-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_14/scaffold_14_15112608-15271642

-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_35251-T1
Valid prediction for GlimmerHMM_glimmerT_35247-T1
Valid prediction for Augustus_model.g23555.t1
Valid prediction for GlimmerHMM_glimmerT_35235-T1
Valid prediction for GlimmerHMM_glimmerT_35246-T1
Valid prediction for snap_scaffold_14-snap.3153-T1
Valid prediction for Augustus_model.g23571.t1
Valid prediction for snap_scaffold_14-snap.3127-T1
Couldn't classify 143620, 143739
Sorry, prediction pasa_asmbl_12584.p1 fails validation.
(GTG)	 GT	143620-143739	GT	AGG
(GCC)	 AG	145146-145346	GT	AGG
(GTG)	 AG	145772-145831	GT	AGG
(GCC)	 AG	145933-145962	CC	GAC
-recovered pasa_asmbl_12584.p1, terminal, 145933, 145962
-recovered pasa_asmbl_12584.p1, internal, 145146, 145346
-recovered pasa_asmbl_12584.p1, internal, 145772, 145831
Valid prediction for snap_scaffold_14-snap.3135-T1
Valid prediction for Augustus_model.g23569.t1
Valid prediction for pasa_asmbl_12577.p1
Valid prediction for snap_scaffold_14-snap.3145-T1
Valid prediction for snap_scaffold_14-snap.3120-T1
Valid prediction for CodingQuarry_transcript_15945-T1
Valid prediction for GlimmerHMM_glimmerT_35224-T1
Valid prediction for Augustus_model.g23565.t1
Couldn't classify 140127, 140171
Sorry, prediction pasa_asmbl_12582.p1 fails validation.
(ATG)	 AC	139009-139202	GT	CAG
(GTT)	 AG	139437-139564	GT	AGG
(GTA)	 AG	139868-140022	GT	AGG
(GTA)	 AG	140127-140171	GA	GTG
-recovered pasa_asmbl_12582.p1, initial, 139009, 139202
-recovered pasa_asmbl_12582.p1, internal, 139437, 139564
-recovered pasa_asmbl_12582.p1, internal, 139868, 140022
Valid prediction for snap_scaffold_14-snap.3148-T1
Valid prediction for Augustus_model.g23570.t1
Couldn't classify 8431, 8519
Sorry, prediction CodingQuarry_transcript_15941-T1 fails validation.
(ATG)	 CC	3663-3798	GT	AGG
(GGT)	 AG	5540-5625	GT	AGG
(ATC)	 AG	5814-5919	GT	AGG
(ATC)	 AG	6164-6228	GT	GGG
(CCA)	 AG	7086-7146	GT	AGG
(CTG)	 CC	8431-8519	GT	AGG
(CGC)	 AG	9249-9362	AC	AAA
-recovered CodingQuarry_transcript_15941-T1, initial, 3663, 3798
-recovered CodingQuarry_transcript_15941-T1, terminal, 9249, 9362
-recovered CodingQuarry_transcript_15941-T1, internal, 5540, 5625
-recovered CodingQuarry_transcript_15941-T1, internal, 5814, 5919
-recovered CodingQuarry_transcript_15941-T1, internal, 6164, 6228
-recovered CodingQuarry_transcript_15941-T1, internal, 7086, 7146
Valid prediction for GlimmerHMM_glimmerT_35241-T1
Valid prediction for snap_scaffold_14-snap.3130-T1
Couldn't classify 140244, 140336
Sorry, prediction pasa_asmbl_12586.p1 fails validation.
(TCC)	 AC	140244-140336	GT	AGG
(GTG)	 AG	140841-141237	GT	TGG
(TGA)	 AG	141404-141500	GT	AGG
(CCC)	 AG	142263-142437	CC	GAC
-recovered pasa_asmbl_12586.p1, terminal, 142263, 142437
-recovered pasa_asmbl_12586.p1, internal, 140841, 141237
-recovered pasa_asmbl_12586.p1, internal, 141404, 141500
Valid prediction for snap_scaffold_14-snap.3138-T1
Valid prediction for snap_scaffold_14-snap.3118-T1
Valid prediction for GlimmerHMM_glimmerT_35244-T1
Valid prediction for Augustus_model.g23563.t1
Valid prediction for snap_scaffold_14-snap.3150-T1
Valid prediction for snap_scaffold_14-snap.3126-T1
Valid prediction for GlimmerHMM_glimmerT_35253-T1
Valid prediction for Augustus_model.g23556.t1
Valid prediction for Augustus_model.g23554.t1
Valid prediction for snap_scaffold_14-snap.3136-T1
Valid prediction for GlimmerHMM_glimmerT_35228-T1
Valid prediction for snap_scaffold_14-snap.3142-T1
Valid prediction for snap_scaffold_14-snap.3125-T1
Valid prediction for snap_scaffold_14-snap.3122-T1
Valid prediction for snap_scaffold_14-snap.3155-T1
Valid prediction for Augustus_model.g23559.t1
Valid prediction for Augustus_model.g23561.t1
Valid prediction for GlimmerHMM_glimmerT_35243-T1
Valid prediction for Augustus_model.g23567.t1
Valid prediction for GlimmerHMM_glimmerT_35231-T1
Valid prediction for GlimmerHMM_glimmerT_35236-T1
Valid prediction for GlimmerHMM_glimmerT_35230-T1
Couldn't classify 104449, 104518
Couldn't classify 106699, 106725
Sorry, prediction pasa_asmbl_12570.p1 fails validation.
(GCC)	 TA	104449-104518	GT	AGG
(CTG)	 AG	104926-105019	GT	TGG
(GTC)	 AG	105287-105368	GT	AGG
(CAT)	 AG	105490-105657	GT	AGG
(GAT)	 AG	106186-106392	GT	TGG
(AGC)	 AG	106699-106725	TA	CGT
-recovered pasa_asmbl_12570.p1, internal, 104926, 105019
-recovered pasa_asmbl_12570.p1, internal, 105287, 105368
-recovered pasa_asmbl_12570.p1, internal, 105490, 105657
-recovered pasa_asmbl_12570.p1, internal, 106186, 106392
Valid prediction for GlimmerHMM_glimmerT_35252-T1
Valid prediction for GlimmerHMM_glimmerT_35239-T1
Couldn't classify 121405, 121539
Couldn't classify 123561, 123634
Sorry, prediction pasa_asmbl_12576.p1 fails validation.
(ATC)	 GC	121405-121539	GT	AGG
(CGT)	 AG	121845-122092	GT	AGG
(GCC)	 AG	122736-122799	GT	CGG
(ACC)	 AG	123140-123311	GT	CAG
(GCT)	 AG	123561-123634	GG	GGG
-recovered pasa_asmbl_12576.p1, internal, 121845, 122092
-recovered pasa_asmbl_12576.p1, internal, 122736, 122799
-recovered pasa_asmbl_12576.p1, internal, 123140, 123311
Valid prediction for snap_scaffold_14-snap.3128-T1
Valid prediction for snap_scaffold_14-snap.3157-T1
Valid prediction for Augustus_model.g23557.t1
Valid prediction for snap_scaffold_14-snap.3147-T1
Valid prediction for GlimmerHMM_glimmerT_35250-T1
Valid prediction for GlimmerHMM_glimmerT_35248-T1
Valid prediction for snap_scaffold_14-snap.3117-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for HiQ_model.g23566.t1
Couldn't classify 106789, 106886
Couldn't classify 107980, 108183
Sorry, prediction pasa_asmbl_12571.p1 fails validation.
(GGG)	 GG	106789-106886	GT	GGG
(GTA)	 AG	107184-107361	GT	AGG
(ACC)	 AG	107574-107702	GT	AGG
(GAG)	 AG	107980-108183	GT	AGG
-recovered pasa_asmbl_12571.p1, internal, 107184, 107361
-recovered pasa_asmbl_12571.p1, internal, 107574, 107702
-recovered pasa_asmbl_12571.p1, internal, 107980, 108183
Valid prediction for GlimmerHMM_glimmerT_35234-T1
Valid prediction for snap_scaffold_14-snap.3134-T1
Valid prediction for GlimmerHMM_glimmerT_35233-T1
Couldn't classify 7247, 7254
Sorry, prediction pasa_asmbl_12562.p1 fails validation.
(ATG)	 CC	2933-2942	GT	ATG
(ATT)	 AG	3652-3798	GT	AGG
(GGT)	 AG	5540-5625	GT	AGG
(ATC)	 AG	5814-5919	GT	AGG
(ATC)	 AG	6164-6228	GT	GGG
(CCA)	 AG	7086-7146	GT	AGG
(ACT)	 AG	7247-7254	GT	AGG
-recovered pasa_asmbl_12562.p1, initial, 2933, 2942
add_exon() Sorry, pasa_asmbl_12562.p1 3652-3798-terminal-1 is invalid.
-recovered pasa_asmbl_12562.p1, terminal, 3652, 3798
-recovered pasa_asmbl_12562.p1, internal, 3652, 3798
-recovered pasa_asmbl_12562.p1, internal, 5540, 5625
-recovered pasa_asmbl_12562.p1, internal, 5814, 5919
-recovered pasa_asmbl_12562.p1, internal, 6164, 6228
-recovered pasa_asmbl_12562.p1, internal, 7086, 7146
-recovered pasa_asmbl_12562.p1, internal, 7247, 7254
Couldn't classify 50028, 50159
Sorry, prediction pasa_asmbl_12567.p1 fails validation.
(ATG)	 CA	49290-49578	GT	AGG
(ATG)	 AG	49682-49788	GT	CGG
(GAG)	 AG	50028-50159	GG	ACG
-recovered pasa_asmbl_12567.p1, initial, 49290, 49578
add_exon() Sorry, pasa_asmbl_12567.p1 49682-49788-initial-1 is invalid.
-recovered pasa_asmbl_12567.p1, initial, 49682, 49788
-recovered pasa_asmbl_12567.p1, internal, 49682, 49788

-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 Augustus_model.g23564.t1
Valid prediction for snap_scaffold_14-snap.3156-T1
Valid prediction for snap_scaffold_14-snap.3129-T1
Valid prediction for snap_scaffold_14-snap.3119-T1
Valid prediction for pasa_asmbl_13806.p1
Valid prediction for snap_scaffold_14-snap.3124-T1
Valid prediction for GlimmerHMM_glimmerT_35249-T1
Valid prediction for GlimmerHMM_glimmerT_35226-T1
Valid prediction for snap_scaffold_14-snap.3154-T1
Valid prediction for GlimmerHMM_glimmerT_35245-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_35232-T1
Valid prediction for snap_scaffold_14-snap.3123-T1
Valid prediction for GlimmerHMM_glimmerT_35225-T1
Valid prediction for snap_scaffold_14-snap.3132-T1
Valid prediction for HiQ_model.g23568.t1
Valid prediction for snap_scaffold_14-snap.3139-T1
Valid prediction for GlimmerHMM_glimmerT_35242-T1
Valid prediction for GlimmerHMM_glimmerT_35237-T1
Valid prediction for Augustus_model.g23558.t1
Valid prediction for Augustus_model.g23553.t1
Valid prediction for snap_scaffold_14-snap.3140-T1
Valid prediction for snap_scaffold_14-snap.3143-T1
Valid prediction for snap_scaffold_14-snap.3149-T1
Valid prediction for GlimmerHMM_glimmerT_35229-T1
Valid prediction for snap_scaffold_14-snap.3151-T1
Valid prediction for Augustus_model.g23552.t1
Valid prediction for snap_scaffold_14-snap.3152-T1
Valid prediction for snap_scaffold_14-snap.3144-T1
Valid prediction for snap_scaffold_14-snap.3121-T1
Valid prediction for CodingQuarry_transcript_15946-T1
Valid prediction for CodingQuarry_transcript_15944-T1
Valid prediction for GlimmerHMM_glimmerT_35240-T1
Valid prediction for snap_scaffold_14-snap.3131-T1
Valid prediction for snap_scaffold_14-snap.3133-T1
Valid prediction for Augustus_model.g23560.t1
Valid prediction for GlimmerHMM_glimmerT_35238-T1
Valid prediction for Augustus_model.g23562.t1
Valid prediction for snap_scaffold_14-snap.3146-T1
Valid prediction for snap_scaffold_14-snap.3141-T1
Valid prediction for snap_scaffold_14-snap.3137-T1
Valid prediction for GlimmerHMM_glimmerT_35227-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 23751, rend_intergenic: 20205  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24216, rend_intergenic: 23966  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27611, rend_intergenic: 24581  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41629, rend_intergenic: 33731  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51730, rend_intergenic: 50149  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64103, rend_intergenic: 52680  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67822, rend_intergenic: 64593  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93952, rend_intergenic: 85275  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102759, rend_intergenic: 100667  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111481, rend_intergenic: 102954  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115846, rend_intergenic: 114120  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119260, rend_intergenic: 116178  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124810, rend_intergenic: 120322  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132769, rend_intergenic: 129298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145962, rend_intergenic: 141378  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150771, rend_intergenic: 147430  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152118, rend_intergenic: 151077  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 159035
-exon list size: 377


building trellis

0.3    
0.5    
0.8    
1.1    
1.3    
1.6    
1.8    
2.1    
2.4    
2.6    
2.9    
3.2    
3.4    
3.7    
4.0    
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4.5    
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5.0    
5.3    
5.5    
5.8    
6.1    
6.3    
6.6    
6.9    
7.1    
7.4    
7.7    
7.9    
8.2    
8.4    
8.7    
9.0    
9.2    
9.5    
9.8    
10.0    
10.3    
10.6    
10.8    
11.1    
11.3    
11.6    
11.9    
12.1    
12.4    
12.7    
12.9    
13.2    
13.5    
13.7    
14.0    
14.2    
14.5    
14.8    
15.0    
15.3    
15.6    
15.8    
16.1    
16.4    
16.6    
16.9    
17.2    
17.4    
17.7    
17.9    
18.2    
18.5    
18.7    
19.0    
19.3    
19.5    
19.8    
20.1    
20.3    
20.6    
20.8    
21.1    
21.4    
21.6    
21.9    
22.2    
22.4    
22.7    
23.0    
23.2    
23.5    
23.7    
24.0    
24.3    
24.5    
24.8    
25.1    
25.3    
25.6    
25.9    
26.1    
26.4    
26.6    
26.9    
27.2    
27.4    
27.7    
28.0    
28.2    
28.5    
28.8    
29.0    
29.3    
29.6    
29.8    
30.1    
30.3    
30.6    
30.9    
31.1    
31.4    
31.7    
31.9    
32.2    
32.5    
32.7    
33.0    
33.2    
33.5    
33.8    
34.0    
34.3    
34.6    
34.8    
35.1    
35.4    
35.6    
35.9    
36.1    
36.4    
36.7    
36.9    
37.2    
37.5    
37.7    
38.0    
38.3    
38.5    
38.8    
39.1    
39.3    
39.6    
39.8    
40.1    
40.4    
40.6    
40.9    
41.2    
41.4    
41.7    
42.0    
42.2    
42.5    
42.7    
43.0    
43.3    
43.5    
43.8    
44.1    
44.3    
44.6    
44.9    
45.1    
45.4    
45.6    
45.9    
46.2    
46.4    
46.7    
47.0    
47.2    
47.5    
47.8    
48.0    
48.3    
48.5    
48.8    
49.1    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
50.9    
51.2    
51.5    
51.7    
52.0    
52.2    
52.5    
52.8    
53.0    
53.3    
53.6    
53.8    
54.1    
54.4    
54.6    
54.9    
55.1    
55.4    
55.7    
55.9    
56.2    
56.5    
56.7    
57.0    
57.3    
57.5    
57.8    
58.0    
58.3    
58.6    
58.8    
59.1    
59.4    
59.6    
59.9    
60.2    
60.4    
60.7    
60.9    
61.2    
61.5    
61.7    
62.0    
62.3    
62.5    
62.8    
63.1    
63.3    
63.6    
63.9    
64.1    
64.4    
64.6    
64.9    
65.2    
65.4    
65.7    
66.0    
66.2    
66.5    
66.8    
67.0    
67.3    
67.5    
67.8    
68.1    
68.3    
68.6    
68.9    
69.1    
69.4    
69.7    
69.9    
70.2    
70.4    
70.7    
71.0    
71.2    
71.5    
71.8    
72.0    
72.3    
72.6    
72.8    
73.1    
73.4    
73.6    
73.9    
74.1    
74.4    
74.7    
74.9    
75.2    
75.5    
75.7    
76.0    
76.3    
76.5    
76.8    
77.0    
77.3    
77.6    
77.8    
78.1    
78.4    
78.6    
78.9    
79.2    
79.4    
79.7    
79.9    
80.2    
80.5    
80.7    
81.0    
81.3    
81.5    
81.8    
82.1    
82.3    
82.6    
82.8    
83.1    
83.4    
83.6    
83.9    
84.2    
84.4    
84.7    
85.0    
85.2    
85.5    
85.8    
86.0    
86.3    
86.5    
86.8    
87.1    
87.3    
87.6    
87.9    
88.1    
88.4    
88.7    
88.9    
89.2    
89.4    
89.7    
90.0    
90.2    
90.5    
90.8    
91.0    
91.3    
91.6    
91.8    
92.1    
92.3    
92.6    
92.9    
93.1    
93.4    
93.7    
93.9    
94.2    
94.5    
94.7    
95.0    
95.3    
95.5    
95.8    
96.0    
96.3    
96.6    
96.8    
97.1    
97.4    
97.6    
97.9    
98.2    
98.4    
98.7    
98.9    
99.2    
99.5    
99.7    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 23751, rend_intergenic: 20205  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24216, rend_intergenic: 23966  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27611, rend_intergenic: 24581  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41629, rend_intergenic: 33731  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51730, rend_intergenic: 50149  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64103, rend_intergenic: 52680  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67822, rend_intergenic: 64593  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93952, rend_intergenic: 85275  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102759, rend_intergenic: 100667  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111481, rend_intergenic: 102954  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115846, rend_intergenic: 114120  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119260, rend_intergenic: 116178  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124810, rend_intergenic: 120322  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132769, rend_intergenic: 129298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145962, rend_intergenic: 141378  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150771, rend_intergenic: 147430  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152118, rend_intergenic: 151077  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support