-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_7931623-8169802

-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_9725-T1
Valid prediction for snap_scaffold_4-snap.1709-T1
Valid prediction for GlimmerHMM_glimmerT_9727-T1
Valid prediction for Augustus_model.g6309.t1
Valid prediction for GlimmerHMM_glimmerT_9717-T1
Valid prediction for Augustus_model.g6305.t1
Valid prediction for GlimmerHMM_glimmerT_9730-T1
Valid prediction for snap_scaffold_4-snap.1700-T1
Valid prediction for snap_scaffold_4-snap.1716-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_4-snap.1702-T1
Valid prediction for snap_scaffold_4-snap.1722-T1
Valid prediction for snap_scaffold_4-snap.1691-T1
Valid prediction for GlimmerHMM_glimmerT_9721-T1
Couldn't classify 79632, 80130
Sorry, prediction pasa_asmbl_41531.p1 fails validation.
(ATG)	 AA	79297-79325	GT	GGG
(CAC)	 AG	79632-80130	CT	ACC
-recovered pasa_asmbl_41531.p1, initial, 79297, 79325
Valid prediction for snap_scaffold_4-snap.1713-T1
Valid prediction for GlimmerHMM_glimmerT_9718-T1
Valid prediction for pasa_asmbl_41526.p1
Valid prediction for GlimmerHMM_glimmerT_9732-T1
Valid prediction for HiQ_model.g6308.t1
Valid prediction for Augustus_model.g6313.t1
Valid prediction for snap_scaffold_4-snap.1698-T1
Couldn't classify 113106, 113182
Couldn't classify 116360, 116383
Sorry, prediction pasa_asmbl_42184.p1 fails validation.
(ATC)	 AC	113106-113182	GT	CGG
(GTT)	 AG	114427-114617	GT	TGG
(GTA)	 AG	116120-116199	GT	AGG
(GTG)	 AG	116360-116383	GA	AGG
-recovered pasa_asmbl_42184.p1, internal, 114427, 114617
-recovered pasa_asmbl_42184.p1, internal, 116120, 116199
Valid prediction for snap_scaffold_4-snap.1725-T1
Valid prediction for GlimmerHMM_glimmerT_9734-T1
Valid prediction for snap_scaffold_4-snap.1710-T1
Couldn't classify 66954, 67154
Couldn't classify 67884, 67912
Sorry, prediction pasa_asmbl_41529.p1 fails validation.
(CCA)	 GT	66954-67154	GT	AGG
(GTG)	 AG	67391-67554	GT	AGG
(GTT)	 AG	67669-67727	GT	AGG
(GGT)	 AG	67884-67912	AT	AGA
-recovered pasa_asmbl_41529.p1, internal, 67391, 67554
-recovered pasa_asmbl_41529.p1, internal, 67669, 67727
Valid prediction for snap_scaffold_4-snap.1727-T1
Valid prediction for Augustus_model.g6321.t1
Valid prediction for snap_scaffold_4-snap.1701-T1
Valid prediction for snap_scaffold_4-snap.1687-T1
Valid prediction for snap_scaffold_4-snap.1689-T1
Valid prediction for GlimmerHMM_glimmerT_9731-T1
Valid prediction for snap_scaffold_4-snap.1696-T1
Valid prediction for snap_scaffold_4-snap.1692-T1
Valid prediction for CodingQuarry_transcript_49066-T1
Valid prediction for GlimmerHMM_glimmerT_9720-T1
Valid prediction for snap_scaffold_4-snap.1697-T1
Valid prediction for HiQ_model.g6315.t1
Valid prediction for snap_scaffold_4-snap.1703-T1
Valid prediction for snap_scaffold_4-snap.1720-T1
Valid prediction for snap_scaffold_4-snap.1685-T1
Valid prediction for Augustus_model.g6324.t1
Valid prediction for GlimmerHMM_glimmerT_9729-T1
Valid prediction for GlimmerHMM_glimmerT_9742-T1
Valid prediction for pasa_asmbl_41536.p1
Valid prediction for snap_scaffold_4-snap.1688-T1
Valid prediction for Augustus_model.g6312.t1
Valid prediction for snap_scaffold_4-snap.1706-T1
Valid prediction for snap_scaffold_4-snap.1690-T1
Valid prediction for Augustus_model.g6311.t1
Valid prediction for GlimmerHMM_glimmerT_9746-T1
Valid prediction for snap_scaffold_4-snap.1686-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.1694-T1
Valid prediction for Augustus_model.g6323.t1
Valid prediction for snap_scaffold_4-snap.1719-T1
Couldn't classify 51442, 51507
Couldn't classify 53624, 53856
Sorry, prediction pasa_asmbl_42751.p1 fails validation.
(TGC)	 CC	51442-51507	GT	GGG
(CAG)	 AG	51914-51977	GT	AAG
(CTC)	 AG	52461-52593	GT	GGG
(GAA)	 AG	52878-52987	GT	GGG
(GAG)	 AG	53244-53387	GT	CGG
(AGC)	 AG	53624-53856	GA	GGG
-recovered pasa_asmbl_42751.p1, internal, 51914, 51977
-recovered pasa_asmbl_42751.p1, internal, 52461, 52593
-recovered pasa_asmbl_42751.p1, internal, 52878, 52987
-recovered pasa_asmbl_42751.p1, internal, 53244, 53387
Valid prediction for GlimmerHMM_glimmerT_9724-T1
Valid prediction for GlimmerHMM_glimmerT_9733-T1
Valid prediction for Augustus_model.g6306.t1
Valid prediction for snap_scaffold_4-snap.1711-T1
Valid prediction for CodingQuarry_transcript_49067-T1
Valid prediction for snap_scaffold_4-snap.1724-T1
Couldn't classify 57299, 57416
Sorry, prediction pasa_asmbl_42750.p1 fails validation.
(GTG)	 CA	57299-57416	GT	CAG
(ATG)	 AG	57559-57617	GT	AGG
(GAC)	 AG	57718-57759	GT	AGG
(GAG)	 AG	57903-57953	GT	AGG
(GCT)	 AG	58317-58694	GT	AGG
(GCT)	 AG	59010-59178	GT	AGG
(ATC)	 AG	60116-60198	CG	AAC
-recovered pasa_asmbl_42750.p1, initial, 57559, 57617
-recovered pasa_asmbl_42750.p1, terminal, 60116, 60198
-recovered pasa_asmbl_42750.p1, internal, 57559, 57617
-recovered pasa_asmbl_42750.p1, internal, 57718, 57759
-recovered pasa_asmbl_42750.p1, internal, 57903, 57953
-recovered pasa_asmbl_42750.p1, internal, 58317, 58694
-recovered pasa_asmbl_42750.p1, internal, 59010, 59178
Valid prediction for snap_scaffold_4-snap.1718-T1
Valid prediction for snap_scaffold_4-snap.1707-T1
Valid prediction for GlimmerHMM_glimmerT_9739-T1
Valid prediction for GlimmerHMM_glimmerT_9743-T1
Couldn't classify 76052, 76137
Couldn't classify 81683, 81745
Sorry, prediction pasa_asmbl_42746.p1 fails validation.
(GAG)	 TG	76052-76137	GT	AGG
(AGG)	 AG	76926-77043	GT	AGG
(GTG)	 AG	77395-77465	GT	GCG
(CAA)	 AG	79628-79703	GT	AGG
(TAC)	 AG	81683-81745	GT	AGG
-recovered pasa_asmbl_42746.p1, internal, 76926, 77043
-recovered pasa_asmbl_42746.p1, internal, 77395, 77465
-recovered pasa_asmbl_42746.p1, internal, 79628, 79703
-recovered pasa_asmbl_42746.p1, internal, 81683, 81745
Valid prediction for snap_scaffold_4-snap.1714-T1
Valid prediction for GlimmerHMM_glimmerT_9738-T1
Valid prediction for GlimmerHMM_glimmerT_9736-T1
Valid prediction for GlimmerHMM_glimmerT_9728-T1
Valid prediction for GlimmerHMM_glimmerT_9737-T1
Valid prediction for Augustus_model.g6316.t1
Valid prediction for Augustus_model.g6307.t1
Valid prediction for GlimmerHMM_glimmerT_9719-T1
Valid prediction for Augustus_model.g6319.t1
Valid prediction for snap_scaffold_4-snap.1717-T1
Valid prediction for Augustus_model.g6310.t1
Valid prediction for snap_scaffold_4-snap.1699-T1
Valid prediction for HiQ_model.g6314.t1
Valid prediction for snap_scaffold_4-snap.1708-T1
Valid prediction for snap_scaffold_4-snap.1715-T1
Valid prediction for snap_scaffold_4-snap.1695-T1
Couldn't classify 14263, 14510
Sorry, prediction pasa_asmbl_42752.p1 fails validation.
(CTG)	 GT	14263-14510	GT	ATG
(AGA)	 AG	14720-14765	GT	AGG
(CCG)	 AG	14912-15001	GT	AGG
(ATG)	 AG	15286-15363	GT	TGG
(AGA)	 AG	15620-15700	AG	GAA
-recovered pasa_asmbl_42752.p1, initial, 15286, 15363
-recovered pasa_asmbl_42752.p1, terminal, 15620, 15700
-recovered pasa_asmbl_42752.p1, internal, 14720, 14765
-recovered pasa_asmbl_42752.p1, internal, 14912, 15001
-recovered pasa_asmbl_42752.p1, internal, 15286, 15363
Valid prediction for GlimmerHMM_glimmerT_9744-T1
Valid prediction for GlimmerHMM_glimmerT_9723-T1
Valid prediction for snap_scaffold_4-snap.1712-T1
Valid prediction for GlimmerHMM_glimmerT_9740-T1
Valid prediction for GlimmerHMM_glimmerT_9716-T1
Valid prediction for snap_scaffold_4-snap.1693-T1
Couldn't classify 10045, 10202
Couldn't classify 12773, 12874
Sorry, prediction pasa_asmbl_42753.p2 fails validation.
(TTC)	 AG	10045-10202	GT	CTG
(TAT)	 AG	12449-12587	GT	AGG
(CCA)	 AG	12773-12874	AG	GGA
-recovered pasa_asmbl_42753.p2, internal, 10045, 10202
-recovered pasa_asmbl_42753.p2, internal, 12449, 12587
Valid prediction for Augustus_model.g6322.t1
Valid prediction for snap_scaffold_4-snap.1705-T1
Valid prediction for Augustus_model.g6320.t1
Couldn't classify 89349, 89450
Sorry, prediction pasa_asmbl_42734.p1 fails validation.
(AAG)	 CA	89349-89450	GT	GGG
(TTG)	 AG	89957-90153	GT	AGG
(AAA)	 AG	90273-90330	GT	AGG
(GTC)	 AG	90419-90505	GT	ACG
(GTC)	 AG	90679-90826	GT	AGG
(GTG)	 AG	92515-92614	GT	ACG
(GTC)	 AG	95153-95225	GT	AAG
(GGA)	 AG	95335-95481	GT	CGG
(ATC)	 AG	95917-95979	GT	AGG
(GTC)	 AG	96350-96409	AC	AGA
-recovered pasa_asmbl_42734.p1, terminal, 96350, 96409
-recovered pasa_asmbl_42734.p1, internal, 89957, 90153
-recovered pasa_asmbl_42734.p1, internal, 90273, 90330
-recovered pasa_asmbl_42734.p1, internal, 90419, 90505
-recovered pasa_asmbl_42734.p1, internal, 90679, 90826
-recovered pasa_asmbl_42734.p1, internal, 92515, 92614
-recovered pasa_asmbl_42734.p1, internal, 95153, 95225
-recovered pasa_asmbl_42734.p1, internal, 95335, 95481
-recovered pasa_asmbl_42734.p1, internal, 95917, 95979
Valid prediction for snap_scaffold_4-snap.1726-T1
Valid prediction for Augustus_model.g6318.t1
Valid prediction for snap_scaffold_4-snap.1721-T1
Valid prediction for GlimmerHMM_glimmerT_9741-T1
Valid prediction for GlimmerHMM_glimmerT_9745-T1
Valid prediction for GlimmerHMM_glimmerT_9722-T1
Valid prediction for snap_scaffold_4-snap.1723-T1
Couldn't classify 55528, 55720
Couldn't classify 56162, 56263
Sorry, prediction pasa_asmbl_43591.p1 fails validation.
(CTG)	 TG	55528-55720	GT	AGG
(ACG)	 AG	55925-56001	GT	TGG
(GAC)	 AG	56162-56263	GT	TGG
-recovered pasa_asmbl_43591.p1, internal, 55925, 56001
-recovered pasa_asmbl_43591.p1, internal, 56162, 56263
Valid prediction for snap_scaffold_4-snap.1704-T1
Valid prediction for GlimmerHMM_glimmerT_9726-T1
Valid prediction for Augustus_model.g6317.t1
Valid prediction for GlimmerHMM_glimmerT_9735-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 164368, rend_intergenic: 159331  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175270, rend_intergenic: 172713  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185106, rend_intergenic: 181582  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197181, rend_intergenic: 185132  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204417, rend_intergenic: 200850  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 217425, rend_intergenic: 214777  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 230688, rend_intergenic: 223667  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 238180
-exon list size: 398


building trellis

0.2    
0.5    
0.8    
1.0    
1.2    
1.5    
1.8    
2.0    
2.2    
2.5    
2.8    
3.0    
3.2    
3.5    
3.8    
4.0    
4.2    
4.5    
4.8    
5.0    
5.2    
5.5    
5.8    
6.0    
6.2    
6.5    
6.8    
7.0    
7.2    
7.5    
7.8    
8.0    
8.2    
8.5    
8.8    
9.0    
9.2    
9.5    
9.8    
10.0    
10.2    
10.5    
10.8    
11.0    
11.2    
11.5    
11.8    
12.0    
12.2    
12.5    
12.8    
13.0    
13.2    
13.5    
13.8    
14.0    
14.2    
14.5    
14.8    
15.0    
15.2    
15.5    
15.8    
16.0    
16.2    
16.5    
16.8    
17.0    
17.2    
17.5    
17.8    
18.0    
18.2    
18.5    
18.8    
19.0    
19.2    
19.5    
19.8    
20.0    
20.2    
20.5    
20.8    
21.0    
21.2    
21.5    
21.8    
22.0    
22.2    
22.5    
22.8    
23.0    
23.2    
23.5    
23.8    
24.0    
24.2    
24.5    
24.8    
25.0    
25.2    
25.5    
25.8    
26.0    
26.2    
26.5    
26.8    
27.0    
27.3    
27.5    
27.8    
28.0    
28.2    
28.5    
28.7    
29.0    
29.2    
29.5    
29.8    
30.0    
30.2    
30.5    
30.8    
31.0    
31.2    
31.5    
31.8    
32.0    
32.2    
32.5    
32.8    
33.0    
33.2    
33.5    
33.8    
34.0    
34.2    
34.5    
34.8    
35.0    
35.2    
35.5    
35.8    
36.0    
36.2    
36.5    
36.8    
37.0    
37.2    
37.5    
37.8    
38.0    
38.2    
38.5    
38.8    
39.0    
39.2    
39.5    
39.8    
40.0    
40.2    
40.5    
40.8    
41.0    
41.2    
41.5    
41.8    
42.0    
42.2    
42.5    
42.8    
43.0    
43.2    
43.5    
43.8    
44.0    
44.2    
44.5    
44.8    
45.0    
45.2    
45.5    
45.8    
46.0    
46.2    
46.5    
46.8    
47.0    
47.2    
47.5    
47.8    
48.0    
48.2    
48.5    
48.8    
49.0    
49.2    
49.5    
49.8    
50.0    
50.2    
50.5    
50.7    
51.0    
51.2    
51.5    
51.7    
52.0    
52.2    
52.5    
52.8    
53.0    
53.2    
53.5    
53.8    
54.0    
54.2    
54.5    
54.8    
55.0    
55.2    
55.5    
55.8    
56.0    
56.2    
56.5    
56.8    
57.0    
57.2    
57.5    
57.8    
58.0    
58.2    
58.5    
58.8    
59.0    
59.2    
59.5    
59.8    
60.0    
60.2    
60.5    
60.8    
61.0    
61.3    
61.5    
61.8    
62.0    
62.3    
62.5    
62.7    
63.0    
63.2    
63.5    
63.7    
64.0    
64.2    
64.5    
64.8    
65.0    
65.2    
65.5    
65.8    
66.0    
66.2    
66.5    
66.8    
67.0    
67.2    
67.5    
67.8    
68.0    
68.2    
68.5    
68.8    
69.0    
69.2    
69.5    
69.8    
70.0    
70.2    
70.5    
70.8    
71.0    
71.2    
71.5    
71.8    
72.0    
72.2    
72.5    
72.8    
73.0    
73.2    
73.5    
73.8    
74.0    
74.2    
74.5    
74.8    
75.0    
75.2    
75.5    
75.8    
76.0    
76.2    
76.5    
76.8    
77.0    
77.2    
77.5    
77.8    
78.0    
78.2    
78.5    
78.8    
79.0    
79.2    
79.5    
79.8    
80.0    
80.2    
80.5    
80.8    
81.0    
81.2    
81.5    
81.8    
82.0    
82.2    
82.5    
82.8    
83.0    
83.2    
83.5    
83.8    
84.0    
84.2    
84.5    
84.8    
85.0    
85.2    
85.5    
85.8    
86.0    
86.2    
86.5    
86.8    
87.0    
87.2    
87.5    
87.8    
88.0    
88.2    
88.5    
88.8    
89.0    
89.2    
89.5    
89.8    
90.0    
90.2    
90.5    
90.8    
91.0    
91.2    
91.5    
91.8    
92.0    
92.2    
92.5    
92.8    
93.0    
93.2    
93.5    
93.8    
94.0    
94.2    
94.5    
94.8    
95.0    
95.2    
95.5    
95.8    
96.0    
96.2    
96.5    
96.8    
97.0    
97.2    
97.5    
97.8    
98.0    
98.2    
98.5    
98.8    
99.0    
99.2    
99.5    
99.8    
-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 164368, rend_intergenic: 159331  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175270, rend_intergenic: 172713  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185106, rend_intergenic: 181582  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197181, rend_intergenic: 185132  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204417, rend_intergenic: 200850  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 217425, rend_intergenic: 214777  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 230688, rend_intergenic: 223667  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 28 predictions persist after filtering for low support