-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_11/scaffold_11_13228767-13421533

-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_28167-T1
Valid prediction for snap_scaffold_11-snap.2805-T1
Valid prediction for Augustus_model.g18645.t1
Valid prediction for Augustus_model.g18649.t1
Valid prediction for GlimmerHMM_glimmerT_28156-T1
Valid prediction for snap_scaffold_11-snap.2820-T1
Couldn't classify 30711, 30712
Sorry, prediction CodingQuarry_transcript_8292-T1 fails validation.
(ATG)	 TC	30711-30712	GT	ATG
(GAT)	 AG	30802-30869	GT	AGG
(GCG)	 AG	31254-31346	GT	ACG
(ACA)	 AG	32036-32096	GT	GGG
(GGG)	 AG	32292-32337	TG	AGT
-recovered CodingQuarry_transcript_8292-T1, terminal, 32292, 32337
-recovered CodingQuarry_transcript_8292-T1, internal, 30802, 30869
-recovered CodingQuarry_transcript_8292-T1, internal, 31254, 31346
-recovered CodingQuarry_transcript_8292-T1, internal, 32036, 32096
Valid prediction for GlimmerHMM_glimmerT_28168-T1
Valid prediction for Augustus_model.g18647.t1
Valid prediction for GlimmerHMM_glimmerT_28170-T1
Couldn't classify 29538, 29611
Sorry, prediction pasa_asmbl_6297.p1 fails validation.
(TGG)	 TG	29538-29611	GT	AGG
(AGC)	 AG	30282-30387	GT	TGG
(TTT)	 AG	30600-30712	GT	ATG
(GAT)	 AG	30802-30869	GT	AGG
(GCG)	 AG	31254-31346	GT	ACG
(ACA)	 AG	32036-32096	GT	GGG
(GGG)	 AG	32292-32337	TG	AGT
-recovered pasa_asmbl_6297.p1, terminal, 32292, 32337
-recovered pasa_asmbl_6297.p1, internal, 30282, 30387
-recovered pasa_asmbl_6297.p1, internal, 30600, 30712
-recovered pasa_asmbl_6297.p1, internal, 30802, 30869
-recovered pasa_asmbl_6297.p1, internal, 31254, 31346
-recovered pasa_asmbl_6297.p1, internal, 32036, 32096
Valid prediction for Augustus_model.g18646.t1
Valid prediction for CodingQuarry_transcript_8283-T1
Valid prediction for pasa_asmbl_6052.p1
Valid prediction for snap_scaffold_11-snap.2832-T1
Valid prediction for GlimmerHMM_glimmerT_28163-T1
Valid prediction for HiQ_model.g18639.t1
Couldn't classify 154374, 154375
Sorry, prediction CodingQuarry_transcript_8295-T1 fails validation.
(ATG)	 TG	154374-154375	GT	ATG
(GGA)	 AG	154460-154514	GT	AGG
(TCG)	 AG	154617-154733	GT	CAG
(GTG)	 AG	154818-154985	GT	AGG
(GCT)	 AG	155282-155356	AC	AAA
-recovered CodingQuarry_transcript_8295-T1, terminal, 155282, 155356
-recovered CodingQuarry_transcript_8295-T1, internal, 154460, 154514
-recovered CodingQuarry_transcript_8295-T1, internal, 154617, 154733
-recovered CodingQuarry_transcript_8295-T1, internal, 154818, 154985
Valid prediction for snap_scaffold_11-snap.2812-T1
Valid prediction for Augustus_model.g18641.t1
Valid prediction for snap_scaffold_11-snap.2833-T1
Valid prediction for CodingQuarry_transcript_8294-T1
Valid prediction for snap_scaffold_11-snap.2835-T1
Valid prediction for snap_scaffold_11-snap.2837-T1
Valid prediction for Augustus_model.g18653.t1
Valid prediction for GlimmerHMM_glimmerT_28173-T1
Valid prediction for Augustus_model.g18655.t1
Valid prediction for GlimmerHMM_glimmerT_28162-T1
Valid prediction for snap_scaffold_11-snap.2814-T1
Valid prediction for CodingQuarry_transcript_8293-T1
Couldn't classify 63075, 63215
Couldn't classify 67016, 67087
Sorry, prediction pasa_asmbl_6268.p1 fails validation.
(CTG)	 AG	63075-63215	GT	CCG
(GCC)	 AG	64415-64527	GT	AGG
(GAT)	 AG	66031-66145	GT	TGG
(GCC)	 AG	67016-67087	GG	AAG
-recovered pasa_asmbl_6268.p1, internal, 63075, 63215
-recovered pasa_asmbl_6268.p1, internal, 64415, 64527
-recovered pasa_asmbl_6268.p1, internal, 66031, 66145
Valid prediction for snap_scaffold_11-snap.2824-T1
Couldn't classify 17639, 17671
Sorry, prediction pasa_asmbl_6039.p1 fails validation.
(TGC)	 TC	17639-17671	GT	AGG
(GAT)	 AG	18107-18181	GT	GGG
(AAC)	 AG	18292-18417	GT	AGG
(GAG)	 AG	18738-18855	GT	AGG
(GTT)	 AG	19396-19490	GG	GAG
-recovered pasa_asmbl_6039.p1, terminal, 19396, 19490
-recovered pasa_asmbl_6039.p1, internal, 18107, 18181
-recovered pasa_asmbl_6039.p1, internal, 18292, 18417
-recovered pasa_asmbl_6039.p1, internal, 18738, 18855
Valid prediction for Augustus_model.g18644.t1
Valid prediction for snap_scaffold_11-snap.2827-T1
Couldn't classify 70566, 70662
Sorry, prediction pasa_asmbl_6049.p1 fails validation.
(GAG)	 CA	70566-70662	GT	AGG
(AGG)	 AG	72837-72958	GT	GGG
(GAG)	 AG	73431-73465	GT	AGG
(ACT)	 AG	76220-76364	AA	GAA
-recovered pasa_asmbl_6049.p1, terminal, 76220, 76364
-recovered pasa_asmbl_6049.p1, internal, 72837, 72958
-recovered pasa_asmbl_6049.p1, internal, 73431, 73465
Valid prediction for snap_scaffold_11-snap.2810-T1
Valid prediction for HiQ_model.g18652.t1
Valid prediction for CodingQuarry_transcript_8291-T1
Valid prediction for snap_scaffold_11-snap.2818-T1
Valid prediction for GlimmerHMM_glimmerT_28149-T1
Valid prediction for snap_scaffold_11-snap.2830-T1
Valid prediction for GlimmerHMM_glimmerT_28157-T1
Valid prediction for GlimmerHMM_glimmerT_28165-T1
Valid prediction for snap_scaffold_11-snap.2840-T1
Valid prediction for Augustus_model.g18643.t1
Valid prediction for GlimmerHMM_glimmerT_28155-T1
Valid prediction for GlimmerHMM_glimmerT_28152-T1
Valid prediction for GlimmerHMM_glimmerT_28150-T1
Valid prediction for GlimmerHMM_glimmerT_28153-T1
Valid prediction for Augustus_model.g18651.t1
Valid prediction for snap_scaffold_11-snap.2807-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_28172-T1
Valid prediction for snap_scaffold_11-snap.2804-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_8289-T1
Valid prediction for Augustus_model.g18638.t1
Valid prediction for CodingQuarry_transcript_8286-T1
Valid prediction for snap_scaffold_11-snap.2828-T1
Valid prediction for snap_scaffold_11-snap.2834-T1
Valid prediction for snap_scaffold_11-snap.2825-T1
Valid prediction for snap_scaffold_11-snap.2836-T1
Valid prediction for GlimmerHMM_glimmerT_28151-T1
Valid prediction for snap_scaffold_11-snap.2806-T1
Valid prediction for CodingQuarry_transcript_8285-T1
Valid prediction for Augustus_model.g18654.t1
Valid prediction for snap_scaffold_11-snap.2809-T1
Valid prediction for CodingQuarry_transcript_8284-T1
Valid prediction for GlimmerHMM_glimmerT_28164-T1
Valid prediction for snap_scaffold_11-snap.2808-T1
Valid prediction for GlimmerHMM_glimmerT_28166-T1
Valid prediction for snap_scaffold_11-snap.2815-T1
Valid prediction for GlimmerHMM_glimmerT_28154-T1
Valid prediction for snap_scaffold_11-snap.2823-T1
Valid prediction for snap_scaffold_11-snap.2839-T1
Valid prediction for Augustus_model.g18642.t1
Valid prediction for GlimmerHMM_glimmerT_28159-T1
Valid prediction for GlimmerHMM_glimmerT_28171-T1
Valid prediction for GlimmerHMM_glimmerT_28158-T1
Valid prediction for Augustus_model.g18650.t1
Valid prediction for snap_scaffold_11-snap.2819-T1
Valid prediction for snap_scaffold_11-snap.2838-T1
Valid prediction for snap_scaffold_11-snap.2817-T1
Valid prediction for CodingQuarry_transcript_8287-T1
Valid prediction for snap_scaffold_11-snap.2829-T1
Valid prediction for GlimmerHMM_glimmerT_28169-T1
Valid prediction for HiQ_model.g18640.t1
Valid prediction for snap_scaffold_11-snap.2822-T1
Valid prediction for snap_scaffold_11-snap.2826-T1
Valid prediction for snap_scaffold_11-snap.2816-T1
Couldn't classify 168226, 168234
Couldn't classify 168621, 168704
Sorry, prediction CodingQuarry_transcript_8288-T1 fails validation.
(ATG)	 GT	168226-168234	AT	AGA
(CAG)	 AA	168621-168704	GT	ATG
(AAC)	 AG	168799-168969	TG	AGT
-recovered CodingQuarry_transcript_8288-T1, terminal, 168799, 168969
Valid prediction for snap_scaffold_11-snap.2821-T1
Valid prediction for Augustus_model.g18648.t1
Valid prediction for snap_scaffold_11-snap.2831-T1
Valid prediction for GlimmerHMM_glimmerT_28161-T1
Valid prediction for snap_scaffold_11-snap.2813-T1
Couldn't classify 168226, 168235
Couldn't classify 168625, 168704
Sorry, prediction CodingQuarry_transcript_8290-T1 fails validation.
(ATG)	 GT	168226-168235	TA	GAT
(ACA)	 GA	168625-168704	GT	ATG
(AAC)	 AG	168799-168969	TG	AGT
-recovered CodingQuarry_transcript_8290-T1, terminal, 168799, 168969
Valid prediction for pasa_asmbl_7124.p1
Valid prediction for snap_scaffold_11-snap.2811-T1
Valid prediction for GlimmerHMM_glimmerT_28160-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 57815, rend_intergenic: 53381  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61080, rend_intergenic: 58751  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64473, rend_intergenic: 61371  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76364, rend_intergenic: 64529  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97005, rend_intergenic: 92162  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102144, rend_intergenic: 97762  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106129, rend_intergenic: 102987  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131499, rend_intergenic: 125438  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145798, rend_intergenic: 143128  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170133, rend_intergenic: 161000  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171880, rend_intergenic: 171087  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175976, rend_intergenic: 173839  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179357, rend_intergenic: 178856  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181560, rend_intergenic: 179369  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186765, rend_intergenic: 182919  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190732, rend_intergenic: 189692  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 192767
-exon list size: 349


building trellis

0.3    
0.6    
0.9    
1.1    
1.4    
1.7    
2.0    
2.3    
2.6    
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3.4    
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5.7    
6.0    
6.3    
6.6    
6.8    
7.1    
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7.7    
8.0    
8.3    
8.5    
8.8    
9.1    
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10.0    
10.3    
10.5    
10.8    
11.1    
11.4    
11.7    
12.0    
12.3    
12.5    
12.8    
13.1    
13.4    
13.7    
14.0    
14.2    
14.5    
14.8    
15.1    
15.4    
15.7    
16.0    
16.2    
16.5    
16.8    
17.1    
17.4    
17.7    
17.9    
18.2    
18.5    
18.8    
19.1    
19.4    
19.7    
19.9    
20.2    
20.5    
20.8    
21.1    
21.4    
21.7    
21.9    
22.2    
22.5    
22.8    
23.1    
23.4    
23.6    
23.9    
24.2    
24.5    
24.8    
25.1    
25.4    
25.6    
25.9    
26.2    
26.5    
26.8    
27.1    
27.4    
27.6    
27.9    
28.2    
28.5    
28.8    
29.1    
29.3    
29.6    
29.9    
30.2    
30.5    
30.8    
31.1    
31.3    
31.6    
31.9    
32.2    
32.5    
32.8    
33.0    
33.3    
33.6    
33.9    
34.2    
34.5    
34.8    
35.0    
35.3    
35.6    
35.9    
36.2    
36.5    
36.8    
37.0    
37.3    
37.6    
37.9    
38.2    
38.5    
38.7    
39.0    
39.3    
39.6    
39.9    
40.2    
40.5    
40.7    
41.0    
41.3    
41.6    
41.9    
42.2    
42.5    
42.7    
43.0    
43.3    
43.6    
43.9    
44.2    
44.4    
44.7    
45.0    
45.3    
45.6    
45.9    
46.2    
46.4    
46.7    
47.0    
47.3    
47.6    
47.9    
48.1    
48.4    
48.7    
49.0    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
51.0    
51.3    
51.6    
51.9    
52.1    
52.4    
52.7    
53.0    
53.3    
53.6    
53.8    
54.1    
54.4    
54.7    
55.0    
55.3    
55.6    
55.8    
56.1    
56.4    
56.7    
57.0    
57.3    
57.5    
57.8    
58.1    
58.4    
58.7    
59.0    
59.3    
59.5    
59.8    
60.1    
60.4    
60.7    
61.0    
61.3    
61.5    
61.8    
62.1    
62.4    
62.7    
63.0    
63.2    
63.5    
63.8    
64.1    
64.4    
64.7    
65.0    
65.2    
65.5    
65.8    
66.1    
66.4    
66.7    
67.0    
67.2    
67.5    
67.8    
68.1    
68.4    
68.7    
68.9    
69.2    
69.5    
69.8    
70.1    
70.4    
70.7    
70.9    
71.2    
71.5    
71.8    
72.1    
72.4    
72.6    
72.9    
73.2    
73.5    
73.8    
74.1    
74.4    
74.6    
74.9    
75.2    
75.5    
75.8    
76.1    
76.4    
76.6    
76.9    
77.2    
77.5    
77.8    
78.1    
78.3    
78.6    
78.9    
79.2    
79.5    
79.8    
80.1    
80.3    
80.6    
80.9    
81.2    
81.5    
81.8    
82.1    
82.3    
82.6    
82.9    
83.2    
83.5    
83.8    
84.0    
84.3    
84.6    
84.9    
85.2    
85.5    
85.8    
86.0    
86.3    
86.6    
86.9    
87.2    
87.5    
87.7    
88.0    
88.3    
88.6    
88.9    
89.2    
89.5    
89.7    
90.0    
90.3    
90.6    
90.9    
91.2    
91.5    
91.7    
92.0    
92.3    
92.6    
92.9    
93.2    
93.4    
93.7    
94.0    
94.3    
94.6    
94.9    
95.2    
95.4    
95.7    
96.0    
96.3    
96.6    
96.9    
97.2    
97.4    
97.7    
98.0    
98.3    
98.6    
98.9    
99.1    
99.4    
99.7    
-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 57815, rend_intergenic: 53381  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61080, rend_intergenic: 58751  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64473, rend_intergenic: 61371  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76364, rend_intergenic: 64529  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97005, rend_intergenic: 92162  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102144, rend_intergenic: 97762  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106129, rend_intergenic: 102987  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131499, rend_intergenic: 125438  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145798, rend_intergenic: 143128  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170133, rend_intergenic: 161000  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171880, rend_intergenic: 171087  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175976, rend_intergenic: 173839  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179357, rend_intergenic: 178856  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181560, rend_intergenic: 179369  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186765, rend_intergenic: 182919  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190732, rend_intergenic: 189692  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 10566
-exon list size: 6


building trellis

12.5    
25.0    
37.5    
50.0    
62.5    
75.0    
87.5    
-found 1 predictions from path traversal

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