-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_2/scaffold_2_794644-955749

-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_2-snap.196-T1
Valid prediction for snap_scaffold_2-snap.198-T1
Valid prediction for CodingQuarry_transcript_28433-T1
Valid prediction for GlimmerHMM_glimmerT_3131-T1
Valid prediction for Augustus_model.g2120.t1
Valid prediction for pasa_asmbl_24114.p1
Valid prediction for HiQ_model.g2126.t1
Valid prediction for GlimmerHMM_glimmerT_3135-T1
Valid prediction for CodingQuarry_transcript_28442-T1
Valid prediction for GlimmerHMM_glimmerT_3134-T1
Valid prediction for snap_scaffold_2-snap.204-T1
Valid prediction for snap_scaffold_2-snap.208-T1
Valid prediction for Augustus_model.g2124.t1
Valid prediction for GlimmerHMM_glimmerT_3128-T1
Valid prediction for CodingQuarry_transcript_28444-T1
Valid prediction for GlimmerHMM_glimmerT_3129-T1
Valid prediction for Augustus_model.g2131.t1
Valid prediction for Augustus_model.g2128.t1
Valid prediction for CodingQuarry_transcript_28441-T1
Valid prediction for snap_scaffold_2-snap.203-T1
Valid prediction for CodingQuarry_transcript_28436-T1
Couldn't classify 9610, 9713
Sorry, prediction pasa_asmbl_24107.p1 fails validation.
(ATG)	 CG	4177-4261	GC	AGG
(AAG)	 AG	4669-4766	GT	TTG
(ACT)	 AG	6196-6325	GT	CGG
(GGC)	 AG	6424-6573	GT	AGG
(GAG)	 AG	6708-6847	GT	AGG
(GAG)	 AG	7247-7312	GT	TGG
(TGC)	 AG	7831-7875	GT	TGG
(ACT)	 AG	8209-8326	GT	CTG
(TCA)	 AG	9610-9713	AG	CCA
-recovered pasa_asmbl_24107.p1, initial, 4177, 4261
-recovered pasa_asmbl_24107.p1, internal, 4669, 4766
-recovered pasa_asmbl_24107.p1, internal, 6196, 6325
-recovered pasa_asmbl_24107.p1, internal, 6424, 6573
-recovered pasa_asmbl_24107.p1, internal, 6708, 6847
-recovered pasa_asmbl_24107.p1, internal, 7247, 7312
-recovered pasa_asmbl_24107.p1, internal, 7831, 7875
-recovered pasa_asmbl_24107.p1, internal, 8209, 8326
Valid prediction for CodingQuarry_transcript_28434-T1
Valid prediction for HiQ_model.g2122.t1
Valid prediction for snap_scaffold_2-snap.213-T1
Valid prediction for CodingQuarry_transcript_28445-T1
Valid prediction for CodingQuarry_transcript_28437-T1
Valid prediction for HiQ_model.g2125.t1
Valid prediction for CodingQuarry_transcript_28440-T1
Couldn't classify 2084, 2117
Sorry, prediction pasa_asmbl_24105.p1 fails validation.
(ATA)	 CA	2084-2117	GT	AGG
(GAC)	 AG	2410-2495	GT	CGG
(CTT)	 AG	2610-2666	GT	TGG
(GAT)	 AG	2815-2982	GC	GAG
-recovered pasa_asmbl_24105.p1, terminal, 2815, 2982
-recovered pasa_asmbl_24105.p1, internal, 2410, 2495
-recovered pasa_asmbl_24105.p1, internal, 2610, 2666
-recovered pasa_asmbl_24105.p1, internal, 2815, 2982
Valid prediction for HiQ_model.g2110.t1
Valid prediction for Augustus_model.g2116.t1
Couldn't classify 138509, 138619
Sorry, prediction pasa_asmbl_24160.p1 fails validation.
(ATG)	 AA	134204-134410	GT	AGG
(AGT)	 AG	135967-136104	GC	AGG
(GAT)	 AG	137021-137119	GT	CGG
(GAC)	 AG	137936-138019	GT	AGG
(GGT)	 AG	138509-138619	GG	CAG
-recovered pasa_asmbl_24160.p1, initial, 134204, 134410
-recovered pasa_asmbl_24160.p1, internal, 135967, 136104
-recovered pasa_asmbl_24160.p1, internal, 137021, 137119
-recovered pasa_asmbl_24160.p1, internal, 137936, 138019
Valid prediction for HiQ_model.g2123.t1
Valid prediction for snap_scaffold_2-snap.188-T1
Valid prediction for snap_scaffold_2-snap.206-T1
Couldn't classify 154865, 154942
Sorry, prediction pasa_asmbl_24169.p1 fails validation.
(GAG)	 AG	154865-154942	GT	AGG
(GAG)	 AG	155374-155487	GT	AGG
(GCG)	 AG	155736-155852	AC	AAA
-recovered pasa_asmbl_24169.p1, terminal, 155736, 155852
-recovered pasa_asmbl_24169.p1, internal, 154865, 154942
-recovered pasa_asmbl_24169.p1, internal, 155374, 155487
Valid prediction for GlimmerHMM_glimmerT_3130-T1
Valid prediction for pasa_asmbl_24142.p2
Valid prediction for GlimmerHMM_glimmerT_3137-T1
Valid prediction for GlimmerHMM_glimmerT_3124-T1
Valid prediction for snap_scaffold_2-snap.200-T1
Valid prediction for Augustus_model.g2132.t1
Valid prediction for CodingQuarry_transcript_28438-T1
Valid prediction for CodingQuarry_transcript_28443-T1
Valid prediction for GlimmerHMM_glimmerT_3122-T1
Valid prediction for Augustus_model.g2117.t1
Valid prediction for Augustus_model.g2113.t1
Valid prediction for snap_scaffold_2-snap.217-T1
Valid prediction for snap_scaffold_2-snap.191-T1
Valid prediction for GlimmerHMM_glimmerT_3117-T1
Valid prediction for GlimmerHMM_glimmerT_3126-T1
Valid prediction for Augustus_model.g2119.t1
Valid prediction for GlimmerHMM_glimmerT_3125-T1
Valid prediction for snap_scaffold_2-snap.195-T1
Valid prediction for GlimmerHMM_glimmerT_3115-T1
Valid prediction for CodingQuarry_transcript_28435-T1
Valid prediction for snap_scaffold_2-snap.211-T1
Valid prediction for snap_scaffold_2-snap.193-T1
Valid prediction for Augustus_model.g2112.t1
Valid prediction for GlimmerHMM_glimmerT_3119-T1
Valid prediction for GlimmerHMM_glimmerT_3111-T1
Valid prediction for pasa_asmbl_24124.p2
Valid prediction for GlimmerHMM_glimmerT_3120-T1
Valid prediction for GlimmerHMM_glimmerT_3112-T1
Valid prediction for Augustus_model.g2111.t1
Couldn't classify 126942, 127113
Couldn't classify 127492, 127634
Sorry, prediction pasa_asmbl_25342.p1 fails validation.
(GGC)	 CA	126942-127113	GT	GGG
(GTC)	 AG	127492-127634	GG	CAG
Valid prediction for snap_scaffold_2-snap.210-T1
Couldn't classify 127978, 128271
Couldn't classify 138509, 138619
Sorry, prediction pasa_asmbl_24155.p1 fails validation.
(GGG)	 TG	127978-128271	GT	AGG
(AAG)	 AG	128374-128507	GT	AGG
(CAC)	 AG	128601-128871	GT	AGG
(GCG)	 AG	129121-129249	GT	AGG
(ATC)	 AG	132120-132163	GT	AGG
(TAA)	 AG	134329-134410	GT	AGG
(AGT)	 AG	135967-136104	GC	AGG
(GAT)	 AG	137021-137119	GT	CGG
(GAC)	 AG	137936-138019	GT	AGG
(GGT)	 AG	138509-138619	GG	CAG
-recovered pasa_asmbl_24155.p1, internal, 128374, 128507
-recovered pasa_asmbl_24155.p1, internal, 128601, 128871
-recovered pasa_asmbl_24155.p1, internal, 129121, 129249
-recovered pasa_asmbl_24155.p1, internal, 132120, 132163
-recovered pasa_asmbl_24155.p1, internal, 134329, 134410
-recovered pasa_asmbl_24155.p1, internal, 135967, 136104
-recovered pasa_asmbl_24155.p1, internal, 137021, 137119
-recovered pasa_asmbl_24155.p1, internal, 137936, 138019
Valid prediction for Augustus_model.g2121.t1
Valid prediction for snap_scaffold_2-snap.184-T1
Valid prediction for snap_scaffold_2-snap.207-T1
Valid prediction for snap_scaffold_2-snap.202-T1
Valid prediction for Augustus_model.g2129.t1
Valid prediction for pasa_asmbl_24147.p1
Valid prediction for snap_scaffold_2-snap.187-T1
Couldn't classify 85574, 85609
Sorry, prediction pasa_asmbl_24121.p1 fails validation.
(TGC)	 GC	85574-85609	GT	AGG
(GAG)	 AG	85996-86085	GT	AGG
(ATT)	 AG	86302-86478	GT	AGG
(GAC)	 AG	86976-87053	AA	AGA
-recovered pasa_asmbl_24121.p1, terminal, 86976, 87053
-recovered pasa_asmbl_24121.p1, internal, 85996, 86085
-recovered pasa_asmbl_24121.p1, internal, 86302, 86478
Valid prediction for snap_scaffold_2-snap.205-T1
Valid prediction for GlimmerHMM_glimmerT_3139-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_2-snap.216-T1
Valid prediction for GlimmerHMM_glimmerT_3123-T1
Valid prediction for Augustus_model.g2127.t1
Valid prediction for GlimmerHMM_glimmerT_3114-T1
Valid prediction for snap_scaffold_2-snap.218-T1
Valid prediction for snap_scaffold_2-snap.215-T1
Valid prediction for GlimmerHMM_glimmerT_3121-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g2114.t1
Valid prediction for GlimmerHMM_glimmerT_3133-T1
Valid prediction for snap_scaffold_2-snap.194-T1
Couldn't classify 99564, 99770
Sorry, prediction pasa_asmbl_22823.p1 fails validation.
(ATG)	 CA	98235-98270	GT	AGG
(AGA)	 AG	98366-98485	GT	AGG
(GCA)	 AG	98718-98847	GT	CGG
(GTC)	 AG	99019-99141	GT	AGG
(GTG)	 AG	99255-99424	GT	AGG
(GAC)	 AG	99564-99770	CT	TCC
-recovered pasa_asmbl_22823.p1, initial, 98235, 98270
-recovered pasa_asmbl_22823.p1, internal, 98366, 98485
-recovered pasa_asmbl_22823.p1, internal, 98718, 98847
-recovered pasa_asmbl_22823.p1, internal, 99019, 99141
-recovered pasa_asmbl_22823.p1, internal, 99255, 99424
Valid prediction for snap_scaffold_2-snap.212-T1
Valid prediction for snap_scaffold_2-snap.201-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_3118-T1
Valid prediction for snap_scaffold_2-snap.185-T1
Valid prediction for GlimmerHMM_glimmerT_3136-T1
Valid prediction for snap_scaffold_2-snap.189-T1
Valid prediction for Augustus_model.g2115.t1
Valid prediction for snap_scaffold_2-snap.199-T1
Valid prediction for GlimmerHMM_glimmerT_3110-T1
Valid prediction for GlimmerHMM_glimmerT_3138-T1
Valid prediction for GlimmerHMM_glimmerT_3116-T1
Valid prediction for snap_scaffold_2-snap.190-T1
Valid prediction for GlimmerHMM_glimmerT_3132-T1
Valid prediction for GlimmerHMM_glimmerT_3113-T1
Valid prediction for snap_scaffold_2-snap.197-T1
Valid prediction for Augustus_model.g2118.t1
Valid prediction for Augustus_model.g2130.t1
Valid prediction for GlimmerHMM_glimmerT_3127-T1
Valid prediction for snap_scaffold_2-snap.209-T1
Valid prediction for snap_scaffold_2-snap.192-T1
Valid prediction for snap_scaffold_2-snap.186-T1
Couldn't classify 19242, 21134
Sorry, prediction pasa_asmbl_22824.p1 fails validation.
(GCT)	 CA	19242-21134	GC	AAG
Valid prediction for snap_scaffold_2-snap.214-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15678, rend_intergenic: 8430  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21529, rend_intergenic: 16930  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30791, rend_intergenic: 27048  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44880, rend_intergenic: 43439  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74776, rend_intergenic: 72997  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122768, rend_intergenic: 112470  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131464, rend_intergenic: 126676  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134568, rend_intergenic: 133989  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138052, rend_intergenic: 135487  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157361, rend_intergenic: 150648  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 161106
-exon list size: 382


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    
3.6    
3.9    
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4.4    
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4.9    
5.2    
5.5    
5.7    
6.0    
6.2    
6.5    
6.8    
7.0    
7.3    
7.6    
7.8    
8.1    
8.3    
8.6    
8.9    
9.1    
9.4    
9.6    
9.9    
10.2    
10.4    
10.7    
10.9    
11.2    
11.5    
11.7    
12.0    
12.2    
12.5    
12.8    
13.0    
13.3    
13.5    
13.8    
14.1    
14.3    
14.6    
14.8    
15.1    
15.4    
15.6    
15.9    
16.1    
16.4    
16.7    
16.9    
17.2    
17.4    
17.7    
18.0    
18.2    
18.5    
18.8    
19.0    
19.3    
19.5    
19.8    
20.1    
20.3    
20.6    
20.8    
21.1    
21.4    
21.6    
21.9    
22.1    
22.4    
22.7    
22.9    
23.2    
23.4    
23.7    
24.0    
24.2    
24.5    
24.7    
25.0    
25.3    
25.5    
25.8    
26.0    
26.3    
26.6    
26.8    
27.1    
27.3    
27.6    
27.9    
28.1    
28.4    
28.6    
28.9    
29.2    
29.4    
29.7    
29.9    
30.2    
30.5    
30.7    
31.0    
31.2    
31.5    
31.8    
32.0    
32.3    
32.6    
32.8    
33.1    
33.3    
33.6    
33.9    
34.1    
34.4    
34.6    
34.9    
35.2    
35.4    
35.7    
35.9    
36.2    
36.5    
36.7    
37.0    
37.2    
37.5    
37.8    
38.0    
38.3    
38.5    
38.8    
39.1    
39.3    
39.6    
39.8    
40.1    
40.4    
40.6    
40.9    
41.1    
41.4    
41.7    
41.9    
42.2    
42.4    
42.7    
43.0    
43.2    
43.5    
43.8    
44.0    
44.3    
44.5    
44.8    
45.1    
45.3    
45.6    
45.8    
46.1    
46.4    
46.6    
46.9    
47.1    
47.4    
47.7    
47.9    
48.2    
48.4    
48.7    
49.0    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.0    
51.3    
51.6    
51.8    
52.1    
52.3    
52.6    
52.9    
53.1    
53.4    
53.6    
53.9    
54.2    
54.4    
54.7    
54.9    
55.2    
55.5    
55.7    
56.0    
56.2    
56.5    
56.8    
57.0    
57.3    
57.6    
57.8    
58.1    
58.3    
58.6    
58.9    
59.1    
59.4    
59.6    
59.9    
60.2    
60.4    
60.7    
60.9    
61.2    
61.5    
61.7    
62.0    
62.2    
62.5    
62.8    
63.0    
63.3    
63.5    
63.8    
64.1    
64.3    
64.6    
64.8    
65.1    
65.4    
65.6    
65.9    
66.1    
66.4    
66.7    
66.9    
67.2    
67.4    
67.7    
68.0    
68.2    
68.5    
68.8    
69.0    
69.3    
69.5    
69.8    
70.1    
70.3    
70.6    
70.8    
71.1    
71.4    
71.6    
71.9    
72.1    
72.4    
72.7    
72.9    
73.2    
73.4    
73.7    
74.0    
74.2    
74.5    
74.7    
75.0    
75.3    
75.5    
75.8    
76.0    
76.3    
76.6    
76.8    
77.1    
77.3    
77.6    
77.9    
78.1    
78.4    
78.6    
78.9    
79.2    
79.4    
79.7    
79.9    
80.2    
80.5    
80.7    
81.0    
81.2    
81.5    
81.8    
82.0    
82.3    
82.6    
82.8    
83.1    
83.3    
83.6    
83.9    
84.1    
84.4    
84.6    
84.9    
85.2    
85.4    
85.7    
85.9    
86.2    
86.5    
86.7    
87.0    
87.2    
87.5    
87.8    
88.0    
88.3    
88.5    
88.8    
89.1    
89.3    
89.6    
89.8    
90.1    
90.4    
90.6    
90.9    
91.1    
91.4    
91.7    
91.9    
92.2    
92.4    
92.7    
93.0    
93.2    
93.5    
93.8    
94.0    
94.3    
94.5    
94.8    
95.1    
95.3    
95.6    
95.8    
96.1    
96.4    
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 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 15678, rend_intergenic: 8430  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21529, rend_intergenic: 16930  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30791, rend_intergenic: 27048  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44880, rend_intergenic: 43439  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74776, rend_intergenic: 72997  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122768, rend_intergenic: 112470  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131464, rend_intergenic: 126676  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134568, rend_intergenic: 133989  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138052, rend_intergenic: 135487  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157361, rend_intergenic: 150648  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support