-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_6/scaffold_6_8162068-8297728

-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.g10278.t1
Couldn't classify 74113, 74188
Couldn't classify 82385, 82421
Sorry, prediction pasa_asmbl_47051.p1 fails validation.
(AGG)	 AC	74113-74188	GT	GGG
(AAT)	 AG	74508-74657	GT	CGG
(TGC)	 AG	74838-75041	GT	GGG
(GGC)	 AG	75181-75279	GT	AGG
(GGT)	 AG	75364-75524	GT	AGG
(CAA)	 AG	75655-75797	GT	CAG
(GAT)	 AG	76047-76182	GT	AGG
(ATT)	 AG	76274-76341	GC	AGG
(AAC)	 AG	77520-77658	GT	AGG
(TTG)	 AG	80024-80110	GT	AGG
(GTC)	 AG	80477-80547	GT	AAG
(TCT)	 AG	82013-82069	GT	AGG
(TGC)	 AG	82385-82421	GC	GAG
-recovered pasa_asmbl_47051.p1, internal, 74508, 74657
-recovered pasa_asmbl_47051.p1, internal, 74838, 75041
-recovered pasa_asmbl_47051.p1, internal, 75181, 75279
-recovered pasa_asmbl_47051.p1, internal, 75364, 75524
-recovered pasa_asmbl_47051.p1, internal, 75655, 75797
-recovered pasa_asmbl_47051.p1, internal, 76047, 76182
-recovered pasa_asmbl_47051.p1, internal, 76274, 76341
-recovered pasa_asmbl_47051.p1, internal, 77520, 77658
-recovered pasa_asmbl_47051.p1, internal, 80024, 80110
-recovered pasa_asmbl_47051.p1, internal, 80477, 80547
-recovered pasa_asmbl_47051.p1, internal, 82013, 82069
-recovered pasa_asmbl_47051.p1, internal, 82385, 82421
Valid prediction for GlimmerHMM_glimmerT_15438-T1
Valid prediction for snap_scaffold_6-snap.1818-T1
Valid prediction for pasa_asmbl_47046.p1
Valid prediction for GlimmerHMM_glimmerT_15428-T1
Valid prediction for GlimmerHMM_glimmerT_15425-T1
Valid prediction for GlimmerHMM_glimmerT_15436-T1
Valid prediction for snap_scaffold_6-snap.1832-T1
Valid prediction for Augustus_model.g10290.t1
Valid prediction for GeneMark_model.26003_t
Valid prediction for snap_scaffold_6-snap.1814-T1
Valid prediction for Augustus_model.g10294.t1
Valid prediction for GlimmerHMM_glimmerT_15417-T1
Couldn't classify 6272, 6361
Sorry, prediction pasa_asmbl_47043.p1 fails validation.
(TCA)	 GC	6272-6361	GT	AGG
(GTC)	 AG	6527-6587	GT	CTG
(GTG)	 AG	6738-6822	GT	ATG
(CTC)	 AG	7156-7267	GT	AGG
(GAA)	 AG	7512-7658	TG	GAT
-recovered pasa_asmbl_47043.p1, terminal, 7512, 7658
-recovered pasa_asmbl_47043.p1, internal, 6527, 6587
-recovered pasa_asmbl_47043.p1, internal, 6738, 6822
-recovered pasa_asmbl_47043.p1, internal, 7156, 7267
Valid prediction for GlimmerHMM_glimmerT_15419-T1
Valid prediction for GeneMark_model.25997_t
Couldn't classify 122843, 122998
Sorry, prediction pasa_asmbl_47054.p1 fails validation.
(TCC)	 CC	122843-122998	GT	CGG
(ATT)	 AG	123595-123881	GT	AGG
(GAA)	 AG	123968-124025	GT	CTG
(TTC)	 AG	125816-125992	GT	TGG
(GCC)	 AG	126228-126329	CA	AGC
-recovered pasa_asmbl_47054.p1, terminal, 126228, 126329
-recovered pasa_asmbl_47054.p1, internal, 123595, 123881
-recovered pasa_asmbl_47054.p1, internal, 123968, 124025
-recovered pasa_asmbl_47054.p1, internal, 125816, 125992
Valid prediction for snap_scaffold_6-snap.1829-T1
Valid prediction for Augustus_model.g10275.t1
Valid prediction for Augustus_model.g10285.t1
Valid prediction for Augustus_model.g10279.t1
Valid prediction for GeneMark_model.25992_t
Valid prediction for GlimmerHMM_glimmerT_15418-T1
Valid prediction for GeneMark_model.25999_t
Valid prediction for GlimmerHMM_glimmerT_15430-T1
Valid prediction for GlimmerHMM_glimmerT_15415-T1
Valid prediction for snap_scaffold_6-snap.1817-T1
Valid prediction for Augustus_model.g10287.t1
Valid prediction for GeneMark_model.25994_t
Valid prediction for GlimmerHMM_glimmerT_15431-T1
Valid prediction for GeneMark_model.26022_t
Valid prediction for GeneMark_model.26032_t
Valid prediction for snap_scaffold_6-snap.1819-T1
Valid prediction for GeneMark_model.25993_t
Valid prediction for HiQ_model.g10277.t1
Valid prediction for GlimmerHMM_glimmerT_15414-T1
Valid prediction for GeneMark_model.26009_t
Valid prediction for GeneMark_model.26013_t
Valid prediction for snap_scaffold_6-snap.1840-T1
Valid prediction for snap_scaffold_6-snap.1835-T1
Couldn't classify 5660, 5812
Sorry, prediction pasa_asmbl_47042.p1 fails validation.
(ATG)	 AA	3351-3698	GT	AGG
(GCT)	 AG	5660-5812	AG	CCA
-recovered pasa_asmbl_47042.p1, initial, 3351, 3698
Valid prediction for GeneMark_model.26011_t
Valid prediction for Augustus_model.g10292.t1
Valid prediction for GeneMark_model.26019_t
Couldn't classify 20959, 21068
Sorry, prediction pasa_asmbl_47047.p1 fails validation.
(ATG)	 AC	19794-20093	GT	AGG
(GTC)	 AG	20209-20394	GT	AGG
(AGA)	 AG	20539-20719	GT	CGG
(ACA)	 AG	20959-21068	CT	AGC
-recovered pasa_asmbl_47047.p1, initial, 19794, 20093
-recovered pasa_asmbl_47047.p1, internal, 20209, 20394
-recovered pasa_asmbl_47047.p1, internal, 20539, 20719
Valid prediction for snap_scaffold_6-snap.1822-T1
Valid prediction for GeneMark_model.26001_t
Valid prediction for CodingQuarry_transcript_54983-T1
Valid prediction for Augustus_model.g10286.t1
Valid prediction for GeneMark_model.26025_t
Valid prediction for snap_scaffold_6-snap.1834-T1
Valid prediction for GeneMark_model.26005_t
Valid prediction for snap_scaffold_6-snap.1831-T1
Valid prediction for Augustus_model.g10288.t1
Valid prediction for GeneMark_model.26030_t
Valid prediction for GeneMark_model.25989_t
Valid prediction for snap_scaffold_6-snap.1823-T1
Valid prediction for GeneMark_model.25995_t
Valid prediction for snap_scaffold_6-snap.1837-T1
Valid prediction for GeneMark_model.26033_t
Valid prediction for snap_scaffold_6-snap.1828-T1
Valid prediction for GeneMark_model.26024_t
Valid prediction for GeneMark_model.26016_t
Valid prediction for GlimmerHMM_glimmerT_15432-T1
Valid prediction for GlimmerHMM_glimmerT_15434-T1
Couldn't classify 87100, 87213
Sorry, prediction pasa_asmbl_47052.p1 fails validation.
(CAG)	 CC	87100-87213	GT	AGG
(GAG)	 AG	89138-89247	GT	AGG
(GAA)	 AG	89545-89656	GT	AGG
(GTG)	 AG	89797-89961	GT	GCG
(GCG)	 AG	90080-90303	GT	AGG
(CCC)	 AG	90503-90739	GT	AGG
(CAG)	 AG	91307-91376	AA	AGA
-recovered pasa_asmbl_47052.p1, terminal, 91307, 91376
-recovered pasa_asmbl_47052.p1, internal, 89138, 89247
-recovered pasa_asmbl_47052.p1, internal, 89545, 89656
-recovered pasa_asmbl_47052.p1, internal, 89797, 89961
-recovered pasa_asmbl_47052.p1, internal, 90080, 90303
-recovered pasa_asmbl_47052.p1, internal, 90503, 90739
Valid prediction for GeneMark_model.26017_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_6-snap.1816-T1
Valid prediction for HiQ_model.g10289.t1
Valid prediction for GeneMark_model.26028_t
Valid prediction for GeneMark_model.26010_t
Valid prediction for GeneMark_model.26002_t
Valid prediction for GlimmerHMM_glimmerT_15423-T1
Valid prediction for GlimmerHMM_glimmerT_15429-T1
Valid prediction for GeneMark_model.26023_t
Valid prediction for GeneMark_model.26004_t
Valid prediction for GeneMark_model.26020_t
Valid prediction for GeneMark_model.26034_t
Valid prediction for snap_scaffold_6-snap.1826-T1
Valid prediction for Augustus_model.g10280.t1
Valid prediction for snap_scaffold_6-snap.1824-T1
Valid prediction for snap_scaffold_6-snap.1841-T1
Valid prediction for GeneMark_model.26015_t
Valid prediction for GlimmerHMM_glimmerT_15439-T1
Valid prediction for snap_scaffold_6-snap.1820-T1
Valid prediction for GeneMark_model.26007_t
Valid prediction for GeneMark_model.26026_t
Valid prediction for GeneMark_model.25991_t
Couldn't classify 69855, 70050
Couldn't classify 70550, 70630
Sorry, prediction pasa_asmbl_48483.p1 fails validation.
(GGT)	 CA	69855-70050	GT	TGG
(AAA)	 AG	70129-70267	GT	GGG
(CTA)	 AG	70370-70445	GT	CAG
(AGG)	 AG	70550-70630	CC	ACC
-recovered pasa_asmbl_48483.p1, internal, 70129, 70267
-recovered pasa_asmbl_48483.p1, internal, 70370, 70445
Valid prediction for Augustus_model.g10281.t1
Valid prediction for GeneMark_model.25996_t
Valid prediction for Augustus_model.g10291.t1
Valid prediction for GeneMark_model.26021_t
Valid prediction for GeneMark_model.26008_t
Valid prediction for GeneMark_model.26031_t
Valid prediction for GlimmerHMM_glimmerT_15426-T1
Valid prediction for GlimmerHMM_glimmerT_15435-T1
Valid prediction for CodingQuarry_transcript_54982-T1
Valid prediction for CodingQuarry_transcript_54981-T1
Valid prediction for GlimmerHMM_glimmerT_15424-T1
Valid prediction for HiQ_model.g10284.t1
Valid prediction for GeneMark_model.25998_t
Valid prediction for pasa_asmbl_48476.p1
Valid prediction for GeneMark_model.26027_t
Valid prediction for snap_scaffold_6-snap.1827-T1
Valid prediction for Augustus_model.g10293.t1
Valid prediction for GlimmerHMM_glimmerT_15416-T1
Valid prediction for GeneMark_model.26006_t
Valid prediction for GeneMark_model.26029_t
Valid prediction for GeneMark_model.26014_t
Valid prediction for GlimmerHMM_glimmerT_15420-T1
Valid prediction for GlimmerHMM_glimmerT_15422-T1
Valid prediction for GeneMark_model.26012_t
Valid prediction for Augustus_model.g10282.t1
Valid prediction for GeneMark_model.26018_t
Valid prediction for snap_scaffold_6-snap.1825-T1
Valid prediction for snap_scaffold_6-snap.1838-T1
Valid prediction for GlimmerHMM_glimmerT_15427-T1
Valid prediction for GeneMark_model.26000_t
Valid prediction for GlimmerHMM_glimmerT_15440-T1
Valid prediction for snap_scaffold_6-snap.1830-T1
Valid prediction for snap_scaffold_6-snap.1833-T1
Valid prediction for GlimmerHMM_glimmerT_15421-T1
Couldn't classify 39463, 39672
Sorry, prediction pasa_asmbl_48488.p1 fails validation.
(ATG)	 GC	37515-37703	GT	AGG
(GTG)	 AG	38838-38935	GT	ACG
(GGT)	 AG	39034-39220	GT	GGG
(GAG)	 AG	39463-39672	CG	TCC
-recovered pasa_asmbl_48488.p1, initial, 37515, 37703
-recovered pasa_asmbl_48488.p1, internal, 38838, 38935
-recovered pasa_asmbl_48488.p1, internal, 39034, 39220
Valid prediction for snap_scaffold_6-snap.1815-T1
Valid prediction for GlimmerHMM_glimmerT_15437-T1
Valid prediction for snap_scaffold_6-snap.1839-T1
Valid prediction for snap_scaffold_6-snap.1836-T1
Valid prediction for snap_scaffold_6-snap.1821-T1
Valid prediction for GlimmerHMM_glimmerT_15433-T1
Valid prediction for Augustus_model.g10276.t1
Valid prediction for Augustus_model.g10283.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 42456, rend_intergenic: 37406  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46857, rend_intergenic: 44753  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90252, rend_intergenic: 88363  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124975, rend_intergenic: 115438  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125898, rend_intergenic: 125226  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 9486, rend_intergenic: 9483  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 135661
-exon list size: 591


building trellis

0.2    
0.3    
0.5    
0.7    
0.8    
1.0    
1.2    
1.3    
1.5    
1.7    
1.9    
2.0    
2.2    
2.4    
2.5    
2.7    
2.9    
3.0    
3.2    
3.4    
3.5    
3.7    
3.9    
4.0    
4.2    
4.4    
4.6    
4.7    
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    
7.1    
7.3    
7.4    
7.6    
7.8    
7.9    
8.1    
8.3    
8.4    
8.6    
8.8    
8.9    
9.1    
9.3    
9.4    
9.6    
9.8    
9.9    
10.1    
10.3    
10.5    
10.6    
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    
13.2    
13.3    
13.5    
13.7    
13.8    
14.0    
14.2    
14.3    
14.5    
14.7    
14.8    
15.0    
15.2    
15.3    
15.5    
15.7    
15.9    
16.0    
16.2    
16.4    
16.5    
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    
19.1    
19.2    
19.4    
19.6    
19.7    
19.9    
20.1    
20.2    
20.4    
20.6    
20.7    
20.9    
21.1    
21.2    
21.4    
21.6    
21.8    
21.9    
22.1    
22.3    
22.4    
22.6    
22.8    
22.9    
23.1    
23.3    
23.4    
23.6    
23.8    
23.9    
24.1    
24.3    
24.5    
24.6    
24.8    
25.0    
25.1    
25.3    
25.5    
25.6    
25.8    
26.0    
26.1    
26.3    
26.5    
26.6    
26.8    
27.0    
27.2    
27.3    
27.5    
27.7    
27.8    
28.0    
28.2    
28.3    
28.5    
28.7    
28.8    
29.0    
29.2    
29.3    
29.5    
29.7    
29.8    
30.0    
30.2    
30.4    
30.5    
30.7    
30.9    
31.0    
31.2    
31.4    
31.5    
31.7    
31.9    
32.0    
32.2    
32.4    
32.5    
32.7    
32.9    
33.1    
33.2    
33.4    
33.6    
33.7    
33.9    
34.1    
34.2    
34.4    
34.6    
34.7    
34.9    
35.1    
35.2    
35.4    
35.6    
35.8    
35.9    
36.1    
36.3    
36.4    
36.6    
36.8    
36.9    
37.1    
37.3    
37.4    
37.6    
37.8    
37.9    
38.1    
38.3    
38.4    
38.6    
38.8    
39.0    
39.1    
39.3    
39.5    
39.6    
39.8    
40.0    
40.1    
40.3    
40.5    
40.6    
40.8    
41.0    
41.1    
41.3    
41.5    
41.7    
41.8    
42.0    
42.2    
42.3    
42.5    
42.7    
42.8    
43.0    
43.2    
43.3    
43.5    
43.7    
43.8    
44.0    
44.2    
44.4    
44.5    
44.7    
44.9    
45.0    
45.2    
45.4    
45.5    
45.7    
45.9    
46.0    
46.2    
46.4    
46.5    
46.7    
46.9    
47.0    
47.2    
47.4    
47.6    
47.7    
47.9    
48.1    
48.2    
48.4    
48.6    
48.7    
48.9    
49.1    
49.2    
49.4    
49.6    
49.7    
49.9    
50.1    
50.3    
50.4    
50.6    
50.8    
50.9    
51.1    
51.3    
51.4    
51.6    
51.8    
51.9    
52.1    
52.3    
52.4    
52.6    
52.8    
53.0    
53.1    
53.3    
53.5    
53.6    
53.8    
54.0    
54.1    
54.3    
54.5    
54.6    
54.8    
55.0    
55.1    
55.3    
55.5    
55.6    
55.8    
56.0    
56.2    
56.3    
56.5    
56.7    
56.8    
57.0    
57.2    
57.3    
57.5    
57.7    
57.8    
58.0    
58.2    
58.3    
58.5    
58.7    
58.9    
59.0    
59.2    
59.4    
59.5    
59.7    
59.9    
60.0    
60.2    
60.4    
60.5    
60.7    
60.9    
61.0    
61.2    
61.4    
61.6    
61.7    
61.9    
62.1    
62.2    
62.4    
62.6    
62.7    
62.9    
63.1    
63.2    
63.4    
63.6    
63.7    
63.9    
64.1    
64.2    
64.4    
64.6    
64.8    
64.9    
65.1    
65.3    
65.4    
65.6    
65.8    
65.9    
66.1    
66.3    
66.4    
66.6    
66.8    
66.9    
67.1    
67.3    
67.5    
67.6    
67.8    
68.0    
68.1    
68.3    
68.5    
68.6    
68.8    
69.0    
69.1    
69.3    
69.5    
69.6    
69.8    
70.0    
70.2    
70.3    
70.5    
70.7    
70.8    
71.0    
71.2    
71.3    
71.5    
71.7    
71.8    
72.0    
72.2    
72.3    
72.5    
72.7    
72.8    
73.0    
73.2    
73.4    
73.5    
73.7    
73.9    
74.0    
74.2    
74.4    
74.5    
74.7    
74.9    
75.0    
75.2    
75.4    
75.5    
75.7    
75.9    
76.1    
76.2    
76.4    
76.6    
76.7    
76.9    
77.1    
77.2    
77.4    
77.6    
77.7    
77.9    
78.1    
78.2    
78.4    
78.6    
78.8    
78.9    
79.1    
79.3    
79.4    
79.6    
79.8    
79.9    
80.1    
80.3    
80.4    
80.6    
80.8    
80.9    
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    
83.5    
83.6    
83.8    
84.0    
84.1    
84.3    
84.5    
84.7    
84.8    
85.0    
85.2    
85.3    
85.5    
85.7    
85.8    
86.0    
86.2    
86.3    
86.5    
86.7    
86.8    
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    
89.4    
89.5    
89.7    
89.9    
90.1    
90.2    
90.4    
90.6    
90.7    
90.9    
91.1    
91.2    
91.4    
91.6    
91.7    
91.9    
92.1    
92.2    
92.4    
92.6    
92.7    
92.9    
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    
95.3    
95.4    
95.6    
95.8    
96.0    
96.1    
96.3    
96.5    
96.6    
96.8    
97.0    
97.1    
97.3    
97.5    
97.6    
97.8    
98.0    
98.1    
98.3    
98.5    
98.7    
98.8    
99.0    
99.2    
99.3    
99.5    
99.7    
99.8    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 42456, rend_intergenic: 37406  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46857, rend_intergenic: 44753  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90252, rend_intergenic: 88363  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124975, rend_intergenic: 115438  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125898, rend_intergenic: 125226  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 9486, rend_intergenic: 9483  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support