, internal, 174830, 174949
-recovered pasa_asmbl_38303.p1, internal, 175341, 175430
Valid prediction for snap_scaffold_28-snap.1295-T1
Valid prediction for GeneMark_model.104943_t
Valid prediction for GeneMark_model.104947_t
Valid prediction for snap_scaffold_28-snap.1294-T1
Valid prediction for HiQ_model.g40141.t1
Valid prediction for GlimmerHMM_glimmerT_60294-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 GeneMark_model.104963_t
Valid prediction for Augustus_model.g40140.t1
Valid prediction for GlimmerHMM_glimmerT_60274-T1
Valid prediction for GlimmerHMM_glimmerT_60265-T1
Valid prediction for GeneMark_model.104957_t
Valid prediction for GlimmerHMM_glimmerT_60263-T1
Valid prediction for GeneMark_model.104941_t
Valid prediction for GeneMark_model.104968_t
Valid prediction for GlimmerHMM_glimmerT_60289-T1
Valid prediction for GlimmerHMM_glimmerT_60273-T1
Valid prediction for GlimmerHMM_glimmerT_60286-T1
Valid prediction for snap_scaffold_28-snap.1313-T1
Valid prediction for GeneMark_model.104964_t
Valid prediction for GlimmerHMM_glimmerT_60288-T1
Valid prediction for GlimmerHMM_glimmerT_60269-T1
Valid prediction for GeneMark_model.104944_t
Valid prediction for snap_scaffold_28-snap.1297-T1
Couldn't classify 78765, 79082
Sorry, prediction pasa_asmbl_37650.p1 fails validation.
(CTT)	 GG	78765-79082	AA	AGA
Valid prediction for snap_scaffold_28-snap.1311-T1
Valid prediction for CodingQuarry_transcript_43589-T1
Valid prediction for snap_scaffold_28-snap.1307-T1
Valid prediction for Augustus_model.g40135.t1
Valid prediction for Augustus_model.g40152.t1
Valid prediction for Augustus_model.g40145.t1
Valid prediction for snap_scaffold_28-snap.1289-T1
Valid prediction for snap_scaffold_28-snap.1305-T1
Valid prediction for GlimmerHMM_glimmerT_60283-T1
Valid prediction for GeneMark_model.104945_t
Valid prediction for GlimmerHMM_glimmerT_60277-T1
Valid prediction for GlimmerHMM_glimmerT_60271-T1
Valid prediction for Augustus_model.g40143.t1
Valid prediction for GeneMark_model.104955_t
Valid prediction for snap_scaffold_28-snap.1296-T1
Valid prediction for GeneMark_model.104948_t
Valid prediction for Augustus_model.g40150.t1
Valid prediction for GeneMark_model.104953_t
Valid prediction for snap_scaffold_28-snap.1287-T1
Valid prediction for GlimmerHMM_glimmerT_60264-T1
Valid prediction for GlimmerHMM_glimmerT_60284-T1
Valid prediction for GlimmerHMM_glimmerT_60279-T1
Valid prediction for Augustus_model.g40149.t1
Valid prediction for Augustus_model.g40136.t1
Valid prediction for GlimmerHMM_glimmerT_60281-T1
Valid prediction for snap_scaffold_28-snap.1308-T1
Valid prediction for Augustus_model.g40144.t1
Valid prediction for snap_scaffold_28-snap.1303-T1
Valid prediction for snap_scaffold_28-snap.1304-T1
Valid prediction for pasa_asmbl_37651.p1
Valid prediction for GeneMark_model.104946_t
Couldn't classify 161566, 161777
Sorry, prediction pasa_asmbl_37881.p1 fails validation.
(ATG)	 TT	160795-161035	GT	GGG
(ATG)	 AG	161566-161777	GT	CAG
-recovered pasa_asmbl_37881.p1, initial, 160795, 161035
add_exon() Sorry, pasa_asmbl_37881.p1 161566-161777-initial-1 is invalid.
-recovered pasa_asmbl_37881.p1, initial, 161566, 161777
-recovered pasa_asmbl_37881.p1, internal, 161566, 161777
Valid prediction for HiQ_model.g40139.t1
Valid prediction for Augustus_model.g40146.t1
Valid prediction for GlimmerHMM_glimmerT_60290-T1
Valid prediction for pasa_asmbl_37642.p1
Valid prediction for GeneMark_model.104942_t
Valid prediction for Augustus_model.g40151.t1
Valid prediction for snap_scaffold_28-snap.1291-T1
Valid prediction for snap_scaffold_28-snap.1310-T1
Valid prediction for GlimmerHMM_glimmerT_60287-T1
Valid prediction for snap_scaffold_28-snap.1301-T1
Valid prediction for GeneMark_model.104959_t
Valid prediction for GlimmerHMM_glimmerT_60275-T1
Couldn't classify 86333, 86443
Couldn't classify 87219, 87354
Sorry, prediction pasa_asmbl_37647.p1 fails validation.
(TTC)	 GC	86333-86443	GT	AGG
(ATA)	 AG	86536-86606	GT	AGG
(ACG)	 AG	86723-86811	GT	AGG
(ACT)	 AG	86923-87133	GT	AGG
(GTT)	 AG	87219-87354	CC	CCC
-recovered pasa_asmbl_37647.p1, internal, 86536, 86606
-recovered pasa_asmbl_37647.p1, internal, 86723, 86811
-recovered pasa_asmbl_37647.p1, internal, 86923, 87133
Valid prediction for Augustus_model.g40134.t1
Valid prediction for snap_scaffold_28-snap.1300-T1
Valid prediction for GeneMark_model.104950_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14248, rend_intergenic: 7473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97444, rend_intergenic: 95407  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114738, rend_intergenic: 114213  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119911, rend_intergenic: 118360  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145709, rend_intergenic: 142657  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149487, rend_intergenic: 145746  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 179029
-exon list size: 608


building trellis

0.2    
0.3    
0.5    
0.7    
0.8    
1.0    
1.1    
1.3    
1.5    
1.6    
1.8    
2.0    
2.1    
2.3    
2.5    
2.6    
2.8    
3.0    
3.1    
3.3    
3.4    
3.6    
3.8    
3.9    
4.1    
4.3    
4.4    
4.6    
4.8    
4.9    
5.1    
5.2    
5.4    
5.6    
5.7    
5.9    
6.1    
6.2    
6.4    
6.6    
6.7    
6.9    
7.0    
7.2    
7.4    
7.5    
7.7    
7.9    
8.0    
8.2    
8.4    
8.5    
8.7    
8.9    
9.0    
9.2    
9.3    
9.5    
9.7    
9.8    
10.0    
10.2    
10.3    
10.5    
10.7    
10.8    
11.0    
11.1    
11.3    
11.5    
11.6    
11.8    
12.0    
12.1    
12.3    
12.5    
12.6    
12.8    
13.0    
13.1    
13.3    
13.4    
13.6    
13.8    
13.9    
14.1    
14.3    
14.4    
14.6    
14.8    
14.9    
15.1    
15.2    
15.4    
15.6    
15.7    
15.9    
16.1    
16.2    
16.4    
16.6    
16.7    
16.9    
17.0    
17.2    
17.4    
17.5    
17.7    
17.9    
18.0    
18.2    
18.4    
18.5    
18.7    
18.9    
19.0    
19.2    
19.3    
19.5    
19.7    
19.8    
20.0    
20.2    
20.3    
20.5    
20.7    
20.8    
21.0    
21.1    
21.3    
21.5    
21.6    
21.8    
22.0    
22.1    
22.3    
22.5    
22.6    
22.8    
23.0    
23.1    
23.3    
23.4    
23.6    
23.8    
23.9    
24.1    
24.3    
24.4    
24.6    
24.8    
24.9    
25.1    
25.2    
25.4    
25.6    
25.7    
25.9    
26.1    
26.2    
26.4    
26.6    
26.7    
26.9    
27.0    
27.2    
27.4    
27.5    
27.7    
27.9    
28.0    
28.2    
28.4    
28.5    
28.7    
28.9    
29.0    
29.2    
29.3    
29.5    
29.7    
29.8    
30.0    
30.2    
30.3    
30.5    
30.7    
30.8    
31.0    
31.1    
31.3    
31.5    
31.6    
31.8    
32.0    
32.1    
32.3    
32.5    
32.6    
32.8    
33.0    
33.1    
33.3    
33.4    
33.6    
33.8    
33.9    
34.1    
34.3    
34.4    
34.6    
34.8    
34.9    
35.1    
35.2    
35.4    
35.6    
35.7    
35.9    
36.1    
36.2    
36.4    
36.6    
36.7    
36.9    
37.0    
37.2    
37.4    
37.5    
37.7    
37.9    
38.0    
38.2    
38.4    
38.5    
38.7    
38.9    
39.0    
39.2    
39.3    
39.5    
39.7    
39.8    
40.0    
40.2    
40.3    
40.5    
40.7    
40.8    
41.0    
41.1    
41.3    
41.5    
41.6    
41.8    
42.0    
42.1    
42.3    
42.5    
42.6    
42.8    
43.0    
43.1    
43.3    
43.4    
43.6    
43.8    
43.9    
44.1    
44.3    
44.4    
44.6    
44.8    
44.9    
45.1    
45.2    
45.4    
45.6    
45.7    
45.9    
46.1    
46.2    
46.4    
46.6    
46.7    
46.9    
47.0    
47.2    
47.4    
47.5    
47.7    
47.9    
48.0    
48.2    
48.4    
48.5    
48.7    
48.9    
49.0    
49.2    
49.3    
49.5    
49.7    
49.8    
50.0    
50.2    
50.3    
50.5    
50.7    
50.8    
51.0    
51.1    
51.3    
51.5    
51.6    
51.8    
52.0    
52.1    
52.3    
52.5    
52.6    
52.8    
53.0    
53.1    
53.3    
53.4    
53.6    
53.8    
53.9    
54.1    
54.3    
54.4    
54.6    
54.8    
54.9    
55.1    
55.2    
55.4    
55.6    
55.7    
55.9    
56.1    
56.2    
56.4    
56.6    
56.7    
56.9    
57.0    
57.2    
57.4    
57.5    
57.7    
57.9    
58.0    
58.2    
58.4    
58.5    
58.7    
58.9    
59.0    
59.2    
59.3    
59.5    
59.7    
59.8    
60.0    
60.2    
60.3    
60.5    
60.7    
60.8    
61.0    
61.1    
61.3    
61.5    
61.6    
61.8    
62.0    
62.1    
62.3    
62.5    
62.6    
62.8    
63.0    
63.1    
63.3    
63.4    
63.6    
63.8    
63.9    
64.1    
64.3    
64.4    
64.6    
64.8    
64.9    
65.1    
65.2    
65.4    
65.6    
65.7    
65.9    
66.1    
66.2    
66.4    
66.6    
66.7    
66.9    
67.0    
67.2    
67.4    
67.5    
67.7    
67.9    
68.0    
68.2    
68.4    
68.5    
68.7    
68.9    
69.0    
69.2    
69.3    
69.5    
69.7    
69.8    
70.0    
70.2    
70.3    
70.5    
70.7    
70.8    
71.0    
71.1    
71.3    
71.5    
71.6    
71.8    
72.0    
72.1    
72.3    
72.5    
72.6    
72.8    
73.0    
73.1    
73.3    
73.4    
73.6    
73.8    
73.9    
74.1    
74.3    
74.4    
74.6    
74.8    
74.9    
75.1    
75.2    
75.4    
75.6    
75.7    
75.9    
76.1    
76.2    
76.4    
76.6    
76.7    
76.9    
77.0    
77.2    
77.4    
77.5    
77.7    
77.9    
78.0    
78.2    
78.4    
78.5    
78.7    
78.9    
79.0    
79.2    
79.3    
79.5    
79.7    
79.8    
80.0    
80.2    
80.3    
80.5    
80.7    
80.8    
81.0    
81.1    
81.3    
81.5    
81.6    
81.8    
82.0    
82.1    
82.3    
82.5    
82.6    
82.8    
83.0    
83.1    
83.3    
83.4    
83.6    
83.8    
83.9    
84.1    
84.3    
84.4    
84.6    
84.8    
84.9    
85.1    
85.2    
85.4    
85.6    
85.7    
85.9    
86.1    
86.2    
86.4    
86.6    
86.7    
86.9    
87.0    
87.2    
87.4    
87.5    
87.7    
87.9    
88.0    
88.2    
88.4    
88.5    
88.7    
88.9    
89.0    
89.2    
89.3    
89.5    
89.7    
89.8    
90.0    
90.2    
90.3    
90.5    
90.7    
90.8    
91.0    
91.1    
91.3    
91.5    
91.6    
91.8    
92.0    
92.1    
92.3    
92.5    
92.6    
92.8    
93.0    
93.1    
93.3    
93.4    
93.6    
93.8    
93.9    
94.1    
94.3    
94.4    
94.6    
94.8    
94.9    
95.1    
95.2    
95.4    
95.6    
95.7    
95.9    
96.1    
96.2    
96.4    
96.6    
96.7    
96.9    
97.0    
97.2    
97.4    
97.5    
97.7    
97.9    
98.0    
98.2    
98.4    
98.5    
98.7    
98.9    
99.0    
99.2    
99.3    
99.5    
99.7    
99.8    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 14248, rend_intergenic: 7473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97444, rend_intergenic: 95407  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114738, rend_intergenic: 114213  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119911, rend_intergenic: 118360  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145709, rend_intergenic: 142657  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149487, rend_intergenic: 145746  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support