-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_15/scaffold_15_7925718-8139841

-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 Augustus_model.g25015.t1
Couldn't classify 5203, 5445
Sorry, prediction pasa_asmbl_14255.p1 fails validation.
(ATG)	 AC	2154-2315	GT	AGG
(GGT)	 AG	5203-5445	TC	CCT
-recovered pasa_asmbl_14255.p1, initial, 2154, 2315
Valid prediction for HiQ_model.g25020.t1
Valid prediction for GlimmerHMM_glimmerT_37312-T1
Valid prediction for snap_scaffold_15-snap.1704-T1
Valid prediction for GeneMark_model.64214_t
Valid prediction for GeneMark_model.64196_t
Valid prediction for GlimmerHMM_glimmerT_37310-T1
Valid prediction for snap_scaffold_15-snap.1697-T1
Valid prediction for GlimmerHMM_glimmerT_37317-T1
Valid prediction for snap_scaffold_15-snap.1681-T1
Valid prediction for GeneMark_model.64191_t
Valid prediction for GeneMark_model.64188_t
Valid prediction for GlimmerHMM_glimmerT_37326-T1
Valid prediction for snap_scaffold_15-snap.1685-T1
Valid prediction for GeneMark_model.64225_t
Valid prediction for GeneMark_model.64217_t
Valid prediction for GeneMark_model.64226_t
Valid prediction for snap_scaffold_15-snap.1690-T1
Valid prediction for GeneMark_model.64202_t
Valid prediction for GeneMark_model.64234_t
Valid prediction for GeneMark_model.64210_t
Valid prediction for GlimmerHMM_glimmerT_37324-T1
Valid prediction for snap_scaffold_15-snap.1687-T1
Valid prediction for GeneMark_model.64212_t
Valid prediction for GeneMark_model.64192_t
Valid prediction for HiQ_model.g25013.t1
Valid prediction for snap_scaffold_15-snap.1677-T1
Valid prediction for Augustus_model.g25016.t1
Valid prediction for GeneMark_model.64200_t
Couldn't classify 163856, 163909
Sorry, prediction GeneMark_model.64218_t fails validation.
(GGC)	 AG	163856-163909	GT	ATG
(ATC)	 AG	165415-165550	TG	AAT
-recovered GeneMark_model.64218_t, terminal, 165415, 165550
-recovered GeneMark_model.64218_t, internal, 163856, 163909
Valid prediction for GeneMark_model.64227_t
Valid prediction for GlimmerHMM_glimmerT_37328-T1
Valid prediction for GeneMark_model.64195_t
Valid prediction for GeneMark_model.64223_t
Valid prediction for GlimmerHMM_glimmerT_37319-T1
Valid prediction for GeneMark_model.64221_t
Couldn't classify 96982, 97362
Sorry, prediction pasa_asmbl_14261.p1 fails validation.
(GAG)	 AT	96982-97362	CA	GAC
Valid prediction for GeneMark_model.64222_t
Valid prediction for GeneMark_model.64187_t
Valid prediction for snap_scaffold_15-snap.1696-T1
Valid prediction for GlimmerHMM_glimmerT_37321-T1
Valid prediction for CodingQuarry_transcript_18016-T1
Valid prediction for pasa_asmbl_14257.p1
Valid prediction for GeneMark_model.64205_t
Valid prediction for snap_scaffold_15-snap.1694-T1
Valid prediction for Augustus_model.g25024.t1
Valid prediction for GlimmerHMM_glimmerT_37308-T1
Valid prediction for GeneMark_model.64231_t
Valid prediction for snap_scaffold_15-snap.1701-T1
Valid prediction for snap_scaffold_15-snap.1700-T1
Valid prediction for pasa_asmbl_14260.p1
Couldn't classify 98896, 99561
Sorry, prediction pasa_asmbl_14262.p1 fails validation.
(AAT)	 GG	98896-99561	GT	GAG
Valid prediction for GlimmerHMM_glimmerT_37313-T1
Valid prediction for pasa_asmbl_14263.p1
Valid prediction for CodingQuarry_transcript_18019-T1
Valid prediction for GeneMark_model.64198_t
Valid prediction for pasa_asmbl_14906.p1
Valid prediction for GeneMark_model.64206_t
Valid prediction for HiQ_model.g25017.t1
Valid prediction for snap_scaffold_15-snap.1686-T1
Valid prediction for GeneMark_model.64229_t
Valid prediction for GeneMark_model.64189_t
Valid prediction for GeneMark_model.64203_t
Valid prediction for snap_scaffold_15-snap.1684-T1
Valid prediction for snap_scaffold_15-snap.1680-T1
Valid prediction for GeneMark_model.64190_t

-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_15-snap.1683-T1
Couldn't classify 103611, 103740
Sorry, prediction pasa_asmbl_15345.p1 fails validation.
(AAG)	 CC	103611-103740	GC	AGG
(GAC)	 AG	103861-103983	GT	TGG
(GTA)	 AG	104174-104328	GT	CGG
(GTT)	 AG	104424-104534	GT	AGG
(GTG)	 AG	104647-104817	CT	AGC
-recovered pasa_asmbl_15345.p1, terminal, 104647, 104817
-recovered pasa_asmbl_15345.p1, internal, 103861, 103983
-recovered pasa_asmbl_15345.p1, internal, 104174, 104328
-recovered pasa_asmbl_15345.p1, internal, 104424, 104534
Couldn't classify 74667, 74748
Sorry, prediction pasa_asmbl_15350.p2 fails validation.
(AGG)	 TA	74667-74748	GT	AGG
(ACG)	 AG	74970-74999	GT	TGG
(GTG)	 AG	75534-75695	GT	AGG
(ATA)	 AG	75805-75927	GT	AGG
(GTT)	 AG	76125-76240	CA	AAC
-recovered pasa_asmbl_15350.p2, terminal, 76125, 76240
-recovered pasa_asmbl_15350.p2, internal, 74970, 74999
-recovered pasa_asmbl_15350.p2, internal, 75534, 75695
-recovered pasa_asmbl_15350.p2, internal, 75805, 75927
Valid prediction for snap_scaffold_15-snap.1699-T1
Valid prediction for snap_scaffold_15-snap.1707-T1
Valid prediction for Augustus_model.g25018.t1
Valid prediction for snap_scaffold_15-snap.1695-T1
Valid prediction for GeneMark_model.64199_t
Valid prediction for snap_scaffold_15-snap.1682-T1
Valid prediction for snap_scaffold_15-snap.1705-T1
Valid prediction for snap_scaffold_15-snap.1692-T1
Valid prediction for pasa_asmbl_15349.p1
Valid prediction for CodingQuarry_transcript_18018-T1
Valid prediction for GlimmerHMM_glimmerT_37327-T1
Valid prediction for Augustus_model.g25023.t1
Valid prediction for HiQ_model.g25021.t1
Valid prediction for GeneMark_model.64220_t
Valid prediction for GlimmerHMM_glimmerT_37325-T1
Valid prediction for GlimmerHMM_glimmerT_37318-T1
Couldn't classify 69730, 69967
Couldn't classify 71114, 71223
Sorry, prediction pasa_asmbl_15351.p1 fails validation.
(GCT)	 TA	69730-69967	GT	AGG
(GCT)	 AG	71114-71223	TG	GGT
Valid prediction for Augustus_model.g25022.t1
Valid prediction for GeneMark_model.64213_t
Valid prediction for snap_scaffold_15-snap.1698-T1
Valid prediction for snap_scaffold_15-snap.1693-T1
Valid prediction for GeneMark_model.64219_t
Valid prediction for GeneMark_model.64228_t
Valid prediction for GlimmerHMM_glimmerT_37315-T1
Valid prediction for Augustus_model.g25019.t1
Valid prediction for snap_scaffold_15-snap.1688-T1
Valid prediction for GeneMark_model.64186_t
Valid prediction for HiQ_model.g25012.t1
Valid prediction for snap_scaffold_15-snap.1689-T1
Valid prediction for GlimmerHMM_glimmerT_37316-T1
Valid prediction for GeneMark_model.64208_t
Valid prediction for snap_scaffold_15-snap.1702-T1
Sorry, intron length (4) is less than minimum required (10)
Couldn't classify 60463, 62824
Couldn't classify 66566, 66675
Sorry, prediction pasa_asmbl_15353.p1 fails validation.
(AGC)	 CC	60463-62824	GT	CGG
(GTA)	 AG	63020-63135	GT	GGG
(GTG)	 AG	63318-63429	GT	TGG
(ACC)	 AG	63550-63924	GT	TGG
(ATG)	 AG	66566-66675	GG	CCG
-recovered pasa_asmbl_15353.p1, internal, 63020, 63135
-recovered pasa_asmbl_15353.p1, internal, 63318, 63429
-recovered pasa_asmbl_15353.p1, internal, 63550, 63924
Valid prediction for CodingQuarry_transcript_18017-T1
Valid prediction for GeneMark_model.64197_t
Valid prediction for GeneMark_model.64233_t
Valid prediction for GeneMark_model.64215_t
Valid prediction for GlimmerHMM_glimmerT_37320-T1
Valid prediction for GeneMark_model.64230_t
Valid prediction for GeneMark_model.64204_t
Valid prediction for snap_scaffold_15-snap.1679-T1
Valid prediction for GeneMark_model.64207_t
Valid prediction for GlimmerHMM_glimmerT_37311-T1
Valid prediction for GeneMark_model.64193_t
Valid prediction for snap_scaffold_15-snap.1678-T1
Couldn't classify 212782, 213092
Sorry, prediction pasa_asmbl_15343.p1 fails validation.
(ATG)	 AG	212407-212518	GT	AGG
(GTT)	 AG	212782-213092	GT	AGG
-recovered pasa_asmbl_15343.p1, initial, 212407, 212518
-recovered pasa_asmbl_15343.p1, internal, 212407, 212518
-recovered pasa_asmbl_15343.p1, internal, 212782, 213092
Valid prediction for GlimmerHMM_glimmerT_37322-T1
Valid prediction for GeneMark_model.64224_t
Valid prediction for GeneMark_model.64194_t
Valid prediction for GlimmerHMM_glimmerT_37314-T1
Valid prediction for CodingQuarry_transcript_18020-T1
Valid prediction for GeneMark_model.64185_t
Valid prediction for GeneMark_model.64201_t
Valid prediction for snap_scaffold_15-snap.1708-T1
Valid prediction for snap_scaffold_15-snap.1703-T1
Valid prediction for snap_scaffold_15-snap.1691-T1
Valid prediction for GlimmerHMM_glimmerT_37309-T1
Valid prediction for GeneMark_model.64211_t
Valid prediction for GeneMark_model.64184_t
Valid prediction for GeneMark_model.64216_t
Valid prediction for GlimmerHMM_glimmerT_37323-T1
Valid prediction for GeneMark_model.64209_t
Valid prediction for HiQ_model.g25014.t1
Valid prediction for GeneMark_model.64232_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14463, rend_intergenic: 4536  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43098, rend_intergenic: 40499  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48180, rend_intergenic: 47447  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99561, rend_intergenic: 79305  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130213, rend_intergenic: 124302  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135854, rend_intergenic: 132661  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156757, rend_intergenic: 139663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189122, rend_intergenic: 171119  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 214124
-exon list size: 633


building trellis

0.2    
0.3    
0.5    
0.6    
0.8    
0.9    
1.1    
1.3    
1.4    
1.6    
1.7    
1.9    
2.0    
2.2    
2.4    
2.5    
2.7    
2.8    
3.0    
3.1    
3.3    
3.5    
3.6    
3.8    
3.9    
4.1    
4.3    
4.4    
4.6    
4.7    
4.9    
5.0    
5.2    
5.4    
5.5    
5.7    
5.8    
6.0    
6.1    
6.3    
6.5    
6.6    
6.8    
6.9    
7.1    
7.2    
7.4    
7.6    
7.7    
7.9    
8.0    
8.2    
8.3    
8.5    
8.7    
8.8    
9.0    
9.1    
9.3    
9.4    
9.6    
9.8    
9.9    
10.1    
10.2    
10.4    
10.6    
10.7    
10.9    
11.0    
11.2    
11.3    
11.5    
11.7    
11.8    
12.0    
12.1    
12.3    
12.4    
12.6    
12.8    
12.9    
13.1    
13.2    
13.4    
13.5    
13.7    
13.9    
14.0    
14.2    
14.3    
14.5    
14.6    
14.8    
15.0    
15.1    
15.3    
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    
17.6    
17.8    
18.0    
18.1    
18.3    
18.4    
18.6    
18.7    
18.9    
19.1    
19.2    
19.4    
19.5    
19.7    
19.8    
20.0    
20.2    
20.3    
20.5    
20.6    
20.8    
20.9    
21.1    
21.3    
21.4    
21.6    
21.7    
21.9    
22.0    
22.2    
22.4    
22.5    
22.7    
22.8    
23.0    
23.1    
23.3    
23.5    
23.6    
23.8    
23.9    
24.1    
24.3    
24.4    
24.6    
24.7    
24.9    
25.0    
25.2    
25.4    
25.5    
25.7    
25.8    
26.0    
26.1    
26.3    
26.5    
26.6    
26.8    
26.9    
27.1    
27.2    
27.4    
27.6    
27.7    
27.9    
28.0    
28.2    
28.3    
28.5    
28.7    
28.8    
29.0    
29.1    
29.3    
29.4    
29.6    
29.8    
29.9    
30.1    
30.2    
30.4    
30.6    
30.7    
30.9    
31.0    
31.2    
31.3    
31.5    
31.7    
31.8    
32.0    
32.1    
32.3    
32.4    
32.6    
32.8    
32.9    
33.1    
33.2    
33.4    
33.5    
33.7    
33.9    
34.0    
34.2    
34.3    
34.5    
34.6    
34.8    
35.0    
35.1    
35.3    
35.4    
35.6    
35.7    
35.9    
36.1    
36.2    
36.4    
36.5    
36.7    
36.9    
37.0    
37.2    
37.3    
37.5    
37.6    
37.8    
38.0    
38.1    
38.3    
38.4    
38.6    
38.7    
38.9    
39.1    
39.2    
39.4    
39.5    
39.7    
39.8    
40.0    
40.2    
40.3    
40.5    
40.6    
40.8    
40.9    
41.1    
41.3    
41.4    
41.6    
41.7    
41.9    
42.0    
42.2    
42.4    
42.5    
42.7    
42.8    
43.0    
43.1    
43.3    
43.5    
43.6    
43.8    
43.9    
44.1    
44.3    
44.4    
44.6    
44.7    
44.9    
45.0    
45.2    
45.4    
45.5    
45.7    
45.8    
46.0    
46.1    
46.3    
46.5    
46.6    
46.8    
46.9    
47.1    
47.2    
47.4    
47.6    
47.7    
47.9    
48.0    
48.2    
48.3    
48.5    
48.7    
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    
51.3    
51.5    
51.7    
51.8    
52.0    
52.1    
52.3    
52.4    
52.6    
52.8    
52.9    
53.1    
53.2    
53.4    
53.5    
53.7    
53.9    
54.0    
54.2    
54.3    
54.5    
54.6    
54.8    
55.0    
55.1    
55.3    
55.4    
55.6    
55.7    
55.9    
56.1    
56.2    
56.4    
56.5    
56.7    
56.9    
57.0    
57.2    
57.3    
57.5    
57.6    
57.8    
58.0    
58.1    
58.3    
58.4    
58.6    
58.7    
58.9    
59.1    
59.2    
59.4    
59.5    
59.7    
59.8    
60.0    
60.2    
60.3    
60.5    
60.6    
60.8    
60.9    
61.1    
61.3    
61.4    
61.6    
61.7    
61.9    
62.0    
62.2    
62.4    
62.5    
62.7    
62.8    
63.0    
63.1    
63.3    
63.5    
63.6    
63.8    
63.9    
64.1    
64.3    
64.4    
64.6    
64.7    
64.9    
65.0    
65.2    
65.4    
65.5    
65.7    
65.8    
66.0    
66.1    
66.3    
66.5    
66.6    
66.8    
66.9    
67.1    
67.2    
67.4    
67.6    
67.7    
67.9    
68.0    
68.2    
68.3    
68.5    
68.7    
68.8    
69.0    
69.1    
69.3    
69.4    
69.6    
69.8    
69.9    
70.1    
70.2    
70.4    
70.6    
70.7    
70.9    
71.0    
71.2    
71.3    
71.5    
71.7    
71.8    
72.0    
72.1    
72.3    
72.4    
72.6    
72.8    
72.9    
73.1    
73.2    
73.4    
73.5    
73.7    
73.9    
74.0    
74.2    
74.3    
74.5    
74.6    
74.8    
75.0    
75.1    
75.3    
75.4    
75.6    
75.7    
75.9    
76.1    
76.2    
76.4    
76.5    
76.7    
76.9    
77.0    
77.2    
77.3    
77.5    
77.6    
77.8    
78.0    
78.1    
78.3    
78.4    
78.6    
78.7    
78.9    
79.1    
79.2    
79.4    
79.5    
79.7    
79.8    
80.0    
80.2    
80.3    
80.5    
80.6    
80.8    
80.9    
81.1    
81.3    
81.4    
81.6    
81.7    
81.9    
82.0    
82.2    
82.4    
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    
84.7    
84.9    
85.0    
85.2    
85.4    
85.5    
85.7    
85.8    
86.0    
86.1    
86.3    
86.5    
86.6    
86.8    
86.9    
87.1    
87.2    
87.4    
87.6    
87.7    
87.9    
88.0    
88.2    
88.3    
88.5    
88.7    
88.8    
89.0    
89.1    
89.3    
89.4    
89.6    
89.8    
89.9    
90.1    
90.2    
90.4    
90.6    
90.7    
90.9    
91.0    
91.2    
91.3    
91.5    
91.7    
91.8    
92.0    
92.1    
92.3    
92.4    
92.6    
92.8    
92.9    
93.1    
93.2    
93.4    
93.5    
93.7    
93.9    
94.0    
94.2    
94.3    
94.5    
94.6    
94.8    
95.0    
95.1    
95.3    
95.4    
95.6    
95.7    
95.9    
96.1    
96.2    
96.4    
96.5    
96.7    
96.9    
97.0    
97.2    
97.3    
97.5    
97.6    
97.8    
98.0    
98.1    
98.3    
98.4    
98.6    
98.7    
98.9    
99.1    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 14463, rend_intergenic: 4536  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43098, rend_intergenic: 40499  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48180, rend_intergenic: 47447  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99561, rend_intergenic: 79305  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130213, rend_intergenic: 124302  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135854, rend_intergenic: 132661  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156757, rend_intergenic: 139663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189122, rend_intergenic: 171119  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