-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_2/scaffold_2_12966579-13210555

-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_4730-T1
Valid prediction for Augustus_model.g3188.t1
Valid prediction for GlimmerHMM_glimmerT_4758-T1
Valid prediction for snap_scaffold_2-snap.2511-T1
Valid prediction for Augustus_model.g3195.t1
Couldn't classify 184950, 186080
Sorry, prediction pasa_asmbl_24825.p1 fails validation.
(ATC)	 AC	184950-186080	AA	CCA
Valid prediction for GlimmerHMM_glimmerT_4736-T1
Valid prediction for GlimmerHMM_glimmerT_4734-T1
Valid prediction for HiQ_model.g3181.t1
Valid prediction for Augustus_model.g3193.t1
Valid prediction for snap_scaffold_2-snap.2496-T1
Valid prediction for Augustus_model.g3189.t1
Valid prediction for pasa_asmbl_24811.p1
Valid prediction for snap_scaffold_2-snap.2529-T1
Valid prediction for CodingQuarry_transcript_28689-T1
Valid prediction for GlimmerHMM_glimmerT_4733-T1
Valid prediction for GlimmerHMM_glimmerT_4743-T1
Valid prediction for Augustus_model.g3182.t1
Valid prediction for snap_scaffold_2-snap.2514-T1
Valid prediction for GlimmerHMM_glimmerT_4751-T1
Valid prediction for snap_scaffold_2-snap.2510-T1
Valid prediction for Augustus_model.g3180.t1
Valid prediction for snap_scaffold_2-snap.2517-T1
Valid prediction for GlimmerHMM_glimmerT_4729-T1
Couldn't classify 99470, 99505
Sorry, prediction pasa_asmbl_24817.p1 fails validation.
(TGG)	 GA	99470-99505	GT	AGG
(GTT)	 AG	99612-99756	GT	AGG
(CCA)	 AG	100074-100215	GT	TGG
(GTC)	 AG	100402-100596	GT	AGG
(TTT)	 AG	101185-101311	GT	CGG
(GAG)	 AG	101664-101844	GT	AGG
(TGA)	 AG	101963-102105	GT	AGG
(ATA)	 AG	102196-102513	GG	GAG
-recovered pasa_asmbl_24817.p1, terminal, 102196, 102513
-recovered pasa_asmbl_24817.p1, internal, 99612, 99756
-recovered pasa_asmbl_24817.p1, internal, 100074, 100215
-recovered pasa_asmbl_24817.p1, internal, 100402, 100596
-recovered pasa_asmbl_24817.p1, internal, 101185, 101311
-recovered pasa_asmbl_24817.p1, internal, 101664, 101844
-recovered pasa_asmbl_24817.p1, internal, 101963, 102105
Valid prediction for Augustus_model.g3177.t1
Valid prediction for snap_scaffold_2-snap.2526-T1
Valid prediction for CodingQuarry_transcript_28690-T1
Valid prediction for snap_scaffold_2-snap.2489-T1
Valid prediction for Augustus_model.g3171.t1
Couldn't classify 186063, 187166
Couldn't classify 187661, 187738
Sorry, prediction pasa_asmbl_24826.p1 fails validation.
(GGA)	 AC	186063-187166	GT	AGG
(AAA)	 AG	187661-187738	AT	ACA
Valid prediction for snap_scaffold_2-snap.2490-T1
Couldn't classify 126587, 126794
Couldn't classify 128313, 128419
Sorry, prediction pasa_asmbl_24820.p1 fails validation.
(TTT)	 TC	126587-126794	GT	AAG
(TCC)	 AG	127851-128126	GT	AGG
(CAA)	 AG	128313-128419	CC	CCC
-recovered pasa_asmbl_24820.p1, internal, 127851, 128126
Valid prediction for GlimmerHMM_glimmerT_4747-T1
Valid prediction for GlimmerHMM_glimmerT_4752-T1
Valid prediction for GlimmerHMM_glimmerT_4726-T1
Valid prediction for GlimmerHMM_glimmerT_4754-T1
Valid prediction for GlimmerHMM_glimmerT_4725-T1
Valid prediction for GlimmerHMM_glimmerT_4742-T1
Valid prediction for snap_scaffold_2-snap.2498-T1
Valid prediction for GlimmerHMM_glimmerT_4738-T1
Valid prediction for snap_scaffold_2-snap.2505-T1
Valid prediction for GlimmerHMM_glimmerT_4722-T1
Valid prediction for snap_scaffold_2-snap.2521-T1
Valid prediction for Augustus_model.g3194.t1
Valid prediction for Augustus_model.g3191.t1
Valid prediction for snap_scaffold_2-snap.2503-T1
Valid prediction for snap_scaffold_2-snap.2512-T1
Valid prediction for snap_scaffold_2-snap.2508-T1
Valid prediction for pasa_asmbl_24807.p1
Valid prediction for snap_scaffold_2-snap.2515-T1
Valid prediction for Augustus_model.g3185.t1
Valid prediction for GlimmerHMM_glimmerT_4737-T1
Valid prediction for snap_scaffold_2-snap.2494-T1
Valid prediction for GlimmerHMM_glimmerT_4721-T1
Valid prediction for Augustus_model.g3173.t1
Valid prediction for GlimmerHMM_glimmerT_4728-T1
Valid prediction for snap_scaffold_2-snap.2520-T1
Valid prediction for CodingQuarry_transcript_28688-T1
Valid prediction for snap_scaffold_2-snap.2502-T1
Valid prediction for GlimmerHMM_glimmerT_4739-T1
Valid prediction for snap_scaffold_2-snap.2507-T1
Valid prediction for GlimmerHMM_glimmerT_4760-T1
Valid prediction for GlimmerHMM_glimmerT_4749-T1
Valid prediction for snap_scaffold_2-snap.2523-T1
Valid prediction for GlimmerHMM_glimmerT_4748-T1
Valid prediction for GlimmerHMM_glimmerT_4745-T1
Valid prediction for Augustus_model.g3192.t1
Valid prediction for snap_scaffold_2-snap.2509-T1
Valid prediction for Augustus_model.g3179.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: -)Couldn't classify 167448, 167595
Sorry, prediction pasa_asmbl_23485.p1 fails validation.
(ATC)	 CC	167448-167595	GT	TGG
(GTC)	 AG	167755-168182	GC	GAG
-recovered pasa_asmbl_23485.p1, terminal, 167755, 168182
-recovered pasa_asmbl_23485.p1, internal, 167755, 168182
Valid prediction for GlimmerHMM_glimmerT_4724-T1
Valid prediction for snap_scaffold_2-snap.2500-T1
Valid prediction for GlimmerHMM_glimmerT_4755-T1
Valid prediction for snap_scaffold_2-snap.2524-T1
Valid prediction for GlimmerHMM_glimmerT_4727-T1
Valid prediction for snap_scaffold_2-snap.2499-T1
Valid prediction for snap_scaffold_2-snap.2518-T1
Valid prediction for GlimmerHMM_glimmerT_4759-T1
Valid prediction for GlimmerHMM_glimmerT_4744-T1
Couldn't classify 127225, 127287
Sorry, prediction pasa_asmbl_23496.p1 fails validation.
(ATG)	 CA	123786-123887	GT	ATG
(ATA)	 AG	124149-124256	GT	AGG
(TTT)	 AG	124636-124728	GT	AGG
(AGT)	 AG	124905-124973	GT	AAG
(GTG)	 AG	125119-125173	GT	TGG
(CTG)	 AG	125507-125710	GT	AGG
(ATT)	 AG	125915-126083	GT	AGG
(TCT)	 AG	126285-126411	GT	AGG
(TCC)	 AG	126584-126694	GT	TGG
(AAT)	 AG	126950-127120	GT	AGG
(CTG)	 AG	127225-127287	CA	GCC
-recovered pasa_asmbl_23496.p1, initial, 123786, 123887
-recovered pasa_asmbl_23496.p1, internal, 124149, 124256
-recovered pasa_asmbl_23496.p1, internal, 124636, 124728
-recovered pasa_asmbl_23496.p1, internal, 124905, 124973
-recovered pasa_asmbl_23496.p1, internal, 125119, 125173
-recovered pasa_asmbl_23496.p1, internal, 125507, 125710
-recovered pasa_asmbl_23496.p1, internal, 125915, 126083
-recovered pasa_asmbl_23496.p1, internal, 126285, 126411
-recovered pasa_asmbl_23496.p1, internal, 126584, 126694
-recovered pasa_asmbl_23496.p1, internal, 126950, 127120
Valid prediction for HiQ_model.g3183.t1
Valid prediction for snap_scaffold_2-snap.2493-T1
Valid prediction for snap_scaffold_2-snap.2497-T1
Valid prediction for GlimmerHMM_glimmerT_4741-T1
Valid prediction for snap_scaffold_2-snap.2495-T1
Valid prediction for GlimmerHMM_glimmerT_4757-T1
Valid prediction for Augustus_model.g3190.t1
Valid prediction for snap_scaffold_2-snap.2522-T1
Valid prediction for snap_scaffold_2-snap.2506-T1
Valid prediction for snap_scaffold_2-snap.2527-T1
Valid prediction for GlimmerHMM_glimmerT_4756-T1
Valid prediction for snap_scaffold_2-snap.2516-T1
Valid prediction for Augustus_model.g3174.t1
Valid prediction for pasa_asmbl_23492.p1
Valid prediction for GlimmerHMM_glimmerT_4731-T1
Valid prediction for GlimmerHMM_glimmerT_4740-T1
Valid prediction for snap_scaffold_2-snap.2525-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for Augustus_model.g3176.t1
Valid prediction for snap_scaffold_2-snap.2488-T1
Valid prediction for GlimmerHMM_glimmerT_4732-T1
Valid prediction for Augustus_model.g3178.t1
Valid prediction for Augustus_model.g3187.t1
Valid prediction for GlimmerHMM_glimmerT_4723-T1
Valid prediction for GlimmerHMM_glimmerT_4735-T1
Valid prediction for Augustus_model.g3175.t1
Valid prediction for Augustus_model.g3186.t1
Valid prediction for snap_scaffold_2-snap.2501-T1
Valid prediction for snap_scaffold_2-snap.2492-T1
Valid prediction for Augustus_model.g3172.t1
Valid prediction for snap_scaffold_2-snap.2504-T1
Valid prediction for snap_scaffold_2-snap.2491-T1
Valid prediction for Augustus_model.g3184.t1
Valid prediction for snap_scaffold_2-snap.2528-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_4750-T1
Valid prediction for GlimmerHMM_glimmerT_4746-T1
Valid prediction for snap_scaffold_2-snap.2513-T1
Valid prediction for GlimmerHMM_glimmerT_4753-T1
Valid prediction for snap_scaffold_2-snap.2519-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15445, rend_intergenic: 10760  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32148, rend_intergenic: 26582  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38034, rend_intergenic: 33377  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39503, rend_intergenic: 38143  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46970, rend_intergenic: 44856  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58463, rend_intergenic: 56555  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64965, rend_intergenic: 64314  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67474, rend_intergenic: 64967  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120192, rend_intergenic: 104623  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169354, rend_intergenic: 142208  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180268, rend_intergenic: 170814  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198373, rend_intergenic: 180346  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200051, rend_intergenic: 198870  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 227814, rend_intergenic: 200071  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 240607, rend_intergenic: 228447  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 243977
-exon list size: 534


building trellis

0.2    
0.4    
0.6    
0.7    
0.9    
1.1    
1.3    
1.5    
1.7    
1.9    
2.1    
2.2    
2.4    
2.6    
2.8    
3.0    
3.2    
3.4    
3.5    
3.7    
3.9    
4.1    
4.3    
4.5    
4.7    
4.9    
5.0    
5.2    
5.4    
5.6    
5.8    
6.0    
6.2    
6.3    
6.5    
6.7    
6.9    
7.1    
7.3    
7.5    
7.6    
7.8    
8.0    
8.2    
8.4    
8.6    
8.8    
9.0    
9.1    
9.3    
9.5    
9.7    
9.9    
10.1    
10.3    
10.4    
10.6    
10.8    
11.0    
11.2    
11.4    
11.6    
11.8    
11.9    
12.1    
12.3    
12.5    
12.7    
12.9    
13.1    
13.2    
13.4    
13.6    
13.8    
14.0    
14.2    
14.4    
14.6    
14.7    
14.9    
15.1    
15.3    
15.5    
15.7    
15.9    
16.0    
16.2    
16.4    
16.6    
16.8    
17.0    
17.2    
17.4    
17.5    
17.7    
17.9    
18.1    
18.3    
18.5    
18.7    
18.8    
19.0    
19.2    
19.4    
19.6    
19.8    
20.0    
20.1    
20.3    
20.5    
20.7    
20.9    
21.1    
21.3    
21.5    
21.6    
21.8    
22.0    
22.2    
22.4    
22.6    
22.8    
22.9    
23.1    
23.3    
23.5    
23.7    
23.9    
24.1    
24.3    
24.4    
24.6    
24.8    
25.0    
25.2    
25.4    
25.6    
25.7    
25.9    
26.1    
26.3    
26.5    
26.7    
26.9    
27.1    
27.2    
27.4    
27.6    
27.8    
28.0    
28.2    
28.4    
28.5    
28.7    
28.9    
29.1    
29.3    
29.5    
29.7    
29.9    
30.0    
30.2    
30.4    
30.6    
30.8    
31.0    
31.2    
31.3    
31.5    
31.7    
31.9    
32.1    
32.3    
32.5    
32.6    
32.8    
33.0    
33.2    
33.4    
33.6    
33.8    
34.0    
34.1    
34.3    
34.5    
34.7    
34.9    
35.1    
35.3    
35.4    
35.6    
35.8    
36.0    
36.2    
36.4    
36.6    
36.8    
36.9    
37.1    
37.3    
37.5    
37.7    
37.9    
38.1    
38.2    
38.4    
38.6    
38.8    
39.0    
39.2    
39.4    
39.6    
39.7    
39.9    
40.1    
40.3    
40.5    
40.7    
40.9    
41.0    
41.2    
41.4    
41.6    
41.8    
42.0    
42.2    
42.4    
42.5    
42.7    
42.9    
43.1    
43.3    
43.5    
43.7    
43.8    
44.0    
44.2    
44.4    
44.6    
44.8    
45.0    
45.1    
45.3    
45.5    
45.7    
45.9    
46.1    
46.3    
46.5    
46.6    
46.8    
47.0    
47.2    
47.4    
47.6    
47.8    
47.9    
48.1    
48.3    
48.5    
48.7    
48.9    
49.1    
49.3    
49.4    
49.6    
49.8    
50.0    
50.2    
50.4    
50.6    
50.7    
50.9    
51.1    
51.3    
51.5    
51.7    
51.9    
52.1    
52.2    
52.4    
52.6    
52.8    
53.0    
53.2    
53.4    
53.5    
53.7    
53.9    
54.1    
54.3    
54.5    
54.7    
54.9    
55.0    
55.2    
55.4    
55.6    
55.8    
56.0    
56.2    
56.3    
56.5    
56.7    
56.9    
57.1    
57.3    
57.5    
57.6    
57.8    
58.0    
58.2    
58.4    
58.6    
58.8    
59.0    
59.1    
59.3    
59.5    
59.7    
59.9    
60.1    
60.3    
60.4    
60.6    
60.8    
61.0    
61.2    
61.4    
61.6    
61.8    
61.9    
62.1    
62.3    
62.5    
62.7    
62.9    
63.1    
63.2    
63.4    
63.6    
63.8    
64.0    
64.2    
64.4    
64.6    
64.7    
64.9    
65.1    
65.3    
65.5    
65.7    
65.9    
66.0    
66.2    
66.4    
66.6    
66.8    
67.0    
67.2    
67.4    
67.5    
67.7    
67.9    
68.1    
68.3    
68.5    
68.7    
68.8    
69.0    
69.2    
69.4    
69.6    
69.8    
70.0    
70.1    
70.3    
70.5    
70.7    
70.9    
71.1    
71.3    
71.5    
71.6    
71.8    
72.0    
72.2    
72.4    
72.6    
72.8    
72.9    
73.1    
73.3    
73.5    
73.7    
73.9    
74.1    
74.3    
74.4    
74.6    
74.8    
75.0    
75.2    
75.4    
75.6    
75.7    
75.9    
76.1    
76.3    
76.5    
76.7    
76.9    
77.1    
77.2    
77.4    
77.6    
77.8    
78.0    
78.2    
78.4    
78.5    
78.7    
78.9    
79.1    
79.3    
79.5    
79.7    
79.9    
80.0    
80.2    
80.4    
80.6    
80.8    
81.0    
81.2    
81.3    
81.5    
81.7    
81.9    
82.1    
82.3    
82.5    
82.6    
82.8    
83.0    
83.2    
83.4    
83.6    
83.8    
84.0    
84.1    
84.3    
84.5    
84.7    
84.9    
85.1    
85.3    
85.4    
85.6    
85.8    
86.0    
86.2    
86.4    
86.6    
86.8    
86.9    
87.1    
87.3    
87.5    
87.7    
87.9    
88.1    
88.2    
88.4    
88.6    
88.8    
89.0    
89.2    
89.4    
89.6    
89.7    
89.9    
90.1    
90.3    
90.5    
90.7    
90.9    
91.0    
91.2    
91.4    
91.6    
91.8    
92.0    
92.2    
92.4    
92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.7    
93.8    
94.0    
94.2    
94.4    
94.6    
94.8    
95.0    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.5    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.8    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.3    
99.4    
99.6    
99.8    
-found 46 predictions from path traversal
Error with prediction: snap lend_intergenic: 15445, rend_intergenic: 10760  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32148, rend_intergenic: 26582  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38034, rend_intergenic: 33377  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39503, rend_intergenic: 38143  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46970, rend_intergenic: 44856  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58463, rend_intergenic: 56555  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64965, rend_intergenic: 64314  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67474, rend_intergenic: 64967  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120192, rend_intergenic: 104623  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169354, rend_intergenic: 142208  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180268, rend_intergenic: 170814  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198373, rend_intergenic: 180346  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200051, rend_intergenic: 198870  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 227814, rend_intergenic: 200071  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 240607, rend_intergenic: 228447  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support