-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_3/scaffold_3_2554702-2729653

-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_3-snap.600-T1
Valid prediction for Augustus_model.g4026.t1
Valid prediction for snap_scaffold_3-snap.592-T1
Valid prediction for GlimmerHMM_glimmerT_6183-T1
Valid prediction for snap_scaffold_3-snap.604-T1
Valid prediction for GlimmerHMM_glimmerT_6175-T1
Valid prediction for GlimmerHMM_glimmerT_6199-T1
Valid prediction for GlimmerHMM_glimmerT_6200-T1
Valid prediction for GlimmerHMM_glimmerT_6191-T1
Valid prediction for pasa_asmbl_39917.p1
Valid prediction for snap_scaffold_3-snap.585-T1
Valid prediction for GlimmerHMM_glimmerT_6187-T1
Valid prediction for snap_scaffold_3-snap.595-T1
Valid prediction for Augustus_model.g4030.t1
Valid prediction for GlimmerHMM_glimmerT_6198-T1
Valid prediction for GlimmerHMM_glimmerT_6186-T1
Valid prediction for snap_scaffold_3-snap.612-T1
Valid prediction for snap_scaffold_3-snap.587-T1
Couldn't classify 91891, 92790
Sorry, prediction pasa_asmbl_39911.p1 fails validation.
(GAC)	 TA	91891-92790	TT	AGT
Valid prediction for GlimmerHMM_glimmerT_6184-T1
Valid prediction for snap_scaffold_3-snap.584-T1
Valid prediction for snap_scaffold_3-snap.580-T1
Valid prediction for snap_scaffold_3-snap.588-T1
Valid prediction for Augustus_model.g4031.t1
Valid prediction for Augustus_model.g4035.t1
Valid prediction for snap_scaffold_3-snap.610-T1
Valid prediction for GlimmerHMM_glimmerT_6196-T1
Valid prediction for snap_scaffold_3-snap.621-T1
Valid prediction for Augustus_model.g4028.t1
Valid prediction for snap_scaffold_3-snap.618-T1
Valid prediction for snap_scaffold_3-snap.616-T1
Valid prediction for GlimmerHMM_glimmerT_6179-T1
Valid prediction for GlimmerHMM_glimmerT_6193-T1
Valid prediction for snap_scaffold_3-snap.615-T1
Couldn't classify 68805, 68828
Couldn't classify 77073, 77179
Sorry, prediction pasa_asmbl_39910.p1 fails validation.
(GAC)	 AC	68805-68828	GT	AAG
(GTG)	 AG	69082-69204	GT	AGG
(GGC)	 AG	70252-70316	GT	AGG
(TGC)	 AG	72234-72317	GT	AGG
(GTA)	 AG	72723-72835	GT	AGG
(GCT)	 AG	73135-73195	GT	TAG
(CAA)	 AG	76079-76154	GT	TGG
(CTC)	 AG	76551-76680	GT	AGG
(ATG)	 AG	76887-76952	GT	CGG
(GGA)	 AG	77073-77179	CC	ACC
-recovered pasa_asmbl_39910.p1, initial, 76887, 76952
-recovered pasa_asmbl_39910.p1, internal, 69082, 69204
-recovered pasa_asmbl_39910.p1, internal, 70252, 70316
-recovered pasa_asmbl_39910.p1, internal, 72234, 72317
-recovered pasa_asmbl_39910.p1, internal, 72723, 72835
-recovered pasa_asmbl_39910.p1, internal, 73135, 73195
-recovered pasa_asmbl_39910.p1, internal, 76079, 76154
-recovered pasa_asmbl_39910.p1, internal, 76551, 76680
-recovered pasa_asmbl_39910.p1, internal, 76887, 76952
Valid prediction for snap_scaffold_3-snap.607-T1
Valid prediction for snap_scaffold_3-snap.602-T1
Valid prediction for snap_scaffold_3-snap.597-T1
Valid prediction for snap_scaffold_3-snap.590-T1
Valid prediction for GlimmerHMM_glimmerT_6190-T1
Valid prediction for snap_scaffold_3-snap.594-T1
Valid prediction for GlimmerHMM_glimmerT_6182-T1
Valid prediction for GlimmerHMM_glimmerT_6178-T1
Couldn't classify 100061, 100243
Couldn't classify 100608, 100730
Sorry, prediction pasa_asmbl_40786.p1 fails validation.
(GGT)	 CA	100061-100243	GT	AGG
(AGA)	 AG	100608-100730	CC	CCC
Valid prediction for snap_scaffold_3-snap.619-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_6176-T1
Valid prediction for snap_scaffold_3-snap.605-T1
Valid prediction for GlimmerHMM_glimmerT_6189-T1
Valid prediction for snap_scaffold_3-snap.611-T1
Valid prediction for snap_scaffold_3-snap.581-T1
Valid prediction for Augustus_model.g4033.t1
Valid prediction for Augustus_model.g4034.t1
Valid prediction for snap_scaffold_3-snap.593-T1
Valid prediction for snap_scaffold_3-snap.617-T1
Valid prediction for GlimmerHMM_glimmerT_6192-T1
Valid prediction for snap_scaffold_3-snap.601-T1
Valid prediction for snap_scaffold_3-snap.591-T1
Valid prediction for GlimmerHMM_glimmerT_6195-T1
Valid prediction for Augustus_model.g4032.t1
Valid prediction for Augustus_model.g4027.t1
Valid prediction for snap_scaffold_3-snap.583-T1
Valid prediction for snap_scaffold_3-snap.613-T1
Valid prediction for GlimmerHMM_glimmerT_6194-T1
Valid prediction for GlimmerHMM_glimmerT_6181-T1
Valid prediction for snap_scaffold_3-snap.599-T1
Valid prediction for GlimmerHMM_glimmerT_6201-T1
Valid prediction for snap_scaffold_3-snap.608-T1
Valid prediction for Augustus_model.g4036.t1
Valid prediction for snap_scaffold_3-snap.596-T1
Valid prediction for Augustus_model.g4029.t1
Valid prediction for snap_scaffold_3-snap.586-T1
Valid prediction for snap_scaffold_3-snap.582-T1
Valid prediction for GlimmerHMM_glimmerT_6188-T1
Valid prediction for GlimmerHMM_glimmerT_6180-T1
Valid prediction for GlimmerHMM_glimmerT_6197-T1
Valid prediction for snap_scaffold_3-snap.620-T1
Valid prediction for snap_scaffold_3-snap.606-T1
Valid prediction for GlimmerHMM_glimmerT_6185-T1
Valid prediction for snap_scaffold_3-snap.614-T1
Valid prediction for GlimmerHMM_glimmerT_6177-T1
Valid prediction for Augustus_model.g4037.t1
Valid prediction for snap_scaffold_3-snap.589-T1
Valid prediction for snap_scaffold_3-snap.603-T1
Valid prediction for snap_scaffold_3-snap.598-T1
Valid prediction for snap_scaffold_3-snap.609-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12723, rend_intergenic: 7365  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18413, rend_intergenic: 12746  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19977, rend_intergenic: 18423  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28073, rend_intergenic: 25956  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37407, rend_intergenic: 34678  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40105, rend_intergenic: 39628  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43935, rend_intergenic: 40509  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54303, rend_intergenic: 45832  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55198, rend_intergenic: 54411  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64539, rend_intergenic: 55569  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73447, rend_intergenic: 69067  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76642, rend_intergenic: 73493  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84955, rend_intergenic: 77020  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97476, rend_intergenic: 87729  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116007, rend_intergenic: 105212  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130136, rend_intergenic: 126450  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164467, rend_intergenic: 162917  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 174952
-exon list size: 318


building trellis

0.3    
0.6    
0.9    
1.2    
1.6    
1.9    
2.2    
2.5    
2.8    
3.1    
3.4    
3.8    
4.1    
4.4    
4.7    
5.0    
5.3    
5.6    
5.9    
6.2    
6.6    
6.9    
7.2    
7.5    
7.8    
8.1    
8.4    
8.8    
9.1    
9.4    
9.7    
10.0    
10.3    
10.6    
10.9    
11.2    
11.6    
11.9    
12.2    
12.5    
12.8    
13.1    
13.4    
13.8    
14.1    
14.4    
14.7    
15.0    
15.3    
15.6    
15.9    
16.2    
16.6    
16.9    
17.2    
17.5    
17.8    
18.1    
18.4    
18.8    
19.1    
19.4    
19.7    
20.0    
20.3    
20.6    
20.9    
21.2    
21.6    
21.9    
22.2    
22.5    
22.8    
23.1    
23.4    
23.8    
24.1    
24.4    
24.7    
25.0    
25.3    
25.6    
25.9    
26.2    
26.6    
26.9    
27.2    
27.5    
27.8    
28.1    
28.4    
28.7    
29.1    
29.4    
29.7    
30.0    
30.3    
30.6    
30.9    
31.2    
31.6    
31.9    
32.2    
32.5    
32.8    
33.1    
33.4    
33.8    
34.1    
34.4    
34.7    
35.0    
35.3    
35.6    
35.9    
36.2    
36.6    
36.9    
37.2    
37.5    
37.8    
38.1    
38.4    
38.8    
39.1    
39.4    
39.7    
40.0    
40.3    
40.6    
40.9    
41.2    
41.6    
41.9    
42.2    
42.5    
42.8    
43.1    
43.4    
43.8    
44.1    
44.4    
44.7    
45.0    
45.3    
45.6    
45.9    
46.2    
46.6    
46.9    
47.2    
47.5    
47.8    
48.1    
48.4    
48.8    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.2    
51.6    
51.9    
52.2    
52.5    
52.8    
53.1    
53.4    
53.8    
54.1    
54.4    
54.7    
55.0    
55.3    
55.6    
55.9    
56.2    
56.6    
56.9    
57.2    
57.5    
57.8    
58.1    
58.4    
58.8    
59.1    
59.4    
59.7    
60.0    
60.3    
60.6    
60.9    
61.3    
61.6    
61.9    
62.2    
62.5    
62.8    
63.1    
63.4    
63.7    
64.1    
64.4    
64.7    
65.0    
65.3    
65.6    
65.9    
66.2    
66.6    
66.9    
67.2    
67.5    
67.8    
68.1    
68.4    
68.8    
69.1    
69.4    
69.7    
70.0    
70.3    
70.6    
70.9    
71.2    
71.6    
71.9    
72.2    
72.5    
72.8    
73.1    
73.4    
73.8    
74.1    
74.4    
74.7    
75.0    
75.3    
75.6    
75.9    
76.2    
76.6    
76.9    
77.2    
77.5    
77.8    
78.1    
78.4    
78.8    
79.1    
79.4    
79.7    
80.0    
80.3    
80.6    
80.9    
81.2    
81.6    
81.9    
82.2    
82.5    
82.8    
83.1    
83.4    
83.8    
84.1    
84.4    
84.7    
85.0    
85.3    
85.6    
85.9    
86.2    
86.6    
86.9    
87.2    
87.5    
87.8    
88.1    
88.4    
88.8    
89.1    
89.4    
89.7    
90.0    
90.3    
90.6    
90.9    
91.2    
91.6    
91.9    
92.2    
92.5    
92.8    
93.1    
93.4    
93.8    
94.1    
94.4    
94.7    
95.0    
95.3    
95.6    
95.9    
96.2    
96.6    
96.9    
97.2    
97.5    
97.8    
98.1    
98.4    
98.8    
99.1    
99.4    
99.7    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 12723, rend_intergenic: 7365  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18413, rend_intergenic: 12746  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19977, rend_intergenic: 18423  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28073, rend_intergenic: 25956  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37407, rend_intergenic: 34678  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40105, rend_intergenic: 39628  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43935, rend_intergenic: 40509  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54303, rend_intergenic: 45832  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55198, rend_intergenic: 54411  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64539, rend_intergenic: 55569  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73447, rend_intergenic: 69067  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76642, rend_intergenic: 73493  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84955, rend_intergenic: 77020  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97476, rend_intergenic: 87729  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116007, rend_intergenic: 105212  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130136, rend_intergenic: 126450  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164467, rend_intergenic: 162917  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support