-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_17/scaffold_17_2467914-2624161

-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 GeneMark_model.70308_t
Valid prediction for GlimmerHMM_glimmerT_40806-T1
Valid prediction for CodingQuarry_transcript_21845-T1
Valid prediction for snap_scaffold_17-snap.535-T1
Valid prediction for HiQ_model.g27331.t1
Valid prediction for snap_scaffold_17-snap.522-T1
Valid prediction for snap_scaffold_17-snap.531-T1
Valid prediction for snap_scaffold_17-snap.530-T1
Valid prediction for snap_scaffold_17-snap.549-T1
Valid prediction for GlimmerHMM_glimmerT_40816-T1
Couldn't classify 8090, 8209
Couldn't classify 10522, 10538
Sorry, prediction pasa_asmbl_17786.p1 fails validation.
(AGC)	 CC	8090-8209	GT	AGG
(TGT)	 AG	8300-8388	GT	GGG
(CTT)	 AG	8499-8643	GT	AGG
(GCG)	 AG	8897-9051	GT	TGG
(GGA)	 AG	9145-9233	GT	GCG
(TGG)	 AG	9370-9500	GT	AGG
(TGT)	 AG	9796-9930	GT	AGG
(GCT)	 AG	10163-10249	GT	GGG
(TTG)	 AG	10362-10428	GT	ACG
(GTG)	 AG	10522-10538	GA	CAG
-recovered pasa_asmbl_17786.p1, internal, 8300, 8388
-recovered pasa_asmbl_17786.p1, internal, 8499, 8643
-recovered pasa_asmbl_17786.p1, internal, 8897, 9051
-recovered pasa_asmbl_17786.p1, internal, 9145, 9233
-recovered pasa_asmbl_17786.p1, internal, 9370, 9500
-recovered pasa_asmbl_17786.p1, internal, 9796, 9930
-recovered pasa_asmbl_17786.p1, internal, 10163, 10249
-recovered pasa_asmbl_17786.p1, internal, 10362, 10428
Valid prediction for Augustus_model.g27318.t1
Valid prediction for snap_scaffold_17-snap.532-T1
Valid prediction for GlimmerHMM_glimmerT_40794-T1
Valid prediction for GlimmerHMM_glimmerT_40822-T1
Valid prediction for GlimmerHMM_glimmerT_40818-T1
Couldn't classify 12881, 13867
Sorry, prediction pasa_asmbl_17788.p1 fails validation.
(ACT)	 GG	12881-13867	AG	GAA
Valid prediction for Augustus_model.g27334.t1
Valid prediction for HiQ_model.g27330.t1
Valid prediction for GeneMark_model.70289_t
Valid prediction for GlimmerHMM_glimmerT_40812-T1
Valid prediction for GlimmerHMM_glimmerT_40820-T1
Valid prediction for GlimmerHMM_glimmerT_40803-T1
Valid prediction for snap_scaffold_17-snap.540-T1
Valid prediction for snap_scaffold_17-snap.524-T1
Valid prediction for pasa_asmbl_17792.p1
Valid prediction for snap_scaffold_17-snap.525-T1
Valid prediction for snap_scaffold_17-snap.542-T1
Valid prediction for GlimmerHMM_glimmerT_40813-T1
Valid prediction for CodingQuarry_transcript_21849-T1
Valid prediction for CodingQuarry_transcript_21859-T1
Couldn't classify 17539, 17648
Sorry, prediction pasa_asmbl_17789.p1 fails validation.
(AAA)	 CC	17539-17648	GT	CGG
(CTT)	 AG	18089-18165	GT	AGG
(GTG)	 AG	18378-18569	GT	AGG
(TGG)	 AG	19793-19869	TC	AAT
-recovered pasa_asmbl_17789.p1, terminal, 19793, 19869
-recovered pasa_asmbl_17789.p1, internal, 18089, 18165
-recovered pasa_asmbl_17789.p1, internal, 18378, 18569
Valid prediction for snap_scaffold_17-snap.547-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_40807-T1
Valid prediction for snap_scaffold_17-snap.541-T1
Valid prediction for GeneMark_model.70290_t
Valid prediction for pasa_asmbl_17791.p1
Valid prediction for GeneMark_model.70300_t
Valid prediction for GeneMark_model.70287_t
Valid prediction for GeneMark_model.70312_t
Valid prediction for GeneMark_model.70315_t
Couldn't classify 10593, 10667
Couldn't classify 12450, 12688
Sorry, prediction pasa_asmbl_17787.p1 fails validation.
(TTA)	 TG	10593-10667	GT	AGG
(ACG)	 AG	10880-11058	GT	AAG
(TTT)	 AG	11639-11690	GT	AGG
(ATG)	 AG	11917-11970	GT	AGG
(GAG)	 AG	12144-12267	GT	AGG
(AAG)	 AG	12450-12688	GA	GGG
-recovered pasa_asmbl_17787.p1, initial, 11917, 11970
-recovered pasa_asmbl_17787.p1, terminal, 12144, 12267
-recovered pasa_asmbl_17787.p1, internal, 10880, 11058
-recovered pasa_asmbl_17787.p1, internal, 11639, 11690
-recovered pasa_asmbl_17787.p1, internal, 11917, 11970
-recovered pasa_asmbl_17787.p1, internal, 12144, 12267
Valid prediction for GlimmerHMM_glimmerT_40802-T1
Valid prediction for Augustus_model.g27317.t1
Valid prediction for GlimmerHMM_glimmerT_40795-T1
Valid prediction for GlimmerHMM_glimmerT_40821-T1
Valid prediction for GeneMark_model.70310_t
Valid prediction for GeneMark_model.70307_t
Valid prediction for GeneMark_model.70295_t
Couldn't classify 105230, 105289
Sorry, prediction pasa_asmbl_17797.p1 fails validation.
(ATG)	 CA	101658-101662	GT	AGG
(AGG)	 AG	102200-102259	GT	GGG
(GTA)	 AG	102420-102462	GT	TGG
(TGT)	 AG	102669-102773	GT	AGG
(TCT)	 AG	102886-102963	GT	TGG
(CAA)	 AG	103061-103163	GT	ATG
(TGG)	 AG	103292-103357	GT	AGG
(TTC)	 AG	103505-103621	GT	CTG
(TGG)	 AG	104130-104208	GT	ACG
(GGT)	 AG	104397-104484	GT	TGG
(GGT)	 AG	104756-104817	GT	AGG
(ACG)	 AG	104934-105048	GT	AGG
(GAT)	 AG	105230-105289	AA	GGA
-recovered pasa_asmbl_17797.p1, initial, 101658, 101662
-recovered pasa_asmbl_17797.p1, internal, 102200, 102259
-recovered pasa_asmbl_17797.p1, internal, 102420, 102462
-recovered pasa_asmbl_17797.p1, internal, 102669, 102773
-recovered pasa_asmbl_17797.p1, internal, 102886, 102963
-recovered pasa_asmbl_17797.p1, internal, 103061, 103163
-recovered pasa_asmbl_17797.p1, internal, 103292, 103357
-recovered pasa_asmbl_17797.p1, internal, 103505, 103621
-recovered pasa_asmbl_17797.p1, internal, 104130, 104208
-recovered pasa_asmbl_17797.p1, internal, 104397, 104484
-recovered pasa_asmbl_17797.p1, internal, 104756, 104817
-recovered pasa_asmbl_17797.p1, internal, 104934, 105048
Valid prediction for pasa_asmbl_17790.p1
Valid prediction for HiQ_model.g27321.t1
Valid prediction for GlimmerHMM_glimmerT_40815-T1
Valid prediction for GlimmerHMM_glimmerT_40796-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_17-snap.546-T1
Valid prediction for Augustus_model.g27327.t1
Valid prediction for HiQ_model.g27323.t1
Valid prediction for pasa_asmbl_18794.p1
Valid prediction for GeneMark_model.70303_t
Valid prediction for CodingQuarry_transcript_21855-T1
Valid prediction for GlimmerHMM_glimmerT_40810-T1
Valid prediction for GeneMark_model.70293_t
Valid prediction for GeneMark_model.70297_t
Valid prediction for snap_scaffold_17-snap.550-T1
Couldn't classify 41111, 41263
Sorry, prediction pasa_asmbl_18812.p1 fails validation.
(GAA)	 CT	41111-41263	GT	TGG
(GAC)	 AG	42064-42117	GT	AGG
(GTC)	 AG	42246-42794	GA	GAG
-recovered pasa_asmbl_18812.p1, terminal, 42246, 42794
-recovered pasa_asmbl_18812.p1, internal, 42064, 42117
Valid prediction for snap_scaffold_17-snap.533-T1
Valid prediction for HiQ_model.g27329.t1
Valid prediction for GlimmerHMM_glimmerT_40804-T1
Valid prediction for pasa_asmbl_18799.p1
Valid prediction for Augustus_model.g27333.t1
Valid prediction for CodingQuarry_transcript_21850-T1
Valid prediction for snap_scaffold_17-snap.537-T1
Valid prediction for GlimmerHMM_glimmerT_40798-T1
Valid prediction for GeneMark_model.70306_t
Valid prediction for GeneMark_model.70288_t
Valid prediction for snap_scaffold_17-snap.543-T1
Valid prediction for GeneMark_model.70314_t
Valid prediction for GeneMark_model.70304_t
Valid prediction for HiQ_model.g27322.t1
Valid prediction for snap_scaffold_17-snap.526-T1
Valid prediction for GlimmerHMM_glimmerT_40819-T1
Couldn't classify 133074, 133709
Sorry, prediction pasa_asmbl_18793.p1 fails validation.
(CCT)	 CA	133074-133709	GC	AGG
Valid prediction for GeneMark_model.70305_t
Valid prediction for GeneMark_model.70298_t
Valid prediction for GeneMark_model.70292_t
Valid prediction for snap_scaffold_17-snap.528-T1
Valid prediction for GlimmerHMM_glimmerT_40809-T1
Valid prediction for Augustus_model.g27328.t1
Valid prediction for GeneMark_model.70299_t
Valid prediction for snap_scaffold_17-snap.539-T1
Valid prediction for CodingQuarry_transcript_21857-T1
Valid prediction for Augustus_model.g27332.t1
Valid prediction for snap_scaffold_17-snap.548-T1
Valid prediction for snap_scaffold_17-snap.538-T1
Valid prediction for snap_scaffold_17-snap.545-T1
Valid prediction for GlimmerHMM_glimmerT_40811-T1
Valid prediction for GeneMark_model.70294_t
Couldn't classify 69174, 69375
Sorry, prediction pasa_asmbl_18807.p1 fails validation.
(TTA)	 GG	69174-69375	GT	GCG
(TGT)	 AG	69778-70008	GT	CAG
(CAA)	 AG	70777-70881	GT	CTG
(GGT)	 AG	71240-71293	GT	AGG
(GGC)	 AG	71409-71592	GT	AGG
(GTT)	 AG	71842-72010	GT	AGG
(GTG)	 AG	72781-72919	GT	CAG
(GTC)	 AG	73055-73266	CT	GAC
-recovered pasa_asmbl_18807.p1, terminal, 73055, 73266
-recovered pasa_asmbl_18807.p1, internal, 69778, 70008
-recovered pasa_asmbl_18807.p1, internal, 70777, 70881
-recovered pasa_asmbl_18807.p1, internal, 71240, 71293
-recovered pasa_asmbl_18807.p1, internal, 71409, 71592
-recovered pasa_asmbl_18807.p1, internal, 71842, 72010
-recovered pasa_asmbl_18807.p1, internal, 72781, 72919
Valid prediction for GeneMark_model.70311_t
Valid prediction for snap_scaffold_17-snap.523-T1
Valid prediction for HiQ_model.g27320.t1
Valid prediction for GlimmerHMM_glimmerT_40808-T1
Valid prediction for GlimmerHMM_glimmerT_40799-T1
Valid prediction for snap_scaffold_17-snap.527-T1
Valid prediction for HiQ_model.g27324.t1
Valid prediction for pasa_asmbl_18795.p1
Valid prediction for GlimmerHMM_glimmerT_40814-T1
Valid prediction for CodingQuarry_transcript_21853-T1
Valid prediction for GlimmerHMM_glimmerT_40817-T1
Valid prediction for GlimmerHMM_glimmerT_40800-T1
Couldn't classify 124224, 124325
Couldn't classify 125584, 125659
Sorry, prediction CodingQuarry_transcript_21848-T1 fails validation.
(ATG)	 AG	123163-123264	GT	TGG
(GAG)	 AG	123507-123680	GT	AGG
(ACG)	 AG	123810-123982	GT	AAG
(ACT)	 AG	124224-124325	CC	GAC
(GAC)	 AA	125584-125659	GT	AGG
(GTT)	 AG	125782-125947	GT	AGG
(TTG)	 AG	126152-126267	GT	AGG
(AAG)	 AG	126700-126917	GT	TGG
(GTA)	 AG	127069-127144	AC	AAA
-recovered CodingQuarry_transcript_21848-T1, initial, 123163, 123264
add_exon() Sorry, CodingQuarry_transcript_21848-T1 125782-125947-terminal-3 is invalid.
-recovered CodingQuarry_transcript_21848-T1, terminal, 125782, 125947
-recovered CodingQuarry_transcript_21848-T1, terminal, 127069, 127144
-recovered CodingQuarry_transcript_21848-T1, internal, 123163, 123264
-recovered CodingQuarry_transcript_21848-T1, internal, 123507, 123680
-recovered CodingQuarry_transcript_21848-T1, internal, 123810, 123982
-recovered CodingQuarry_transcript_21848-T1, internal, 125782, 125947
-recovered CodingQuarry_transcript_21848-T1, internal, 126152, 126267
-recovered CodingQuarry_transcript_21848-T1, internal, 126700, 126917
Valid prediction for GlimmerHMM_glimmerT_40805-T1
Valid prediction for pasa_asmbl_18798.p1
Valid prediction for CodingQuarry_transcript_21847-T1
Valid prediction for pasa_asmbl_18801.p1
Couldn't classify 60813, 60934
Sorry, prediction pasa_asmbl_18811.p1 fails validation.
(CCA)	 CG	60813-60934	GT	AGG
(GGA)	 AG	61756-61802	GT	TGG
(AGC)	 AG	61933-62051	GT	AGG
(GAG)	 AG	62578-62685	CT	AAC
-recovered pasa_asmbl_18811.p1, terminal, 62578, 62685
-recovered pasa_asmbl_18811.p1, internal, 61756, 61802
-recovered pasa_asmbl_18811.p1, internal, 61933, 62051
Valid prediction for snap_scaffold_17-snap.544-T1
Valid prediction for snap_scaffold_17-snap.536-T1
Valid prediction for CodingQuarry_transcript_21852-T1
Valid prediction for Augustus_model.g27325.t1
Valid prediction for snap_scaffold_17-snap.534-T1
Valid prediction for GeneMark_model.70301_t
Valid prediction for Augustus_model.g27319.t1
Valid prediction for CodingQuarry_transcript_21858-T1
Valid prediction for GeneMark_model.70313_t
Valid prediction for snap_scaffold_17-snap.529-T1
Valid prediction for GeneMark_model.70291_t
Valid prediction for pasa_asmbl_18796.p1
Valid prediction for CodingQuarry_transcript_21856-T1
Valid prediction for GeneMark_model.70296_t
Valid prediction for GlimmerHMM_glimmerT_40797-T1
Valid prediction for GlimmerHMM_glimmerT_40793-T1
Valid prediction for HiQ_model.g27326.t1
Valid prediction for GeneMark_model.70302_t
Valid prediction for GeneMark_model.70309_t
Valid prediction for GlimmerHMM_glimmerT_40801-T1
Valid prediction for CodingQuarry_transcript_21851-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13867, rend_intergenic: 4138  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88344, rend_intergenic: 84819  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 156248
-exon list size: 375


building trellis

0.3    
0.5    
0.8    
1.1    
1.3    
1.6    
1.9    
2.1    
2.4    
2.7    
2.9    
3.2    
3.4    
3.7    
4.0    
4.2    
4.5    
4.8    
5.0    
5.3    
5.6    
5.8    
6.1    
6.4    
6.6    
6.9    
7.2    
7.4    
7.7    
8.0    
8.2    
8.5    
8.8    
9.0    
9.3    
9.5    
9.8    
10.1    
10.3    
10.6    
10.9    
11.1    
11.4    
11.7    
11.9    
12.2    
12.5    
12.7    
13.0    
13.3    
13.5    
13.8    
14.1    
14.3    
14.6    
14.9    
15.1    
15.4    
15.6    
15.9    
16.2    
16.4    
16.7    
17.0    
17.2    
17.5    
17.8    
18.0    
18.3    
18.6    
18.8    
19.1    
19.4    
19.6    
19.9    
20.2    
20.4    
20.7    
21.0    
21.2    
21.5    
21.8    
22.0    
22.3    
22.5    
22.8    
23.1    
23.3    
23.6    
23.9    
24.1    
24.4    
24.7    
24.9    
25.2    
25.5    
25.7    
26.0    
26.3    
26.5    
26.8    
27.1    
27.3    
27.6    
27.9    
28.1    
28.4    
28.6    
28.9    
29.2    
29.4    
29.7    
30.0    
30.2    
30.5    
30.8    
31.0    
31.3    
31.6    
31.8    
32.1    
32.4    
32.6    
32.9    
33.2    
33.4    
33.7    
34.0    
34.2    
34.5    
34.7    
35.0    
35.3    
35.5    
35.8    
36.1    
36.3    
36.6    
36.9    
37.1    
37.4    
37.7    
37.9    
38.2    
38.5    
38.7    
39.0    
39.3    
39.5    
39.8    
40.1    
40.3    
40.6    
40.8    
41.1    
41.4    
41.6    
41.9    
42.2    
42.4    
42.7    
43.0    
43.2    
43.5    
43.8    
44.0    
44.3    
44.6    
44.8    
45.1    
45.4    
45.6    
45.9    
46.2    
46.4    
46.7    
46.9    
47.2    
47.5    
47.7    
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    
52.3    
52.5    
52.8    
53.1    
53.3    
53.6    
53.8    
54.1    
54.4    
54.6    
54.9    
55.2    
55.4    
55.7    
56.0    
56.2    
56.5    
56.8    
57.0    
57.3    
57.6    
57.8    
58.1    
58.4    
58.6    
58.9    
59.2    
59.4    
59.7    
59.9    
60.2    
60.5    
60.7    
61.0    
61.3    
61.5    
61.8    
62.1    
62.3    
62.6    
62.9    
63.1    
63.4    
63.7    
63.9    
64.2    
64.5    
64.7    
65.0    
65.3    
65.5    
65.8    
66.0    
66.3    
66.6    
66.8    
67.1    
67.4    
67.6    
67.9    
68.2    
68.4    
68.7    
69.0    
69.2    
69.5    
69.8    
70.0    
70.3    
70.6    
70.8    
71.1    
71.4    
71.6    
71.9    
72.1    
72.4    
72.7    
72.9    
73.2    
73.5    
73.7    
74.0    
74.3    
74.5    
74.8    
75.1    
75.3    
75.6    
75.9    
76.1    
76.4    
76.7    
76.9    
77.2    
77.5    
77.7    
78.0    
78.2    
78.5    
78.8    
79.0    
79.3    
79.6    
79.8    
80.1    
80.4    
80.6    
80.9    
81.2    
81.4    
81.7    
82.0    
82.2    
82.5    
82.8    
83.0    
83.3    
83.6    
83.8    
84.1    
84.4    
84.6    
84.9    
85.1    
85.4    
85.7    
85.9    
86.2    
86.5    
86.7    
87.0    
87.3    
87.5    
87.8    
88.1    
88.3    
88.6    
88.9    
89.1    
89.4    
89.7    
89.9    
90.2    
90.5    
90.7    
91.0    
91.2    
91.5    
91.8    
92.0    
92.3    
92.6    
92.8    
93.1    
93.4    
93.6    
93.9    
94.2    
94.4    
94.7    
95.0    
95.2    
95.5    
95.8    
96.0    
96.3    
96.6    
96.8    
97.1    
97.3    
97.6    
97.9    
98.1    
98.4    
98.7    
98.9    
99.2    
99.5    
99.7    
-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 13867, rend_intergenic: 4138  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88344, rend_intergenic: 84819  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support