-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_21/scaffold_21_11958845-12129199

-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_21-snap.2601-T1
Valid prediction for snap_scaffold_21-snap.2613-T1
Valid prediction for GeneMark_model.86547_t
Valid prediction for GeneMark_model.86578_t
Valid prediction for GeneMark_model.86552_t
Valid prediction for snap_scaffold_21-snap.2599-T1
Valid prediction for GeneMark_model.86554_t
Valid prediction for GeneMark_model.86567_t
Valid prediction for GlimmerHMM_glimmerT_49954-T1
Valid prediction for GlimmerHMM_glimmerT_49939-T1
Valid prediction for snap_scaffold_21-snap.2603-T1
Valid prediction for GlimmerHMM_glimmerT_49938-T1
Couldn't classify 170054, 170143
Sorry, prediction GlimmerHMM_glimmerT_49958-T1 fails validation.
(ATG)	 CT	164576-165097	GT	CGG
(CTG)	 AG	170054-170143	GT	AGG
-recovered GlimmerHMM_glimmerT_49958-T1, initial, 164576, 165097
-recovered GlimmerHMM_glimmerT_49958-T1, internal, 170054, 170143
Valid prediction for GeneMark_model.86587_t
Valid prediction for GeneMark_model.86580_t
Valid prediction for snap_scaffold_21-snap.2596-T1
Valid prediction for GeneMark_model.86560_t
Valid prediction for snap_scaffold_21-snap.2616-T1
Valid prediction for snap_scaffold_21-snap.2615-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_49930-T1
Valid prediction for GeneMark_model.86563_t
Valid prediction for GeneMark_model.86549_t
Valid prediction for snap_scaffold_21-snap.2621-T1
Valid prediction for snap_scaffold_21-snap.2606-T1
Valid prediction for GeneMark_model.86551_t
Valid prediction for GeneMark_model.86574_t
Valid prediction for snap_scaffold_21-snap.2605-T1
Valid prediction for snap_scaffold_21-snap.2598-T1
Valid prediction for GlimmerHMM_glimmerT_49944-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.86556_t
Valid prediction for snap_scaffold_21-snap.2620-T1
Valid prediction for snap_scaffold_21-snap.2600-T1
Valid prediction for GeneMark_model.86562_t
Valid prediction for GlimmerHMM_glimmerT_49949-T1
Valid prediction for snap_scaffold_21-snap.2627-T1
Valid prediction for GlimmerHMM_glimmerT_49957-T1
Valid prediction for GeneMark_model.86572_t
Valid prediction for snap_scaffold_21-snap.2623-T1
Valid prediction for GeneMark_model.86569_t
Valid prediction for GeneMark_model.86571_t
Valid prediction for GeneMark_model.86558_t
Valid prediction for GlimmerHMM_glimmerT_49953-T1
Valid prediction for GeneMark_model.86565_t
Valid prediction for GeneMark_model.86588_t
Valid prediction for GeneMark_model.86584_t
Valid prediction for snap_scaffold_21-snap.2625-T1
Valid prediction for GlimmerHMM_glimmerT_49943-T1
Valid prediction for GeneMark_model.86576_t
Valid prediction for GeneMark_model.86586_t
Valid prediction for GeneMark_model.86582_t
Valid prediction for snap_scaffold_21-snap.2618-T1
Valid prediction for GlimmerHMM_glimmerT_49941-T1
Valid prediction for GlimmerHMM_glimmerT_49946-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 pasa_asmbl_28165.p3
Valid prediction for GlimmerHMM_glimmerT_49952-T1
Valid prediction for snap_scaffold_21-snap.2609-T1
Valid prediction for GeneMark_model.86577_t
Valid prediction for snap_scaffold_21-snap.2610-T1
Valid prediction for snap_scaffold_21-snap.2597-T1
Valid prediction for CodingQuarry_transcript_32695-T1
Valid prediction for GlimmerHMM_glimmerT_49932-T1
Valid prediction for GeneMark_model.86555_t
Valid prediction for snap_scaffold_21-snap.2617-T1
Valid prediction for GlimmerHMM_glimmerT_49948-T1
Valid prediction for GeneMark_model.86550_t
Valid prediction for snap_scaffold_21-snap.2626-T1
Valid prediction for GeneMark_model.86570_t
Valid prediction for GlimmerHMM_glimmerT_49951-T1
Valid prediction for GeneMark_model.86566_t
Valid prediction for snap_scaffold_21-snap.2628-T1
Valid prediction for snap_scaffold_21-snap.2624-T1
Valid prediction for GeneMark_model.86553_t
Valid prediction for snap_scaffold_21-snap.2608-T1
Couldn't classify 153962, 154063
Couldn't classify 154893, 154940
Sorry, prediction pasa_asmbl_28200.p1 fails validation.
(AAC)	 TC	153962-154063	GT	AGG
(GCT)	 AG	154327-154473	GT	AGG
(ATC)	 AG	154893-154940	TC	CGT
-recovered pasa_asmbl_28200.p1, internal, 154327, 154473
Valid prediction for GlimmerHMM_glimmerT_49933-T1
Valid prediction for GeneMark_model.86559_t
Valid prediction for snap_scaffold_21-snap.2611-T1
Valid prediction for GeneMark_model.86583_t
Valid prediction for snap_scaffold_21-snap.2604-T1
Valid prediction for snap_scaffold_21-snap.2607-T1
Couldn't classify 100396, 100497
Sorry, prediction pasa_asmbl_28171.p1 fails validation.
(CTG)	 AT	100396-100497	GT	AGG
(GGA)	 AG	100640-101062	CA	AAC
-recovered pasa_asmbl_28171.p1, terminal, 100640, 101062
Couldn't classify 143194, 143220
Couldn't classify 144931, 145011
Sorry, prediction pasa_asmbl_28244.p2 fails validation.
(AAA)	 AG	143194-143220	GT	TCG
(GAC)	 AG	143859-143972	GT	AGG
(GTG)	 AG	144741-144854	GT	AGG
(AAA)	 AG	144931-145011	GC	CCG
-recovered pasa_asmbl_28244.p2, internal, 143194, 143220
-recovered pasa_asmbl_28244.p2, internal, 143859, 143972
-recovered pasa_asmbl_28244.p2, internal, 144741, 144854
-recovered pasa_asmbl_28244.p2, internal, 144931, 145011
Valid prediction for GlimmerHMM_glimmerT_49940-T1
Valid prediction for Augustus_model.g33498.t1
Valid prediction for GlimmerHMM_glimmerT_49956-T1
Valid prediction for CodingQuarry_transcript_32697-T1
Valid prediction for GeneMark_model.86575_t
Valid prediction for GeneMark_model.86561_t
Valid prediction for GeneMark_model.86573_t
Valid prediction for snap_scaffold_21-snap.2629-T1
Valid prediction for GlimmerHMM_glimmerT_49945-T1
Valid prediction for snap_scaffold_21-snap.2619-T1
Valid prediction for snap_scaffold_21-snap.2612-T1
Valid prediction for GeneMark_model.86564_t
Couldn't classify 150102, 150107
Couldn't classify 153550, 153591
Sorry, prediction pasa_asmbl_28168.p1 fails validation.
(CAG)	 CA	150102-150107	GT	AGG
(GAT)	 AG	150582-150626	GT	ATG
(AGA)	 AG	152149-152190	GT	AGG
(TTT)	 AG	152935-153150	GT	AGG
(GAA)	 AG	153253-153408	GT	AGG
(ATC)	 AG	153550-153591	CG	GCC
-recovered pasa_asmbl_28168.p1, internal, 150582, 150626
-recovered pasa_asmbl_28168.p1, internal, 152149, 152190
-recovered pasa_asmbl_28168.p1, internal, 152935, 153150
-recovered pasa_asmbl_28168.p1, internal, 153253, 153408
Valid prediction for GlimmerHMM_glimmerT_49931-T1
Couldn't classify 42, 116
Sorry, prediction GeneMark_model.86590_t fails validation.
(AGA)	 AG	42-116	GT	CAG
(AGA)	 AG	151-165	GT	GAG
(ACC)	 AG	187-426	GT	CAG
(AGG)	 AG	2906-2945	GT	TGG
(ACT)	 AG	3120-3166	GT	GGG
(GAT)	 AG	3189-3278	GT	CGG
(AGA)	 AG	3470-3595	GT	AAG
(AGA)	 AG	3630-3648	AC	GAA
-recovered GeneMark_model.86590_t, terminal, 151, 165
-recovered GeneMark_model.86590_t, terminal, 3630, 3648
-recovered GeneMark_model.86590_t, internal, 42, 116
-recovered GeneMark_model.86590_t, internal, 151, 165
-recovered GeneMark_model.86590_t, internal, 187, 426
-recovered GeneMark_model.86590_t, internal, 2906, 2945
-recovered GeneMark_model.86590_t, internal, 3120, 3166
-recovered GeneMark_model.86590_t, internal, 3189, 3278
-recovered GeneMark_model.86590_t, internal, 3470, 3595
Valid prediction for snap_scaffold_21-snap.2602-T1
Valid prediction for GeneMark_model.86557_t
Valid prediction for GeneMark_model.86548_t
Valid prediction for GlimmerHMM_glimmerT_49934-T1
Valid prediction for GlimmerHMM_glimmerT_49936-T1
Valid prediction for GeneMark_model.86585_t
Couldn't classify 135543, 135584
Couldn't classify 137884, 137929
Sorry, prediction pasa_asmbl_28169.p1 fails validation.
(GAC)	 TT	135543-135584	GT	AGG
(GCT)	 AG	135720-135823	GT	AGG
(GGG)	 AG	137108-137335	GT	AGG
(GTA)	 AG	137884-137929	AA	AGA
-recovered pasa_asmbl_28169.p1, internal, 135720, 135823
-recovered pasa_asmbl_28169.p1, internal, 137108, 137335
Valid prediction for snap_scaffold_21-snap.2614-T1
Valid prediction for snap_scaffold_21-snap.2622-T1
Valid prediction for GlimmerHMM_glimmerT_49935-T1
Valid prediction for GlimmerHMM_glimmerT_49937-T1
Valid prediction for GlimmerHMM_glimmerT_49947-T1
Valid prediction for GlimmerHMM_glimmerT_49955-T1
Valid prediction for GeneMark_model.86568_t
Valid prediction for GlimmerHMM_glimmerT_49950-T1
Valid prediction for GeneMark_model.86581_t
Valid prediction for GlimmerHMM_glimmerT_49942-T1
Couldn't classify 99150, 99270
Couldn't classify 99941, 100248
Sorry, prediction pasa_asmbl_28172.p1 fails validation.
(CAG)	 AC	99150-99270	GT	AGG
(ATG)	 AG	99941-100248	CC	GCC

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 6475, rend_intergenic: 6472  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 8370, rend_intergenic: 6224  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37711, rend_intergenic: 8394  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48767, rend_intergenic: 45066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63403, rend_intergenic: 54646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84290, rend_intergenic: 83120  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90012, rend_intergenic: 88439  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96475, rend_intergenic: 90071  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102979, rend_intergenic: 98737  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113183, rend_intergenic: 103835  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123302, rend_intergenic: 120160  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134583, rend_intergenic: 124417  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139233, rend_intergenic: 135901  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155666, rend_intergenic: 151642  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 170355
-exon list size: 621


building trellis

0.2    
0.3    
0.5    
0.6    
0.8    
1.0    
1.1    
1.3    
1.4    
1.6    
1.8    
1.9    
2.1    
2.2    
2.4    
2.6    
2.7    
2.9    
3.0    
3.2    
3.4    
3.5    
3.7    
3.9    
4.0    
4.2    
4.3    
4.5    
4.7    
4.8    
5.0    
5.1    
5.3    
5.5    
5.6    
5.8    
5.9    
6.1    
6.3    
6.4    
6.6    
6.7    
6.9    
7.1    
7.2    
7.4    
7.5    
7.7    
7.9    
8.0    
8.2    
8.3    
8.5    
8.7    
8.8    
9.0    
9.1    
9.3    
9.5    
9.6    
9.8    
10.0    
10.1    
10.3    
10.4    
10.6    
10.8    
10.9    
11.1    
11.2    
11.4    
11.6    
11.7    
11.9    
12.0    
12.2    
12.4    
12.5    
12.7    
12.8    
13.0    
13.2    
13.3    
13.5    
13.6    
13.8    
14.0    
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    
16.5    
16.7    
16.9    
17.0    
17.2    
17.3    
17.5    
17.7    
17.8    
18.0    
18.1    
18.3    
18.5    
18.6    
18.8    
18.9    
19.1    
19.3    
19.4    
19.6    
19.7    
19.9    
20.1    
20.2    
20.4    
20.5    
20.7    
20.9    
21.0    
21.2    
21.3    
21.5    
21.7    
21.8    
22.0    
22.2    
22.3    
22.5    
22.6    
22.8    
23.0    
23.1    
23.3    
23.4    
23.6    
23.8    
23.9    
24.1    
24.2    
24.4    
24.6    
24.7    
24.9    
25.0    
25.2    
25.4    
25.5    
25.7    
25.8    
26.0    
26.2    
26.3    
26.5    
26.6    
26.8    
27.0    
27.1    
27.3    
27.4    
27.6    
27.8    
27.9    
28.1    
28.3    
28.4    
28.6    
28.7    
28.9    
29.1    
29.2    
29.4    
29.5    
29.7    
29.9    
30.0    
30.2    
30.3    
30.5    
30.7    
30.8    
31.0    
31.1    
31.3    
31.5    
31.6    
31.8    
31.9    
32.1    
32.3    
32.4    
32.6    
32.7    
32.9    
33.1    
33.2    
33.4    
33.5    
33.7    
33.9    
34.0    
34.2    
34.3    
34.5    
34.7    
34.8    
35.0    
35.2    
35.3    
35.5    
35.6    
35.8    
36.0    
36.1    
36.3    
36.4    
36.6    
36.8    
36.9    
37.1    
37.2    
37.4    
37.6    
37.7    
37.9    
38.0    
38.2    
38.4    
38.5    
38.7    
38.8    
39.0    
39.2    
39.3    
39.5    
39.6    
39.8    
40.0    
40.1    
40.3    
40.4    
40.6    
40.8    
40.9    
41.1    
41.3    
41.4    
41.6    
41.7    
41.9    
42.1    
42.2    
42.4    
42.5    
42.7    
42.9    
43.0    
43.2    
43.3    
43.5    
43.7    
43.8    
44.0    
44.1    
44.3    
44.5    
44.6    
44.8    
44.9    
45.1    
45.3    
45.4    
45.6    
45.7    
45.9    
46.1    
46.2    
46.4    
46.5    
46.7    
46.9    
47.0    
47.2    
47.4    
47.5    
47.7    
47.8    
48.0    
48.2    
48.3    
48.5    
48.6    
48.8    
49.0    
49.1    
49.3    
49.4    
49.6    
49.8    
49.9    
50.1    
50.2    
50.4    
50.6    
50.7    
50.9    
51.0    
51.2    
51.4    
51.5    
51.7    
51.8    
52.0    
52.2    
52.3    
52.5    
52.6    
52.8    
53.0    
53.1    
53.3    
53.5    
53.6    
53.8    
53.9    
54.1    
54.3    
54.4    
54.6    
54.7    
54.9    
55.1    
55.2    
55.4    
55.5    
55.7    
55.9    
56.0    
56.2    
56.3    
56.5    
56.7    
56.8    
57.0    
57.1    
57.3    
57.5    
57.6    
57.8    
57.9    
58.1    
58.3    
58.4    
58.6    
58.7    
58.9    
59.1    
59.2    
59.4    
59.6    
59.7    
59.9    
60.0    
60.2    
60.4    
60.5    
60.7    
60.8    
61.0    
61.2    
61.3    
61.5    
61.6    
61.8    
62.0    
62.1    
62.3    
62.4    
62.6    
62.8    
62.9    
63.1    
63.2    
63.4    
63.6    
63.7    
63.9    
64.0    
64.2    
64.4    
64.5    
64.7    
64.8    
65.0    
65.2    
65.3    
65.5    
65.7    
65.8    
66.0    
66.1    
66.3    
66.5    
66.6    
66.8    
66.9    
67.1    
67.3    
67.4    
67.6    
67.7    
67.9    
68.1    
68.2    
68.4    
68.5    
68.7    
68.9    
69.0    
69.2    
69.3    
69.5    
69.7    
69.8    
70.0    
70.1    
70.3    
70.5    
70.6    
70.8    
70.9    
71.1    
71.3    
71.4    
71.6    
71.7    
71.9    
72.1    
72.2    
72.4    
72.6    
72.7    
72.9    
73.0    
73.2    
73.4    
73.5    
73.7    
73.8    
74.0    
74.2    
74.3    
74.5    
74.6    
74.8    
75.0    
75.1    
75.3    
75.4    
75.6    
75.8    
75.9    
76.1    
76.2    
76.4    
76.6    
76.7    
76.9    
77.0    
77.2    
77.4    
77.5    
77.7    
77.8    
78.0    
78.2    
78.3    
78.5    
78.7    
78.8    
79.0    
79.1    
79.3    
79.5    
79.6    
79.8    
79.9    
80.1    
80.3    
80.4    
80.6    
80.7    
80.9    
81.1    
81.2    
81.4    
81.5    
81.7    
81.9    
82.0    
82.2    
82.3    
82.5    
82.7    
82.8    
83.0    
83.1    
83.3    
83.5    
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    
86.0    
86.2    
86.4    
86.5    
86.7    
86.8    
87.0    
87.2    
87.3    
87.5    
87.6    
87.8    
88.0    
88.1    
88.3    
88.4    
88.6    
88.8    
88.9    
89.1    
89.2    
89.4    
89.6    
89.7    
89.9    
90.0    
90.2    
90.4    
90.5    
90.7    
90.9    
91.0    
91.2    
91.3    
91.5    
91.7    
91.8    
92.0    
92.1    
92.3    
92.5    
92.6    
92.8    
92.9    
93.1    
93.3    
93.4    
93.6    
93.7    
93.9    
94.1    
94.2    
94.4    
94.5    
94.7    
94.9    
95.0    
95.2    
95.3    
95.5    
95.7    
95.8    
96.0    
96.1    
96.3    
96.5    
96.6    
96.8    
97.0    
97.1    
97.3    
97.4    
97.6    
97.8    
97.9    
98.1    
98.2    
98.4    
98.6    
98.7    
98.9    
99.0    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 29 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 6475, rend_intergenic: 6472  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 8370, rend_intergenic: 6224  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37711, rend_intergenic: 8394  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48767, rend_intergenic: 45066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63403, rend_intergenic: 54646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84290, rend_intergenic: 83120  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90012, rend_intergenic: 88439  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96475, rend_intergenic: 90071  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102979, rend_intergenic: 98737  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113183, rend_intergenic: 103835  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123302, rend_intergenic: 120160  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134583, rend_intergenic: 124417  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139233, rend_intergenic: 135901  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155666, rend_intergenic: 151642  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 12 predictions persist after filtering for low support