-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_9/scaffold_9_2543662-2854709

-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 CodingQuarry_transcript_62126-T1
Valid prediction for GlimmerHMM_glimmerT_21768-T1
Valid prediction for snap_scaffold_9-snap.576-T1
Valid prediction for snap_scaffold_9-snap.569-T1
Valid prediction for snap_scaffold_9-snap.586-T1
Valid prediction for snap_scaffold_9-snap.592-T1
Valid prediction for snap_scaffold_9-snap.547-T1
Valid prediction for snap_scaffold_9-snap.594-T1
Couldn't classify 93238, 93324
Sorry, prediction pasa_asmbl_53849.p1 fails validation.
(GAG)	 CA	93238-93324	GT	TGG
(GAA)	 AG	94917-95037	GC	AGG
(GTG)	 AG	95829-95923	GT	AGG
(TCC)	 AG	96266-96386	GT	GGG
(CTT)	 AG	97416-97504	GT	AGG
(GTG)	 AG	97955-98044	AG	AGA
add_exon() Sorry, pasa_asmbl_53849.p1 94917-95037-terminal-3 is invalid.
-recovered pasa_asmbl_53849.p1, terminal, 94917, 95037
-recovered pasa_asmbl_53849.p1, terminal, 97955, 98044
-recovered pasa_asmbl_53849.p1, internal, 94917, 95037
-recovered pasa_asmbl_53849.p1, internal, 95829, 95923
-recovered pasa_asmbl_53849.p1, internal, 96266, 96386
-recovered pasa_asmbl_53849.p1, internal, 97416, 97504
Couldn't classify 279629, 279782
Couldn't classify 280089, 280174
Sorry, prediction pasa_asmbl_53870.p1 fails validation.
(CCT)	 AT	279629-279782	GT	GTG
(ATC)	 AG	279877-279948	GT	GGG
(GTT)	 AG	280089-280174	AC	AGA
-recovered pasa_asmbl_53870.p1, internal, 279877, 279948
Valid prediction for Augustus_model.g14467.t1
Valid prediction for snap_scaffold_9-snap.550-T1
Valid prediction for snap_scaffold_9-snap.560-T1
Valid prediction for Augustus_model.g14471.t1
Valid prediction for CodingQuarry_transcript_62123-T1
Valid prediction for pasa_asmbl_53868.p1
Valid prediction for snap_scaffold_9-snap.573-T1
Valid prediction for CodingQuarry_transcript_62121-T1
Valid prediction for snap_scaffold_9-snap.552-T1
Valid prediction for pasa_asmbl_54695.p1
Valid prediction for HiQ_model.g14488.t1
Valid prediction for GlimmerHMM_glimmerT_21787-T1
Valid prediction for GlimmerHMM_glimmerT_21757-T1
Valid prediction for Augustus_model.g14476.t1
Valid prediction for Augustus_model.g14478.t1
Valid prediction for Augustus_model.g14479.t1
Valid prediction for Augustus_model.g14486.t1
Valid prediction for GlimmerHMM_glimmerT_21774-T1
Valid prediction for snap_scaffold_9-snap.585-T1
Valid prediction for snap_scaffold_9-snap.575-T1
Valid prediction for GlimmerHMM_glimmerT_21761-T1
Valid prediction for snap_scaffold_9-snap.583-T1
Valid prediction for GlimmerHMM_glimmerT_21777-T1
Valid prediction for snap_scaffold_9-snap.588-T1
Valid prediction for snap_scaffold_9-snap.564-T1
Valid prediction for GlimmerHMM_glimmerT_21775-T1
Valid prediction for Augustus_model.g14480.t1
Valid prediction for snap_scaffold_9-snap.589-T1
Valid prediction for snap_scaffold_9-snap.556-T1
Valid prediction for GlimmerHMM_glimmerT_21780-T1
Valid prediction for CodingQuarry_transcript_62122-T1
Valid prediction for Augustus_model.g14470.t1
Valid prediction for GlimmerHMM_glimmerT_21765-T1
Valid prediction for Augustus_model.g14468.t1
Valid prediction for snap_scaffold_9-snap.551-T1
Valid prediction for Augustus_model.g14484.t1
Valid prediction for GlimmerHMM_glimmerT_21785-T1
Couldn't classify 280877, 281024
Sorry, prediction pasa_asmbl_54716.p1 fails validation.
(CAG)	 GA	280877-281024	GT	AGG
(CAT)	 AG	281381-281524	GT	AGG
(ATG)	 AG	281627-281770	GT	GAG
(CCA)	 AG	281955-282346	AT	GAA
add_exon() Sorry, pasa_asmbl_54716.p1 281627-281770-initial-1 is invalid.
-recovered pasa_asmbl_54716.p1, initial, 281627, 281770
-recovered pasa_asmbl_54716.p1, terminal, 281955, 282346
-recovered pasa_asmbl_54716.p1, internal, 281381, 281524
-recovered pasa_asmbl_54716.p1, internal, 281627, 281770
Valid prediction for pasa_asmbl_53852.p1
Valid prediction for HiQ_model.g14482.t1
Valid prediction for pasa_asmbl_53863.p1
Valid prediction for CodingQuarry_transcript_62124-T1
Valid prediction for GlimmerHMM_glimmerT_21762-T1
Valid prediction for Augustus_model.g14469.t1
Valid prediction for Augustus_model.g14475.t1
Valid prediction for GlimmerHMM_glimmerT_21770-T1
Couldn't classify 85827, 85906
Couldn't classify 89209, 89294
Sorry, prediction pasa_asmbl_54775.p1 fails validation.
(GTA)	 AG	85827-85906	GT	AAG
(GGC)	 AG	86032-86076	GT	AGG
(ACG)	 AG	86963-87007	GT	AAG
(AGC)	 AG	88779-88822	GT	GGG
(GTC)	 AG	89209-89294	GG	AGG
-recovered pasa_asmbl_54775.p1, internal, 85827, 85906
-recovered pasa_asmbl_54775.p1, internal, 86032, 86076
-recovered pasa_asmbl_54775.p1, internal, 86963, 87007
-recovered pasa_asmbl_54775.p1, internal, 88779, 88822
Couldn't classify 247460, 247855
Sorry, prediction pasa_asmbl_53858.p1 fails validation.
(CAC)	 CA	247460-247855	AA	GAA
Valid prediction for Augustus_model.g14483.t1
Valid prediction for Augustus_model.g14474.t1
Valid prediction for snap_scaffold_9-snap.584-T1
Valid prediction for GlimmerHMM_glimmerT_21766-T1
Valid prediction for GlimmerHMM_glimmerT_21778-T1
Valid prediction for GlimmerHMM_glimmerT_21759-T1
Valid prediction for Augustus_model.g14481.t1
Valid prediction for GlimmerHMM_glimmerT_21781-T1
Couldn't classify 134892, 135077
Couldn't classify 136043, 136228
Sorry, prediction pasa_asmbl_54756.p1 fails validation.
(GGC)	 GG	134892-135077	GT	AGG
(CCG)	 AG	136043-136228	CA	TCC
Valid prediction for GlimmerHMM_glimmerT_21772-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 GlimmerHMM_glimmerT_21767-T1
Valid prediction for GlimmerHMM_glimmerT_21764-T1
Valid prediction for GlimmerHMM_glimmerT_21786-T1
Valid prediction for snap_scaffold_9-snap.570-T1
Valid prediction for snap_scaffold_9-snap.590-T1
Valid prediction for snap_scaffold_9-snap.554-T1
Valid prediction for snap_scaffold_9-snap.580-T1
Valid prediction for snap_scaffold_9-snap.577-T1
Valid prediction for GlimmerHMM_glimmerT_21779-T1
Valid prediction for GlimmerHMM_glimmerT_21784-T1
Valid prediction for snap_scaffold_9-snap.555-T1
Valid prediction for snap_scaffold_9-snap.582-T1
Valid prediction for GlimmerHMM_glimmerT_21758-T1
Valid prediction for GlimmerHMM_glimmerT_21773-T1
Valid prediction for CodingQuarry_transcript_62125-T1
Valid prediction for Augustus_model.g14487.t1
Valid prediction for snap_scaffold_9-snap.557-T1
Valid prediction for GlimmerHMM_glimmerT_21776-T1
Valid prediction for HiQ_model.g14485.t1
Valid prediction for pasa_asmbl_54882.p1
Valid prediction for snap_scaffold_9-snap.574-T1
Valid prediction for snap_scaffold_9-snap.548-T1
Valid prediction for HiQ_model.g14472.t1
Valid prediction for pasa_asmbl_54885.p1
Valid prediction for snap_scaffold_9-snap.553-T1
Valid prediction for GlimmerHMM_glimmerT_21783-T1
Valid prediction for snap_scaffold_9-snap.565-T1
Valid prediction for snap_scaffold_9-snap.593-T1
Valid prediction for snap_scaffold_9-snap.572-T1
Valid prediction for snap_scaffold_9-snap.558-T1
Valid prediction for snap_scaffold_9-snap.578-T1
Valid prediction for CodingQuarry_transcript_62117-T1
Valid prediction for GlimmerHMM_glimmerT_21771-T1
Valid prediction for snap_scaffold_9-snap.563-T1
Valid prediction for snap_scaffold_9-snap.579-T1
Valid prediction for snap_scaffold_9-snap.559-T1
Valid prediction for Augustus_model.g14473.t1
Valid prediction for snap_scaffold_9-snap.561-T1
Valid prediction for snap_scaffold_9-snap.566-T1
Valid prediction for GlimmerHMM_glimmerT_21763-T1
Valid prediction for snap_scaffold_9-snap.568-T1
Valid prediction for GlimmerHMM_glimmerT_21782-T1
Valid prediction for snap_scaffold_9-snap.562-T1
Valid prediction for GlimmerHMM_glimmerT_21760-T1
Valid prediction for snap_scaffold_9-snap.567-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_9-snap.549-T1
Valid prediction for Augustus_model.g14477.t1
Valid prediction for snap_scaffold_9-snap.571-T1
Valid prediction for GlimmerHMM_glimmerT_21769-T1
Valid prediction for snap_scaffold_9-snap.591-T1
Valid prediction for snap_scaffold_9-snap.587-T1
Valid prediction for snap_scaffold_9-snap.581-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 26410, rend_intergenic: 12634  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47645, rend_intergenic: 27447  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87011, rend_intergenic: 48009  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98998, rend_intergenic: 87824  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109963, rend_intergenic: 104543  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120934, rend_intergenic: 110024  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139391, rend_intergenic: 124601  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158007, rend_intergenic: 139932  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176307, rend_intergenic: 165124  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196560, rend_intergenic: 177139  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 215511, rend_intergenic: 196566  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 249550, rend_intergenic: 216037  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 305080, rend_intergenic: 302380  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 311048
-exon list size: 434


building trellis

0.2    
0.5    
0.7    
0.9    
1.1    
1.4    
1.6    
1.8    
2.1    
2.3    
2.5    
2.8    
3.0    
3.2    
3.4    
3.7    
3.9    
4.1    
4.4    
4.6    
4.8    
5.0    
5.3    
5.5    
5.7    
6.0    
6.2    
6.4    
6.7    
6.9    
7.1    
7.3    
7.6    
7.8    
8.0    
8.3    
8.5    
8.7    
8.9    
9.2    
9.4    
9.6    
9.9    
10.1    
10.3    
10.6    
10.8    
11.0    
11.2    
11.5    
11.7    
11.9    
12.2    
12.4    
12.6    
12.8    
13.1    
13.3    
13.5    
13.8    
14.0    
14.2    
14.4    
14.7    
14.9    
15.1    
15.4    
15.6    
15.8    
16.1    
16.3    
16.5    
16.7    
17.0    
17.2    
17.4    
17.7    
17.9    
18.1    
18.3    
18.6    
18.8    
19.0    
19.3    
19.5    
19.7    
20.0    
20.2    
20.4    
20.6    
20.9    
21.1    
21.3    
21.6    
21.8    
22.0    
22.2    
22.5    
22.7    
22.9    
23.2    
23.4    
23.6    
23.9    
24.1    
24.3    
24.5    
24.8    
25.0    
25.2    
25.5    
25.7    
25.9    
26.1    
26.4    
26.6    
26.8    
27.1    
27.3    
27.5    
27.8    
28.0    
28.2    
28.4    
28.7    
28.9    
29.1    
29.4    
29.6    
29.8    
30.0    
30.3    
30.5    
30.7    
31.0    
31.2    
31.4    
31.7    
31.9    
32.1    
32.3    
32.6    
32.8    
33.0    
33.3    
33.5    
33.7    
33.9    
34.2    
34.4    
34.6    
34.9    
35.1    
35.3    
35.6    
35.8    
36.0    
36.2    
36.5    
36.7    
36.9    
37.2    
37.4    
37.6    
37.8    
38.1    
38.3    
38.5    
38.8    
39.0    
39.2    
39.4    
39.7    
39.9    
40.1    
40.4    
40.6    
40.8    
41.1    
41.3    
41.5    
41.7    
42.0    
42.2    
42.4    
42.7    
42.9    
43.1    
43.3    
43.6    
43.8    
44.0    
44.3    
44.5    
44.7    
45.0    
45.2    
45.4    
45.6    
45.9    
46.1    
46.3    
46.6    
46.8    
47.0    
47.2    
47.5    
47.7    
47.9    
48.2    
48.4    
48.6    
48.9    
49.1    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
50.7    
50.9    
51.1    
51.4    
51.6    
51.8    
52.1    
52.3    
52.5    
52.8    
53.0    
53.2    
53.4    
53.7    
53.9    
54.1    
54.4    
54.6    
54.8    
55.0    
55.3    
55.5    
55.7    
56.0    
56.2    
56.4    
56.7    
56.9    
57.1    
57.3    
57.6    
57.8    
58.0    
58.3    
58.5    
58.7    
58.9    
59.2    
59.4    
59.6    
59.9    
60.1    
60.3    
60.6    
60.8    
61.0    
61.2    
61.5    
61.7    
61.9    
62.2    
62.4    
62.6    
62.8    
63.1    
63.3    
63.5    
63.8    
64.0    
64.2    
64.4    
64.7    
64.9    
65.1    
65.4    
65.6    
65.8    
66.1    
66.3    
66.5    
66.7    
67.0    
67.2    
67.4    
67.7    
67.9    
68.1    
68.3    
68.6    
68.8    
69.0    
69.3    
69.5    
69.7    
70.0    
70.2    
70.4    
70.6    
70.9    
71.1    
71.3    
71.6    
71.8    
72.0    
72.2    
72.5    
72.7    
72.9    
73.2    
73.4    
73.6    
73.9    
74.1    
74.3    
74.5    
74.8    
75.0    
75.2    
75.5    
75.7    
75.9    
76.1    
76.4    
76.6    
76.8    
77.1    
77.3    
77.5    
77.8    
78.0    
78.2    
78.4    
78.7    
78.9    
79.1    
79.4    
79.6    
79.8    
80.0    
80.3    
80.5    
80.7    
81.0    
81.2    
81.4    
81.7    
81.9    
82.1    
82.3    
82.6    
82.8    
83.0    
83.3    
83.5    
83.7    
83.9    
84.2    
84.4    
84.6    
84.9    
85.1    
85.3    
85.6    
85.8    
86.0    
86.2    
86.5    
86.7    
86.9    
87.2    
87.4    
87.6    
87.8    
88.1    
88.3    
88.5    
88.8    
89.0    
89.2    
89.4    
89.7    
89.9    
90.1    
90.4    
90.6    
90.8    
91.1    
91.3    
91.5    
91.7    
92.0    
92.2    
92.4    
92.7    
92.9    
93.1    
93.3    
93.6    
93.8    
94.0    
94.3    
94.5    
94.7    
95.0    
95.2    
95.4    
95.6    
95.9    
96.1    
96.3    
96.6    
96.8    
97.0    
97.2    
97.5    
97.7    
97.9    
98.2    
98.4    
98.6    
98.9    
99.1    
99.3    
99.5    
99.8    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 26410, rend_intergenic: 12634  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47645, rend_intergenic: 27447  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87011, rend_intergenic: 48009  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98998, rend_intergenic: 87824  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109963, rend_intergenic: 104543  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120934, rend_intergenic: 110024  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139391, rend_intergenic: 124601  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158007, rend_intergenic: 139932  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176307, rend_intergenic: 165124  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196560, rend_intergenic: 177139  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 215511, rend_intergenic: 196566  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 249550, rend_intergenic: 216037  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 305080, rend_intergenic: 302380  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 16658
-exon list size: 5


building trellis

14.3    
28.6    
42.9    
57.1    
71.4    
85.7    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 2284 - 16658
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 2284 - 12633
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support