-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_2/scaffold_2_19694267-19897149

-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.9531_t
Couldn't classify 134034, 136745
Sorry, prediction pasa_asmbl_25325.p1 fails validation.
(CTG)	 CT	134034-136745	AG	TCA
Valid prediction for GlimmerHMM_glimmerT_5834-T1
Valid prediction for GlimmerHMM_glimmerT_5833-T1
Valid prediction for HiQ_model.g3906.t1
Valid prediction for HiQ_model.g3904.t1
Valid prediction for snap_scaffold_2-snap.3887-T1
Valid prediction for HiQ_model.g3900.t1
Valid prediction for pasa_asmbl_25327.p1
Valid prediction for Augustus_model.g3902.t1
Valid prediction for GeneMark_model.9512_t
Couldn't classify 145592, 146203
Sorry, prediction pasa_asmbl_25326.p1 fails validation.
(GCC)	 TC	145592-146203	GT	AGG
(ATC)	 AG	147949-149436	GA	GAG
-recovered pasa_asmbl_25326.p1, terminal, 147949, 149436
Valid prediction for GlimmerHMM_glimmerT_5828-T1
Valid prediction for CodingQuarry_transcript_28823-T1
Valid prediction for snap_scaffold_2-snap.3901-T1
Valid prediction for CodingQuarry_transcript_28824-T1
Valid prediction for GeneMark_model.9511_t
Valid prediction for GeneMark_model.9532_t
Valid prediction for Augustus_model.g3901.t1
Valid prediction for GlimmerHMM_glimmerT_5825-T1
Valid prediction for pasa_asmbl_25318.p1
Valid prediction for snap_scaffold_2-snap.3888-T1
Valid prediction for GeneMark_model.9529_t
Valid prediction for snap_scaffold_2-snap.3886-T1
Valid prediction for GlimmerHMM_glimmerT_5824-T1
Valid prediction for GeneMark_model.9535_t
Valid prediction for snap_scaffold_2-snap.3906-T1
Valid prediction for GeneMark_model.9534_t
Couldn't classify 185155, 185334
Sorry, prediction pasa_asmbl_25330.p1 fails validation.
(CCG)	 CC	185155-185334	GT	AGG
(GTT)	 AG	185998-186111	GT	AGG
(AAA)	 AG	186382-186475	GT	AGG
(GCA)	 AG	186678-186862	GT	TGG
(GAC)	 AG	187206-187328	AA	AGA
-recovered pasa_asmbl_25330.p1, terminal, 187206, 187328
-recovered pasa_asmbl_25330.p1, internal, 185998, 186111
-recovered pasa_asmbl_25330.p1, internal, 186382, 186475
-recovered pasa_asmbl_25330.p1, internal, 186678, 186862
Valid prediction for GlimmerHMM_glimmerT_5832-T1
Valid prediction for snap_scaffold_2-snap.3903-T1
Valid prediction for CodingQuarry_transcript_28825-T1
Valid prediction for snap_scaffold_2-snap.3893-T1
Valid prediction for snap_scaffold_2-snap.3884-T1
Valid prediction for snap_scaffold_2-snap.3882-T1
Valid prediction for snap_scaffold_2-snap.3896-T1
Valid prediction for snap_scaffold_2-snap.3910-T1
Valid prediction for snap_scaffold_2-snap.3883-T1
Valid prediction for GlimmerHMM_glimmerT_5823-T1
Valid prediction for Augustus_model.g3903.t1
Couldn't classify 182034, 182456
Sorry, prediction pasa_asmbl_25329.p1 fails validation.
(CTA)	 TT	182034-182456	CG	AGC
Valid prediction for GeneMark_model.9520_t
Valid prediction for Augustus_model.g3905.t1
Couldn't classify 171266, 171304
Sorry, prediction pasa_asmbl_25369.p1 fails validation.
(ATG)	 AG	167984-168049	GT	AGG
(AGA)	 AG	169123-169294	GT	AGG
(GAG)	 AG	170702-170812	GT	CGG
(CTG)	 AG	171051-171181	GT	TGG
(TTT)	 AG	171266-171304	NN	NNN
-recovered pasa_asmbl_25369.p1, initial, 167984, 168049
-recovered pasa_asmbl_25369.p1, internal, 167984, 168049
-recovered pasa_asmbl_25369.p1, internal, 169123, 169294
-recovered pasa_asmbl_25369.p1, internal, 170702, 170812
-recovered pasa_asmbl_25369.p1, internal, 171051, 171181
Valid prediction for GeneMark_model.9517_t
Valid prediction for GeneMark_model.9519_t
Valid prediction for snap_scaffold_2-snap.3889-T1
Valid prediction for GeneMark_model.9515_t
Valid prediction for snap_scaffold_2-snap.3894-T1
Valid prediction for GeneMark_model.9516_t
Valid prediction for snap_scaffold_2-snap.3898-T1
Valid prediction for GeneMark_model.9528_t
Valid prediction for snap_scaffold_2-snap.3907-T1
Valid prediction for GlimmerHMM_glimmerT_5822-T1
Valid prediction for GlimmerHMM_glimmerT_5831-T1
Valid prediction for GeneMark_model.9522_t
Valid prediction for GlimmerHMM_glimmerT_5820-T1
Valid prediction for GeneMark_model.9513_t
Valid prediction for GeneMark_model.9509_t
Valid prediction for CodingQuarry_transcript_28822-T1
Valid prediction for GlimmerHMM_glimmerT_5821-T1
Valid prediction for GeneMark_model.9536_t
Valid prediction for snap_scaffold_2-snap.3899-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 GlimmerHMM_glimmerT_5835-T1
Valid prediction for CodingQuarry_transcript_28827-T1
Valid prediction for GeneMark_model.9505_t
Valid prediction for GeneMark_model.9518_t
Valid prediction for GeneMark_model.9525_t
Valid prediction for HiQ_model.g3908.t1
Valid prediction for pasa_asmbl_23892.p1
Valid prediction for GeneMark_model.9527_t
Valid prediction for snap_scaffold_2-snap.3897-T1
Valid prediction for snap_scaffold_2-snap.3911-T1
Valid prediction for snap_scaffold_2-snap.3908-T1
Valid prediction for GeneMark_model.9537_t
Valid prediction for GeneMark_model.9510_t
Valid prediction for HiQ_model.g3907.t1
Valid prediction for GlimmerHMM_glimmerT_5830-T1
Valid prediction for GlimmerHMM_glimmerT_5829-T1
Valid prediction for snap_scaffold_2-snap.3902-T1
Valid prediction for GlimmerHMM_glimmerT_5836-T1
Couldn't classify 2156, 2374
Couldn't classify 2483, 3707
Sorry, prediction CodingQuarry_transcript_28828-T1 fails validation.
(ATG)	 GT	757-882	GT	CGG
(ACA)	 AG	2156-2374	AA	CCA
(GCT)	 CC	2483-3707	GT	AGG
(AAG)	 AG	4024-4163	GT	AGG
(TTG)	 AG	4360-4426	GT	GGG
(GTG)	 AG	4668-4711	GT	AGG
(ACG)	 AG	4875-5016	GT	GGG
(GCA)	 AG	5090-5168	GT	AGG
(ATA)	 AG	5693-5768	GT	AGG
(TTG)	 AG	5916-6029	GT	TTG
(TGG)	 AG	6402-6495	GT	AGG
(AGC)	 AG	6713-6918	GT	GGG
(GCA)	 AG	7199-7342	GT	AGG
(TGG)	 AG	8014-8094	GT	AGG
(AAA)	 AG	8210-8281	GT	AGG
(TTG)	 AG	8637-8687	TT	GAT
-recovered CodingQuarry_transcript_28828-T1, initial, 757, 882
-recovered CodingQuarry_transcript_28828-T1, terminal, 8637, 8687
-recovered CodingQuarry_transcript_28828-T1, internal, 4024, 4163
-recovered CodingQuarry_transcript_28828-T1, internal, 4360, 4426
-recovered CodingQuarry_transcript_28828-T1, internal, 4668, 4711
-recovered CodingQuarry_transcript_28828-T1, internal, 4875, 5016
-recovered CodingQuarry_transcript_28828-T1, internal, 5090, 5168
-recovered CodingQuarry_transcript_28828-T1, internal, 5693, 5768
-recovered CodingQuarry_transcript_28828-T1, internal, 5916, 6029
-recovered CodingQuarry_transcript_28828-T1, internal, 6402, 6495
-recovered CodingQuarry_transcript_28828-T1, internal, 6713, 6918
-recovered CodingQuarry_transcript_28828-T1, internal, 7199, 7342
-recovered CodingQuarry_transcript_28828-T1, internal, 8014, 8094
-recovered CodingQuarry_transcript_28828-T1, internal, 8210, 8281
Valid prediction for GeneMark_model.9514_t
Valid prediction for GeneMark_model.9533_t
Valid prediction for snap_scaffold_2-snap.3905-T1
Valid prediction for snap_scaffold_2-snap.3909-T1
Valid prediction for GlimmerHMM_glimmerT_5827-T1
Valid prediction for snap_scaffold_2-snap.3912-T1
Valid prediction for GeneMark_model.9523_t
Valid prediction for GeneMark_model.9524_t
Valid prediction for snap_scaffold_2-snap.3892-T1
Valid prediction for GlimmerHMM_glimmerT_5826-T1
Valid prediction for GeneMark_model.9530_t
Valid prediction for snap_scaffold_2-snap.3895-T1
Valid prediction for snap_scaffold_2-snap.3904-T1
Valid prediction for pasa_asmbl_25324.p1
Valid prediction for GeneMark_model.9508_t
Valid prediction for snap_scaffold_2-snap.3900-T1
Valid prediction for snap_scaffold_2-snap.3890-T1
Valid prediction for GeneMark_model.9506_t
Valid prediction for GeneMark_model.9507_t
Valid prediction for CodingQuarry_transcript_28826-T1
Valid prediction for snap_scaffold_2-snap.3891-T1
Valid prediction for GeneMark_model.9521_t
Valid prediction for snap_scaffold_2-snap.3885-T1
Valid prediction for pasa_asmbl_23894.p1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 58233, rend_intergenic: 58041  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62025, rend_intergenic: 58768  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95479, rend_intergenic: 87242  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126753, rend_intergenic: 124163  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149436, rend_intergenic: 145412  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165895, rend_intergenic: 157064  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175158, rend_intergenic: 171065  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198196, rend_intergenic: 195930  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 202883
-exon list size: 416


building trellis

0.2    
0.5    
0.7    
1.0    
1.2    
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1.9    
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2.9    
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3.3    
3.6    
3.8    
4.1    
4.3    
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5.0    
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5.5    
5.7    
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6.5    
6.7    
6.9    
7.2    
7.4    
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7.9    
8.1    
8.4    
8.6    
8.9    
9.1    
9.3    
9.6    
9.8    
10.0    
10.3    
10.5    
10.8    
11.0    
11.2    
11.5    
11.7    
12.0    
12.2    
12.4    
12.7    
12.9    
13.2    
13.4    
13.6    
13.9    
14.1    
14.4    
14.6    
14.8    
15.1    
15.3    
15.6    
15.8    
16.0    
16.3    
16.5    
16.7    
17.0    
17.2    
17.5    
17.7    
17.9    
18.2    
18.4    
18.7    
18.9    
19.1    
19.4    
19.6    
19.9    
20.1    
20.3    
20.6    
20.8    
21.1    
21.3    
21.5    
21.8    
22.0    
22.2    
22.5    
22.7    
23.0    
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    
27.0    
27.3    
27.5    
27.8    
28.0    
28.2    
28.5    
28.7    
28.9    
29.2    
29.4    
29.7    
29.9    
30.1    
30.4    
30.6    
30.9    
31.1    
31.3    
31.6    
31.8    
32.1    
32.3    
32.5    
32.8    
33.0    
33.3    
33.5    
33.7    
34.0    
34.2    
34.4    
34.7    
34.9    
35.2    
35.4    
35.6    
35.9    
36.1    
36.4    
36.6    
36.8    
37.1    
37.3    
37.6    
37.8    
38.0    
38.3    
38.5    
38.8    
39.0    
39.2    
39.5    
39.7    
40.0    
40.2    
40.4    
40.7    
40.9    
41.1    
41.4    
41.6    
41.9    
42.1    
42.3    
42.6    
42.8    
43.1    
43.3    
43.5    
43.8    
44.0    
44.3    
44.5    
44.7    
45.0    
45.2    
45.5    
45.7    
45.9    
46.2    
46.4    
46.7    
46.9    
47.1    
47.4    
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    
52.6    
52.9    
53.1    
53.3    
53.6    
53.8    
54.1    
54.3    
54.5    
54.8    
55.0    
55.3    
55.5    
55.7    
56.0    
56.2    
56.5    
56.7    
56.9    
57.2    
57.4    
57.7    
57.9    
58.1    
58.4    
58.6    
58.9    
59.1    
59.3    
59.6    
59.8    
60.0    
60.3    
60.5    
60.8    
61.0    
61.2    
61.5    
61.7    
62.0    
62.2    
62.4    
62.7    
62.9    
63.2    
63.4    
63.6    
63.9    
64.1    
64.4    
64.6    
64.8    
65.1    
65.3    
65.6    
65.8    
66.0    
66.3    
66.5    
66.7    
67.0    
67.2    
67.5    
67.7    
67.9    
68.2    
68.4    
68.7    
68.9    
69.1    
69.4    
69.6    
69.9    
70.1    
70.3    
70.6    
70.8    
71.1    
71.3    
71.5    
71.8    
72.0    
72.2    
72.5    
72.7    
73.0    
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    
77.0    
77.3    
77.5    
77.8    
78.0    
78.2    
78.5    
78.7    
78.9    
79.2    
79.4    
79.7    
79.9    
80.1    
80.4    
80.6    
80.9    
81.1    
81.3    
81.6    
81.8    
82.1    
82.3    
82.5    
82.8    
83.0    
83.3    
83.5    
83.7    
84.0    
84.2    
84.4    
84.7    
84.9    
85.2    
85.4    
85.6    
85.9    
86.1    
86.4    
86.6    
86.8    
87.1    
87.3    
87.6    
87.8    
88.0    
88.3    
88.5    
88.8    
89.0    
89.2    
89.5    
89.7    
90.0    
90.2    
90.4    
90.7    
90.9    
91.1    
91.4    
91.6    
91.9    
92.1    
92.3    
92.6    
92.8    
93.1    
93.3    
93.5    
93.8    
94.0    
94.3    
94.5    
94.7    
95.0    
95.2    
95.5    
95.7    
95.9    
96.2    
96.4    
96.7    
96.9    
97.1    
97.4    
97.6    
97.8    
98.1    
98.3    
98.6    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 58233, rend_intergenic: 58041  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62025, rend_intergenic: 58768  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95479, rend_intergenic: 87242  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126753, rend_intergenic: 124163  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149436, rend_intergenic: 145412  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165895, rend_intergenic: 157064  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175158, rend_intergenic: 171065  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198196, rend_intergenic: 195930  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 12 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 20760
-exon list size: 11


building trellis

7.7    
15.4    
23.1    
30.8    
38.5    
46.2    
53.8    
61.5    
69.2    
76.9    
84.6    
92.3    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 19988
-exon list size: 8


building trellis

10.0    
20.0    
30.0    
40.0    
50.0    
60.0    
70.0    
80.0    
90.0    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 2064 - 19988
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support
	-no exons in range 2064 - 12266