-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_6/scaffold_6_11942166-12172934

-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 snap_scaffold_6-snap.2518-T1
Valid prediction for snap_scaffold_6-snap.2531-T1
Valid prediction for GlimmerHMM_glimmerT_15598-T1
Couldn't classify 39042, 39137
Couldn't classify 40784, 40906
Sorry, prediction pasa_asmbl_47365.p1 fails validation.
(TGT)	 CA	39042-39137	GT	AGG
(GCC)	 AG	39495-39656	GT	AGG
(AAC)	 AG	39854-39946	GT	AGG
(GTA)	 AG	40426-40629	GT	TGG
(GTG)	 AG	40784-40906	AT	CCA
-recovered pasa_asmbl_47365.p1, internal, 39495, 39656
-recovered pasa_asmbl_47365.p1, internal, 39854, 39946
-recovered pasa_asmbl_47365.p1, internal, 40426, 40629
Valid prediction for Augustus_model.g10396.t1
Valid prediction for snap_scaffold_6-snap.2557-T1
Valid prediction for GlimmerHMM_glimmerT_15580-T1
Couldn't classify 32943, 33017
Couldn't classify 34841, 35066
Sorry, prediction pasa_asmbl_47942.p1 fails validation.
(CTT)	 TG	32943-33017	GT	AGG
(CCC)	 AG	33303-33428	GT	CAG
(AAT)	 AG	34190-34251	GT	GGG
(GCT)	 AG	34538-34669	GT	AGG
(GCT)	 AG	34841-35066	AG	TCA
-recovered pasa_asmbl_47942.p1, internal, 33303, 33428
-recovered pasa_asmbl_47942.p1, internal, 34190, 34251
-recovered pasa_asmbl_47942.p1, internal, 34538, 34669
Valid prediction for GlimmerHMM_glimmerT_15592-T1
Valid prediction for snap_scaffold_6-snap.2523-T1
Valid prediction for snap_scaffold_6-snap.2521-T1
Valid prediction for snap_scaffold_6-snap.2553-T1
Valid prediction for snap_scaffold_6-snap.2558-T1
Valid prediction for snap_scaffold_6-snap.2532-T1
Valid prediction for GlimmerHMM_glimmerT_15583-T1
Valid prediction for CodingQuarry_transcript_55247-T1
Valid prediction for Augustus_model.g10388.t1
Valid prediction for CodingQuarry_transcript_55242-T1
Valid prediction for Augustus_model.g10397.t1
Valid prediction for GlimmerHMM_glimmerT_15584-T1
Valid prediction for snap_scaffold_6-snap.2546-T1
Valid prediction for GlimmerHMM_glimmerT_15596-T1
Valid prediction for snap_scaffold_6-snap.2516-T1
Valid prediction for GlimmerHMM_glimmerT_15594-T1
Valid prediction for snap_scaffold_6-snap.2533-T1
Valid prediction for snap_scaffold_6-snap.2522-T1
Valid prediction for snap_scaffold_6-snap.2559-T1
Valid prediction for pasa_asmbl_47377.p1
Valid prediction for Augustus_model.g10391.t1
Valid prediction for snap_scaffold_6-snap.2529-T1
Valid prediction for Augustus_model.g10415.t1
Valid prediction for Augustus_model.g10409.t1
Valid prediction for Augustus_model.g10414.t1
Valid prediction for GlimmerHMM_glimmerT_15573-T1
Valid prediction for GlimmerHMM_glimmerT_15578-T1
Couldn't classify 67058, 67253
Sorry, prediction pasa_asmbl_47370.p1 fails validation.
(ATG)	 TC	55933-56046	GT	AGG
(GGA)	 AG	56211-56378	GT	GGG
(ACT)	 AG	57520-57697	GT	CGG
(AAG)	 AG	58317-58364	GT	AGG
(ACA)	 AG	59705-59756	GT	GGG
(CTC)	 AG	60140-60254	GT	GGG
(GTG)	 AG	60948-61155	GT	AGG
(GGG)	 AG	61297-61607	GT	AGG
(AGG)	 AG	62095-62294	GT	CGG
(TTG)	 AG	62481-62607	GT	AGG
(CTG)	 AG	63188-63289	GT	AGG
(GCT)	 AG	63443-63589	GT	AGG
(GTA)	 AG	63812-63970	GC	AGG
(GAC)	 AG	64752-64918	GT	AGG
(TCT)	 AG	67058-67253	TA	GGT
-recovered pasa_asmbl_47370.p1, initial, 55933, 56046
-recovered pasa_asmbl_47370.p1, internal, 56211, 56378
-recovered pasa_asmbl_47370.p1, internal, 57520, 57697
-recovered pasa_asmbl_47370.p1, internal, 58317, 58364
-recovered pasa_asmbl_47370.p1, internal, 59705, 59756
-recovered pasa_asmbl_47370.p1, internal, 60140, 60254
-recovered pasa_asmbl_47370.p1, internal, 60948, 61155
-recovered pasa_asmbl_47370.p1, internal, 61297, 61607
-recovered pasa_asmbl_47370.p1, internal, 62095, 62294
-recovered pasa_asmbl_47370.p1, internal, 62481, 62607
-recovered pasa_asmbl_47370.p1, internal, 63188, 63289
-recovered pasa_asmbl_47370.p1, internal, 63443, 63589
-recovered pasa_asmbl_47370.p1, internal, 63812, 63970
-recovered pasa_asmbl_47370.p1, internal, 64752, 64918
Valid prediction for Augustus_model.g10405.t1
Valid prediction for HiQ_model.g10413.t1
Valid prediction for snap_scaffold_6-snap.2535-T1
Valid prediction for snap_scaffold_6-snap.2530-T1
Valid prediction for snap_scaffold_6-snap.2543-T1
Valid prediction for snap_scaffold_6-snap.2554-T1
Valid prediction for Augustus_model.g10392.t1
Valid prediction for snap_scaffold_6-snap.2567-T1
Valid prediction for GlimmerHMM_glimmerT_15597-T1
Valid prediction for snap_scaffold_6-snap.2551-T1
Valid prediction for GlimmerHMM_glimmerT_15569-T1
Valid prediction for snap_scaffold_6-snap.2556-T1
Valid prediction for Augustus_model.g10411.t1
Valid prediction for snap_scaffold_6-snap.2517-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_15577-T1
Valid prediction for snap_scaffold_6-snap.2520-T1
Valid prediction for GlimmerHMM_glimmerT_15590-T1
Valid prediction for Augustus_model.g10420.t1
Valid prediction for Augustus_model.g10416.t1
Valid prediction for Augustus_model.g10402.t1
Valid prediction for GlimmerHMM_glimmerT_15601-T1
Valid prediction for GlimmerHMM_glimmerT_15586-T1
Valid prediction for snap_scaffold_6-snap.2524-T1
Valid prediction for CodingQuarry_transcript_55243-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 snap_scaffold_6-snap.2534-T1
Valid prediction for snap_scaffold_6-snap.2527-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_6-snap.2547-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_6-snap.2549-T1
Valid prediction for snap_scaffold_6-snap.2539-T1
Valid prediction for snap_scaffold_6-snap.2519-T1
Valid prediction for GlimmerHMM_glimmerT_15587-T1
Valid prediction for snap_scaffold_6-snap.2563-T1
Couldn't classify 94908, 95124
Sorry, prediction pasa_asmbl_48789.p1 fails validation.
(GAC)	 AC	94908-95124	GT	TGG
(AGT)	 AG	96040-96178	GT	AAG
(GAT)	 AG	96411-96523	GT	TGG
(GTG)	 AG	96614-96879	GT	AGG
-recovered pasa_asmbl_48789.p1, terminal, 96614, 96879
-recovered pasa_asmbl_48789.p1, internal, 96040, 96178
-recovered pasa_asmbl_48789.p1, internal, 96411, 96523
-recovered pasa_asmbl_48789.p1, internal, 96614, 96879
Valid prediction for snap_scaffold_6-snap.2561-T1
Valid prediction for snap_scaffold_6-snap.2538-T1
Valid prediction for Augustus_model.g10395.t1
Valid prediction for Augustus_model.g10410.t1
Valid prediction for Augustus_model.g10417.t1
Valid prediction for snap_scaffold_6-snap.2566-T1
Valid prediction for pasa_asmbl_48775.p1
Valid prediction for snap_scaffold_6-snap.2548-T1
Valid prediction for Augustus_model.g10393.t1
Valid prediction for snap_scaffold_6-snap.2528-T1
Valid prediction for GlimmerHMM_glimmerT_15571-T1
Valid prediction for GlimmerHMM_glimmerT_15575-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_15593-T1
Valid prediction for GlimmerHMM_glimmerT_15588-T1
Valid prediction for Augustus_model.g10406.t1
Couldn't classify 118434, 118513
Sorry, prediction pasa_asmbl_48784.p1 fails validation.
(AAT)	 AG	118434-118513	GT	AGG
(ATT)	 AG	119187-119358	GT	AAG
(ATA)	 AG	119537-119683	CC	AAC
-recovered pasa_asmbl_48784.p1, terminal, 119537, 119683
-recovered pasa_asmbl_48784.p1, internal, 118434, 118513
-recovered pasa_asmbl_48784.p1, internal, 119187, 119358
Valid prediction for snap_scaffold_6-snap.2515-T1
Valid prediction for HiQ_model.g10404.t1
Valid prediction for GlimmerHMM_glimmerT_15599-T1
Valid prediction for GlimmerHMM_glimmerT_15572-T1
Valid prediction for Augustus_model.g10412.t1
Valid prediction for Augustus_model.g10418.t1
Valid prediction for Augustus_model.g10401.t1
Valid prediction for HiQ_model.g10399.t1
Valid prediction for GlimmerHMM_glimmerT_15576-T1
Valid prediction for CodingQuarry_transcript_55245-T1
Valid prediction for snap_scaffold_6-snap.2564-T1
Valid prediction for GlimmerHMM_glimmerT_15600-T1
Couldn't classify 133333, 133542
Couldn't classify 137972, 138124
Sorry, prediction pasa_asmbl_48780.p1 fails validation.
(TCC)	 AG	133333-133542	GT	AGG
(ATG)	 AG	133702-133758	GT	AGG
(ACG)	 AG	136448-136583	GT	AGG
(ACC)	 AG	136792-136896	GT	TGG
(AGC)	 AG	137097-137225	GT	CTG
(ATG)	 AG	137694-137743	GT	AGG
(GAG)	 AG	137972-138124	GT	AGG
-recovered pasa_asmbl_48780.p1, initial, 133702, 133758
add_exon() Sorry, pasa_asmbl_48780.p1 137694-137743-initial-1 is invalid.
-recovered pasa_asmbl_48780.p1, initial, 137694, 137743
-recovered pasa_asmbl_48780.p1, internal, 133333, 133542
-recovered pasa_asmbl_48780.p1, internal, 133702, 133758
-recovered pasa_asmbl_48780.p1, internal, 136448, 136583
-recovered pasa_asmbl_48780.p1, internal, 136792, 136896
-recovered pasa_asmbl_48780.p1, internal, 137097, 137225
-recovered pasa_asmbl_48780.p1, internal, 137694, 137743
-recovered pasa_asmbl_48780.p1, internal, 137972, 138124
Valid prediction for snap_scaffold_6-snap.2565-T1
Valid prediction for GlimmerHMM_glimmerT_15570-T1
Valid prediction for snap_scaffold_6-snap.2550-T1
Valid prediction for GlimmerHMM_glimmerT_15579-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_6-snap.2541-T1
Valid prediction for snap_scaffold_6-snap.2562-T1
Valid prediction for snap_scaffold_6-snap.2545-T1
Valid prediction for snap_scaffold_6-snap.2555-T1
Valid prediction for Augustus_model.g10419.t1
Valid prediction for snap_scaffold_6-snap.2536-T1
Valid prediction for GlimmerHMM_glimmerT_15581-T1
Valid prediction for GlimmerHMM_glimmerT_15574-T1
Valid prediction for snap_scaffold_6-snap.2552-T1
Valid prediction for CodingQuarry_transcript_55246-T1
Couldn't classify 79733, 79943
Sorry, prediction pasa_asmbl_48796.p1 fails validation.
(CAG)	 CT	79733-79943	GT	GGG
(GCG)	 AG	80292-80379	GT	AGG
(GCA)	 AG	82395-82512	CT	AGC
add_exon() Sorry, pasa_asmbl_48796.p1 80292-80379-terminal-3 is invalid.
-recovered pasa_asmbl_48796.p1, terminal, 80292, 80379
-recovered pasa_asmbl_48796.p1, terminal, 82395, 82512
-recovered pasa_asmbl_48796.p1, internal, 80292, 80379
Valid prediction for Augustus_model.g10400.t1
Valid prediction for Augustus_model.g10398.t1
Valid prediction for snap_scaffold_6-snap.2542-T1
Valid prediction for Augustus_model.g10394.t1
Valid prediction for GlimmerHMM_glimmerT_15582-T1
Valid prediction for Augustus_model.g10407.t1
Valid prediction for pasa_asmbl_48794.p1
Valid prediction for snap_scaffold_6-snap.2560-T1
Valid prediction for GlimmerHMM_glimmerT_15595-T1
Valid prediction for Augustus_model.g10403.t1
Valid prediction for snap_scaffold_6-snap.2537-T1
Valid prediction for snap_scaffold_6-snap.2526-T1
Valid prediction for Augustus_model.g10389.t1
Valid prediction for GlimmerHMM_glimmerT_15585-T1
Valid prediction for snap_scaffold_6-snap.2544-T1
Valid prediction for Augustus_model.g10390.t1
Valid prediction for CodingQuarry_transcript_55244-T1
Valid prediction for snap_scaffold_6-snap.2525-T1
Valid prediction for snap_scaffold_6-snap.2540-T1
Valid prediction for GlimmerHMM_glimmerT_15589-T1
Valid prediction for GlimmerHMM_glimmerT_15591-T1
Valid prediction for Augustus_model.g10408.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 42176, rend_intergenic: 42173  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 230769
-exon list size: 393


building trellis

0.3    
0.5    
0.8    
1.0    
1.3    
1.5    
1.8    
2.0    
2.3    
2.5    
2.8    
3.0    
3.3    
3.5    
3.8    
4.1    
4.3    
4.6    
4.8    
5.1    
5.3    
5.6    
5.8    
6.1    
6.3    
6.6    
6.8    
7.1    
7.3    
7.6    
7.8    
8.1    
8.4    
8.6    
8.9    
9.1    
9.4    
9.6    
9.9    
10.1    
10.4    
10.6    
10.9    
11.1    
11.4    
11.6    
11.9    
12.2    
12.4    
12.7    
12.9    
13.2    
13.4    
13.7    
13.9    
14.2    
14.4    
14.7    
14.9    
15.2    
15.4    
15.7    
15.9    
16.2    
16.5    
16.7    
17.0    
17.2    
17.5    
17.7    
18.0    
18.2    
18.5    
18.7    
19.0    
19.2    
19.5    
19.7    
20.0    
20.3    
20.5    
20.8    
21.0    
21.3    
21.5    
21.8    
22.0    
22.3    
22.5    
22.8    
23.0    
23.3    
23.5    
23.8    
24.1    
24.3    
24.6    
24.8    
25.1    
25.3    
25.6    
25.8    
26.1    
26.3    
26.6    
26.8    
27.1    
27.3    
27.6    
27.8    
28.1    
28.4    
28.6    
28.9    
29.1    
29.4    
29.6    
29.9    
30.1    
30.4    
30.6    
30.9    
31.1    
31.4    
31.6    
31.9    
32.2    
32.4    
32.7    
32.9    
33.2    
33.4    
33.7    
33.9    
34.2    
34.4    
34.7    
34.9    
35.2    
35.4    
35.7    
35.9    
36.2    
36.5    
36.7    
37.0    
37.2    
37.5    
37.7    
38.0    
38.2    
38.5    
38.7    
39.0    
39.2    
39.5    
39.7    
40.0    
40.3    
40.5    
40.8    
41.0    
41.3    
41.5    
41.8    
42.0    
42.3    
42.5    
42.8    
43.0    
43.3    
43.5    
43.8    
44.1    
44.3    
44.6    
44.8    
45.1    
45.3    
45.6    
45.8    
46.1    
46.3    
46.6    
46.8    
47.1    
47.3    
47.6    
47.8    
48.1    
48.4    
48.6    
48.9    
49.1    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.9    
51.1    
51.4    
51.6    
51.9    
52.2    
52.4    
52.7    
52.9    
53.2    
53.4    
53.7    
53.9    
54.2    
54.4    
54.7    
54.9    
55.2    
55.4    
55.7    
55.9    
56.2    
56.5    
56.7    
57.0    
57.2    
57.5    
57.7    
58.0    
58.2    
58.5    
58.7    
59.0    
59.2    
59.5    
59.7    
60.0    
60.3    
60.5    
60.8    
61.0    
61.3    
61.5    
61.8    
62.0    
62.3    
62.5    
62.8    
63.0    
63.3    
63.5    
63.8    
64.1    
64.3    
64.6    
64.8    
65.1    
65.3    
65.6    
65.8    
66.1    
66.3    
66.6    
66.8    
67.1    
67.3    
67.6    
67.8    
68.1    
68.4    
68.6    
68.9    
69.1    
69.4    
69.6    
69.9    
70.1    
70.4    
70.6    
70.9    
71.1    
71.4    
71.6    
71.9    
72.2    
72.4    
72.7    
72.9    
73.2    
73.4    
73.7    
73.9    
74.2    
74.4    
74.7    
74.9    
75.2    
75.4    
75.7    
75.9    
76.2    
76.5    
76.7    
77.0    
77.2    
77.5    
77.7    
78.0    
78.2    
78.5    
78.7    
79.0    
79.2    
79.5    
79.7    
80.0    
80.3    
80.5    
80.8    
81.0    
81.3    
81.5    
81.8    
82.0    
82.3    
82.5    
82.8    
83.0    
83.3    
83.5    
83.8    
84.1    
84.3    
84.6    
84.8    
85.1    
85.3    
85.6    
85.8    
86.1    
86.3    
86.6    
86.8    
87.1    
87.3    
87.6    
87.8    
88.1    
88.4    
88.6    
88.9    
89.1    
89.4    
89.6    
89.9    
90.1    
90.4    
90.6    
90.9    
91.1    
91.4    
91.6    
91.9    
92.2    
92.4    
92.7    
92.9    
93.2    
93.4    
93.7    
93.9    
94.2    
94.4    
94.7    
94.9    
95.2    
95.4    
95.7    
95.9    
96.2    
96.5    
96.7    
97.0    
97.2    
97.5    
97.7    
98.0    
98.2    
98.5    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 39 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 42176, rend_intergenic: 42173  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 37 predictions persist after filtering for low support