-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_25/scaffold_25_2511213-2674059

-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_25-snap.514-T1
Valid prediction for snap_scaffold_25-snap.521-T1
Valid prediction for Augustus_model.g35689.t1
Valid prediction for GlimmerHMM_glimmerT_53749-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_25-snap.534-T1
Valid prediction for GlimmerHMM_glimmerT_53759-T1
Valid prediction for GlimmerHMM_glimmerT_53743-T1
Valid prediction for snap_scaffold_25-snap.538-T1
Valid prediction for GlimmerHMM_glimmerT_53739-T1
Valid prediction for GlimmerHMM_glimmerT_53752-T1
Valid prediction for snap_scaffold_25-snap.516-T1
Couldn't classify 135750, 135792
Sorry, prediction pasa_asmbl_33394.p1 fails validation.
(ATG)	 TC	126969-126987	GT	AGG
(AAC)	 AG	128142-128441	GT	GGG
(GTC)	 AG	128695-128985	GT	CGG
(CCC)	 AG	130804-130997	GT	CGG
(GGA)	 AG	131720-131930	GT	GGG
(AGT)	 AG	132625-132735	GT	AGG
(GCT)	 AG	134243-134433	GT	AGG
(TTC)	 AG	134548-134661	GT	TGG
(GGC)	 AG	134801-134871	GT	GTG
(ATG)	 AG	135750-135792	AA	GTA
-recovered pasa_asmbl_33394.p1, initial, 126969, 126987
-recovered pasa_asmbl_33394.p1, internal, 128142, 128441
-recovered pasa_asmbl_33394.p1, internal, 128695, 128985
-recovered pasa_asmbl_33394.p1, internal, 130804, 130997
-recovered pasa_asmbl_33394.p1, internal, 131720, 131930
-recovered pasa_asmbl_33394.p1, internal, 132625, 132735
-recovered pasa_asmbl_33394.p1, internal, 134243, 134433
-recovered pasa_asmbl_33394.p1, internal, 134548, 134661
-recovered pasa_asmbl_33394.p1, internal, 134801, 134871
Valid prediction for Augustus_model.g35690.t1
Valid prediction for GlimmerHMM_glimmerT_53757-T1
Valid prediction for GlimmerHMM_glimmerT_53746-T1
Valid prediction for Augustus_model.g35683.t1
Couldn't classify 125584, 125661
Sorry, prediction pasa_asmbl_33393.p1 fails validation.
(ATG)	 CT	119623-119680	GT	AGG
(GTG)	 AG	120330-120623	GT	AGG
(GAC)	 AG	120775-120885	GT	CGG
(GAA)	 AG	121220-121375	GT	GGG
(ACT)	 AG	122220-122351	GT	AGG
(CCT)	 AG	123006-123146	GT	ATG
(CCT)	 AG	124457-124585	GT	AGG
(ATC)	 AG	125014-125159	GT	AGG
(GCC)	 AG	125584-125661	CT	GCC
-recovered pasa_asmbl_33393.p1, initial, 119623, 119680
-recovered pasa_asmbl_33393.p1, internal, 120330, 120623
-recovered pasa_asmbl_33393.p1, internal, 120775, 120885
-recovered pasa_asmbl_33393.p1, internal, 121220, 121375
-recovered pasa_asmbl_33393.p1, internal, 122220, 122351
-recovered pasa_asmbl_33393.p1, internal, 123006, 123146
-recovered pasa_asmbl_33393.p1, internal, 124457, 124585
-recovered pasa_asmbl_33393.p1, internal, 125014, 125159
Valid prediction for GlimmerHMM_glimmerT_53753-T1
Valid prediction for GlimmerHMM_glimmerT_53761-T1
Valid prediction for snap_scaffold_25-snap.530-T1
Valid prediction for GlimmerHMM_glimmerT_53747-T1
Valid prediction for GlimmerHMM_glimmerT_53764-T1
Valid prediction for GlimmerHMM_glimmerT_53751-T1
Valid prediction for snap_scaffold_25-snap.529-T1
Valid prediction for Augustus_model.g35687.t1
Valid prediction for snap_scaffold_25-snap.524-T1
Valid prediction for HiQ_model.g35693.t1
Valid prediction for snap_scaffold_25-snap.537-T1
Couldn't classify 139657, 139687
Couldn't classify 142275, 142422
Sorry, prediction pasa_asmbl_33920.p1 fails validation.
(GCT)	 GC	139657-139687	GT	AGG
(ATG)	 AG	140250-140370	GT	GGG
(GAG)	 AG	142275-142422	CG	CAC
add_exon() Sorry, pasa_asmbl_33920.p1 140250-140370-initial-1 is invalid.
-recovered pasa_asmbl_33920.p1, initial, 140250, 140370
-recovered pasa_asmbl_33920.p1, internal, 140250, 140370
Valid prediction for snap_scaffold_25-snap.528-T1
Valid prediction for snap_scaffold_25-snap.525-T1
Valid prediction for CodingQuarry_transcript_38652-T1
Valid prediction for snap_scaffold_25-snap.505-T1
Valid prediction for snap_scaffold_25-snap.522-T1
Valid prediction for GlimmerHMM_glimmerT_53766-T1
Valid prediction for GlimmerHMM_glimmerT_53744-T1
Valid prediction for Augustus_model.g35695.t1
Valid prediction for GlimmerHMM_glimmerT_53755-T1
Valid prediction for snap_scaffold_25-snap.504-T1
Valid prediction for snap_scaffold_25-snap.513-T1
Valid prediction for GlimmerHMM_glimmerT_53760-T1
Valid prediction for Augustus_model.g35685.t1
Valid prediction for snap_scaffold_25-snap.539-T1
Valid prediction for snap_scaffold_25-snap.501-T1
Valid prediction for GlimmerHMM_glimmerT_53765-T1
Valid prediction for CodingQuarry_transcript_38653-T1
Valid prediction for snap_scaffold_25-snap.527-T1
Valid prediction for snap_scaffold_25-snap.532-T1
Sorry, intron length (3) is less than minimum required (10)
Sorry, intron length (5) is less than minimum required (10)
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_25-snap.542-T1
Valid prediction for snap_scaffold_25-snap.507-T1
Valid prediction for GlimmerHMM_glimmerT_53750-T1
Valid prediction for snap_scaffold_25-snap.541-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_53763-T1
Valid prediction for snap_scaffold_25-snap.503-T1
Valid prediction for snap_scaffold_25-snap.533-T1
Valid prediction for snap_scaffold_25-snap.506-T1
Valid prediction for snap_scaffold_25-snap.509-T1
Valid prediction for GlimmerHMM_glimmerT_53758-T1
Valid prediction for snap_scaffold_25-snap.535-T1
Valid prediction for GlimmerHMM_glimmerT_53754-T1
Valid prediction for snap_scaffold_25-snap.523-T1
Valid prediction for snap_scaffold_25-snap.518-T1
Valid prediction for snap_scaffold_25-snap.536-T1
Valid prediction for snap_scaffold_25-snap.500-T1
Valid prediction for snap_scaffold_25-snap.502-T1
Valid prediction for snap_scaffold_25-snap.508-T1
Valid prediction for GlimmerHMM_glimmerT_53748-T1
Valid prediction for snap_scaffold_25-snap.498-T1
Valid prediction for HiQ_model.g35686.t1
Valid prediction for GlimmerHMM_glimmerT_53756-T1
Valid prediction for GlimmerHMM_glimmerT_53740-T1
Valid prediction for snap_scaffold_25-snap.511-T1
Valid prediction for Augustus_model.g35694.t1
Valid prediction for GlimmerHMM_glimmerT_53741-T1
Valid prediction for snap_scaffold_25-snap.510-T1
Valid prediction for Augustus_model.g35688.t1
Valid prediction for Augustus_model.g35696.t1
Valid prediction for Augustus_model.g35691.t1
Valid prediction for GlimmerHMM_glimmerT_53762-T1
Valid prediction for snap_scaffold_25-snap.526-T1
Valid prediction for snap_scaffold_25-snap.515-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_25-snap.499-T1
Valid prediction for GlimmerHMM_glimmerT_53742-T1
Valid prediction for snap_scaffold_25-snap.543-T1
Valid prediction for snap_scaffold_25-snap.519-T1
Valid prediction for CodingQuarry_transcript_38651-T1
Valid prediction for GlimmerHMM_glimmerT_53745-T1
Valid prediction for snap_scaffold_25-snap.512-T1
Valid prediction for snap_scaffold_25-snap.540-T1
Valid prediction for GlimmerHMM_glimmerT_53768-T1
Valid prediction for pasa_asmbl_34068.p1
Valid prediction for snap_scaffold_25-snap.520-T1
Valid prediction for snap_scaffold_25-snap.497-T1
Valid prediction for snap_scaffold_25-snap.517-T1
Valid prediction for snap_scaffold_25-snap.531-T1
Valid prediction for Augustus_model.g35684.t1
Valid prediction for GlimmerHMM_glimmerT_53767-T1
Valid prediction for Augustus_model.g35692.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15039, rend_intergenic: 14104  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35455, rend_intergenic: 15101  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70021, rend_intergenic: 50671  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76296, rend_intergenic: 71851  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77308, rend_intergenic: 76332  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78437, rend_intergenic: 77633  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89278, rend_intergenic: 78865  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96250, rend_intergenic: 90122  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98878, rend_intergenic: 97202  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118717, rend_intergenic: 105601  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123679, rend_intergenic: 121230  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128430, rend_intergenic: 124381  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129099, rend_intergenic: 128612  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134829, rend_intergenic: 129200  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143187, rend_intergenic: 138433  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158620, rend_intergenic: 153357  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 162847
-exon list size: 390


building trellis

0.3    
0.5    
0.8    
1.0    
1.3    
1.5    
1.8    
2.0    
2.3    
2.6    
2.8    
3.1    
3.3    
3.6    
3.8    
4.1    
4.3    
4.6    
4.8    
5.1    
5.4    
5.6    
5.9    
6.1    
6.4    
6.6    
6.9    
7.1    
7.4    
7.7    
7.9    
8.2    
8.4    
8.7    
8.9    
9.2    
9.4    
9.7    
9.9    
10.2    
10.5    
10.7    
11.0    
11.2    
11.5    
11.7    
12.0    
12.2    
12.5    
12.8    
13.0    
13.3    
13.5    
13.8    
14.0    
14.3    
14.5    
14.8    
15.1    
15.3    
15.6    
15.8    
16.1    
16.3    
16.6    
16.8    
17.1    
17.3    
17.6    
17.9    
18.1    
18.4    
18.6    
18.9    
19.1    
19.4    
19.6    
19.9    
20.2    
20.4    
20.7    
20.9    
21.2    
21.4    
21.7    
21.9    
22.2    
22.4    
22.7    
23.0    
23.2    
23.5    
23.7    
24.0    
24.2    
24.5    
24.7    
25.0    
25.3    
25.5    
25.8    
26.0    
26.3    
26.5    
26.8    
27.0    
27.3    
27.6    
27.8    
28.1    
28.3    
28.6    
28.8    
29.1    
29.3    
29.6    
29.8    
30.1    
30.4    
30.6    
30.9    
31.1    
31.4    
31.6    
31.9    
32.1    
32.4    
32.7    
32.9    
33.2    
33.4    
33.7    
33.9    
34.2    
34.4    
34.7    
34.9    
35.2    
35.5    
35.7    
36.0    
36.2    
36.5    
36.7    
37.0    
37.2    
37.5    
37.8    
38.0    
38.3    
38.5    
38.8    
39.0    
39.3    
39.5    
39.8    
40.1    
40.3    
40.6    
40.8    
41.1    
41.3    
41.6    
41.8    
42.1    
42.3    
42.6    
42.9    
43.1    
43.4    
43.6    
43.9    
44.1    
44.4    
44.6    
44.9    
45.2    
45.4    
45.7    
45.9    
46.2    
46.4    
46.7    
46.9    
47.2    
47.4    
47.7    
48.0    
48.2    
48.5    
48.7    
49.0    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.0    
51.3    
51.5    
51.8    
52.0    
52.3    
52.6    
52.8    
53.1    
53.3    
53.6    
53.8    
54.1    
54.3    
54.6    
54.8    
55.1    
55.4    
55.6    
55.9    
56.1    
56.4    
56.6    
56.9    
57.1    
57.4    
57.7    
57.9    
58.2    
58.4    
58.7    
58.9    
59.2    
59.4    
59.7    
59.9    
60.2    
60.5    
60.7    
61.0    
61.2    
61.5    
61.7    
62.0    
62.2    
62.5    
62.8    
63.0    
63.3    
63.5    
63.8    
64.0    
64.3    
64.5    
64.8    
65.1    
65.3    
65.6    
65.8    
66.1    
66.3    
66.6    
66.8    
67.1    
67.3    
67.6    
67.9    
68.1    
68.4    
68.6    
68.9    
69.1    
69.4    
69.6    
69.9    
70.2    
70.4    
70.7    
70.9    
71.2    
71.4    
71.7    
71.9    
72.2    
72.4    
72.7    
73.0    
73.2    
73.5    
73.7    
74.0    
74.2    
74.5    
74.7    
75.0    
75.3    
75.5    
75.8    
76.0    
76.3    
76.5    
76.8    
77.0    
77.3    
77.6    
77.8    
78.1    
78.3    
78.6    
78.8    
79.1    
79.3    
79.6    
79.8    
80.1    
80.4    
80.6    
80.9    
81.1    
81.4    
81.6    
81.9    
82.1    
82.4    
82.7    
82.9    
83.2    
83.4    
83.7    
83.9    
84.2    
84.4    
84.7    
84.9    
85.2    
85.5    
85.7    
86.0    
86.2    
86.5    
86.7    
87.0    
87.2    
87.5    
87.8    
88.0    
88.3    
88.5    
88.8    
89.0    
89.3    
89.5    
89.8    
90.1    
90.3    
90.6    
90.8    
91.1    
91.3    
91.6    
91.8    
92.1    
92.3    
92.6    
92.9    
93.1    
93.4    
93.6    
93.9    
94.1    
94.4    
94.6    
94.9    
95.2    
95.4    
95.7    
95.9    
96.2    
96.4    
96.7    
96.9    
97.2    
97.4    
97.7    
98.0    
98.2    
98.5    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 15039, rend_intergenic: 14104  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35455, rend_intergenic: 15101  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70021, rend_intergenic: 50671  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76296, rend_intergenic: 71851  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77308, rend_intergenic: 76332  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78437, rend_intergenic: 77633  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89278, rend_intergenic: 78865  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96250, rend_intergenic: 90122  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98878, rend_intergenic: 97202  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118717, rend_intergenic: 105601  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123679, rend_intergenic: 121230  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128430, rend_intergenic: 124381  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129099, rend_intergenic: 128612  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134829, rend_intergenic: 129200  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143187, rend_intergenic: 138433  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158620, rend_intergenic: 153357  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support