-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_4/scaffold_4_4236294-4394673

-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 GlimmerHMM_glimmerT_9231-T1
Valid prediction for GlimmerHMM_glimmerT_9240-T1
Valid prediction for GlimmerHMM_glimmerT_9234-T1
Valid prediction for GlimmerHMM_glimmerT_9223-T1
Valid prediction for HiQ_model.g5938.t1
Valid prediction for snap_scaffold_4-snap.1003-T1
Valid prediction for Augustus_model.g5942.t1
Valid prediction for snap_scaffold_4-snap.1002-T1
Valid prediction for snap_scaffold_4-snap.989-T1
Valid prediction for snap_scaffold_4-snap.991-T1
Valid prediction for snap_scaffold_4-snap.1004-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for snap_scaffold_4-snap.996-T1
Valid prediction for Augustus_model.g5941.t1
Valid prediction for Augustus_model.g5933.t1
Valid prediction for pasa_asmbl_41240.p1
Valid prediction for GlimmerHMM_glimmerT_9230-T1
Valid prediction for GlimmerHMM_glimmerT_9237-T1
Valid prediction for CodingQuarry_transcript_48944-T1
Valid prediction for Augustus_model.g5937.t1
Valid prediction for GlimmerHMM_glimmerT_9217-T1
Valid prediction for GlimmerHMM_glimmerT_9219-T1
Valid prediction for GlimmerHMM_glimmerT_9222-T1
Valid prediction for GlimmerHMM_glimmerT_9216-T1
Valid prediction for snap_scaffold_4-snap.979-T1
Valid prediction for snap_scaffold_4-snap.986-T1
Valid prediction for snap_scaffold_4-snap.994-T1
Valid prediction for GlimmerHMM_glimmerT_9229-T1
Valid prediction for GlimmerHMM_glimmerT_9218-T1
Valid prediction for snap_scaffold_4-snap.969-T1
Valid prediction for GlimmerHMM_glimmerT_9233-T1
Valid prediction for Augustus_model.g5929.t1
Valid prediction for Augustus_model.g5928.t1
Valid prediction for snap_scaffold_4-snap.1006-T1
Valid prediction for snap_scaffold_4-snap.990-T1
Valid prediction for Augustus_model.g5935.t1
Valid prediction for snap_scaffold_4-snap.998-T1
Valid prediction for GlimmerHMM_glimmerT_9220-T1
Valid prediction for Augustus_model.g5926.t1
Valid prediction for GlimmerHMM_glimmerT_9235-T1
Valid prediction for Augustus_model.g5927.t1
Valid prediction for GlimmerHMM_glimmerT_9225-T1
Valid prediction for Augustus_model.g5934.t1
Valid prediction for snap_scaffold_4-snap.980-T1
Valid prediction for snap_scaffold_4-snap.974-T1
Valid prediction for snap_scaffold_4-snap.972-T1
Valid prediction for Augustus_model.g5936.t1
Valid prediction for snap_scaffold_4-snap.1005-T1
Valid prediction for snap_scaffold_4-snap.1001-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_4-snap.1000-T1
Valid prediction for snap_scaffold_4-snap.984-T1
Valid prediction for CodingQuarry_transcript_48945-T1
Valid prediction for Augustus_model.g5930.t1
Valid prediction for snap_scaffold_4-snap.995-T1
Valid prediction for GlimmerHMM_glimmerT_9239-T1
Valid prediction for Augustus_model.g5925.t1
Valid prediction for GlimmerHMM_glimmerT_9215-T1
Valid prediction for snap_scaffold_4-snap.985-T1
Valid prediction for snap_scaffold_4-snap.970-T1
Valid prediction for snap_scaffold_4-snap.971-T1
Valid prediction for HiQ_model.g5939.t1
Valid prediction for GlimmerHMM_glimmerT_9224-T1
Valid prediction for snap_scaffold_4-snap.973-T1
Valid prediction for CodingQuarry_transcript_48946-T1
Valid prediction for GlimmerHMM_glimmerT_9226-T1
Valid prediction for GlimmerHMM_glimmerT_9227-T1
Valid prediction for GlimmerHMM_glimmerT_9238-T1
Valid prediction for snap_scaffold_4-snap.981-T1
Valid prediction for GlimmerHMM_glimmerT_9214-T1
Valid prediction for snap_scaffold_4-snap.992-T1
Valid prediction for snap_scaffold_4-snap.977-T1
Valid prediction for GlimmerHMM_glimmerT_9228-T1
Valid prediction for GlimmerHMM_glimmerT_9236-T1
Couldn't classify 13365, 13419
Sorry, prediction pasa_asmbl_42509.p1 fails validation.
(GCA)	 CA	13365-13419	GT	AGG
(CTA)	 AG	13938-13970	GT	AGG
(AAG)	 AG	14117-14146	GT	CAG
(GGA)	 AG	15376-15450	GT	ACG
(ATC)	 AG	15613-15681	GT	GGG
(CTG)	 AG	16209-16251	GT	GGG
(GAT)	 AG	18365-18410	CC	AAC
-recovered pasa_asmbl_42509.p1, terminal, 18365, 18410
-recovered pasa_asmbl_42509.p1, internal, 13938, 13970
-recovered pasa_asmbl_42509.p1, internal, 14117, 14146
-recovered pasa_asmbl_42509.p1, internal, 15376, 15450
-recovered pasa_asmbl_42509.p1, internal, 15613, 15681
-recovered pasa_asmbl_42509.p1, internal, 16209, 16251
Valid prediction for Augustus_model.g5932.t1
Valid prediction for snap_scaffold_4-snap.999-T1
Valid prediction for GlimmerHMM_glimmerT_9232-T1
Valid prediction for snap_scaffold_4-snap.997-T1
Valid prediction for snap_scaffold_4-snap.988-T1
Valid prediction for CodingQuarry_transcript_48947-T1
Valid prediction for snap_scaffold_4-snap.987-T1
Valid prediction for snap_scaffold_4-snap.976-T1
Valid prediction for snap_scaffold_4-snap.983-T1
Valid prediction for GlimmerHMM_glimmerT_9221-T1
Valid prediction for Augustus_model.g5931.t1
Valid prediction for Augustus_model.g5940.t1
Valid prediction for snap_scaffold_4-snap.993-T1
Valid prediction for snap_scaffold_4-snap.982-T1
Valid prediction for snap_scaffold_4-snap.975-T1
Valid prediction for snap_scaffold_4-snap.978-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11106, rend_intergenic: 6221  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15749, rend_intergenic: 13019  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22233, rend_intergenic: 16674  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49057, rend_intergenic: 46748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71300, rend_intergenic: 65259  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74093, rend_intergenic: 73248  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78334, rend_intergenic: 74721  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87863, rend_intergenic: 85371  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105924, rend_intergenic: 97144  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111046, rend_intergenic: 108507  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119308, rend_intergenic: 111395  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126017, rend_intergenic: 120289  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128083, rend_intergenic: 126408  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 158380
-exon list size: 333


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.8    
2.1    
2.4    
2.7    
3.0    
3.3    
3.6    
3.9    
4.2    
4.5    
4.8    
5.1    
5.4    
5.7    
6.0    
6.3    
6.6    
6.9    
7.2    
7.5    
7.8    
8.1    
8.4    
8.7    
9.0    
9.3    
9.6    
9.9    
10.1    
10.4    
10.7    
11.0    
11.3    
11.6    
11.9    
12.2    
12.5    
12.8    
13.1    
13.4    
13.7    
14.0    
14.3    
14.6    
14.9    
15.2    
15.5    
15.8    
16.1    
16.4    
16.7    
17.0    
17.3    
17.6    
17.9    
18.2    
18.5    
18.8    
19.1    
19.4    
19.7    
20.0    
20.3    
20.6    
20.9    
21.2    
21.5    
21.8    
22.1    
22.4    
22.7    
23.0    
23.3    
23.6    
23.9    
24.2    
24.5    
24.8    
25.1    
25.4    
25.7    
26.0    
26.3    
26.6    
26.9    
27.2    
27.5    
27.8    
28.1    
28.4    
28.7    
29.0    
29.3    
29.6    
29.9    
30.1    
30.4    
30.7    
31.0    
31.3    
31.6    
31.9    
32.2    
32.5    
32.8    
33.1    
33.4    
33.7    
34.0    
34.3    
34.6    
34.9    
35.2    
35.5    
35.8    
36.1    
36.4    
36.7    
37.0    
37.3    
37.6    
37.9    
38.2    
38.5    
38.8    
39.1    
39.4    
39.7    
40.0    
40.3    
40.6    
40.9    
41.2    
41.5    
41.8    
42.1    
42.4    
42.7    
43.0    
43.3    
43.6    
43.9    
44.2    
44.5    
44.8    
45.1    
45.4    
45.7    
46.0    
46.3    
46.6    
46.9    
47.2    
47.5    
47.8    
48.1    
48.4    
48.7    
49.0    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
51.0    
51.3    
51.6    
51.9    
52.2    
52.5    
52.8    
53.1    
53.4    
53.7    
54.0    
54.3    
54.6    
54.9    
55.2    
55.5    
55.8    
56.1    
56.4    
56.7    
57.0    
57.3    
57.6    
57.9    
58.2    
58.5    
58.8    
59.1    
59.4    
59.7    
60.0    
60.3    
60.6    
60.9    
61.2    
61.5    
61.8    
62.1    
62.4    
62.7    
63.0    
63.3    
63.6    
63.9    
64.2    
64.5    
64.8    
65.1    
65.4    
65.7    
66.0    
66.3    
66.6    
66.9    
67.2    
67.5    
67.8    
68.1    
68.4    
68.7    
69.0    
69.3    
69.6    
69.9    
70.1    
70.4    
70.7    
71.0    
71.3    
71.6    
71.9    
72.2    
72.5    
72.8    
73.1    
73.4    
73.7    
74.0    
74.3    
74.6    
74.9    
75.2    
75.5    
75.8    
76.1    
76.4    
76.7    
77.0    
77.3    
77.6    
77.9    
78.2    
78.5    
78.8    
79.1    
79.4    
79.7    
80.0    
80.3    
80.6    
80.9    
81.2    
81.5    
81.8    
82.1    
82.4    
82.7    
83.0    
83.3    
83.6    
83.9    
84.2    
84.5    
84.8    
85.1    
85.4    
85.7    
86.0    
86.3    
86.6    
86.9    
87.2    
87.5    
87.8    
88.1    
88.4    
88.7    
89.0    
89.3    
89.6    
89.9    
90.1    
90.4    
90.7    
91.0    
91.3    
91.6    
91.9    
92.2    
92.5    
92.8    
93.1    
93.4    
93.7    
94.0    
94.3    
94.6    
94.9    
95.2    
95.5    
95.8    
96.1    
96.4    
96.7    
97.0    
97.3    
97.6    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 11106, rend_intergenic: 6221  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15749, rend_intergenic: 13019  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22233, rend_intergenic: 16674  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49057, rend_intergenic: 46748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71300, rend_intergenic: 65259  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74093, rend_intergenic: 73248  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78334, rend_intergenic: 74721  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87863, rend_intergenic: 85371  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105924, rend_intergenic: 97144  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111046, rend_intergenic: 108507  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119308, rend_intergenic: 111395  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126017, rend_intergenic: 120289  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128083, rend_intergenic: 126408  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support