-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_10/scaffold_10_9283900-9431553

-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.43931_t
Valid prediction for GeneMark_model.43925_t
Valid prediction for Augustus_model.g17248.t1
Valid prediction for GeneMark_model.43921_t
Valid prediction for GeneMark_model.43930_t
Valid prediction for GeneMark_model.43941_t
Valid prediction for GeneMark_model.43923_t
Couldn't classify 51167, 51295
Sorry, prediction pasa_asmbl_4646.p1 fails validation.
(AGG)	 AC	51167-51295	GT	GGG
(GAG)	 AG	51772-51897	GT	GGG
(GAC)	 AG	52004-52158	GT	AGG
(TGC)	 AG	52454-52589	GT	AGG
(GAC)	 AG	53718-53786	TC	AGT
add_exon() Sorry, pasa_asmbl_4646.p1 52004-52158-terminal-2 is invalid.
-recovered pasa_asmbl_4646.p1, terminal, 52004, 52158
-recovered pasa_asmbl_4646.p1, terminal, 53718, 53786
-recovered pasa_asmbl_4646.p1, internal, 51772, 51897
-recovered pasa_asmbl_4646.p1, internal, 52004, 52158
-recovered pasa_asmbl_4646.p1, internal, 52454, 52589
Valid prediction for snap_scaffold_10-snap.1809-T1
Valid prediction for snap_scaffold_10-snap.1812-T1
Valid prediction for GlimmerHMM_glimmerT_25686-T1
Valid prediction for GlimmerHMM_glimmerT_25688-T1
Valid prediction for GlimmerHMM_glimmerT_25696-T1
Valid prediction for Augustus_model.g17242.t1
Valid prediction for GlimmerHMM_glimmerT_25694-T1
Couldn't classify 132451, 132504
Sorry, prediction pasa_asmbl_4655.p1 fails validation.
(ATG)	 AG	128652-128736	GT	AGG
(ATG)	 AG	129071-129125	GT	AGG
(TGC)	 AG	129313-129382	GT	AGG
(CCG)	 AG	129668-129792	GT	ACG
(AAC)	 AG	130100-130164	GT	AGG
(TGG)	 AG	130414-130524	GT	AGG
(GAG)	 AG	130696-130826	GT	CCG
(GTG)	 AG	130984-131117	GT	AGG
(GTT)	 AG	131577-131630	GT	ACG
(TAA)	 AG	132245-132344	GT	AGG
(GTG)	 AG	132451-132504	CC	CCC
-recovered pasa_asmbl_4655.p1, initial, 128652, 128736
add_exon() Sorry, pasa_asmbl_4655.p1 129071-129125-initial-1 is invalid.
-recovered pasa_asmbl_4655.p1, initial, 129071, 129125
-recovered pasa_asmbl_4655.p1, internal, 128652, 128736
-recovered pasa_asmbl_4655.p1, internal, 129071, 129125
-recovered pasa_asmbl_4655.p1, internal, 129313, 129382
-recovered pasa_asmbl_4655.p1, internal, 129668, 129792
-recovered pasa_asmbl_4655.p1, internal, 130100, 130164
-recovered pasa_asmbl_4655.p1, internal, 130414, 130524
-recovered pasa_asmbl_4655.p1, internal, 130696, 130826
-recovered pasa_asmbl_4655.p1, internal, 130984, 131117
-recovered pasa_asmbl_4655.p1, internal, 131577, 131630
-recovered pasa_asmbl_4655.p1, internal, 132245, 132344
Valid prediction for CodingQuarry_transcript_5515-T1
Valid prediction for snap_scaffold_10-snap.1813-T1
Valid prediction for snap_scaffold_10-snap.1820-T1
Valid prediction for snap_scaffold_10-snap.1827-T1
Valid prediction for GeneMark_model.43937_t
Valid prediction for GeneMark_model.43935_t
Valid prediction for snap_scaffold_10-snap.1802-T1
Valid prediction for snap_scaffold_10-snap.1814-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g17251.t1
Valid prediction for snap_scaffold_10-snap.1826-T1
Valid prediction for GeneMark_model.43944_t
Valid prediction for pasa_asmbl_4658.p1
Valid prediction for CodingQuarry_transcript_5511-T1
Valid prediction for snap_scaffold_10-snap.1804-T1
Valid prediction for GlimmerHMM_glimmerT_25687-T1
Valid prediction for GeneMark_model.43950_t
Valid prediction for snap_scaffold_10-snap.1816-T1
Valid prediction for GeneMark_model.43952_t
Valid prediction for GeneMark_model.43939_t
Valid prediction for GeneMark_model.43927_t
Couldn't classify 135029, 135120
Sorry, prediction pasa_asmbl_4657.p1 fails validation.
(GCT)	 AC	135029-135120	GT	ACG
(CCT)	 AG	135421-135482	GT	AGG
(TGA)	 AG	135632-135745	GT	GAG
(GTA)	 AG	135892-135990	GT	TGG
(ATC)	 AG	136193-136371	AG	AGA
add_exon() Sorry, pasa_asmbl_4657.p1 135421-135482-terminal-2 is invalid.
-recovered pasa_asmbl_4657.p1, terminal, 135421, 135482
add_exon() Sorry, pasa_asmbl_4657.p1 135632-135745-terminal-1 is invalid.
-recovered pasa_asmbl_4657.p1, terminal, 135632, 135745
-recovered pasa_asmbl_4657.p1, terminal, 136193, 136371
-recovered pasa_asmbl_4657.p1, internal, 135421, 135482
-recovered pasa_asmbl_4657.p1, internal, 135632, 135745
-recovered pasa_asmbl_4657.p1, internal, 135892, 135990
Valid prediction for GlimmerHMM_glimmerT_25683-T1
Valid prediction for CodingQuarry_transcript_5517-T1
Valid prediction for HiQ_model.g17245.t1
Valid prediction for HiQ_model.g17249.t1
Valid prediction for CodingQuarry_transcript_5516-T1
Valid prediction for pasa_asmbl_4653.p1
Valid prediction for GeneMark_model.43933_t
Valid prediction for GeneMark_model.43942_t
Valid prediction for GlimmerHMM_glimmerT_25698-T1
Valid prediction for CodingQuarry_transcript_5518-T1
Valid prediction for GeneMark_model.43947_t
Valid prediction for snap_scaffold_10-snap.1830-T1
Valid prediction for snap_scaffold_10-snap.1831-T1
Valid prediction for GlimmerHMM_glimmerT_25682-T1
Valid prediction for GlimmerHMM_glimmerT_25692-T1
Valid prediction for GlimmerHMM_glimmerT_25697-T1
Valid prediction for GlimmerHMM_glimmerT_25691-T1
Valid prediction for snap_scaffold_10-snap.1829-T1
Valid prediction for snap_scaffold_10-snap.1823-T1
Valid prediction for pasa_asmbl_4649.p1

-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_10-snap.1805-T1
Valid prediction for CodingQuarry_transcript_5514-T1
Valid prediction for Augustus_model.g17241.t1
Valid prediction for GlimmerHMM_glimmerT_25699-T1
Valid prediction for GeneMark_model.43932_t
Valid prediction for CodingQuarry_transcript_5519-T1
Valid prediction for snap_scaffold_10-snap.1808-T1
Valid prediction for GeneMark_model.43929_t
Valid prediction for GeneMark_model.43948_t
Valid prediction for snap_scaffold_10-snap.1821-T1
Valid prediction for CodingQuarry_transcript_5521-T1
Couldn't classify 73062, 73165
Couldn't classify 73823, 73987
Sorry, prediction pasa_asmbl_4032.p1 fails validation.
(ATC)	 CG	73062-73165	GT	AAG
(ATA)	 AG	73442-73556	GT	AGG
(GAC)	 AG	73823-73987	TA	ACT
-recovered pasa_asmbl_4032.p1, internal, 73442, 73556
Valid prediction for CodingQuarry_transcript_5513-T1
Valid prediction for GeneMark_model.43928_t
Valid prediction for snap_scaffold_10-snap.1825-T1
Valid prediction for GeneMark_model.43924_t
Valid prediction for CodingQuarry_transcript_5512-T1
Valid prediction for GlimmerHMM_glimmerT_25680-T1
Valid prediction for GeneMark_model.43936_t
Valid prediction for GlimmerHMM_glimmerT_25685-T1
Valid prediction for Augustus_model.g17243.t1
Valid prediction for GlimmerHMM_glimmerT_25690-T1
Valid prediction for snap_scaffold_10-snap.1807-T1
Valid prediction for snap_scaffold_10-snap.1819-T1
Valid prediction for snap_scaffold_10-snap.1817-T1
Valid prediction for Augustus_model.g17246.t1
Valid prediction for GeneMark_model.43919_t
Valid prediction for Augustus_model.g17244.t1
Valid prediction for GeneMark_model.43940_t
Valid prediction for GlimmerHMM_glimmerT_25695-T1
Valid prediction for GlimmerHMM_glimmerT_25689-T1
Couldn't classify 51832, 51940
Couldn't classify 52387, 52491
Sorry, prediction pasa_asmbl_3596.p1 fails validation.
(CAG)	 AG	51832-51940	GT	TGG
(AGG)	 AG	52059-52252	GT	AGG
(GAG)	 AG	52387-52491	CA	AGC
-recovered pasa_asmbl_3596.p1, internal, 51832, 51940
-recovered pasa_asmbl_3596.p1, internal, 52059, 52252
Valid prediction for GeneMark_model.43917_t
Valid prediction for GeneMark_model.43949_t
Valid prediction for snap_scaffold_10-snap.1811-T1
Valid prediction for GeneMark_model.43926_t
Valid prediction for Augustus_model.g17247.t1
Valid prediction for snap_scaffold_10-snap.1803-T1
Valid prediction for GlimmerHMM_glimmerT_25693-T1
Valid prediction for HiQ_model.g17252.t1
Valid prediction for snap_scaffold_10-snap.1806-T1
Valid prediction for GeneMark_model.43920_t
Valid prediction for snap_scaffold_10-snap.1810-T1
Valid prediction for GeneMark_model.43945_t
Valid prediction for pasa_asmbl_3599.p1
Valid prediction for snap_scaffold_10-snap.1818-T1
Valid prediction for pasa_asmbl_3598.p2
Valid prediction for GlimmerHMM_glimmerT_25681-T1
Valid prediction for CodingQuarry_transcript_5520-T1
Valid prediction for GeneMark_model.43918_t
Couldn't classify 78191, 79279
Couldn't classify 80761, 80811
Sorry, prediction pasa_asmbl_3593.p1 fails validation.
(CCT)	 CG	78191-79279	GT	CTG
(TAT)	 AG	79471-79582	GT	TGG
(AAC)	 AG	80481-80662	GT	AGG
(CCC)	 AG	80761-80811	AG	AGA
-recovered pasa_asmbl_3593.p1, internal, 79471, 79582
-recovered pasa_asmbl_3593.p1, internal, 80481, 80662
Valid prediction for snap_scaffold_10-snap.1828-T1
Valid prediction for GeneMark_model.43946_t
Couldn't classify 75808, 75840
Couldn't classify 76769, 76817
Sorry, prediction pasa_asmbl_3594.p1 fails validation.
(GTC)	 CT	75808-75840	GT	AGG
(ATC)	 AG	76128-76265	GT	AGG
(TGC)	 AG	76362-76555	GT	AGG
(CAA)	 AG	76769-76817	GA	AGG
-recovered pasa_asmbl_3594.p1, internal, 76128, 76265
-recovered pasa_asmbl_3594.p1, internal, 76362, 76555
Valid prediction for GeneMark_model.43951_t
Valid prediction for Augustus_model.g17250.t1
Valid prediction for GlimmerHMM_glimmerT_25684-T1
Valid prediction for GeneMark_model.43943_t
Valid prediction for snap_scaffold_10-snap.1815-T1
Valid prediction for snap_scaffold_10-snap.1822-T1
Valid prediction for pasa_asmbl_3589.p1
Valid prediction for snap_scaffold_10-snap.1824-T1
Valid prediction for GeneMark_model.43938_t
Valid prediction for GeneMark_model.43922_t
Valid prediction for snap_scaffold_10-snap.1832-T1
Valid prediction for HiQ_model.g17253.t1
Valid prediction for GeneMark_model.43934_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9377, rend_intergenic: 8770  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12717, rend_intergenic: 9623  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41520, rend_intergenic: 13005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45224, rend_intergenic: 42193  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53786, rend_intergenic: 47096  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72264, rend_intergenic: 59343  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91935, rend_intergenic: 82917  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99135, rend_intergenic: 96636  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114606, rend_intergenic: 108649  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124518, rend_intergenic: 121043  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135124, rend_intergenic: 130385  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 147654
-exon list size: 609


building trellis

0.2    
0.3    
0.5    
0.7    
0.8    
1.0    
1.1    
1.3    
1.5    
1.6    
1.8    
2.0    
2.1    
2.3    
2.5    
2.6    
2.8    
2.9    
3.1    
3.3    
3.4    
3.6    
3.8    
3.9    
4.1    
4.3    
4.4    
4.6    
4.7    
4.9    
5.1    
5.2    
5.4    
5.6    
5.7    
5.9    
6.1    
6.2    
6.4    
6.5    
6.7    
6.9    
7.0    
7.2    
7.4    
7.5    
7.7    
7.9    
8.0    
8.2    
8.3    
8.5    
8.7    
8.8    
9.0    
9.2    
9.3    
9.5    
9.7    
9.8    
10.0    
10.1    
10.3    
10.5    
10.6    
10.8    
11.0    
11.1    
11.3    
11.5    
11.6    
11.8    
11.9    
12.1    
12.3    
12.4    
12.6    
12.8    
12.9    
13.1    
13.3    
13.4    
13.6    
13.7    
13.9    
14.1    
14.2    
14.4    
14.6    
14.7    
14.9    
15.1    
15.2    
15.4    
15.5    
15.7    
15.9    
16.0    
16.2    
16.4    
16.5    
16.7    
16.9    
17.0    
17.2    
17.3    
17.5    
17.7    
17.8    
18.0    
18.2    
18.3    
18.5    
18.7    
18.8    
19.0    
19.1    
19.3    
19.5    
19.6    
19.8    
20.0    
20.1    
20.3    
20.5    
20.6    
20.8    
20.9    
21.1    
21.3    
21.4    
21.6    
21.8    
21.9    
22.1    
22.3    
22.4    
22.6    
22.7    
22.9    
23.1    
23.2    
23.4    
23.6    
23.7    
23.9    
24.1    
24.2    
24.4    
24.5    
24.7    
24.9    
25.0    
25.2    
25.4    
25.5    
25.7    
25.9    
26.0    
26.2    
26.4    
26.5    
26.7    
26.8    
27.0    
27.2    
27.3    
27.5    
27.7    
27.8    
28.0    
28.2    
28.3    
28.5    
28.6    
28.8    
29.0    
29.1    
29.3    
29.5    
29.6    
29.8    
30.0    
30.1    
30.3    
30.4    
30.6    
30.8    
30.9    
31.1    
31.3    
31.4    
31.6    
31.8    
31.9    
32.1    
32.2    
32.4    
32.6    
32.7    
32.9    
33.1    
33.2    
33.4    
33.6    
33.7    
33.9    
34.0    
34.2    
34.4    
34.5    
34.7    
34.9    
35.0    
35.2    
35.4    
35.5    
35.7    
35.8    
36.0    
36.2    
36.3    
36.5    
36.7    
36.8    
37.0    
37.2    
37.3    
37.5    
37.6    
37.8    
38.0    
38.1    
38.3    
38.5    
38.6    
38.8    
39.0    
39.1    
39.3    
39.4    
39.6    
39.8    
39.9    
40.1    
40.3    
40.4    
40.6    
40.8    
40.9    
41.1    
41.2    
41.4    
41.6    
41.7    
41.9    
42.1    
42.2    
42.4    
42.6    
42.7    
42.9    
43.0    
43.2    
43.4    
43.5    
43.7    
43.9    
44.0    
44.2    
44.4    
44.5    
44.7    
44.8    
45.0    
45.2    
45.3    
45.5    
45.7    
45.8    
46.0    
46.2    
46.3    
46.5    
46.6    
46.8    
47.0    
47.1    
47.3    
47.5    
47.6    
47.8    
48.0    
48.1    
48.3    
48.4    
48.6    
48.8    
48.9    
49.1    
49.3    
49.4    
49.6    
49.8    
49.9    
50.1    
50.2    
50.4    
50.6    
50.7    
50.9    
51.1    
51.2    
51.4    
51.6    
51.7    
51.9    
52.0    
52.2    
52.4    
52.5    
52.7    
52.9    
53.0    
53.2    
53.4    
53.5    
53.7    
53.8    
54.0    
54.2    
54.3    
54.5    
54.7    
54.8    
55.0    
55.2    
55.3    
55.5    
55.6    
55.8    
56.0    
56.1    
56.3    
56.5    
56.6    
56.8    
57.0    
57.1    
57.3    
57.4    
57.6    
57.8    
57.9    
58.1    
58.3    
58.4    
58.6    
58.8    
58.9    
59.1    
59.2    
59.4    
59.6    
59.7    
59.9    
60.1    
60.2    
60.4    
60.6    
60.7    
60.9    
61.0    
61.2    
61.4    
61.5    
61.7    
61.9    
62.0    
62.2    
62.4    
62.5    
62.7    
62.8    
63.0    
63.2    
63.3    
63.5    
63.7    
63.8    
64.0    
64.2    
64.3    
64.5    
64.6    
64.8    
65.0    
65.1    
65.3    
65.5    
65.6    
65.8    
66.0    
66.1    
66.3    
66.4    
66.6    
66.8    
66.9    
67.1    
67.3    
67.4    
67.6    
67.8    
67.9    
68.1    
68.2    
68.4    
68.6    
68.7    
68.9    
69.1    
69.2    
69.4    
69.6    
69.7    
69.9    
70.0    
70.2    
70.4    
70.5    
70.7    
70.9    
71.0    
71.2    
71.4    
71.5    
71.7    
71.8    
72.0    
72.2    
72.3    
72.5    
72.7    
72.8    
73.0    
73.2    
73.3    
73.5    
73.6    
73.8    
74.0    
74.1    
74.3    
74.5    
74.6    
74.8    
75.0    
75.1    
75.3    
75.5    
75.6    
75.8    
75.9    
76.1    
76.3    
76.4    
76.6    
76.8    
76.9    
77.1    
77.3    
77.4    
77.6    
77.7    
77.9    
78.1    
78.2    
78.4    
78.6    
78.7    
78.9    
79.1    
79.2    
79.4    
79.5    
79.7    
79.9    
80.0    
80.2    
80.4    
80.5    
80.7    
80.9    
81.0    
81.2    
81.3    
81.5    
81.7    
81.8    
82.0    
82.2    
82.3    
82.5    
82.7    
82.8    
83.0    
83.1    
83.3    
83.5    
83.6    
83.8    
84.0    
84.1    
84.3    
84.5    
84.6    
84.8    
84.9    
85.1    
85.3    
85.4    
85.6    
85.8    
85.9    
86.1    
86.3    
86.4    
86.6    
86.7    
86.9    
87.1    
87.2    
87.4    
87.6    
87.7    
87.9    
88.1    
88.2    
88.4    
88.5    
88.7    
88.9    
89.0    
89.2    
89.4    
89.5    
89.7    
89.9    
90.0    
90.2    
90.3    
90.5    
90.7    
90.8    
91.0    
91.2    
91.3    
91.5    
91.7    
91.8    
92.0    
92.1    
92.3    
92.5    
92.6    
92.8    
93.0    
93.1    
93.3    
93.5    
93.6    
93.8    
93.9    
94.1    
94.3    
94.4    
94.6    
94.8    
94.9    
95.1    
95.3    
95.4    
95.6    
95.7    
95.9    
96.1    
96.2    
96.4    
96.6    
96.7    
96.9    
97.1    
97.2    
97.4    
97.5    
97.7    
97.9    
98.0    
98.2    
98.4    
98.5    
98.7    
98.9    
99.0    
99.2    
99.3    
99.5    
99.7    
99.8    
-found 20 predictions from path traversal
Error with prediction: snap lend_intergenic: 9377, rend_intergenic: 8770  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12717, rend_intergenic: 9623  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41520, rend_intergenic: 13005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45224, rend_intergenic: 42193  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53786, rend_intergenic: 47096  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72264, rend_intergenic: 59343  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91935, rend_intergenic: 82917  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99135, rend_intergenic: 96636  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114606, rend_intergenic: 108649  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124518, rend_intergenic: 121043  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135124, rend_intergenic: 130385  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