-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_28/scaffold_28_2113128-2248964

-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_28-snap.548-T1
Valid prediction for Augustus_model.g38591.t1
Valid prediction for pasa_asmbl_37338.p1
Valid prediction for GlimmerHMM_glimmerT_58294-T1
Valid prediction for snap_scaffold_28-snap.541-T1
Valid prediction for CodingQuarry_transcript_43552-T1
Valid prediction for snap_scaffold_28-snap.540-T1
Valid prediction for GlimmerHMM_glimmerT_58301-T1
Valid prediction for CodingQuarry_transcript_43545-T1
Valid prediction for GlimmerHMM_glimmerT_58298-T1
Valid prediction for snap_scaffold_28-snap.544-T1
Valid prediction for Augustus_model.g38597.t1
Valid prediction for snap_scaffold_28-snap.526-T1
Valid prediction for snap_scaffold_28-snap.528-T1
Valid prediction for HiQ_model.g38581.t1
Valid prediction for snap_scaffold_28-snap.533-T1
Valid prediction for GlimmerHMM_glimmerT_58297-T1
Valid prediction for snap_scaffold_28-snap.522-T1
Valid prediction for snap_scaffold_28-snap.545-T1
Valid prediction for GlimmerHMM_glimmerT_58299-T1
Couldn't classify 18556, 18609
Sorry, prediction pasa_asmbl_37330.p1 fails validation.
(AAA)	 AA	18556-18609	GT	AAG
(GCC)	 AG	19097-19216	GT	AGG
(GCA)	 AG	19417-19532	GT	AGG
(GAT)	 AG	19626-19704	GT	AGG
(TGT)	 AG	19793-19837	GT	AGG
(GAT)	 AG	19931-19989	GT	AAG
(GAC)	 AG	20126-20155	GT	GGG
(AGC)	 AG	20274-20394	GT	AGG
(ATC)	 AG	20583-20765	TG	GAT
-recovered pasa_asmbl_37330.p1, terminal, 19931, 19989
-recovered pasa_asmbl_37330.p1, terminal, 20583, 20765
-recovered pasa_asmbl_37330.p1, internal, 19097, 19216
-recovered pasa_asmbl_37330.p1, internal, 19417, 19532
-recovered pasa_asmbl_37330.p1, internal, 19626, 19704
-recovered pasa_asmbl_37330.p1, internal, 19793, 19837
-recovered pasa_asmbl_37330.p1, internal, 19931, 19989
-recovered pasa_asmbl_37330.p1, internal, 20126, 20155
-recovered pasa_asmbl_37330.p1, internal, 20274, 20394
Valid prediction for snap_scaffold_28-snap.518-T1
Valid prediction for Augustus_model.g38600.t1
Valid prediction for CodingQuarry_transcript_43549-T1
Valid prediction for GlimmerHMM_glimmerT_58293-T1
Couldn't classify 90886, 90907
Sorry, prediction pasa_asmbl_37351.p1 fails validation.
(ATG)	 CC	89583-89735	GT	TGG
(ATG)	 AG	89911-89996	GT	AGG
(GTT)	 AG	90140-90243	GT	GAG
(GTC)	 AG	90514-90637	GT	GGG
(CAT)	 AG	90886-90907	GC	GCG
-recovered pasa_asmbl_37351.p1, initial, 89583, 89735
-recovered pasa_asmbl_37351.p1, initial, 89911, 89996
add_exon() Sorry, pasa_asmbl_37351.p1 90140-90243-terminal-2 is invalid.
-recovered pasa_asmbl_37351.p1, terminal, 90140, 90243
-recovered pasa_asmbl_37351.p1, internal, 89911, 89996
-recovered pasa_asmbl_37351.p1, internal, 90140, 90243
-recovered pasa_asmbl_37351.p1, internal, 90514, 90637
-recovered pasa_asmbl_37351.p1, internal, 90886, 90907
Valid prediction for Augustus_model.g38599.t1
Valid prediction for GlimmerHMM_glimmerT_58295-T1
Valid prediction for HiQ_model.g38586.t1
Valid prediction for Augustus_model.g38577.t1
Couldn't classify 85973, 85983
Sorry, prediction pasa_asmbl_37348.p1 fails validation.
(CTC)	 GC	85973-85983	GT	AGG
(GAT)	 AG	86057-86190	GT	AGG
(GTA)	 AG	86286-86494	GT	AGG
(GAG)	 AG	86587-87576	AG	GAA
-recovered pasa_asmbl_37348.p1, terminal, 86587, 87576
-recovered pasa_asmbl_37348.p1, internal, 86057, 86190
-recovered pasa_asmbl_37348.p1, internal, 86286, 86494
Couldn't classify 37179, 37233
Sorry, prediction pasa_asmbl_37334.p1 fails validation.
(GGT)	 CA	37179-37233	GT	GGG
(ACC)	 AG	37390-37602	GT	AGG
(GAA)	 AG	37781-37918	GT	AGG
(GTT)	 AG	38043-38187	GT	AGG
(GCG)	 AG	38331-38454	TG	AAT
add_exon() Sorry, pasa_asmbl_37334.p1 37390-37602-terminal-1 is invalid.
-recovered pasa_asmbl_37334.p1, terminal, 37390, 37602
add_exon() Sorry, pasa_asmbl_37334.p1 38043-38187-terminal-3 is invalid.
-recovered pasa_asmbl_37334.p1, terminal, 38043, 38187
-recovered pasa_asmbl_37334.p1, terminal, 38331, 38454
-recovered pasa_asmbl_37334.p1, internal, 37390, 37602
-recovered pasa_asmbl_37334.p1, internal, 37781, 37918
-recovered pasa_asmbl_37334.p1, internal, 38043, 38187
Couldn't classify 6083, 6329
Sorry, prediction pasa_asmbl_37329.p1 fails validation.
(GAT)	 CA	6083-6329	GT	AGG
(GTC)	 AG	6493-6614	GT	AGG
(GAC)	 AG	6774-6899	GT	AGG
(GTG)	 AG	7088-7164	GT	AAG
(ATG)	 AG	7260-7360	GT	AGG
(AGA)	 AG	7492-7592	GA	AAG
-recovered pasa_asmbl_37329.p1, initial, 7260, 7360
-recovered pasa_asmbl_37329.p1, terminal, 7492, 7592
-recovered pasa_asmbl_37329.p1, internal, 6493, 6614
-recovered pasa_asmbl_37329.p1, internal, 6774, 6899
-recovered pasa_asmbl_37329.p1, internal, 7088, 7164
-recovered pasa_asmbl_37329.p1, internal, 7260, 7360
Valid prediction for snap_scaffold_28-snap.527-T1
Valid prediction for snap_scaffold_28-snap.535-T1
Couldn't classify 4436, 4509
Sorry, prediction pasa_asmbl_37325.p1 fails validation.
(ATG)	 AA	3642-3787	GT	TGG
(CCC)	 AG	3992-4132	GT	CAG
(AGT)	 AG	4267-4349	GT	AGG
(GTT)	 AG	4436-4509	AA	GGA
-recovered pasa_asmbl_37325.p1, initial, 3642, 3787
-recovered pasa_asmbl_37325.p1, internal, 3992, 4132
-recovered pasa_asmbl_37325.p1, internal, 4267, 4349
Valid prediction for GlimmerHMM_glimmerT_58282-T1
Valid prediction for GlimmerHMM_glimmerT_58292-T1
Couldn't classify 127509, 127523
Couldn't classify 129451, 129516
Sorry, prediction pasa_asmbl_37353.p1 fails validation.
(CTT)	 AC	127509-127523	GT	CGG
(ACC)	 AG	127747-127820	GT	CCG
(GAA)	 AG	127925-127976	GT	AGG
(ACA)	 AG	128153-128302	GT	AGG
(AAT)	 AG	129090-129137	GT	CTG
(ACG)	 AG	129451-129516	GC	ACG
-recovered pasa_asmbl_37353.p1, internal, 127747, 127820
-recovered pasa_asmbl_37353.p1, internal, 127925, 127976
-recovered pasa_asmbl_37353.p1, internal, 128153, 128302
-recovered pasa_asmbl_37353.p1, internal, 129090, 129137
-recovered pasa_asmbl_37353.p1, internal, 129451, 129516
Valid prediction for snap_scaffold_28-snap.536-T1
Valid prediction for GlimmerHMM_glimmerT_58281-T1
Valid prediction for Augustus_model.g38590.t1
Valid prediction for snap_scaffold_28-snap.546-T1
Couldn't classify 34677, 34837
Couldn't classify 36689, 36819
Sorry, prediction pasa_asmbl_37333.p1 fails validation.
(GGG)	 CA	34677-34837	GT	AGG
(CAA)	 AG	36058-36147	GT	AGG
(ATC)	 AG	36353-36546	GT	AGG
(TCT)	 AG	36689-36819	CC	TAC
-recovered pasa_asmbl_37333.p1, internal, 36058, 36147
-recovered pasa_asmbl_37333.p1, internal, 36353, 36546
Valid prediction for snap_scaffold_28-snap.550-T1
Valid prediction for Augustus_model.g38593.t1
Valid prediction for GlimmerHMM_glimmerT_58287-T1
Valid prediction for Augustus_model.g38588.t1
Valid prediction for snap_scaffold_28-snap.520-T1
Valid prediction for Augustus_model.g38594.t1
Valid prediction for CodingQuarry_transcript_43548-T1
Valid prediction for snap_scaffold_28-snap.529-T1
Valid prediction for pasa_asmbl_37336.p1
Valid prediction for snap_scaffold_28-snap.549-T1
Valid prediction for snap_scaffold_28-snap.517-T1
Couldn't classify 83928, 84120
Sorry, prediction pasa_asmbl_37343.p1 fails validation.
(GAG)	 CC	83928-84120	GT	TGG
(GTA)	 AG	84252-84383	GT	AGG
(GTA)	 AG	84493-84657	GT	AGG
(AGC)	 AG	84813-84973	TT	AGT
add_exon() Sorry, pasa_asmbl_37343.p1 84252-84383-terminal-1 is invalid.
-recovered pasa_asmbl_37343.p1, terminal, 84252, 84383
-recovered pasa_asmbl_37343.p1, terminal, 84813, 84973
-recovered pasa_asmbl_37343.p1, internal, 84252, 84383
-recovered pasa_asmbl_37343.p1, internal, 84493, 84657
Valid prediction for GlimmerHMM_glimmerT_58290-T1
Valid prediction for GlimmerHMM_glimmerT_58303-T1
Valid prediction for snap_scaffold_28-snap.532-T1
Valid prediction for snap_scaffold_28-snap.538-T1
Valid prediction for snap_scaffold_28-snap.530-T1
Valid prediction for HiQ_model.g38587.t1
Valid prediction for GlimmerHMM_glimmerT_58283-T1
Valid prediction for Augustus_model.g38585.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_28-snap.542-T1
Couldn't classify 113622, 113939
Sorry, prediction pasa_asmbl_38547.p3 fails validation.
(ACC)	 CG	113622-113939	CC	ACC
Valid prediction for GlimmerHMM_glimmerT_58296-T1
Valid prediction for snap_scaffold_28-snap.543-T1
Valid prediction for snap_scaffold_28-snap.534-T1
Valid prediction for Augustus_model.g38592.t1
Valid prediction for snap_scaffold_28-snap.547-T1
Valid prediction for HiQ_model.g38596.t1
Valid prediction for GlimmerHMM_glimmerT_58300-T1
Valid prediction for snap_scaffold_28-snap.539-T1
Valid prediction for GlimmerHMM_glimmerT_58285-T1
Valid prediction for snap_scaffold_28-snap.519-T1
Valid prediction for HiQ_model.g38579.t1
Valid prediction for Augustus_model.g38589.t1
Valid prediction for pasa_asmbl_38022.p1
Couldn't classify 127100, 127242
Sorry, prediction pasa_asmbl_38016.p1 fails validation.
(ATG)	 AC	126115-126131	GT	AGG
(AAT)	 AG	126379-126493	GT	GAG
(TAC)	 AG	126597-126733	GT	GGG
(ATT)	 AG	126867-126979	GT	AGG
(GTG)	 AG	127100-127242	CA	TCC
-recovered pasa_asmbl_38016.p1, initial, 126115, 126131
-recovered pasa_asmbl_38016.p1, internal, 126379, 126493
-recovered pasa_asmbl_38016.p1, internal, 126597, 126733
-recovered pasa_asmbl_38016.p1, internal, 126867, 126979
Valid prediction for CodingQuarry_transcript_43546-T1
Valid prediction for GlimmerHMM_glimmerT_58286-T1
Valid prediction for GlimmerHMM_glimmerT_58302-T1
Valid prediction for GlimmerHMM_glimmerT_58291-T1
Valid prediction for snap_scaffold_28-snap.531-T1
Valid prediction for GlimmerHMM_glimmerT_58304-T1
Valid prediction for snap_scaffold_28-snap.523-T1
Valid prediction for snap_scaffold_28-snap.524-T1
Valid prediction for Augustus_model.g38583.t1
Valid prediction for CodingQuarry_transcript_43551-T1
Valid prediction for Augustus_model.g38582.t1
Valid prediction for GlimmerHMM_glimmerT_58288-T1
Couldn't classify 58069, 58191
Sorry, prediction pasa_asmbl_38019.p1 fails validation.
(GAG)	 GT	58069-58191	GT	AGG
(CTG)	 AG	58415-58535	GT	TGG
(GTG)	 AG	58877-58965	CA	GAC
-recovered pasa_asmbl_38019.p1, terminal, 58877, 58965
-recovered pasa_asmbl_38019.p1, internal, 58415, 58535
Valid prediction for Augustus_model.g38595.t1
Valid prediction for Augustus_model.g38580.t1
Valid prediction for CodingQuarry_transcript_43547-T1
Valid prediction for snap_scaffold_28-snap.521-T1
Valid prediction for GlimmerHMM_glimmerT_58284-T1
Valid prediction for Augustus_model.g38598.t1
Valid prediction for snap_scaffold_28-snap.537-T1
Valid prediction for GlimmerHMM_glimmerT_58289-T1
Valid prediction for snap_scaffold_28-snap.525-T1
Valid prediction for Augustus_model.g38578.t1
Valid prediction for CodingQuarry_transcript_43550-T1
Valid prediction for CodingQuarry_transcript_43553-T1
Valid prediction for Augustus_model.g38584.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 65170, rend_intergenic: 58787  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 135837
-exon list size: 412


building trellis

0.2    
0.5    
0.7    
1.0    
1.2    
1.4    
1.7    
1.9    
2.2    
2.4    
2.7    
2.9    
3.1    
3.4    
3.6    
3.9    
4.1    
4.3    
4.6    
4.8    
5.1    
5.3    
5.6    
5.8    
6.0    
6.3    
6.5    
6.8    
7.0    
7.2    
7.5    
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8.0    
8.2    
8.5    
8.7    
8.9    
9.2    
9.4    
9.7    
9.9    
10.1    
10.4    
10.6    
10.9    
11.1    
11.4    
11.6    
11.8    
12.1    
12.3    
12.6    
12.8    
13.0    
13.3    
13.5    
13.8    
14.0    
14.3    
14.5    
14.7    
15.0    
15.2    
15.5    
15.7    
15.9    
16.2    
16.4    
16.7    
16.9    
17.1    
17.4    
17.6    
17.9    
18.1    
18.4    
18.6    
18.8    
19.1    
19.3    
19.6    
19.8    
20.0    
20.3    
20.5    
20.8    
21.0    
21.3    
21.5    
21.7    
22.0    
22.2    
22.5    
22.7    
22.9    
23.2    
23.4    
23.7    
23.9    
24.2    
24.4    
24.6    
24.9    
25.1    
25.4    
25.6    
25.8    
26.1    
26.3    
26.6    
26.8    
27.1    
27.3    
27.5    
27.8    
28.0    
28.3    
28.5    
28.7    
29.0    
29.2    
29.5    
29.7    
30.0    
30.2    
30.4    
30.7    
30.9    
31.2    
31.4    
31.6    
31.9    
32.1    
32.4    
32.6    
32.9    
33.1    
33.3    
33.6    
33.8    
34.1    
34.3    
34.5    
34.8    
35.0    
35.3    
35.5    
35.7    
36.0    
36.2    
36.5    
36.7    
37.0    
37.2    
37.4    
37.7    
37.9    
38.2    
38.4    
38.6    
38.9    
39.1    
39.4    
39.6    
39.9    
40.1    
40.3    
40.6    
40.8    
41.1    
41.3    
41.5    
41.8    
42.0    
42.3    
42.5    
42.8    
43.0    
43.2    
43.5    
43.7    
44.0    
44.2    
44.4    
44.7    
44.9    
45.2    
45.4    
45.7    
45.9    
46.1    
46.4    
46.6    
46.9    
47.1    
47.3    
47.6    
47.8    
48.1    
48.3    
48.6    
48.8    
49.0    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
50.7    
51.0    
51.2    
51.4    
51.7    
51.9    
52.2    
52.4    
52.7    
52.9    
53.1    
53.4    
53.6    
53.9    
54.1    
54.3    
54.6    
54.8    
55.1    
55.3    
55.6    
55.8    
56.0    
56.3    
56.5    
56.8    
57.0    
57.2    
57.5    
57.7    
58.0    
58.2    
58.5    
58.7    
58.9    
59.2    
59.4    
59.7    
59.9    
60.1    
60.4    
60.6    
60.9    
61.1    
61.4    
61.6    
61.8    
62.1    
62.3    
62.6    
62.8    
63.0    
63.3    
63.5    
63.8    
64.0    
64.3    
64.5    
64.7    
65.0    
65.2    
65.5    
65.7    
65.9    
66.2    
66.4    
66.7    
66.9    
67.1    
67.4    
67.6    
67.9    
68.1    
68.4    
68.6    
68.8    
69.1    
69.3    
69.6    
69.8    
70.0    
70.3    
70.5    
70.8    
71.0    
71.3    
71.5    
71.7    
72.0    
72.2    
72.5    
72.7    
72.9    
73.2    
73.4    
73.7    
73.9    
74.2    
74.4    
74.6    
74.9    
75.1    
75.4    
75.6    
75.8    
76.1    
76.3    
76.6    
76.8    
77.1    
77.3    
77.5    
77.8    
78.0    
78.3    
78.5    
78.7    
79.0    
79.2    
79.5    
79.7    
80.0    
80.2    
80.4    
80.7    
80.9    
81.2    
81.4    
81.6    
81.9    
82.1    
82.4    
82.6    
82.9    
83.1    
83.3    
83.6    
83.8    
84.1    
84.3    
84.5    
84.8    
85.0    
85.3    
85.5    
85.7    
86.0    
86.2    
86.5    
86.7    
87.0    
87.2    
87.4    
87.7    
87.9    
88.2    
88.4    
88.6    
88.9    
89.1    
89.4    
89.6    
89.9    
90.1    
90.3    
90.6    
90.8    
91.1    
91.3    
91.5    
91.8    
92.0    
92.3    
92.5    
92.8    
93.0    
93.2    
93.5    
93.7    
94.0    
94.2    
94.4    
94.7    
94.9    
95.2    
95.4    
95.7    
95.9    
96.1    
96.4    
96.6    
96.9    
97.1    
97.3    
97.6    
97.8    
98.1    
98.3    
98.6    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 65170, rend_intergenic: 58787  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 28 predictions persist after filtering for low support