-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_13/scaffold_13_14141630-14359400

-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 CodingQuarry_transcript_13305-T1
Valid prediction for snap_scaffold_13-snap.2742-T1
Valid prediction for GlimmerHMM_glimmerT_32755-T1
Valid prediction for GlimmerHMM_glimmerT_32764-T1
Valid prediction for CodingQuarry_transcript_13306-T1
Valid prediction for snap_scaffold_13-snap.2731-T1
Valid prediction for GlimmerHMM_glimmerT_32748-T1
Valid prediction for snap_scaffold_13-snap.2702-T1
Valid prediction for Augustus_model.g21858.t1
Valid prediction for snap_scaffold_13-snap.2707-T1
Valid prediction for snap_scaffold_13-snap.2721-T1
Valid prediction for pasa_asmbl_11424.p1
Valid prediction for GlimmerHMM_glimmerT_32760-T1
Valid prediction for snap_scaffold_13-snap.2739-T1
Couldn't classify 32872, 33030
Couldn't classify 33230, 33310
Sorry, prediction CodingQuarry_transcript_13301-T1 fails validation.
(ATG)	 AT	32872-33030	GG	TAG
(GTT)	 AT	33230-33310	AT	AGA
Valid prediction for Augustus_model.g21855.t1
Valid prediction for GlimmerHMM_glimmerT_32757-T1
Valid prediction for snap_scaffold_13-snap.2726-T1
Valid prediction for snap_scaffold_13-snap.2714-T1
Valid prediction for snap_scaffold_13-snap.2709-T1
Valid prediction for GlimmerHMM_glimmerT_32765-T1
Valid prediction for GlimmerHMM_glimmerT_32741-T1
Valid prediction for CodingQuarry_transcript_13299-T1
Couldn't classify 32860, 33030
Couldn't classify 33230, 33234
Sorry, prediction CodingQuarry_transcript_13304-T1 fails validation.
(ATG)	 AA	31934-32033	GT	AGG
(TTG)	 AG	32140-32246	GT	AAG
(ACT)	 AG	32541-32676	GT	AGG
(GTG)	 AG	32860-33030	GG	TAG
(GTT)	 AT	33230-33234	GG	AGG
-recovered CodingQuarry_transcript_13304-T1, initial, 31934, 32033
-recovered CodingQuarry_transcript_13304-T1, internal, 32140, 32246
-recovered CodingQuarry_transcript_13304-T1, internal, 32541, 32676
Valid prediction for snap_scaffold_13-snap.2716-T1
Valid prediction for snap_scaffold_13-snap.2738-T1
Valid prediction for GlimmerHMM_glimmerT_32743-T1
Couldn't classify 104867, 105193
Sorry, prediction pasa_asmbl_11440.p1 fails validation.
(GAG)	 CA	104867-105193	GA	GAG
Valid prediction for GlimmerHMM_glimmerT_32756-T1
Valid prediction for snap_scaffold_13-snap.2701-T1
Valid prediction for GlimmerHMM_glimmerT_32761-T1
Valid prediction for snap_scaffold_13-snap.2740-T1
Valid prediction for snap_scaffold_13-snap.2717-T1
Valid prediction for snap_scaffold_13-snap.2711-T1
Couldn't classify 89560, 89691
Sorry, prediction pasa_asmbl_11674.p1 fails validation.
(ATG)	 TC	87313-87433	GT	AGG
(GTG)	 AG	87594-87676	GT	AGG
(GCC)	 AG	87915-88491	GT	AGG
(CCC)	 AG	88884-89029	GT	AGG
(GAC)	 AG	89560-89691	GT	AGG
-recovered pasa_asmbl_11674.p1, initial, 87313, 87433
-recovered pasa_asmbl_11674.p1, internal, 87594, 87676
-recovered pasa_asmbl_11674.p1, internal, 87915, 88491
-recovered pasa_asmbl_11674.p1, internal, 88884, 89029
-recovered pasa_asmbl_11674.p1, internal, 89560, 89691
Valid prediction for CodingQuarry_transcript_13303-T1
Valid prediction for Augustus_model.g21847.t1
Valid prediction for Augustus_model.g21853.t1
Valid prediction for snap_scaffold_13-snap.2734-T1
Valid prediction for pasa_asmbl_11432.p1
Valid prediction for snap_scaffold_13-snap.2723-T1
Valid prediction for GlimmerHMM_glimmerT_32762-T1
Valid prediction for snap_scaffold_13-snap.2706-T1
Valid prediction for Augustus_model.g21843.t1
Valid prediction for HiQ_model.g21844.t1
Valid prediction for snap_scaffold_13-snap.2715-T1
Valid prediction for Augustus_model.g21859.t1
Valid prediction for CodingQuarry_transcript_13302-T1
Valid prediction for snap_scaffold_13-snap.2745-T1
Valid prediction for GlimmerHMM_glimmerT_32766-T1
Valid prediction for Augustus_model.g21854.t1
Valid prediction for GlimmerHMM_glimmerT_32759-T1
Valid prediction for GlimmerHMM_glimmerT_32753-T1
Valid prediction for GlimmerHMM_glimmerT_32751-T1
Valid prediction for Augustus_model.g21857.t1
Valid prediction for GlimmerHMM_glimmerT_32749-T1
Valid prediction for GlimmerHMM_glimmerT_32737-T1
Valid prediction for GlimmerHMM_glimmerT_32738-T1
Valid prediction for snap_scaffold_13-snap.2729-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 CodingQuarry_transcript_13300-T1
Valid prediction for GlimmerHMM_glimmerT_32739-T1
Valid prediction for snap_scaffold_13-snap.2733-T1
Valid prediction for snap_scaffold_13-snap.2705-T1
Valid prediction for GlimmerHMM_glimmerT_32746-T1
Valid prediction for GlimmerHMM_glimmerT_32750-T1
Valid prediction for Augustus_model.g21856.t1
Valid prediction for snap_scaffold_13-snap.2720-T1
Valid prediction for snap_scaffold_13-snap.2730-T1
Couldn't classify 132809, 132901
Sorry, prediction pasa_asmbl_10179.p1 fails validation.
(ATG)	 GA	131281-131514	GT	CGG
(TGG)	 AG	131762-131779	GT	AAG
(ATT)	 AG	131966-132031	GT	AGG
(AAC)	 AG	132453-132548	GT	CGG
(CAA)	 AG	132809-132901	AG	CCA
-recovered pasa_asmbl_10179.p1, initial, 131281, 131514
-recovered pasa_asmbl_10179.p1, internal, 131762, 131779
-recovered pasa_asmbl_10179.p1, internal, 131966, 132031
-recovered pasa_asmbl_10179.p1, internal, 132453, 132548
Valid prediction for GlimmerHMM_glimmerT_32758-T1
Valid prediction for GlimmerHMM_glimmerT_32744-T1
Valid prediction for snap_scaffold_13-snap.2746-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for pasa_asmbl_10176.p1
Valid prediction for snap_scaffold_13-snap.2712-T1
Valid prediction for snap_scaffold_13-snap.2737-T1
Valid prediction for snap_scaffold_13-snap.2743-T1
Valid prediction for GlimmerHMM_glimmerT_32747-T1
Valid prediction for Augustus_model.g21849.t1
Valid prediction for snap_scaffold_13-snap.2719-T1
Couldn't classify 137549, 137635
Couldn't classify 141041, 141168
Sorry, prediction pasa_asmbl_10354.p1 fails validation.
(CAG)	 CT	137549-137635	GT	AGG
(CTC)	 AG	138031-138080	GT	AGG
(CTC)	 AG	139269-139346	GT	AAG
(GAG)	 AG	139598-139709	GT	GGG
(GAG)	 AG	140464-140554	GT	GGG
(ACC)	 AG	141041-141168	GT	GTG
-recovered pasa_asmbl_10354.p1, internal, 138031, 138080
-recovered pasa_asmbl_10354.p1, internal, 139269, 139346
-recovered pasa_asmbl_10354.p1, internal, 139598, 139709
-recovered pasa_asmbl_10354.p1, internal, 140464, 140554
-recovered pasa_asmbl_10354.p1, internal, 141041, 141168
Couldn't classify 178610, 178784
Sorry, prediction pasa_asmbl_10174.p1 fails validation.
(CAT)	 TT	178610-178784	GT	CGG
(GCT)	 AG	179367-179566	AA	AGA
-recovered pasa_asmbl_10174.p1, terminal, 179367, 179566
Valid prediction for GlimmerHMM_glimmerT_32752-T1
Valid prediction for snap_scaffold_13-snap.2741-T1
Valid prediction for snap_scaffold_13-snap.2732-T1
Valid prediction for snap_scaffold_13-snap.2728-T1
Valid prediction for GlimmerHMM_glimmerT_32740-T1
Valid prediction for Augustus_model.g21848.t1
Couldn't classify 196835, 196979
Sorry, prediction pasa_asmbl_10172.p1 fails validation.
(TGT)	 AG	196835-196979	GT	TGG
(CAA)	 AG	197378-197570	GT	GGG
(GTG)	 AG	197780-197924	GT	CGG
(ATG)	 AG	198357-198432	GT	ACG
(GGA)	 AG	198697-198773	CT	GAC
-recovered pasa_asmbl_10172.p1, initial, 198357, 198432
-recovered pasa_asmbl_10172.p1, terminal, 198697, 198773
-recovered pasa_asmbl_10172.p1, internal, 196835, 196979
-recovered pasa_asmbl_10172.p1, internal, 197378, 197570
-recovered pasa_asmbl_10172.p1, internal, 197780, 197924
-recovered pasa_asmbl_10172.p1, internal, 198357, 198432
Valid prediction for CodingQuarry_transcript_13308-T1
Valid prediction for snap_scaffold_13-snap.2735-T1
Couldn't classify 52664, 52783
Couldn't classify 53331, 53466
Sorry, prediction pasa_asmbl_10323.p1 fails validation.
(AGG)	 AG	52664-52783	GT	AGG
(AGT)	 AG	52950-53056	GT	AGG
(CCA)	 AG	53331-53466	CC	GGC
-recovered pasa_asmbl_10323.p1, internal, 52664, 52783
-recovered pasa_asmbl_10323.p1, internal, 52950, 53056
Valid prediction for snap_scaffold_13-snap.2704-T1
Valid prediction for snap_scaffold_13-snap.2713-T1
Valid prediction for Augustus_model.g21852.t1
Couldn't classify 47906, 47998
Couldn't classify 49094, 49252
Sorry, prediction pasa_asmbl_10183.p1 fails validation.
(TCC)	 AG	47906-47998	GT	AGG
(TCC)	 AG	48616-48846	GT	AGG
(GAG)	 AG	49094-49252	GT	AGG
-recovered pasa_asmbl_10183.p1, internal, 47906, 47998
-recovered pasa_asmbl_10183.p1, internal, 48616, 48846
-recovered pasa_asmbl_10183.p1, internal, 49094, 49252
Valid prediction for GlimmerHMM_glimmerT_32767-T1
Valid prediction for snap_scaffold_13-snap.2725-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_32763-T1
Valid prediction for GlimmerHMM_glimmerT_32745-T1
Valid prediction for snap_scaffold_13-snap.2718-T1
Valid prediction for snap_scaffold_13-snap.2744-T1
Valid prediction for snap_scaffold_13-snap.2724-T1
Valid prediction for GlimmerHMM_glimmerT_32742-T1
Valid prediction for GlimmerHMM_glimmerT_32754-T1
Valid prediction for snap_scaffold_13-snap.2727-T1
Valid prediction for snap_scaffold_13-snap.2708-T1
Valid prediction for snap_scaffold_13-snap.2722-T1
Valid prediction for snap_scaffold_13-snap.2710-T1
Valid prediction for Augustus_model.g21845.t1
Valid prediction for Augustus_model.g21851.t1
Valid prediction for Augustus_model.g21846.t1
Valid prediction for Augustus_model.g21850.t1
Valid prediction for snap_scaffold_13-snap.2703-T1
Valid prediction for snap_scaffold_13-snap.2736-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17899, rend_intergenic: 11377  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41114, rend_intergenic: 39025  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44410, rend_intergenic: 43127  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67016, rend_intergenic: 47582  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78832, rend_intergenic: 75217  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84967, rend_intergenic: 79688  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91556, rend_intergenic: 88049  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96313, rend_intergenic: 94037  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105193, rend_intergenic: 96544  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106948, rend_intergenic: 105214  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121858, rend_intergenic: 112993  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127067, rend_intergenic: 122277  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137647, rend_intergenic: 127144  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163027, rend_intergenic: 153057  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174362, rend_intergenic: 164291  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180755, rend_intergenic: 178270  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188743, rend_intergenic: 180972  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188796, rend_intergenic: 188767  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 213615, rend_intergenic: 188856  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 217771
-exon list size: 429


building trellis

0.2    
0.5    
0.7    
0.9    
1.2    
1.4    
1.6    
1.9    
2.1    
2.3    
2.6    
2.8    
3.0    
3.2    
3.5    
3.7    
3.9    
4.2    
4.4    
4.6    
4.9    
5.1    
5.3    
5.6    
5.8    
6.0    
6.3    
6.5    
6.7    
7.0    
7.2    
7.4    
7.7    
7.9    
8.1    
8.4    
8.6    
8.8    
9.0    
9.3    
9.5    
9.7    
10.0    
10.2    
10.4    
10.7    
10.9    
11.1    
11.4    
11.6    
11.8    
12.1    
12.3    
12.5    
12.8    
13.0    
13.2    
13.5    
13.7    
13.9    
14.2    
14.4    
14.6    
14.8    
15.1    
15.3    
15.5    
15.8    
16.0    
16.2    
16.5    
16.7    
16.9    
17.2    
17.4    
17.6    
17.9    
18.1    
18.3    
18.6    
18.8    
19.0    
19.3    
19.5    
19.7    
20.0    
20.2    
20.4    
20.6    
20.9    
21.1    
21.3    
21.6    
21.8    
22.0    
22.3    
22.5    
22.7    
23.0    
23.2    
23.4    
23.7    
23.9    
24.1    
24.4    
24.6    
24.8    
25.1    
25.3    
25.5    
25.8    
26.0    
26.2    
26.5    
26.7    
26.9    
27.1    
27.4    
27.6    
27.8    
28.1    
28.3    
28.5    
28.8    
29.0    
29.2    
29.5    
29.7    
29.9    
30.2    
30.4    
30.6    
30.9    
31.1    
31.3    
31.6    
31.8    
32.0    
32.3    
32.5    
32.7    
32.9    
33.2    
33.4    
33.6    
33.9    
34.1    
34.3    
34.6    
34.8    
35.0    
35.3    
35.5    
35.7    
36.0    
36.2    
36.4    
36.7    
36.9    
37.1    
37.4    
37.6    
37.8    
38.1    
38.3    
38.5    
38.7    
39.0    
39.2    
39.4    
39.7    
39.9    
40.1    
40.4    
40.6    
40.8    
41.1    
41.3    
41.5    
41.8    
42.0    
42.2    
42.5    
42.7    
42.9    
43.2    
43.4    
43.6    
43.9    
44.1    
44.3    
44.5    
44.8    
45.0    
45.2    
45.5    
45.7    
45.9    
46.2    
46.4    
46.6    
46.9    
47.1    
47.3    
47.6    
47.8    
48.0    
48.3    
48.5    
48.7    
49.0    
49.2    
49.4    
49.7    
49.9    
50.1    
50.3    
50.6    
50.8    
51.0    
51.3    
51.5    
51.7    
52.0    
52.2    
52.4    
52.7    
52.9    
53.1    
53.4    
53.6    
53.8    
54.1    
54.3    
54.5    
54.8    
55.0    
55.2    
55.5    
55.7    
55.9    
56.1    
56.4    
56.6    
56.8    
57.1    
57.3    
57.5    
57.8    
58.0    
58.2    
58.5    
58.7    
58.9    
59.2    
59.4    
59.6    
59.9    
60.1    
60.3    
60.6    
60.8    
61.0    
61.3    
61.5    
61.7    
61.9    
62.2    
62.4    
62.6    
62.9    
63.1    
63.3    
63.6    
63.8    
64.0    
64.3    
64.5    
64.7    
65.0    
65.2    
65.4    
65.7    
65.9    
66.1    
66.4    
66.6    
66.8    
67.1    
67.3    
67.5    
67.7    
68.0    
68.2    
68.4    
68.7    
68.9    
69.1    
69.4    
69.6    
69.8    
70.1    
70.3    
70.5    
70.8    
71.0    
71.2    
71.5    
71.7    
71.9    
72.2    
72.4    
72.6    
72.9    
73.1    
73.3    
73.5    
73.8    
74.0    
74.2    
74.5    
74.7    
74.9    
75.2    
75.4    
75.6    
75.9    
76.1    
76.3    
76.6    
76.8    
77.0    
77.3    
77.5    
77.7    
78.0    
78.2    
78.4    
78.7    
78.9    
79.1    
79.4    
79.6    
79.8    
80.0    
80.3    
80.5    
80.7    
81.0    
81.2    
81.4    
81.7    
81.9    
82.1    
82.4    
82.6    
82.8    
83.1    
83.3    
83.5    
83.8    
84.0    
84.2    
84.5    
84.7    
84.9    
85.2    
85.4    
85.6    
85.8    
86.1    
86.3    
86.5    
86.8    
87.0    
87.2    
87.5    
87.7    
87.9    
88.2    
88.4    
88.6    
88.9    
89.1    
89.3    
89.6    
89.8    
90.0    
90.3    
90.5    
90.7    
91.0    
91.2    
91.4    
91.6    
91.9    
92.1    
92.3    
92.6    
92.8    
93.0    
93.3    
93.5    
93.7    
94.0    
94.2    
94.4    
94.7    
94.9    
95.1    
95.4    
95.6    
95.8    
96.1    
96.3    
96.5    
96.8    
97.0    
97.2    
97.4    
97.7    
97.9    
98.1    
98.4    
98.6    
98.8    
99.1    
99.3    
99.5    
99.8    
-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 17899, rend_intergenic: 11377  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41114, rend_intergenic: 39025  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44410, rend_intergenic: 43127  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67016, rend_intergenic: 47582  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78832, rend_intergenic: 75217  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84967, rend_intergenic: 79688  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91556, rend_intergenic: 88049  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96313, rend_intergenic: 94037  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105193, rend_intergenic: 96544  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106948, rend_intergenic: 105214  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121858, rend_intergenic: 112993  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127067, rend_intergenic: 122277  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137647, rend_intergenic: 127144  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163027, rend_intergenic: 153057  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174362, rend_intergenic: 164291  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180755, rend_intergenic: 178270  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188743, rend_intergenic: 180972  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188796, rend_intergenic: 188767  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 213615, rend_intergenic: 188856  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 26 predictions persist after filtering for low support