-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_6/scaffold_6_8725585-8863724

-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_6-snap.1945-T1
Valid prediction for Augustus_model.g10067.t1
Valid prediction for snap_scaffold_6-snap.1955-T1
Valid prediction for Augustus_model.g10078.t1
Valid prediction for snap_scaffold_6-snap.1936-T1
Valid prediction for GlimmerHMM_glimmerT_15180-T1
Valid prediction for snap_scaffold_6-snap.1964-T1
Valid prediction for snap_scaffold_6-snap.1953-T1
Valid prediction for GlimmerHMM_glimmerT_15189-T1
Valid prediction for GlimmerHMM_glimmerT_15184-T1
Valid prediction for HiQ_model.g10068.t1
Valid prediction for Augustus_model.g10076.t1
Valid prediction for CodingQuarry_transcript_55148-T1
Valid prediction for Augustus_model.g10071.t1
Valid prediction for snap_scaffold_6-snap.1948-T1
Valid prediction for GlimmerHMM_glimmerT_15186-T1
Valid prediction for pasa_asmbl_47176.p1
Valid prediction for snap_scaffold_6-snap.1954-T1
Valid prediction for snap_scaffold_6-snap.1949-T1
Valid prediction for snap_scaffold_6-snap.1965-T1
Valid prediction for snap_scaffold_6-snap.1939-T1
Valid prediction for Augustus_model.g10065.t1
Valid prediction for Augustus_model.g10075.t1
Valid prediction for CodingQuarry_transcript_55147-T1
Valid prediction for GlimmerHMM_glimmerT_15182-T1
Valid prediction for GlimmerHMM_glimmerT_15174-T1
Couldn't classify 12885, 13070
Couldn't classify 25212, 25319
Sorry, prediction pasa_asmbl_47174.p1 fails validation.
(CTC)	 AC	12885-13070	GT	AGG
(GCG)	 AG	13933-14052	GT	ACG
(GTT)	 AG	14150-14269	GT	AGG
(GCG)	 AG	14370-14423	GT	CGG
(GGC)	 AG	14510-14551	GT	AGG
(GGA)	 AG	14673-14735	GT	TGG
(GGT)	 AG	15683-15757	GT	CCG
(TTC)	 AG	15957-16040	GT	AGG
(CTG)	 AG	16293-16349	GT	TAG
(GGT)	 AG	16727-16780	GT	CTG
(GGT)	 AG	16908-16961	GT	GGG
(GGA)	 AG	17189-17242	GT	AGG
(GGT)	 AG	18031-18084	GT	GAG
(GGG)	 AG	18328-18381	GT	AGG
(GGA)	 AG	18688-18732	GT	CTG
(GGG)	 AG	19619-19672	GT	CGG
(GGT)	 AG	19945-19989	GT	TGG
(GGG)	 AG	20179-20232	GT	AGG
(GGT)	 AG	20480-20524	GT	AGG
(GGT)	 AG	21019-21072	GT	CTG
(GGT)	 AG	21477-21521	GT	AGG
(GGT)	 AG	21890-21943	GT	AGG
(GGA)	 AG	22528-22572	GT	AGG
(GGT)	 AG	22813-22866	GT	GGG
(GGT)	 AG	23041-23148	GT	AGG
(GGC)	 AG	23231-23284	GT	AGG
(GGG)	 AG	23590-23643	GT	GGG
(GGA)	 AG	23758-23802	GT	ATG
(GGC)	 AG	23942-23995	GT	AGG
(GGT)	 AG	24296-24340	GT	AGG
(GGC)	 AG	24556-24609	GT	ACG
(GGG)	 AG	24784-24837	GT	CTG
(GGC)	 AG	25019-25072	GT	AGG
(GGT)	 AG	25212-25319	GT	AGG
-recovered pasa_asmbl_47174.p1, internal, 13933, 14052
-recovered pasa_asmbl_47174.p1, internal, 14150, 14269
-recovered pasa_asmbl_47174.p1, internal, 14370, 14423
-recovered pasa_asmbl_47174.p1, internal, 14510, 14551
-recovered pasa_asmbl_47174.p1, internal, 14673, 14735
-recovered pasa_asmbl_47174.p1, internal, 15683, 15757
-recovered pasa_asmbl_47174.p1, internal, 15957, 16040
-recovered pasa_asmbl_47174.p1, internal, 16293, 16349
-recovered pasa_asmbl_47174.p1, internal, 16727, 16780
-recovered pasa_asmbl_47174.p1, internal, 16908, 16961
-recovered pasa_asmbl_47174.p1, internal, 17189, 17242
-recovered pasa_asmbl_47174.p1, internal, 18031, 18084
-recovered pasa_asmbl_47174.p1, internal, 18328, 18381
-recovered pasa_asmbl_47174.p1, internal, 18688, 18732
-recovered pasa_asmbl_47174.p1, internal, 19619, 19672
-recovered pasa_asmbl_47174.p1, internal, 19945, 19989
-recovered pasa_asmbl_47174.p1, internal, 20179, 20232
-recovered pasa_asmbl_47174.p1, internal, 20480, 20524
-recovered pasa_asmbl_47174.p1, internal, 21019, 21072
-recovered pasa_asmbl_47174.p1, internal, 21477, 21521
-recovered pasa_asmbl_47174.p1, internal, 21890, 21943
-recovered pasa_asmbl_47174.p1, internal, 22528, 22572
-recovered pasa_asmbl_47174.p1, internal, 22813, 22866
-recovered pasa_asmbl_47174.p1, internal, 23041, 23148
-recovered pasa_asmbl_47174.p1, internal, 23231, 23284
-recovered pasa_asmbl_47174.p1, internal, 23590, 23643
-recovered pasa_asmbl_47174.p1, internal, 23758, 23802
-recovered pasa_asmbl_47174.p1, internal, 23942, 23995
-recovered pasa_asmbl_47174.p1, internal, 24296, 24340
-recovered pasa_asmbl_47174.p1, internal, 24556, 24609
-recovered pasa_asmbl_47174.p1, internal, 24784, 24837
-recovered pasa_asmbl_47174.p1, internal, 25019, 25072
-recovered pasa_asmbl_47174.p1, internal, 25212, 25319
Couldn't classify 5988, 6060
Couldn't classify 6677, 6842
Sorry, prediction pasa_asmbl_47173.p1 fails validation.
(GAG)	 CG	5988-6060	GT	AGG
(ACT)	 AG	6173-6386	GT	AAG
(GTG)	 AG	6677-6842	GA	TAG
-recovered pasa_asmbl_47173.p1, internal, 6173, 6386
Valid prediction for snap_scaffold_6-snap.1934-T1
Valid prediction for snap_scaffold_6-snap.1962-T1
Valid prediction for GlimmerHMM_glimmerT_15190-T1
Valid prediction for snap_scaffold_6-snap.1944-T1
Valid prediction for CodingQuarry_transcript_55149-T1
Valid prediction for Augustus_model.g10073.t1
Valid prediction for snap_scaffold_6-snap.1959-T1
Valid prediction for GlimmerHMM_glimmerT_15188-T1
Valid prediction for snap_scaffold_6-snap.1951-T1
Valid prediction for GlimmerHMM_glimmerT_15179-T1
Valid prediction for snap_scaffold_6-snap.1942-T1
Valid prediction for GlimmerHMM_glimmerT_15187-T1
Valid prediction for snap_scaffold_6-snap.1957-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 Augustus_model.g10069.t1
Valid prediction for snap_scaffold_6-snap.1967-T1
Valid prediction for snap_scaffold_6-snap.1947-T1
Couldn't classify 9756, 9886
Sorry, prediction pasa_asmbl_48591.p1 fails validation.
(CCG)	 AC	9756-9886	GT	AGG
(GAA)	 AG	10965-11021	GT	CGG
(GTT)	 AG	11326-11473	GT	TGG
(CAT)	 AG	12341-12403	GT	GTG
(AGT)	 AG	12964-13068	GT	AAG
(GCA)	 AG	13448-13576	GT	ACG
(AAA)	 AG	13723-13869	GT	GTG
(GAC)	 AG	14011-14199	GT	AGG
(CTC)	 AG	16558-16722	GT	CGG
(CCC)	 AG	17708-17817	GT	AGG
(CGA)	 AG	18102-18234	GT	AGG
(TCG)	 AG	18521-18609	GT	AGG
(CCC)	 AG	18743-18876	GT	GGG
(GTG)	 AG	19031-19182	CC	GAC
-recovered pasa_asmbl_48591.p1, terminal, 19031, 19182
-recovered pasa_asmbl_48591.p1, internal, 10965, 11021
-recovered pasa_asmbl_48591.p1, internal, 11326, 11473
-recovered pasa_asmbl_48591.p1, internal, 12341, 12403
-recovered pasa_asmbl_48591.p1, internal, 12964, 13068
-recovered pasa_asmbl_48591.p1, internal, 13448, 13576
-recovered pasa_asmbl_48591.p1, internal, 13723, 13869
-recovered pasa_asmbl_48591.p1, internal, 14011, 14199
-recovered pasa_asmbl_48591.p1, internal, 16558, 16722
-recovered pasa_asmbl_48591.p1, internal, 17708, 17817
-recovered pasa_asmbl_48591.p1, internal, 18102, 18234
-recovered pasa_asmbl_48591.p1, internal, 18521, 18609
-recovered pasa_asmbl_48591.p1, internal, 18743, 18876
Valid prediction for snap_scaffold_6-snap.1960-T1
Couldn't classify 2441, 2636
Couldn't classify 3423, 3640
Sorry, prediction pasa_asmbl_48596.p1 fails validation.
(AAC)	 GG	2441-2636	GT	ATG
(ACG)	 AG	3011-3238	GT	GCG
(ACG)	 AG	3423-3640	AC	CCA
-recovered pasa_asmbl_48596.p1, internal, 3011, 3238
Valid prediction for GlimmerHMM_glimmerT_15191-T1
Valid prediction for HiQ_model.g10079.t1
Valid prediction for GlimmerHMM_glimmerT_15181-T1
Valid prediction for snap_scaffold_6-snap.1938-T1
Valid prediction for GlimmerHMM_glimmerT_15176-T1
Valid prediction for snap_scaffold_6-snap.1958-T1
Valid prediction for GlimmerHMM_glimmerT_15185-T1
Valid prediction for snap_scaffold_6-snap.1941-T1
Valid prediction for snap_scaffold_6-snap.1963-T1
Valid prediction for snap_scaffold_6-snap.1956-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_15177-T1
Valid prediction for snap_scaffold_6-snap.1946-T1
Valid prediction for GlimmerHMM_glimmerT_15178-T1
Valid prediction for Augustus_model.g10070.t1
Valid prediction for snap_scaffold_6-snap.1940-T1
Valid prediction for Augustus_model.g10077.t1
Valid prediction for Augustus_model.g10072.t1
Valid prediction for Augustus_model.g10074.t1
Valid prediction for Augustus_model.g10080.t1
Valid prediction for Augustus_model.g10066.t1
Valid prediction for snap_scaffold_6-snap.1952-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_6-snap.1966-T1
Valid prediction for snap_scaffold_6-snap.1943-T1
Valid prediction for GlimmerHMM_glimmerT_15175-T1
Valid prediction for snap_scaffold_6-snap.1937-T1
Valid prediction for snap_scaffold_6-snap.1961-T1
Valid prediction for snap_scaffold_6-snap.1935-T1
Valid prediction for snap_scaffold_6-snap.1950-T1
Valid prediction for GlimmerHMM_glimmerT_15183-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11261, rend_intergenic: 10050  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28942, rend_intergenic: 18691  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31025, rend_intergenic: 29294  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36993, rend_intergenic: 31551  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40084, rend_intergenic: 39688  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44381, rend_intergenic: 41404  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46358, rend_intergenic: 44480  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83570, rend_intergenic: 79669  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88675, rend_intergenic: 84179  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93979, rend_intergenic: 90070  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105327, rend_intergenic: 99203  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111500, rend_intergenic: 109259  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129480, rend_intergenic: 119348  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 138140
-exon list size: 381


building trellis

0.3    
0.5    
0.8    
1.0    
1.3    
1.6    
1.8    
2.1    
2.3    
2.6    
2.9    
3.1    
3.4    
3.7    
3.9    
4.2    
4.4    
4.7    
5.0    
5.2    
5.5    
5.7    
6.0    
6.3    
6.5    
6.8    
7.0    
7.3    
7.6    
7.8    
8.1    
8.4    
8.6    
8.9    
9.1    
9.4    
9.7    
9.9    
10.2    
10.4    
10.7    
11.0    
11.2    
11.5    
11.7    
12.0    
12.3    
12.5    
12.8    
13.1    
13.3    
13.6    
13.8    
14.1    
14.4    
14.6    
14.9    
15.1    
15.4    
15.7    
15.9    
16.2    
16.4    
16.7    
17.0    
17.2    
17.5    
17.8    
18.0    
18.3    
18.5    
18.8    
19.1    
19.3    
19.6    
19.8    
20.1    
20.4    
20.6    
20.9    
21.1    
21.4    
21.7    
21.9    
22.2    
22.5    
22.7    
23.0    
23.2    
23.5    
23.8    
24.0    
24.3    
24.5    
24.8    
25.1    
25.3    
25.6    
25.8    
26.1    
26.4    
26.6    
26.9    
27.2    
27.4    
27.7    
27.9    
28.2    
28.5    
28.7    
29.0    
29.2    
29.5    
29.8    
30.0    
30.3    
30.5    
30.8    
31.1    
31.3    
31.6    
31.9    
32.1    
32.4    
32.6    
32.9    
33.2    
33.4    
33.7    
33.9    
34.2    
34.5    
34.7    
35.0    
35.2    
35.5    
35.8    
36.0    
36.3    
36.6    
36.8    
37.1    
37.3    
37.6    
37.9    
38.1    
38.4    
38.6    
38.9    
39.2    
39.4    
39.7    
39.9    
40.2    
40.5    
40.7    
41.0    
41.3    
41.5    
41.8    
42.0    
42.3    
42.6    
42.8    
43.1    
43.3    
43.6    
43.9    
44.1    
44.4    
44.6    
44.9    
45.2    
45.4    
45.7    
46.0    
46.2    
46.5    
46.7    
47.0    
47.3    
47.5    
47.8    
48.0    
48.3    
48.6    
48.8    
49.1    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
50.9    
51.2    
51.4    
51.7    
52.0    
52.2    
52.5    
52.7    
53.0    
53.3    
53.5    
53.8    
54.0    
54.3    
54.6    
54.8    
55.1    
55.4    
55.6    
55.9    
56.1    
56.4    
56.7    
56.9    
57.2    
57.4    
57.7    
58.0    
58.2    
58.5    
58.7    
59.0    
59.3    
59.5    
59.8    
60.1    
60.3    
60.6    
60.8    
61.1    
61.4    
61.6    
61.9    
62.1    
62.4    
62.7    
62.9    
63.2    
63.4    
63.7    
64.0    
64.2    
64.5    
64.8    
65.0    
65.3    
65.5    
65.8    
66.1    
66.3    
66.6    
66.8    
67.1    
67.4    
67.6    
67.9    
68.1    
68.4    
68.7    
68.9    
69.2    
69.5    
69.7    
70.0    
70.2    
70.5    
70.8    
71.0    
71.3    
71.5    
71.8    
72.1    
72.3    
72.6    
72.8    
73.1    
73.4    
73.6    
73.9    
74.2    
74.4    
74.7    
74.9    
75.2    
75.5    
75.7    
76.0    
76.2    
76.5    
76.8    
77.0    
77.3    
77.5    
77.8    
78.1    
78.3    
78.6    
78.9    
79.1    
79.4    
79.6    
79.9    
80.2    
80.4    
80.7    
80.9    
81.2    
81.5    
81.7    
82.0    
82.2    
82.5    
82.8    
83.0    
83.3    
83.6    
83.8    
84.1    
84.3    
84.6    
84.9    
85.1    
85.4    
85.6    
85.9    
86.2    
86.4    
86.7    
86.9    
87.2    
87.5    
87.7    
88.0    
88.3    
88.5    
88.8    
89.0    
89.3    
89.6    
89.8    
90.1    
90.3    
90.6    
90.9    
91.1    
91.4    
91.6    
91.9    
92.2    
92.4    
92.7    
93.0    
93.2    
93.5    
93.7    
94.0    
94.3    
94.5    
94.8    
95.0    
95.3    
95.6    
95.8    
96.1    
96.3    
96.6    
96.9    
97.1    
97.4    
97.7    
97.9    
98.2    
98.4    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 11261, rend_intergenic: 10050  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28942, rend_intergenic: 18691  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31025, rend_intergenic: 29294  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36993, rend_intergenic: 31551  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40084, rend_intergenic: 39688  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44381, rend_intergenic: 41404  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46358, rend_intergenic: 44480  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83570, rend_intergenic: 79669  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88675, rend_intergenic: 84179  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93979, rend_intergenic: 90070  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105327, rend_intergenic: 99203  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111500, rend_intergenic: 109259  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129480, rend_intergenic: 119348  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

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