-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_7/scaffold_7_18534577-18668715

-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 GeneMark_model.32926_t
Valid prediction for GeneMark_model.32899_t
Valid prediction for GeneMark_model.32903_t
Valid prediction for snap_scaffold_7-snap.3643-T1
Valid prediction for Augustus_model.g13082.t1
Valid prediction for snap_scaffold_7-snap.3648-T1
Valid prediction for snap_scaffold_7-snap.3627-T1
Valid prediction for snap_scaffold_7-snap.3631-T1
Valid prediction for snap_scaffold_7-snap.3626-T1
Valid prediction for snap_scaffold_7-snap.3647-T1
Valid prediction for GeneMark_model.32917_t
Valid prediction for snap_scaffold_7-snap.3646-T1
Valid prediction for snap_scaffold_7-snap.3641-T1
Valid prediction for GlimmerHMM_glimmerT_19447-T1
Valid prediction for GeneMark_model.32909_t
Valid prediction for GeneMark_model.32915_t
Valid prediction for GlimmerHMM_glimmerT_19437-T1
Valid prediction for GeneMark_model.32913_t
Valid prediction for GlimmerHMM_glimmerT_19433-T1
Valid prediction for GlimmerHMM_glimmerT_19445-T1
Valid prediction for CodingQuarry_transcript_57615-T1
Valid prediction for snap_scaffold_7-snap.3634-T1
Valid prediction for GlimmerHMM_glimmerT_19435-T1
Valid prediction for GeneMark_model.32920_t
Valid prediction for Augustus_model.g13087.t1
Valid prediction for snap_scaffold_7-snap.3637-T1
Valid prediction for GlimmerHMM_glimmerT_19439-T1
Valid prediction for snap_scaffold_7-snap.3629-T1
Valid prediction for GeneMark_model.32897_t
Valid prediction for GeneMark_model.32924_t
Valid prediction for snap_scaffold_7-snap.3625-T1
Valid prediction for snap_scaffold_7-snap.3622-T1
Valid prediction for GeneMark_model.32911_t
Valid prediction for GeneMark_model.32905_t
Valid prediction for HiQ_model.g13080.t1
Couldn't classify 52230, 52452
Sorry, prediction pasa_asmbl_51415.p1 fails validation.
(ATG)	 CC	34401-34448	GT	AGG
(GTG)	 AG	35957-36119	GT	AGG
(ATC)	 AG	37690-37781	GT	AGG
(GAT)	 AG	38865-38945	GT	GGG
(CAA)	 AG	39608-39667	GT	AGG
(GTT)	 AG	40215-40366	GT	AAG
(GCC)	 AG	40509-40602	GT	CTG
(ATT)	 AG	43509-43598	GT	GGG
(CTT)	 AG	45161-45327	GT	AGG
(AGC)	 AG	45614-45743	GT	AGG
(GTT)	 AG	46160-46264	GT	AGG
(TAC)	 AG	46647-46753	GT	TTG
(CTG)	 AG	47085-47239	GT	CGG
(GTT)	 AG	47338-47448	GT	TGG
(AGA)	 AG	48470-48572	GT	AGG
(CCC)	 AG	50014-50056	GT	GGG
(GTT)	 AG	50180-50222	GT	AGG
(TGG)	 AG	51081-51219	GT	GGG
(CTC)	 AG	52230-52452	GG	AAG
-recovered pasa_asmbl_51415.p1, initial, 34401, 34448
-recovered pasa_asmbl_51415.p1, internal, 35957, 36119
-recovered pasa_asmbl_51415.p1, internal, 37690, 37781
-recovered pasa_asmbl_51415.p1, internal, 38865, 38945
-recovered pasa_asmbl_51415.p1, internal, 39608, 39667
-recovered pasa_asmbl_51415.p1, internal, 40215, 40366
-recovered pasa_asmbl_51415.p1, internal, 40509, 40602
-recovered pasa_asmbl_51415.p1, internal, 43509, 43598
-recovered pasa_asmbl_51415.p1, internal, 45161, 45327
-recovered pasa_asmbl_51415.p1, internal, 45614, 45743
-recovered pasa_asmbl_51415.p1, internal, 46160, 46264
-recovered pasa_asmbl_51415.p1, internal, 46647, 46753
-recovered pasa_asmbl_51415.p1, internal, 47085, 47239
-recovered pasa_asmbl_51415.p1, internal, 47338, 47448
-recovered pasa_asmbl_51415.p1, internal, 48470, 48572
-recovered pasa_asmbl_51415.p1, internal, 50014, 50056
-recovered pasa_asmbl_51415.p1, internal, 50180, 50222
-recovered pasa_asmbl_51415.p1, internal, 51081, 51219

-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 CodingQuarry_transcript_57620-T1
Valid prediction for pasa_asmbl_50302.p1
Valid prediction for GeneMark_model.32902_t
Valid prediction for GeneMark_model.32916_t
Valid prediction for GlimmerHMM_glimmerT_19438-T1
Couldn't classify 60418, 60526
Sorry, prediction pasa_asmbl_50301.p1 fails validation.
(GGA)	 AT	60418-60526	GT	CTG
(CGG)	 AG	60733-60878	GT	AGG
(GGA)	 AG	61076-61237	CA	AGC
-recovered pasa_asmbl_50301.p1, terminal, 61076, 61237
-recovered pasa_asmbl_50301.p1, internal, 60733, 60878
Valid prediction for Augustus_model.g13081.t1
Valid prediction for snap_scaffold_7-snap.3642-T1
Valid prediction for GlimmerHMM_glimmerT_19431-T1
Valid prediction for GeneMark_model.32923_t
Valid prediction for CodingQuarry_transcript_57616-T1
Valid prediction for GeneMark_model.32901_t
Valid prediction for GlimmerHMM_glimmerT_19440-T1
Valid prediction for Augustus_model.g13086.t1
Valid prediction for Augustus_model.g13083.t1
Valid prediction for GlimmerHMM_glimmerT_19441-T1
Valid prediction for GlimmerHMM_glimmerT_19442-T1
Valid prediction for GlimmerHMM_glimmerT_19449-T1
Couldn't classify 39419, 39542
Couldn't classify 41075, 41224
Sorry, prediction pasa_asmbl_50389.p1 fails validation.
(CAA)	 CC	39419-39542	GT	TGG
(GCT)	 AG	40567-40652	GT	AGG
(ATC)	 AG	41075-41224	AA	CCA
-recovered pasa_asmbl_50389.p1, internal, 40567, 40652
Valid prediction for snap_scaffold_7-snap.3636-T1
Valid prediction for CodingQuarry_transcript_57617-T1
Valid prediction for GlimmerHMM_glimmerT_19443-T1
Valid prediction for snap_scaffold_7-snap.3639-T1
Valid prediction for Augustus_model.g13085.t1
Valid prediction for snap_scaffold_7-snap.3633-T1
Valid prediction for GeneMark_model.32922_t
Valid prediction for GlimmerHMM_glimmerT_19432-T1
Valid prediction for GlimmerHMM_glimmerT_19430-T1
Valid prediction for CodingQuarry_transcript_57618-T1
Valid prediction for GeneMark_model.32921_t
Valid prediction for snap_scaffold_7-snap.3645-T1
Valid prediction for GeneMark_model.32914_t
Valid prediction for snap_scaffold_7-snap.3632-T1
Valid prediction for CodingQuarry_transcript_57619-T1
Valid prediction for GlimmerHMM_glimmerT_19444-T1
Valid prediction for snap_scaffold_7-snap.3650-T1
Valid prediction for GeneMark_model.32908_t
Valid prediction for snap_scaffold_7-snap.3640-T1
Valid prediction for Augustus_model.g13084.t1
Valid prediction for snap_scaffold_7-snap.3644-T1
Valid prediction for GlimmerHMM_glimmerT_19436-T1
Valid prediction for snap_scaffold_7-snap.3623-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_7-snap.3630-T1
Valid prediction for snap_scaffold_7-snap.3635-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_7-snap.3624-T1
Valid prediction for GeneMark_model.32900_t
Valid prediction for snap_scaffold_7-snap.3628-T1
Valid prediction for GeneMark_model.32918_t
Valid prediction for GlimmerHMM_glimmerT_19434-T1
Valid prediction for GlimmerHMM_glimmerT_19429-T1
Valid prediction for GeneMark_model.32904_t
Valid prediction for GeneMark_model.32919_t
Valid prediction for GeneMark_model.32910_t
Valid prediction for snap_scaffold_7-snap.3638-T1
Valid prediction for GlimmerHMM_glimmerT_19446-T1
Valid prediction for GeneMark_model.32898_t
Valid prediction for CodingQuarry_transcript_57621-T1
Valid prediction for GeneMark_model.32925_t
Valid prediction for GlimmerHMM_glimmerT_19448-T1
Valid prediction for GeneMark_model.32906_t
Valid prediction for pasa_asmbl_50300.p1
Valid prediction for snap_scaffold_7-snap.3649-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 21847, rend_intergenic: 10289  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24189, rend_intergenic: 21850  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31832, rend_intergenic: 24926  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39257, rend_intergenic: 31963  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52509, rend_intergenic: 40530  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71670, rend_intergenic: 68876  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84690, rend_intergenic: 84460  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94745, rend_intergenic: 91067  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124333, rend_intergenic: 99671  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129265, rend_intergenic: 126117  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 134139
-exon list size: 529


building trellis

0.2    
0.4    
0.6    
0.8    
0.9    
1.1    
1.3    
1.5    
1.7    
1.9    
2.1    
2.3    
2.4    
2.6    
2.8    
3.0    
3.2    
3.4    
3.6    
3.8    
4.0    
4.1    
4.3    
4.5    
4.7    
4.9    
5.1    
5.3    
5.5    
5.6    
5.8    
6.0    
6.2    
6.4    
6.6    
6.8    
7.0    
7.2    
7.3    
7.5    
7.7    
7.9    
8.1    
8.3    
8.5    
8.7    
8.9    
9.0    
9.2    
9.4    
9.6    
9.8    
10.0    
10.2    
10.4    
10.5    
10.7    
10.9    
11.1    
11.3    
11.5    
11.7    
11.9    
12.1    
12.2    
12.4    
12.6    
12.8    
13.0    
13.2    
13.4    
13.6    
13.7    
13.9    
14.1    
14.3    
14.5    
14.7    
14.9    
15.1    
15.3    
15.4    
15.6    
15.8    
16.0    
16.2    
16.4    
16.6    
16.8    
16.9    
17.1    
17.3    
17.5    
17.7    
17.9    
18.1    
18.3    
18.5    
18.6    
18.8    
19.0    
19.2    
19.4    
19.6    
19.8    
20.0    
20.2    
20.3    
20.5    
20.7    
20.9    
21.1    
21.3    
21.5    
21.7    
21.8    
22.0    
22.2    
22.4    
22.6    
22.8    
23.0    
23.2    
23.4    
23.5    
23.7    
23.9    
24.1    
24.3    
24.5    
24.7    
24.9    
25.0    
25.2    
25.4    
25.6    
25.8    
26.0    
26.2    
26.4    
26.6    
26.7    
26.9    
27.1    
27.3    
27.5    
27.7    
27.9    
28.1    
28.2    
28.4    
28.6    
28.8    
29.0    
29.2    
29.4    
29.6    
29.8    
29.9    
30.1    
30.3    
30.5    
30.7    
30.9    
31.1    
31.3    
31.5    
31.6    
31.8    
32.0    
32.2    
32.4    
32.6    
32.8    
33.0    
33.1    
33.3    
33.5    
33.7    
33.9    
34.1    
34.3    
34.5    
34.7    
34.8    
35.0    
35.2    
35.4    
35.6    
35.8    
36.0    
36.2    
36.3    
36.5    
36.7    
36.9    
37.1    
37.3    
37.5    
37.7    
37.9    
38.0    
38.2    
38.4    
38.6    
38.8    
39.0    
39.2    
39.4    
39.5    
39.7    
39.9    
40.1    
40.3    
40.5    
40.7    
40.9    
41.1    
41.2    
41.4    
41.6    
41.8    
42.0    
42.2    
42.4    
42.6    
42.7    
42.9    
43.1    
43.3    
43.5    
43.7    
43.9    
44.1    
44.3    
44.4    
44.6    
44.8    
45.0    
45.2    
45.4    
45.6    
45.8    
46.0    
46.1    
46.3    
46.5    
46.7    
46.9    
47.1    
47.3    
47.5    
47.6    
47.8    
48.0    
48.2    
48.4    
48.6    
48.8    
49.0    
49.2    
49.3    
49.5    
49.7    
49.9    
50.1    
50.3    
50.5    
50.7    
50.8    
51.0    
51.2    
51.4    
51.6    
51.8    
52.0    
52.2    
52.4    
52.5    
52.7    
52.9    
53.1    
53.3    
53.5    
53.7    
53.9    
54.0    
54.2    
54.4    
54.6    
54.8    
55.0    
55.2    
55.4    
55.6    
55.7    
55.9    
56.1    
56.3    
56.5    
56.7    
56.9    
57.1    
57.3    
57.4    
57.6    
57.8    
58.0    
58.2    
58.4    
58.6    
58.8    
58.9    
59.1    
59.3    
59.5    
59.7    
59.9    
60.1    
60.3    
60.5    
60.6    
60.8    
61.0    
61.2    
61.4    
61.6    
61.8    
62.0    
62.1    
62.3    
62.5    
62.7    
62.9    
63.1    
63.3    
63.5    
63.7    
63.8    
64.0    
64.2    
64.4    
64.6    
64.8    
65.0    
65.2    
65.3    
65.5    
65.7    
65.9    
66.1    
66.3    
66.5    
66.7    
66.9    
67.0    
67.2    
67.4    
67.6    
67.8    
68.0    
68.2    
68.4    
68.5    
68.7    
68.9    
69.1    
69.3    
69.5    
69.7    
69.9    
70.1    
70.2    
70.4    
70.6    
70.8    
71.0    
71.2    
71.4    
71.6    
71.8    
71.9    
72.1    
72.3    
72.5    
72.7    
72.9    
73.1    
73.3    
73.4    
73.6    
73.8    
74.0    
74.2    
74.4    
74.6    
74.8    
75.0    
75.1    
75.3    
75.5    
75.7    
75.9    
76.1    
76.3    
76.5    
76.6    
76.8    
77.0    
77.2    
77.4    
77.6    
77.8    
78.0    
78.2    
78.3    
78.5    
78.7    
78.9    
79.1    
79.3    
79.5    
79.7    
79.8    
80.0    
80.2    
80.4    
80.6    
80.8    
81.0    
81.2    
81.4    
81.5    
81.7    
81.9    
82.1    
82.3    
82.5    
82.7    
82.9    
83.1    
83.2    
83.4    
83.6    
83.8    
84.0    
84.2    
84.4    
84.6    
84.7    
84.9    
85.1    
85.3    
85.5    
85.7    
85.9    
86.1    
86.3    
86.4    
86.6    
86.8    
87.0    
87.2    
87.4    
87.6    
87.8    
87.9    
88.1    
88.3    
88.5    
88.7    
88.9    
89.1    
89.3    
89.5    
89.6    
89.8    
90.0    
90.2    
90.4    
90.6    
90.8    
91.0    
91.1    
91.3    
91.5    
91.7    
91.9    
92.1    
92.3    
92.5    
92.7    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
94.0    
94.2    
94.4    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.9    
96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.2    
99.4    
99.6    
99.8    
-found 21 predictions from path traversal
Error with prediction: snap lend_intergenic: 21847, rend_intergenic: 10289  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24189, rend_intergenic: 21850  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31832, rend_intergenic: 24926  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39257, rend_intergenic: 31963  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52509, rend_intergenic: 40530  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71670, rend_intergenic: 68876  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84690, rend_intergenic: 84460  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94745, rend_intergenic: 91067  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124333, rend_intergenic: 99671  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129265, rend_intergenic: 126117  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 13 predictions persist after filtering for low support