-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_21/scaffold_21_4686444-4907744

-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_47583-T1
Valid prediction for Augustus_model.g31731.t1
Valid prediction for CodingQuarry_transcript_32504-T1
Valid prediction for Augustus_model.g31724.t1
Valid prediction for snap_scaffold_21-snap.943-T1
Valid prediction for GlimmerHMM_glimmerT_47589-T1
Valid prediction for snap_scaffold_21-snap.924-T1
Valid prediction for CodingQuarry_transcript_32506-T1
Valid prediction for GlimmerHMM_glimmerT_47587-T1
Valid prediction for Augustus_model.g31711.t1
Valid prediction for snap_scaffold_21-snap.947-T1
Valid prediction for GlimmerHMM_glimmerT_47579-T1
Valid prediction for snap_scaffold_21-snap.935-T1
Valid prediction for Augustus_model.g31709.t1
Valid prediction for pasa_asmbl_28530.p1
Valid prediction for HiQ_model.g31707.t1
Valid prediction for snap_scaffold_21-snap.944-T1
Valid prediction for Augustus_model.g31720.t1
Valid prediction for snap_scaffold_21-snap.957-T1
Valid prediction for GlimmerHMM_glimmerT_47595-T1
Valid prediction for Augustus_model.g31729.t1
Valid prediction for GlimmerHMM_glimmerT_47592-T1
Valid prediction for GlimmerHMM_glimmerT_47593-T1
Valid prediction for GlimmerHMM_glimmerT_47597-T1
Valid prediction for Augustus_model.g31721.t1
Valid prediction for snap_scaffold_21-snap.950-T1
Valid prediction for snap_scaffold_21-snap.936-T1
Valid prediction for Augustus_model.g31714.t1
Valid prediction for Augustus_model.g31725.t1
Valid prediction for snap_scaffold_21-snap.937-T1
Valid prediction for GlimmerHMM_glimmerT_47601-T1
Valid prediction for snap_scaffold_21-snap.929-T1
Valid prediction for pasa_asmbl_28532.p1
Couldn't classify 132576, 133415
Sorry, prediction pasa_asmbl_28537.p1 fails validation.
(GAT)	 GT	132576-133415	GG	AAG
Valid prediction for GlimmerHMM_glimmerT_47586-T1
Valid prediction for snap_scaffold_21-snap.932-T1
Valid prediction for snap_scaffold_21-snap.958-T1
Valid prediction for snap_scaffold_21-snap.933-T1
Valid prediction for snap_scaffold_21-snap.934-T1
Valid prediction for GlimmerHMM_glimmerT_47599-T1
Couldn't classify 89472, 89506
Couldn't classify 95013, 95179
Sorry, prediction pasa_asmbl_28535.p1 fails validation.
(TTA)	 CG	89472-89506	GT	AGG
(AGA)	 AG	91802-91889	GT	TGG
(GCC)	 AG	92274-92334	GT	AGG
(CCA)	 AG	95013-95179	TA	AGT
-recovered pasa_asmbl_28535.p1, internal, 91802, 91889
-recovered pasa_asmbl_28535.p1, internal, 92274, 92334
Valid prediction for CodingQuarry_transcript_32505-T1
Valid prediction for snap_scaffold_21-snap.926-T1
Valid prediction for Augustus_model.g31716.t1
Valid prediction for Augustus_model.g31719.t1
Couldn't classify 71357, 71410
Sorry, prediction pasa_asmbl_28534.p1 fails validation.
(ATG)	 GG	66012-66116	GT	AGG
(AGG)	 AG	68555-68672	GT	AGG
(GCT)	 AG	69334-69368	GT	TGG
(AAT)	 AG	70904-71065	GT	AGG
(ATC)	 AG	71175-71249	GT	AGG
(GAC)	 AG	71357-71410	AG	TCA
-recovered pasa_asmbl_28534.p1, initial, 66012, 66116
-recovered pasa_asmbl_28534.p1, internal, 68555, 68672
-recovered pasa_asmbl_28534.p1, internal, 69334, 69368
-recovered pasa_asmbl_28534.p1, internal, 70904, 71065
-recovered pasa_asmbl_28534.p1, internal, 71175, 71249
Valid prediction for snap_scaffold_21-snap.928-T1
Valid prediction for snap_scaffold_21-snap.945-T1
Valid prediction for GlimmerHMM_glimmerT_47582-T1
Valid prediction for GlimmerHMM_glimmerT_47588-T1
Valid prediction for snap_scaffold_21-snap.949-T1
Valid prediction for GlimmerHMM_glimmerT_47584-T1
Valid prediction for Augustus_model.g31730.t1
Valid prediction for snap_scaffold_21-snap.955-T1
Valid prediction for snap_scaffold_21-snap.940-T1
Valid prediction for Augustus_model.g31712.t1
Valid prediction for snap_scaffold_21-snap.938-T1
Valid prediction for Augustus_model.g31726.t1
Valid prediction for GlimmerHMM_glimmerT_47577-T1
Valid prediction for Augustus_model.g31717.t1
Valid prediction for GlimmerHMM_glimmerT_47600-T1
Valid prediction for Augustus_model.g31728.t1
Valid prediction for snap_scaffold_21-snap.956-T1
Valid prediction for snap_scaffold_21-snap.946-T1
Valid prediction for HiQ_model.g31713.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_47596-T1
Valid prediction for GlimmerHMM_glimmerT_47581-T1
Valid prediction for snap_scaffold_21-snap.969-T1
Valid prediction for snap_scaffold_21-snap.961-T1
Valid prediction for Augustus_model.g31715.t1
Valid prediction for snap_scaffold_21-snap.968-T1
Valid prediction for snap_scaffold_21-snap.925-T1
Valid prediction for GlimmerHMM_glimmerT_47580-T1
Valid prediction for snap_scaffold_21-snap.964-T1
Valid prediction for Augustus_model.g31735.t1
Valid prediction for GlimmerHMM_glimmerT_47585-T1
Valid prediction for snap_scaffold_21-snap.953-T1
Valid prediction for HiQ_model.g31732.t1
Valid prediction for CodingQuarry_transcript_32508-T1
Valid prediction for HiQ_model.g31737.t1
Valid prediction for snap_scaffold_21-snap.930-T1
Valid prediction for snap_scaffold_21-snap.959-T1
Valid prediction for snap_scaffold_21-snap.965-T1
Valid prediction for pasa_asmbl_27592.p1
Couldn't classify 201103, 202566
Sorry, prediction pasa_asmbl_27588.p1 fails validation.
(AAA)	 CG	201103-202566	GA	GGG
Valid prediction for snap_scaffold_21-snap.963-T1
Valid prediction for snap_scaffold_21-snap.966-T1
Couldn't classify 17393, 17641
Couldn't classify 18067, 18320
Sorry, prediction pasa_asmbl_27596.p1 fails validation.
(CAA)	 CC	17393-17641	GT	ATG
(GTT)	 AG	17892-17952	GT	TGG
(AAC)	 AG	18067-18320	CA	TGC
-recovered pasa_asmbl_27596.p1, internal, 17892, 17952
Valid prediction for GlimmerHMM_glimmerT_47604-T1
Valid prediction for GlimmerHMM_glimmerT_47602-T1
Valid prediction for GlimmerHMM_glimmerT_47594-T1
Valid prediction for snap_scaffold_21-snap.939-T1
Valid prediction for GlimmerHMM_glimmerT_47607-T1
Valid prediction for snap_scaffold_21-snap.942-T1
Valid prediction for GlimmerHMM_glimmerT_47590-T1
Valid prediction for snap_scaffold_21-snap.952-T1
Valid prediction for CodingQuarry_transcript_32510-T1
Valid prediction for Augustus_model.g31718.t1
Valid prediction for GlimmerHMM_glimmerT_47576-T1
Valid prediction for Augustus_model.g31723.t1
Valid prediction for Augustus_model.g31734.t1
Valid prediction for snap_scaffold_21-snap.941-T1
Valid prediction for GlimmerHMM_glimmerT_47591-T1
Valid prediction for Augustus_model.g31708.t1
Valid prediction for snap_scaffold_21-snap.962-T1
Couldn't classify 202952, 203341
Sorry, prediction pasa_asmbl_27587.p1 fails validation.
(AGA)	 CA	202952-203341	AT	GAA
Valid prediction for Augustus_model.g31706.t1
Couldn't classify 212098, 212178
Sorry, prediction pasa_asmbl_27586.p1 fails validation.
(ATG)	 GG	207798-208082	GT	TGG
(GAT)	 AG	208388-208483	GT	AGG
(ACT)	 AG	209582-209701	GT	AGG
(CTG)	 AG	211546-211647	GT	AGG
(GAA)	 AG	211768-211884	GT	AGG
(GAG)	 AG	212098-212178	AC	TCA
-recovered pasa_asmbl_27586.p1, initial, 207798, 208082
-recovered pasa_asmbl_27586.p1, internal, 208388, 208483
-recovered pasa_asmbl_27586.p1, internal, 209582, 209701
-recovered pasa_asmbl_27586.p1, internal, 211546, 211647
-recovered pasa_asmbl_27586.p1, internal, 211768, 211884
Couldn't classify 21035, 21604
Sorry, prediction pasa_asmbl_27595.p1 fails validation.
(ATT)	 CC	21035-21604	AG	GGA
Valid prediction for snap_scaffold_21-snap.954-T1
Valid prediction for pasa_asmbl_27597.p1
Valid prediction for snap_scaffold_21-snap.931-T1
Couldn't classify 47589, 47655
Sorry, prediction pasa_asmbl_27591.p1 fails validation.
(ATG)	 CC	41689-41771	GT	CTG
(GGC)	 AG	42949-43193	GT	AGG
(GCA)	 AG	44466-44743	GT	AGG
(GCC)	 AG	44921-45213	GT	AGG
(GCA)	 AG	47589-47655	CC	ACC
-recovered pasa_asmbl_27591.p1, initial, 41689, 41771
-recovered pasa_asmbl_27591.p1, internal, 42949, 43193
-recovered pasa_asmbl_27591.p1, internal, 44466, 44743
-recovered pasa_asmbl_27591.p1, internal, 44921, 45213
Valid prediction for Augustus_model.g31733.t1
Valid prediction for GlimmerHMM_glimmerT_47606-T1
Valid prediction for CodingQuarry_transcript_32509-T1
Valid prediction for GlimmerHMM_glimmerT_47608-T1
Valid prediction for snap_scaffold_21-snap.948-T1
Valid prediction for GlimmerHMM_glimmerT_47578-T1
Valid prediction for HiQ_model.g31736.t1
Valid prediction for Augustus_model.g31727.t1
Valid prediction for GlimmerHMM_glimmerT_47603-T1
Valid prediction for pasa_asmbl_27599.p1
Valid prediction for GlimmerHMM_glimmerT_47598-T1
Couldn't classify 28846, 29322
Sorry, prediction pasa_asmbl_27593.p2 fails validation.
(GAT)	 CT	28846-29322	GC	GGG
Valid prediction for Augustus_model.g31710.t1
Couldn't classify 213955, 214026
Couldn't classify 215905, 216083
Sorry, prediction pasa_asmbl_27585.p1 fails validation.
(AAG)	 AA	213955-214026	GT	AGG
(TTT)	 AG	214161-214329	GT	AGG
(AAT)	 AG	214453-214694	GT	AGG
(ACT)	 AG	214793-215072	GT	AGG
(GCA)	 AG	215905-216083	AA	GCA
add_exon() Sorry, pasa_asmbl_27585.p1 214161-214329-terminal-3 is invalid.
-recovered pasa_asmbl_27585.p1, terminal, 214161, 214329
-recovered pasa_asmbl_27585.p1, internal, 214161, 214329
-recovered pasa_asmbl_27585.p1, internal, 214453, 214694
-recovered pasa_asmbl_27585.p1, internal, 214793, 215072
Valid prediction for snap_scaffold_21-snap.951-T1
Valid prediction for snap_scaffold_21-snap.927-T1
Valid prediction for snap_scaffold_21-snap.960-T1
Valid prediction for GlimmerHMM_glimmerT_47605-T1
Valid prediction for CodingQuarry_transcript_32503-T1
Valid prediction for snap_scaffold_21-snap.967-T1
Valid prediction for Augustus_model.g31722.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 82701, rend_intergenic: 80116  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87082, rend_intergenic: 82764  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94225, rend_intergenic: 87662  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101197, rend_intergenic: 99907  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127336, rend_intergenic: 124827  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129740, rend_intergenic: 128482  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151043, rend_intergenic: 147769  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 221301
-exon list size: 420


building trellis

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14.0    
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14.5    
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14.9    
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15.6    
15.9    
16.1    
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16.6    
16.8    
17.1    
17.3    
17.5    
17.8    
18.0    
18.2    
18.5    
18.7    
19.0    
19.2    
19.4    
19.7    
19.9    
20.1    
20.4    
20.6    
20.9    
21.1    
21.3    
21.6    
21.8    
22.0    
22.3    
22.5    
22.7    
23.0    
23.2    
23.5    
23.7    
23.9    
24.2    
24.4    
24.6    
24.9    
25.1    
25.4    
25.6    
25.8    
26.1    
26.3    
26.5    
26.8    
27.0    
27.3    
27.5    
27.7    
28.0    
28.2    
28.4    
28.7    
28.9    
29.1    
29.4    
29.6    
29.9    
30.1    
30.3    
30.6    
30.8    
31.0    
31.3    
31.5    
31.8    
32.0    
32.2    
32.5    
32.7    
32.9    
33.2    
33.4    
33.6    
33.9    
34.1    
34.4    
34.6    
34.8    
35.1    
35.3    
35.5    
35.8    
36.0    
36.3    
36.5    
36.7    
37.0    
37.2    
37.4    
37.7    
37.9    
38.2    
38.4    
38.6    
38.9    
39.1    
39.3    
39.6    
39.8    
40.0    
40.3    
40.5    
40.8    
41.0    
41.2    
41.5    
41.7    
41.9    
42.2    
42.4    
42.7    
42.9    
43.1    
43.4    
43.6    
43.8    
44.1    
44.3    
44.5    
44.8    
45.0    
45.3    
45.5    
45.7    
46.0    
46.2    
46.4    
46.7    
46.9    
47.2    
47.4    
47.6    
47.9    
48.1    
48.3    
48.6    
48.8    
49.1    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
50.7    
50.9    
51.2    
51.4    
51.7    
51.9    
52.1    
52.4    
52.6    
52.8    
53.1    
53.3    
53.6    
53.8    
54.0    
54.3    
54.5    
54.7    
55.0    
55.2    
55.5    
55.7    
55.9    
56.2    
56.4    
56.6    
56.9    
57.1    
57.3    
57.6    
57.8    
58.1    
58.3    
58.5    
58.8    
59.0    
59.2    
59.5    
59.7    
60.0    
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60.9    
61.1    
61.4    
61.6    
61.8    
62.1    
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63.0    
63.3    
63.5    
63.7    
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64.2    
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65.6    
65.9    
66.1    
66.4    
66.6    
66.8    
67.1    
67.3    
67.5    
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68.0    
68.2    
68.5    
68.7    
69.0    
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69.9    
70.1    
70.4    
70.6    
70.9    
71.1    
71.3    
71.6    
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72.3    
72.5    
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73.0    
73.2    
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73.7    
73.9    
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74.6    
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75.1    
75.4    
75.6    
75.8    
76.1    
76.3    
76.5    
76.8    
77.0    
77.3    
77.5    
77.7    
78.0    
78.2    
78.4    
78.7    
78.9    
79.1    
79.4    
79.6    
79.9    
80.1    
80.3    
80.6    
80.8    
81.0    
81.3    
81.5    
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82.0    
82.2    
82.5    
82.7    
82.9    
83.2    
83.4    
83.6    
83.9    
84.1    
84.4    
84.6    
84.8    
85.1    
85.3    
85.5    
85.8    
86.0    
86.3    
86.5    
86.7    
87.0    
87.2    
87.4    
87.7    
87.9    
88.2    
88.4    
88.6    
88.9    
89.1    
89.3    
89.6    
89.8    
90.0    
90.3    
90.5    
90.8    
91.0    
91.2    
91.5    
91.7    
91.9    
92.2    
92.4    
92.7    
92.9    
93.1    
93.4    
93.6    
93.8    
94.1    
94.3    
94.5    
94.8    
95.0    
95.3    
95.5    
95.7    
96.0    
96.2    
96.4    
96.7    
96.9    
97.2    
97.4    
97.6    
97.9    
98.1    
98.3    
98.6    
98.8    
99.1    
99.3    
99.5    
99.8    
-found 40 predictions from path traversal
Error with prediction: snap lend_intergenic: 82701, rend_intergenic: 80116  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87082, rend_intergenic: 82764  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94225, rend_intergenic: 87662  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101197, rend_intergenic: 99907  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127336, rend_intergenic: 124827  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129740, rend_intergenic: 128482  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151043, rend_intergenic: 147769  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 35 predictions persist after filtering for low support