-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_14839840-15069492

-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.12966_t
Valid prediction for Augustus_model.g5300.t1
Valid prediction for snap_scaffold_3-snap.2868-T1
Valid prediction for snap_scaffold_3-snap.2836-T1
Valid prediction for snap_scaffold_3-snap.2847-T1
Valid prediction for snap_scaffold_3-snap.2839-T1
Valid prediction for GeneMark_model.12970_t
Valid prediction for snap_scaffold_3-snap.2857-T1
Couldn't classify 208734, 208880
Couldn't classify 214242, 214309
Sorry, prediction pasa_asmbl_40524.p1 fails validation.
(GAA)	 TA	208734-208880	GT	AGG
(GGC)	 AG	211098-211245	GT	AGG
(CCA)	 AG	213309-213452	GT	TGG
(ACT)	 AG	214242-214309	GG	AAG
-recovered pasa_asmbl_40524.p1, internal, 211098, 211245
-recovered pasa_asmbl_40524.p1, internal, 213309, 213452
Valid prediction for snap_scaffold_3-snap.2854-T1
Couldn't classify 71328, 71484
Sorry, prediction pasa_asmbl_40817.p1 fails validation.
(TCC)	 GT	71328-71484	GT	AGG
(GTG)	 AG	71696-71877	GC	GAG
-recovered pasa_asmbl_40817.p1, terminal, 71696, 71877
-recovered pasa_asmbl_40817.p1, internal, 71696, 71877
Valid prediction for GlimmerHMM_glimmerT_7981-T1
Valid prediction for GeneMark_model.12973_t
Valid prediction for Augustus_model.g5303.t1
Valid prediction for GlimmerHMM_glimmerT_7982-T1
Valid prediction for GlimmerHMM_glimmerT_7980-T1
Valid prediction for snap_scaffold_3-snap.2828-T1
Valid prediction for GlimmerHMM_glimmerT_7964-T1
Valid prediction for GeneMark_model.12979_t
Valid prediction for GeneMark_model.12985_t
Valid prediction for snap_scaffold_3-snap.2850-T1
Valid prediction for snap_scaffold_3-snap.2867-T1
Valid prediction for GeneMark_model.12984_t
Valid prediction for GlimmerHMM_glimmerT_7965-T1
Valid prediction for snap_scaffold_3-snap.2827-T1
Valid prediction for snap_scaffold_3-snap.2852-T1
Valid prediction for GeneMark_model.12990_t
Valid prediction for GeneMark_model.12981_t
Valid prediction for GeneMark_model.12951_t
Valid prediction for GlimmerHMM_glimmerT_7961-T1
Valid prediction for GlimmerHMM_glimmerT_7967-T1
Valid prediction for snap_scaffold_3-snap.2830-T1
Valid prediction for snap_scaffold_3-snap.2848-T1
Valid prediction for snap_scaffold_3-snap.2845-T1
Couldn't classify 192292, 192420
Couldn't classify 193103, 193203
Sorry, prediction pasa_asmbl_40819.p1 fails validation.
(GTC)	 CA	192292-192420	GT	AGG
(GAG)	 AG	192659-192794	GT	ACG
(CGA)	 AG	193103-193203	CA	GCC
-recovered pasa_asmbl_40819.p1, internal, 192659, 192794
Valid prediction for GeneMark_model.12955_t
Valid prediction for GlimmerHMM_glimmerT_7972-T1
Valid prediction for GeneMark_model.12952_t
Valid prediction for snap_scaffold_3-snap.2841-T1
Valid prediction for CodingQuarry_transcript_46274-T1
Valid prediction for GeneMark_model.12976_t
Valid prediction for Augustus_model.g5299.t1
Valid prediction for GeneMark_model.12992_t
Valid prediction for snap_scaffold_3-snap.2855-T1
Valid prediction for snap_scaffold_3-snap.2837-T1
Valid prediction for GeneMark_model.12957_t
Valid prediction for GeneMark_model.12968_t
Valid prediction for GlimmerHMM_glimmerT_7970-T1
Valid prediction for Augustus_model.g5295.t1
Valid prediction for GlimmerHMM_glimmerT_7969-T1
Valid prediction for Augustus_model.g5297.t1
Valid prediction for GlimmerHMM_glimmerT_7975-T1
Valid prediction for snap_scaffold_3-snap.2859-T1
Valid prediction for Augustus_model.g5294.t1
Valid prediction for GeneMark_model.12995_t
Valid prediction for GlimmerHMM_glimmerT_7984-T1
Valid prediction for snap_scaffold_3-snap.2831-T1
Valid prediction for snap_scaffold_3-snap.2843-T1
Valid prediction for GlimmerHMM_glimmerT_7977-T1
Valid prediction for GeneMark_model.12978_t
Valid prediction for GeneMark_model.12961_t
Valid prediction for snap_scaffold_3-snap.2851-T1
Valid prediction for GeneMark_model.12954_t
Valid prediction for snap_scaffold_3-snap.2835-T1
Valid prediction for GlimmerHMM_glimmerT_7974-T1
Valid prediction for GeneMark_model.12964_t
Valid prediction for GeneMark_model.12959_t
Valid prediction for Augustus_model.g5301.t1
Valid prediction for Augustus_model.g5298.t1
Valid prediction for snap_scaffold_3-snap.2832-T1
Valid prediction for snap_scaffold_3-snap.2866-T1
Valid prediction for GeneMark_model.12974_t
Valid prediction for Augustus_model.g5293.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_3-snap.2834-T1
Valid prediction for Augustus_model.g5302.t1
Valid prediction for GlimmerHMM_glimmerT_7976-T1
Valid prediction for GlimmerHMM_glimmerT_7973-T1
Valid prediction for pasa_asmbl_39381.p1
Valid prediction for snap_scaffold_3-snap.2856-T1
Valid prediction for snap_scaffold_3-snap.2869-T1
Valid prediction for snap_scaffold_3-snap.2862-T1
Valid prediction for GeneMark_model.12994_t
Valid prediction for GeneMark_model.12983_t
Valid prediction for snap_scaffold_3-snap.2844-T1
Valid prediction for snap_scaffold_3-snap.2864-T1
Valid prediction for GeneMark_model.12971_t
Valid prediction for GlimmerHMM_glimmerT_7963-T1
Valid prediction for snap_scaffold_3-snap.2849-T1
Valid prediction for GeneMark_model.12967_t
Valid prediction for snap_scaffold_3-snap.2863-T1
Valid prediction for GlimmerHMM_glimmerT_7983-T1
Valid prediction for snap_scaffold_3-snap.2833-T1
Valid prediction for GeneMark_model.12963_t
Valid prediction for snap_scaffold_3-snap.2846-T1
Valid prediction for GeneMark_model.12980_t
Valid prediction for HiQ_model.g5296.t1
Valid prediction for snap_scaffold_3-snap.2840-T1
Valid prediction for snap_scaffold_3-snap.2865-T1
Valid prediction for snap_scaffold_3-snap.2838-T1
Valid prediction for GeneMark_model.12965_t
Valid prediction for GeneMark_model.12953_t
Valid prediction for GeneMark_model.12982_t
Valid prediction for GlimmerHMM_glimmerT_7966-T1
Valid prediction for GeneMark_model.12986_t
Valid prediction for GeneMark_model.12956_t
Valid prediction for CodingQuarry_transcript_46277-T1
Valid prediction for snap_scaffold_3-snap.2829-T1
Valid prediction for GeneMark_model.12993_t
Valid prediction for GlimmerHMM_glimmerT_7971-T1
Valid prediction for GlimmerHMM_glimmerT_7979-T1
Valid prediction for GeneMark_model.12958_t
Valid prediction for GeneMark_model.12969_t
Valid prediction for snap_scaffold_3-snap.2860-T1
Valid prediction for snap_scaffold_3-snap.2853-T1
Valid prediction for GeneMark_model.12987_t
Valid prediction for GlimmerHMM_glimmerT_7968-T1
Valid prediction for GeneMark_model.12962_t
Valid prediction for GlimmerHMM_glimmerT_7962-T1
Valid prediction for GeneMark_model.12996_t
Valid prediction for GeneMark_model.12997_t
Valid prediction for snap_scaffold_3-snap.2858-T1
Valid prediction for snap_scaffold_3-snap.2861-T1
Valid prediction for GeneMark_model.12989_t
Valid prediction for GeneMark_model.12991_t
Valid prediction for snap_scaffold_3-snap.2842-T1
Valid prediction for GeneMark_model.12960_t
Valid prediction for GeneMark_model.12975_t
Valid prediction for GeneMark_model.12988_t
Valid prediction for GeneMark_model.12977_t
Valid prediction for GlimmerHMM_glimmerT_7978-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15036, rend_intergenic: 12458  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32686, rend_intergenic: 26434  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37917, rend_intergenic: 33038  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49217, rend_intergenic: 47526  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52265, rend_intergenic: 50498  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56846, rend_intergenic: 52872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62252, rend_intergenic: 60860  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63758, rend_intergenic: 62495  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70108, rend_intergenic: 63935  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157344, rend_intergenic: 154617  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171884, rend_intergenic: 171726  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179350, rend_intergenic: 173968  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 208855, rend_intergenic: 207096  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 229653
-exon list size: 554


building trellis

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28.8    
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30.8    
30.9    
31.1    
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31.7    
31.8    
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32.2    
32.4    
32.6    
32.7    
32.9    
33.1    
33.3    
33.5    
33.6    
33.8    
34.0    
34.2    
34.4    
34.5    
34.7    
34.9    
35.1    
35.3    
35.4    
35.6    
35.8    
36.0    
36.2    
36.3    
36.5    
36.7    
36.9    
37.1    
37.2    
37.4    
37.6    
37.8    
37.9    
38.1    
38.3    
38.5    
38.7    
38.8    
39.0    
39.2    
39.4    
39.6    
39.7    
39.9    
40.1    
40.3    
40.5    
40.6    
40.8    
41.0    
41.2    
41.4    
41.5    
41.7    
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42.1    
42.3    
42.4    
42.6    
42.8    
43.0    
43.2    
43.3    
43.5    
43.7    
43.9    
44.1    
44.2    
44.4    
44.6    
44.8    
45.0    
45.1    
45.3    
45.5    
45.7    
45.9    
46.0    
46.2    
46.4    
46.6    
46.8    
46.9    
47.1    
47.3    
47.5    
47.7    
47.8    
48.0    
48.2    
48.4    
48.6    
48.7    
48.9    
49.1    
49.3    
49.5    
49.6    
49.8    
50.0    
50.2    
50.4    
50.5    
50.7    
50.9    
51.1    
51.3    
51.4    
51.6    
51.8    
52.0    
52.2    
52.3    
52.5    
52.7    
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53.1    
53.2    
53.4    
53.6    
53.8    
54.0    
54.1    
54.3    
54.5    
54.7    
54.9    
55.0    
55.2    
55.4    
55.6    
55.8    
55.9    
56.1    
56.3    
56.5    
56.7    
56.8    
57.0    
57.2    
57.4    
57.6    
57.7    
57.9    
58.1    
58.3    
58.5    
58.6    
58.8    
59.0    
59.2    
59.4    
59.5    
59.7    
59.9    
60.1    
60.3    
60.4    
60.6    
60.8    
61.0    
61.2    
61.3    
61.5    
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62.1    
62.2    
62.4    
62.6    
62.8    
62.9    
63.1    
63.3    
63.5    
63.7    
63.8    
64.0    
64.2    
64.4    
64.6    
64.7    
64.9    
65.1    
65.3    
65.5    
65.6    
65.8    
66.0    
66.2    
66.4    
66.5    
66.7    
66.9    
67.1    
67.3    
67.4    
67.6    
67.8    
68.0    
68.2    
68.3    
68.5    
68.7    
68.9    
69.1    
69.2    
69.4    
69.6    
69.8    
70.0    
70.1    
70.3    
70.5    
70.7    
70.9    
71.0    
71.2    
71.4    
71.6    
71.8    
71.9    
72.1    
72.3    
72.5    
72.7    
72.8    
73.0    
73.2    
73.4    
73.6    
73.7    
73.9    
74.1    
74.3    
74.5    
74.6    
74.8    
75.0    
75.2    
75.4    
75.5    
75.7    
75.9    
76.1    
76.3    
76.4    
76.6    
76.8    
77.0    
77.2    
77.3    
77.5    
77.7    
77.9    
78.1    
78.2    
78.4    
78.6    
78.8    
79.0    
79.1    
79.3    
79.5    
79.7    
79.9    
80.0    
80.2    
80.4    
80.6    
80.8    
80.9    
81.1    
81.3    
81.5    
81.7    
81.8    
82.0    
82.2    
82.4    
82.6    
82.7    
82.9    
83.1    
83.3    
83.5    
83.6    
83.8    
84.0    
84.2    
84.4    
84.5    
84.7    
84.9    
85.1    
85.3    
85.4    
85.6    
85.8    
86.0    
86.2    
86.3    
86.5    
86.7    
86.9    
87.1    
87.2    
87.4    
87.6    
87.8    
87.9    
88.1    
88.3    
88.5    
88.7    
88.8    
89.0    
89.2    
89.4    
89.6    
89.7    
89.9    
90.1    
90.3    
90.5    
90.6    
90.8    
91.0    
91.2    
91.4    
91.5    
91.7    
91.9    
92.1    
92.3    
92.4    
92.6    
92.8    
93.0    
93.2    
93.3    
93.5    
93.7    
93.9    
94.1    
94.2    
94.4    
94.6    
94.8    
95.0    
95.1    
95.3    
95.5    
95.7    
95.9    
96.0    
96.2    
96.4    
96.6    
96.8    
96.9    
97.1    
97.3    
97.5    
97.7    
97.8    
98.0    
98.2    
98.4    
98.6    
98.7    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 15036, rend_intergenic: 12458  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32686, rend_intergenic: 26434  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37917, rend_intergenic: 33038  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49217, rend_intergenic: 47526  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52265, rend_intergenic: 50498  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56846, rend_intergenic: 52872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62252, rend_intergenic: 60860  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63758, rend_intergenic: 62495  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70108, rend_intergenic: 63935  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157344, rend_intergenic: 154617  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171884, rend_intergenic: 171726  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179350, rend_intergenic: 173968  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 208855, rend_intergenic: 207096  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support