-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_4/scaffold_4_9879255-10029524

-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_10027-T1
Valid prediction for Augustus_model.g6517.t1
Valid prediction for GlimmerHMM_glimmerT_10020-T1
Valid prediction for GlimmerHMM_glimmerT_10016-T1
Valid prediction for snap_scaffold_4-snap.2095-T1
Valid prediction for GlimmerHMM_glimmerT_10024-T1
Valid prediction for Augustus_model.g6501.t1
Valid prediction for Augustus_model.g6503.t1
Valid prediction for GlimmerHMM_glimmerT_10022-T1
Valid prediction for Augustus_model.g6504.t1
Valid prediction for GlimmerHMM_glimmerT_10011-T1
Valid prediction for snap_scaffold_4-snap.2123-T1
Valid prediction for snap_scaffold_4-snap.2128-T1
Valid prediction for snap_scaffold_4-snap.2124-T1
Valid prediction for snap_scaffold_4-snap.2097-T1
Couldn't classify 114917, 115042
Sorry, prediction pasa_asmbl_41638.p1 fails validation.
(CAG)	 GC	114917-115042	GT	AGG
(CAC)	 AG	115374-115533	GT	GGG
(ATG)	 AG	115643-115833	GT	TTG
(GAT)	 AG	115938-116090	GT	TGG
(ATG)	 AG	116240-116339	GT	AGG
(CGC)	 AG	117073-117126	GT	GAG
(GCG)	 AG	117493-117687	GT	GGG
(AAA)	 AG	117821-118859	GT	AGG
(GTC)	 AG	119402-119432	GG	GAG
add_exon() Sorry, pasa_asmbl_41638.p1 115643-115833-initial-1 is invalid.
-recovered pasa_asmbl_41638.p1, initial, 115643, 115833
-recovered pasa_asmbl_41638.p1, initial, 116240, 116339
add_exon() Sorry, pasa_asmbl_41638.p1 117073-117126-terminal-1 is invalid.
-recovered pasa_asmbl_41638.p1, terminal, 117073, 117126
-recovered pasa_asmbl_41638.p1, terminal, 119402, 119432
-recovered pasa_asmbl_41638.p1, internal, 115374, 115533
-recovered pasa_asmbl_41638.p1, internal, 115643, 115833
-recovered pasa_asmbl_41638.p1, internal, 115938, 116090
-recovered pasa_asmbl_41638.p1, internal, 116240, 116339
-recovered pasa_asmbl_41638.p1, internal, 117073, 117126
-recovered pasa_asmbl_41638.p1, internal, 117493, 117687
-recovered pasa_asmbl_41638.p1, internal, 117821, 118859
Valid prediction for snap_scaffold_4-snap.2116-T1
Valid prediction for snap_scaffold_4-snap.2113-T1
Valid prediction for Augustus_model.g6507.t1
Valid prediction for snap_scaffold_4-snap.2126-T1
Couldn't classify 114810, 114810
Sorry, prediction CodingQuarry_transcript_49106-T1 fails validation.
(ATG)	 CA	114207-114262	GT	AGG
(GCC)	 AG	114454-114636	GT	TGG
(AAT)	 AG	114810-114810	AT	GAA
-recovered CodingQuarry_transcript_49106-T1, initial, 114207, 114262
-recovered CodingQuarry_transcript_49106-T1, internal, 114454, 114636
Valid prediction for Augustus_model.g6500.t1
Couldn't classify 124458, 124808
Sorry, prediction pasa_asmbl_41642.p2 fails validation.
(ATG)	 GA	124458-124808	TG	GGT
Valid prediction for GlimmerHMM_glimmerT_10009-T1
Valid prediction for GlimmerHMM_glimmerT_10021-T1
Valid prediction for HiQ_model.g6516.t1
Valid prediction for GlimmerHMM_glimmerT_10012-T1
Valid prediction for Augustus_model.g6514.t1
Valid prediction for Augustus_model.g6506.t1
Valid prediction for Augustus_model.g6518.t1
Valid prediction for Augustus_model.g6513.t1
Couldn't classify 114810, 114835
Sorry, prediction pasa_asmbl_41636.p2 fails validation.
(ATG)	 TG	114175-114262	GT	AGG
(GCC)	 AG	114454-114636	GT	TGG
(AAT)	 AG	114810-114835	CC	CCC
-recovered pasa_asmbl_41636.p2, initial, 114175, 114262
-recovered pasa_asmbl_41636.p2, internal, 114454, 114636
Valid prediction for pasa_asmbl_41628.p1
Valid prediction for snap_scaffold_4-snap.2101-T1
Valid prediction for Augustus_model.g6499.t1
Valid prediction for GlimmerHMM_glimmerT_10005-T1
Valid prediction for snap_scaffold_4-snap.2118-T1
Couldn't classify 103616, 103702
Couldn't classify 107789, 107842
Sorry, prediction pasa_asmbl_41633.p1 fails validation.
(GCT)	 GG	103616-103702	GT	AGG
(AGG)	 AG	106344-106425	GT	AGG
(CCT)	 AG	107393-107484	GT	ACG
(ATC)	 AG	107639-107695	GT	GGG
(ATG)	 AG	107789-107842	GC	ACG
-recovered pasa_asmbl_41633.p1, initial, 107789, 107842
-recovered pasa_asmbl_41633.p1, internal, 106344, 106425
-recovered pasa_asmbl_41633.p1, internal, 107393, 107484
-recovered pasa_asmbl_41633.p1, internal, 107639, 107695
-recovered pasa_asmbl_41633.p1, internal, 107789, 107842
Valid prediction for GlimmerHMM_glimmerT_10010-T1
Valid prediction for GlimmerHMM_glimmerT_10007-T1
Valid prediction for snap_scaffold_4-snap.2098-T1
Valid prediction for GlimmerHMM_glimmerT_10018-T1
Valid prediction for GlimmerHMM_glimmerT_10006-T1
Valid prediction for snap_scaffold_4-snap.2131-T1
Couldn't classify 146285, 146597
Sorry, prediction pasa_asmbl_41647.p1 fails validation.
(ATT)	 AG	146285-146597	GT	GGG
(GTA)	 AG	146696-146859	CG	GAC
-recovered pasa_asmbl_41647.p1, terminal, 146696, 146859
-recovered pasa_asmbl_41647.p1, internal, 146285, 146597
Valid prediction for snap_scaffold_4-snap.2105-T1
Valid prediction for GlimmerHMM_glimmerT_10026-T1
Couldn't classify 109549, 109623
Sorry, prediction pasa_asmbl_41634.p2 fails validation.
(CTG)	 AC	109549-109623	GT	AGG
(AAC)	 AG	110070-110214	GT	AGG
(GTC)	 AG	110875-111005	GA	AGG
-recovered pasa_asmbl_41634.p2, terminal, 110875, 111005
-recovered pasa_asmbl_41634.p2, internal, 110070, 110214
Couldn't classify 141458, 141912
Couldn't classify 144171, 144384
Sorry, prediction pasa_asmbl_41646.p1 fails validation.
(CGT)	 GG	141458-141912	GT	AGG
(GTG)	 AG	142046-142376	GT	AGG
(CTG)	 AG	143169-143413	GT	AGG
(CTT)	 AG	144171-144384	GT	AGG
-recovered pasa_asmbl_41646.p1, internal, 142046, 142376
-recovered pasa_asmbl_41646.p1, internal, 143169, 143413
-recovered pasa_asmbl_41646.p1, internal, 144171, 144384
Valid prediction for snap_scaffold_4-snap.2129-T1
Valid prediction for snap_scaffold_4-snap.2108-T1
Valid prediction for snap_scaffold_4-snap.2102-T1
Valid prediction for snap_scaffold_4-snap.2120-T1
Valid prediction for CodingQuarry_transcript_49103-T1
Valid prediction for Augustus_model.g6515.t1
Valid prediction for GlimmerHMM_glimmerT_10025-T1
Valid prediction for snap_scaffold_4-snap.2132-T1
Valid prediction for snap_scaffold_4-snap.2109-T1
Valid prediction for snap_scaffold_4-snap.2094-T1
Valid prediction for Augustus_model.g6511.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_4-snap.2115-T1
Valid prediction for snap_scaffold_4-snap.2127-T1
Valid prediction for snap_scaffold_4-snap.2100-T1
Valid prediction for snap_scaffold_4-snap.2117-T1
Valid prediction for GlimmerHMM_glimmerT_10023-T1
Valid prediction for snap_scaffold_4-snap.2104-T1
Valid prediction for snap_scaffold_4-snap.2107-T1
Valid prediction for snap_scaffold_4-snap.2114-T1
Valid prediction for snap_scaffold_4-snap.2096-T1
Valid prediction for snap_scaffold_4-snap.2112-T1
Valid prediction for snap_scaffold_4-snap.2122-T1
Valid prediction for Augustus_model.g6505.t1
Valid prediction for pasa_asmbl_42830.p1
Valid prediction for snap_scaffold_4-snap.2099-T1
Valid prediction for snap_scaffold_4-snap.2111-T1
Valid prediction for snap_scaffold_4-snap.2103-T1
Valid prediction for GlimmerHMM_glimmerT_10013-T1
Valid prediction for GlimmerHMM_glimmerT_10015-T1
Valid prediction for CodingQuarry_transcript_49105-T1
Valid prediction for GlimmerHMM_glimmerT_10004-T1
Valid prediction for GlimmerHMM_glimmerT_10019-T1
Valid prediction for Augustus_model.g6509.t1
Valid prediction for GlimmerHMM_glimmerT_10008-T1
Valid prediction for snap_scaffold_4-snap.2133-T1
Valid prediction for snap_scaffold_4-snap.2106-T1
Valid prediction for snap_scaffold_4-snap.2119-T1
Valid prediction for CodingQuarry_transcript_49104-T1
Valid prediction for snap_scaffold_4-snap.2110-T1
Valid prediction for Augustus_model.g6498.t1
Valid prediction for snap_scaffold_4-snap.2121-T1
Valid prediction for GlimmerHMM_glimmerT_10017-T1
Valid prediction for Augustus_model.g6502.t1
Valid prediction for GlimmerHMM_glimmerT_10014-T1
Valid prediction for snap_scaffold_4-snap.2130-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for Augustus_model.g6508.t1
Valid prediction for Augustus_model.g6512.t1
Valid prediction for Augustus_model.g6510.t1
Valid prediction for snap_scaffold_4-snap.2125-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6402, rend_intergenic: 3734  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18304, rend_intergenic: 9373  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30988, rend_intergenic: 21571  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47833, rend_intergenic: 44258  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56475, rend_intergenic: 51248  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61863, rend_intergenic: 58851  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82865, rend_intergenic: 76624  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92049, rend_intergenic: 90721  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97972, rend_intergenic: 95576  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101382, rend_intergenic: 97992  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113031, rend_intergenic: 103626  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124419, rend_intergenic: 117506  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130996, rend_intergenic: 128390  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134821, rend_intergenic: 132330  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139203, rend_intergenic: 135224  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146592, rend_intergenic: 139235  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148688, rend_intergenic: 146652  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 90777, rend_intergenic: 90774  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 150270
-exon list size: 430


building trellis

0.2    
0.5    
0.7    
0.9    
1.2    
1.4    
1.6    
1.9    
2.1    
2.3    
2.5    
2.8    
3.0    
3.2    
3.5    
3.7    
3.9    
4.2    
4.4    
4.6    
4.9    
5.1    
5.3    
5.6    
5.8    
6.0    
6.2    
6.5    
6.7    
6.9    
7.2    
7.4    
7.6    
7.9    
8.1    
8.3    
8.6    
8.8    
9.0    
9.3    
9.5    
9.7    
10.0    
10.2    
10.4    
10.6    
10.9    
11.1    
11.3    
11.6    
11.8    
12.0    
12.3    
12.5    
12.7    
13.0    
13.2    
13.4    
13.7    
13.9    
14.1    
14.4    
14.6    
14.8    
15.0    
15.3    
15.5    
15.7    
16.0    
16.2    
16.4    
16.7    
16.9    
17.1    
17.4    
17.6    
17.8    
18.1    
18.3    
18.5    
18.8    
19.0    
19.2    
19.4    
19.7    
19.9    
20.1    
20.4    
20.6    
20.8    
21.1    
21.3    
21.5    
21.8    
22.0    
22.2    
22.5    
22.7    
22.9    
23.1    
23.4    
23.6    
23.8    
24.1    
24.3    
24.5    
24.8    
25.0    
25.2    
25.5    
25.7    
25.9    
26.2    
26.4    
26.6    
26.9    
27.1    
27.3    
27.5    
27.8    
28.0    
28.2    
28.5    
28.7    
28.9    
29.2    
29.4    
29.6    
29.9    
30.1    
30.3    
30.6    
30.8    
31.0    
31.2    
31.5    
31.7    
31.9    
32.2    
32.4    
32.6    
32.9    
33.1    
33.3    
33.6    
33.8    
34.0    
34.3    
34.5    
34.7    
35.0    
35.2    
35.4    
35.6    
35.9    
36.1    
36.3    
36.6    
36.8    
37.0    
37.3    
37.5    
37.7    
38.0    
38.2    
38.4    
38.7    
38.9    
39.1    
39.4    
39.6    
39.8    
40.0    
40.3    
40.5    
40.7    
41.0    
41.2    
41.4    
41.7    
41.9    
42.1    
42.4    
42.6    
42.8    
43.1    
43.3    
43.5    
43.8    
44.0    
44.2    
44.4    
44.7    
44.9    
45.1    
45.4    
45.6    
45.8    
46.1    
46.3    
46.5    
46.8    
47.0    
47.2    
47.5    
47.7    
47.9    
48.1    
48.4    
48.6    
48.8    
49.1    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
50.7    
50.9    
51.2    
51.4    
51.6    
51.9    
52.1    
52.3    
52.5    
52.8    
53.0    
53.2    
53.5    
53.7    
53.9    
54.2    
54.4    
54.6    
54.9    
55.1    
55.3    
55.6    
55.8    
56.0    
56.2    
56.5    
56.7    
56.9    
57.2    
57.4    
57.6    
57.9    
58.1    
58.3    
58.6    
58.8    
59.0    
59.3    
59.5    
59.7    
60.0    
60.2    
60.4    
60.6    
60.9    
61.1    
61.3    
61.6    
61.8    
62.0    
62.3    
62.5    
62.7    
63.0    
63.2    
63.4    
63.7    
63.9    
64.1    
64.4    
64.6    
64.8    
65.0    
65.3    
65.5    
65.7    
66.0    
66.2    
66.4    
66.7    
66.9    
67.1    
67.4    
67.6    
67.8    
68.1    
68.3    
68.5    
68.8    
69.0    
69.2    
69.4    
69.7    
69.9    
70.1    
70.4    
70.6    
70.8    
71.1    
71.3    
71.5    
71.8    
72.0    
72.2    
72.5    
72.7    
72.9    
73.1    
73.4    
73.6    
73.8    
74.1    
74.3    
74.5    
74.8    
75.0    
75.2    
75.5    
75.7    
75.9    
76.2    
76.4    
76.6    
76.9    
77.1    
77.3    
77.5    
77.8    
78.0    
78.2    
78.5    
78.7    
78.9    
79.2    
79.4    
79.6    
79.9    
80.1    
80.3    
80.6    
80.8    
81.0    
81.2    
81.5    
81.7    
81.9    
82.2    
82.4    
82.6    
82.9    
83.1    
83.3    
83.6    
83.8    
84.0    
84.3    
84.5    
84.7    
85.0    
85.2    
85.4    
85.6    
85.9    
86.1    
86.3    
86.6    
86.8    
87.0    
87.3    
87.5    
87.7    
88.0    
88.2    
88.4    
88.7    
88.9    
89.1    
89.4    
89.6    
89.8    
90.0    
90.3    
90.5    
90.7    
91.0    
91.2    
91.4    
91.7    
91.9    
92.1    
92.4    
92.6    
92.8    
93.1    
93.3    
93.5    
93.8    
94.0    
94.2    
94.4    
94.7    
94.9    
95.1    
95.4    
95.6    
95.8    
96.1    
96.3    
96.5    
96.8    
97.0    
97.2    
97.5    
97.7    
97.9    
98.1    
98.4    
98.6    
98.8    
99.1    
99.3    
99.5    
99.8    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 6402, rend_intergenic: 3734  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18304, rend_intergenic: 9373  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30988, rend_intergenic: 21571  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47833, rend_intergenic: 44258  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56475, rend_intergenic: 51248  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61863, rend_intergenic: 58851  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82865, rend_intergenic: 76624  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92049, rend_intergenic: 90721  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97972, rend_intergenic: 95576  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101382, rend_intergenic: 97992  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113031, rend_intergenic: 103626  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124419, rend_intergenic: 117506  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130996, rend_intergenic: 128390  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134821, rend_intergenic: 132330  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139203, rend_intergenic: 135224  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146592, rend_intergenic: 139235  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148688, rend_intergenic: 146652  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 90777, rend_intergenic: 90774  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support