-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_17/scaffold_17_13138515-13341012

-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_17-snap.2729-T1
Valid prediction for snap_scaffold_17-snap.2726-T1
Valid prediction for Augustus_model.g27547.t1
Valid prediction for snap_scaffold_17-snap.2696-T1
Valid prediction for GlimmerHMM_glimmerT_41337-T1
Valid prediction for Augustus_model.g27545.t1
Valid prediction for snap_scaffold_17-snap.2700-T1
Valid prediction for snap_scaffold_17-snap.2713-T1
Valid prediction for snap_scaffold_17-snap.2716-T1
Valid prediction for snap_scaffold_17-snap.2697-T1
Valid prediction for GlimmerHMM_glimmerT_41326-T1
Valid prediction for snap_scaffold_17-snap.2705-T1
Valid prediction for snap_scaffold_17-snap.2695-T1
Valid prediction for GlimmerHMM_glimmerT_41327-T1
Valid prediction for snap_scaffold_17-snap.2690-T1
Valid prediction for snap_scaffold_17-snap.2728-T1
Valid prediction for snap_scaffold_17-snap.2703-T1
Valid prediction for GlimmerHMM_glimmerT_41336-T1
Valid prediction for pasa_asmbl_19319.p1
Valid prediction for Augustus_model.g27548.t1
Valid prediction for snap_scaffold_17-snap.2714-T1
Valid prediction for snap_scaffold_17-snap.2691-T1
Valid prediction for Augustus_model.g27533.t1
Valid prediction for Augustus_model.g27538.t1
Valid prediction for GlimmerHMM_glimmerT_41324-T1
Valid prediction for Augustus_model.g27542.t1
Valid prediction for snap_scaffold_17-snap.2712-T1
Couldn't classify 176404, 176499
Couldn't classify 186552, 186661
Sorry, prediction pasa_asmbl_19322.p1 fails validation.
(GAA)	 GT	176404-176499	GT	AGG
(GAT)	 AG	177263-177357	GT	AGG
(GCT)	 AG	177700-177798	GT	AGG
(GAC)	 AG	178969-179059	GT	ACG
(GAG)	 AG	181336-181515	GT	GGG
(TAC)	 AG	183074-183192	GT	AGG
(TGC)	 AG	185492-185598	GT	CGG
(GGA)	 AG	186552-186661	CG	GAC
-recovered pasa_asmbl_19322.p1, internal, 177263, 177357
-recovered pasa_asmbl_19322.p1, internal, 177700, 177798
-recovered pasa_asmbl_19322.p1, internal, 178969, 179059
-recovered pasa_asmbl_19322.p1, internal, 181336, 181515
-recovered pasa_asmbl_19322.p1, internal, 183074, 183192
-recovered pasa_asmbl_19322.p1, internal, 185492, 185598
Valid prediction for snap_scaffold_17-snap.2689-T1
Valid prediction for GlimmerHMM_glimmerT_41331-T1
Valid prediction for GlimmerHMM_glimmerT_41338-T1
Valid prediction for GlimmerHMM_glimmerT_41323-T1
Valid prediction for Augustus_model.g27543.t1
Valid prediction for snap_scaffold_17-snap.2717-T1
Valid prediction for Augustus_model.g27544.t1
Valid prediction for GlimmerHMM_glimmerT_41341-T1
Valid prediction for snap_scaffold_17-snap.2707-T1
Valid prediction for GlimmerHMM_glimmerT_41342-T1
Valid prediction for snap_scaffold_17-snap.2709-T1
Valid prediction for snap_scaffold_17-snap.2720-T1
Valid prediction for Augustus_model.g27535.t1
Valid prediction for GlimmerHMM_glimmerT_41339-T1
Valid prediction for GlimmerHMM_glimmerT_41332-T1
Valid prediction for snap_scaffold_17-snap.2688-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_41335-T1
Valid prediction for Augustus_model.g27546.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.2719-T1
Valid prediction for GlimmerHMM_glimmerT_41329-T1
Valid prediction for snap_scaffold_17-snap.2704-T1
Valid prediction for pasa_asmbl_18361.p1
Valid prediction for Augustus_model.g27541.t1
Valid prediction for snap_scaffold_17-snap.2715-T1
Valid prediction for CodingQuarry_transcript_22230-T1
Valid prediction for snap_scaffold_17-snap.2693-T1
Valid prediction for snap_scaffold_17-snap.2722-T1
Valid prediction for snap_scaffold_17-snap.2730-T1
Valid prediction for GlimmerHMM_glimmerT_41333-T1
Valid prediction for CodingQuarry_transcript_22233-T1
Valid prediction for GlimmerHMM_glimmerT_41334-T1
Valid prediction for snap_scaffold_17-snap.2727-T1
Valid prediction for snap_scaffold_17-snap.2724-T1
Valid prediction for snap_scaffold_17-snap.2731-T1
Valid prediction for GlimmerHMM_glimmerT_41328-T1
Valid prediction for HiQ_model.g27537.t1
Valid prediction for CodingQuarry_transcript_22234-T1
Valid prediction for Augustus_model.g27536.t1
Valid prediction for snap_scaffold_17-snap.2708-T1
Valid prediction for snap_scaffold_17-snap.2725-T1
Valid prediction for snap_scaffold_17-snap.2692-T1
Valid prediction for snap_scaffold_17-snap.2699-T1
Valid prediction for GlimmerHMM_glimmerT_41325-T1
Valid prediction for snap_scaffold_17-snap.2711-T1
Valid prediction for Augustus_model.g27539.t1
Valid prediction for CodingQuarry_transcript_22231-T1
Valid prediction for snap_scaffold_17-snap.2718-T1
Valid prediction for Augustus_model.g27549.t1
Valid prediction for snap_scaffold_17-snap.2698-T1
Valid prediction for snap_scaffold_17-snap.2710-T1
Valid prediction for snap_scaffold_17-snap.2702-T1
Valid prediction for snap_scaffold_17-snap.2701-T1
Couldn't classify 150700, 150798
Sorry, prediction pasa_asmbl_18358.p1 fails validation.
(CTC)	 AC	150700-150798	GT	CTG
(GGG)	 AG	151281-151457	GT	AGG
(GTC)	 AG	151907-152053	GT	TGG
(GGC)	 AG	152548-152676	AC	AGA
-recovered pasa_asmbl_18358.p1, terminal, 152548, 152676
-recovered pasa_asmbl_18358.p1, internal, 151281, 151457
-recovered pasa_asmbl_18358.p1, internal, 151907, 152053
Valid prediction for GlimmerHMM_glimmerT_41340-T1
Couldn't classify 172603, 172845
Sorry, prediction pasa_asmbl_18353.p1 fails validation.
(GAG)	 AG	172603-172845	GT	TGG
(GGC)	 AG	173914-174099	GT	CAG
(GAA)	 AG	174540-174673	GT	CTG
(CTA)	 AG	175463-175547	TG	GAT
-recovered pasa_asmbl_18353.p1, terminal, 175463, 175547
-recovered pasa_asmbl_18353.p1, internal, 172603, 172845
-recovered pasa_asmbl_18353.p1, internal, 173914, 174099
-recovered pasa_asmbl_18353.p1, internal, 174540, 174673
Valid prediction for snap_scaffold_17-snap.2694-T1
Valid prediction for CodingQuarry_transcript_22229-T1
Valid prediction for snap_scaffold_17-snap.2706-T1
Valid prediction for snap_scaffold_17-snap.2687-T1
Valid prediction for GlimmerHMM_glimmerT_41330-T1
Valid prediction for CodingQuarry_transcript_22232-T1
Valid prediction for snap_scaffold_17-snap.2723-T1
Couldn't classify 159221, 159400
Couldn't classify 162156, 162265
Sorry, prediction pasa_asmbl_18356.p1 fails validation.
(GGA)	 GT	159221-159400	GT	GGG
(GTA)	 AG	159717-159836	GT	TGG
(CCA)	 AG	160978-161101	GT	GGG
(GGA)	 AG	162156-162265	GT	AGG
-recovered pasa_asmbl_18356.p1, internal, 159717, 159836
-recovered pasa_asmbl_18356.p1, internal, 160978, 161101
-recovered pasa_asmbl_18356.p1, internal, 162156, 162265
Couldn't classify 158553, 158692
Sorry, prediction pasa_asmbl_18357.p1 fails validation.
(ATG)	 CT	157088-157195	GT	AGG
(AAC)	 AG	157456-157602	GT	AGG
(GGA)	 AG	157726-157809	GT	TGG
(GAG)	 AG	158088-158202	GT	AGG
(GAT)	 AG	158553-158692	AA	CCA
-recovered pasa_asmbl_18357.p1, initial, 157088, 157195
add_exon() Sorry, pasa_asmbl_18357.p1 158088-158202-terminal-3 is invalid.
-recovered pasa_asmbl_18357.p1, terminal, 158088, 158202
-recovered pasa_asmbl_18357.p1, internal, 157456, 157602
-recovered pasa_asmbl_18357.p1, internal, 157726, 157809
-recovered pasa_asmbl_18357.p1, internal, 158088, 158202
Valid prediction for snap_scaffold_17-snap.2686-T1
Valid prediction for snap_scaffold_17-snap.2721-T1
Valid prediction for Augustus_model.g27540.t1
Valid prediction for Augustus_model.g27534.t1
Couldn't classify 167219, 167307
Couldn't classify 170359, 170471
Sorry, prediction pasa_asmbl_18355.p1 fails validation.
(CAG)	 CA	167219-167307	GT	GGG
(TGG)	 AG	167856-167988	GT	AGG
(GGA)	 AG	168528-168624	GT	AGG
(GGA)	 AG	168928-169098	GT	GAG
(GTG)	 AG	169640-169794	GT	AGG
(GCC)	 AG	170077-170263	GT	AGG
(GGA)	 AG	170359-170471	GG	GCG
-recovered pasa_asmbl_18355.p1, internal, 167856, 167988
-recovered pasa_asmbl_18355.p1, internal, 168528, 168624
-recovered pasa_asmbl_18355.p1, internal, 168928, 169098
-recovered pasa_asmbl_18355.p1, internal, 169640, 169794
-recovered pasa_asmbl_18355.p1, internal, 170077, 170263

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9203, rend_intergenic: 4603  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22563, rend_intergenic: 19688  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45015, rend_intergenic: 27479  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59513, rend_intergenic: 56477  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64921, rend_intergenic: 64296  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66412, rend_intergenic: 65223  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76562, rend_intergenic: 67205  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95055, rend_intergenic: 82856  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95775, rend_intergenic: 95102  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100677, rend_intergenic: 96174  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123434, rend_intergenic: 118889  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130357, rend_intergenic: 124595  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152251, rend_intergenic: 138739  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153250, rend_intergenic: 153206  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175356, rend_intergenic: 153516  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179938, rend_intergenic: 176454  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196651, rend_intergenic: 185762  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 202498
-exon list size: 383


building trellis

0.3    
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3.4    
3.6    
3.9    
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10.1    
10.4    
10.6    
10.9    
11.2    
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11.7    
11.9    
12.2    
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14.5    
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15.1    
15.3    
15.6    
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16.4    
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16.9    
17.1    
17.4    
17.7    
17.9    
18.2    
18.4    
18.7    
19.0    
19.2    
19.5    
19.7    
20.0    
20.3    
20.5    
20.8    
21.0    
21.3    
21.6    
21.8    
22.1    
22.3    
22.6    
22.9    
23.1    
23.4    
23.6    
23.9    
24.2    
24.4    
24.7    
24.9    
25.2    
25.5    
25.7    
26.0    
26.2    
26.5    
26.8    
27.0    
27.3    
27.5    
27.8    
28.1    
28.3    
28.6    
28.8    
29.1    
29.4    
29.6    
29.9    
30.1    
30.4    
30.6    
30.9    
31.2    
31.4    
31.7    
31.9    
32.2    
32.5    
32.7    
33.0    
33.2    
33.5    
33.8    
34.0    
34.3    
34.5    
34.8    
35.1    
35.3    
35.6    
35.8    
36.1    
36.4    
36.6    
36.9    
37.1    
37.4    
37.7    
37.9    
38.2    
38.4    
38.7    
39.0    
39.2    
39.5    
39.7    
40.0    
40.3    
40.5    
40.8    
41.0    
41.3    
41.6    
41.8    
42.1    
42.3    
42.6    
42.9    
43.1    
43.4    
43.6    
43.9    
44.2    
44.4    
44.7    
44.9    
45.2    
45.5    
45.7    
46.0    
46.2    
46.5    
46.8    
47.0    
47.3    
47.5    
47.8    
48.1    
48.3    
48.6    
48.8    
49.1    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.9    
51.2    
51.4    
51.7    
51.9    
52.2    
52.5    
52.7    
53.0    
53.2    
53.5    
53.8    
54.0    
54.3    
54.5    
54.8    
55.1    
55.3    
55.6    
55.8    
56.1    
56.4    
56.6    
56.9    
57.1    
57.4    
57.7    
57.9    
58.2    
58.4    
58.7    
59.0    
59.2    
59.5    
59.7    
60.0    
60.3    
60.5    
60.8    
61.0    
61.3    
61.6    
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62.1    
62.3    
62.6    
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63.4    
63.6    
63.9    
64.2    
64.4    
64.7    
64.9    
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66.0    
66.2    
66.5    
66.8    
67.0    
67.3    
67.5    
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68.1    
68.3    
68.6    
68.8    
69.1    
69.4    
69.6    
69.9    
70.1    
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70.6    
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71.7    
71.9    
72.2    
72.5    
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73.0    
73.2    
73.5    
73.8    
74.0    
74.3    
74.5    
74.8    
75.1    
75.3    
75.6    
75.8    
76.1    
76.4    
76.6    
76.9    
77.1    
77.4    
77.7    
77.9    
78.2    
78.4    
78.7    
79.0    
79.2    
79.5    
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80.0    
80.3    
80.5    
80.8    
81.0    
81.3    
81.6    
81.8    
82.1    
82.3    
82.6    
82.9    
83.1    
83.4    
83.6    
83.9    
84.2    
84.4    
84.7    
84.9    
85.2    
85.5    
85.7    
86.0    
86.2    
86.5    
86.8    
87.0    
87.3    
87.5    
87.8    
88.1    
88.3    
88.6    
88.8    
89.1    
89.4    
89.6    
89.9    
90.1    
90.4    
90.6    
90.9    
91.2    
91.4    
91.7    
91.9    
92.2    
92.5    
92.7    
93.0    
93.2    
93.5    
93.8    
94.0    
94.3    
94.5    
94.8    
95.1    
95.3    
95.6    
95.8    
96.1    
96.4    
96.6    
96.9    
97.1    
97.4    
97.7    
97.9    
98.2    
98.4    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 9203, rend_intergenic: 4603  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22563, rend_intergenic: 19688  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45015, rend_intergenic: 27479  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59513, rend_intergenic: 56477  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64921, rend_intergenic: 64296  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66412, rend_intergenic: 65223  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76562, rend_intergenic: 67205  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95055, rend_intergenic: 82856  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95775, rend_intergenic: 95102  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100677, rend_intergenic: 96174  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123434, rend_intergenic: 118889  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130357, rend_intergenic: 124595  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152251, rend_intergenic: 138739  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153250, rend_intergenic: 153206  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175356, rend_intergenic: 153516  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179938, rend_intergenic: 176454  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196651, rend_intergenic: 185762  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support