-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_23/scaffold_23_9274867-9454672

-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_23-snap.1802-T1
Valid prediction for GlimmerHMM_glimmerT_51578-T1
Valid prediction for Augustus_model.g34486.t1
Valid prediction for snap_scaffold_23-snap.1792-T1
Couldn't classify 54519, 54553
Sorry, prediction pasa_asmbl_31790.p1 fails validation.
(CAT)	 AG	54519-54553	GT	TGG
(GCA)	 AG	54805-54895	GT	AGG
(GTA)	 AG	57005-57175	GT	AGG
(GTC)	 AG	57849-58023	GT	CGG
(GTG)	 AG	58332-58453	GT	TGG
(ATT)	 AG	58766-58843	GT	AGG
(GTG)	 AG	59060-59120	GT	AGG
(CTG)	 AG	59570-59739	AC	GAA
-recovered pasa_asmbl_31790.p1, terminal, 59570, 59739
-recovered pasa_asmbl_31790.p1, internal, 54519, 54553
-recovered pasa_asmbl_31790.p1, internal, 54805, 54895
-recovered pasa_asmbl_31790.p1, internal, 57005, 57175
-recovered pasa_asmbl_31790.p1, internal, 57849, 58023
-recovered pasa_asmbl_31790.p1, internal, 58332, 58453
-recovered pasa_asmbl_31790.p1, internal, 58766, 58843
-recovered pasa_asmbl_31790.p1, internal, 59060, 59120
Valid prediction for GlimmerHMM_glimmerT_51572-T1
Valid prediction for snap_scaffold_23-snap.1807-T1
Valid prediction for GlimmerHMM_glimmerT_51580-T1
Valid prediction for snap_scaffold_23-snap.1780-T1
Valid prediction for Augustus_model.g34483.t1
Valid prediction for snap_scaffold_23-snap.1809-T1
Valid prediction for GlimmerHMM_glimmerT_51598-T1
Valid prediction for snap_scaffold_23-snap.1786-T1
Valid prediction for snap_scaffold_23-snap.1798-T1
Valid prediction for snap_scaffold_23-snap.1805-T1
Valid prediction for GlimmerHMM_glimmerT_51595-T1
Valid prediction for Augustus_model.g34488.t1
Valid prediction for snap_scaffold_23-snap.1789-T1
Valid prediction for snap_scaffold_23-snap.1797-T1
Valid prediction for GlimmerHMM_glimmerT_51587-T1
Couldn't classify 49687, 49722
Couldn't classify 53598, 53902
Sorry, prediction pasa_asmbl_31957.p1 fails validation.
(TTC)	 TC	49687-49722	GT	TGG
(AAA)	 AG	49903-50064	GT	GTG
(GAG)	 AG	50687-50836	GT	AGG
(GTG)	 AG	51196-51285	GT	AGG
(GTA)	 AG	52756-52888	GT	AGG
(GCA)	 AG	53598-53902	GT	AGG
-recovered pasa_asmbl_31957.p1, internal, 49903, 50064
-recovered pasa_asmbl_31957.p1, internal, 50687, 50836
-recovered pasa_asmbl_31957.p1, internal, 51196, 51285
-recovered pasa_asmbl_31957.p1, internal, 52756, 52888
-recovered pasa_asmbl_31957.p1, internal, 53598, 53902
Valid prediction for GlimmerHMM_glimmerT_51582-T1
Valid prediction for GlimmerHMM_glimmerT_51597-T1
Valid prediction for snap_scaffold_23-snap.1791-T1
Valid prediction for snap_scaffold_23-snap.1800-T1
Valid prediction for GlimmerHMM_glimmerT_51599-T1
Valid prediction for snap_scaffold_23-snap.1808-T1
Valid prediction for GlimmerHMM_glimmerT_51573-T1
Valid prediction for GlimmerHMM_glimmerT_51593-T1
Valid prediction for Augustus_model.g34492.t1
Valid prediction for GlimmerHMM_glimmerT_51581-T1
Valid prediction for snap_scaffold_23-snap.1782-T1
Valid prediction for Augustus_model.g34490.t1
Valid prediction for snap_scaffold_23-snap.1784-T1
Valid prediction for Augustus_model.g34494.t1
Valid prediction for snap_scaffold_23-snap.1796-T1
Valid prediction for snap_scaffold_23-snap.1811-T1
Couldn't classify 147613, 148506
Sorry, prediction pasa_asmbl_31793.p1 fails validation.
(TCC)	 TC	147613-148506	GT	AGG
(GTG)	 AG	148779-148909	GT	AGG
(GTG)	 AG	150034-150122	GT	GGG
(ACC)	 AG	150384-150448	AA	AGA
-recovered pasa_asmbl_31793.p1, terminal, 150384, 150448
-recovered pasa_asmbl_31793.p1, internal, 148779, 148909
-recovered pasa_asmbl_31793.p1, internal, 150034, 150122
Valid prediction for HiQ_model.g34484.t1
Valid prediction for snap_scaffold_23-snap.1803-T1
Valid prediction for snap_scaffold_23-snap.1788-T1
Couldn't classify 145947, 146237
Couldn't classify 146758, 147498
Sorry, prediction pasa_asmbl_31792.p1 fails validation.
(AAC)	 CG	145947-146237	GT	AGG
(GTA)	 AG	146758-147498	AT	AGA
Valid prediction for GlimmerHMM_glimmerT_51577-T1
Valid prediction for GlimmerHMM_glimmerT_51588-T1
Valid prediction for snap_scaffold_23-snap.1812-T1
Valid prediction for GlimmerHMM_glimmerT_51585-T1
Valid prediction for snap_scaffold_23-snap.1794-T1
Valid prediction for GlimmerHMM_glimmerT_51594-T1
Valid prediction for snap_scaffold_23-snap.1817-T1
Valid prediction for GlimmerHMM_glimmerT_51591-T1
Valid prediction for GlimmerHMM_glimmerT_51590-T1
Valid prediction for HiQ_model.g34493.t1
Valid prediction for GlimmerHMM_glimmerT_51596-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_23-snap.1810-T1
Valid prediction for snap_scaffold_23-snap.1790-T1
Valid prediction for GlimmerHMM_glimmerT_51584-T1
Valid prediction for GlimmerHMM_glimmerT_51571-T1
Valid prediction for pasa_asmbl_31234.p1
Valid prediction for snap_scaffold_23-snap.1815-T1
Valid prediction for CodingQuarry_transcript_35770-T1
Valid prediction for snap_scaffold_23-snap.1781-T1
Valid prediction for snap_scaffold_23-snap.1813-T1
Valid prediction for snap_scaffold_23-snap.1799-T1
Valid prediction for snap_scaffold_23-snap.1814-T1
Valid prediction for snap_scaffold_23-snap.1795-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_23-snap.1793-T1
Valid prediction for snap_scaffold_23-snap.1783-T1
Valid prediction for snap_scaffold_23-snap.1816-T1
Valid prediction for GlimmerHMM_glimmerT_51583-T1
Valid prediction for snap_scaffold_23-snap.1779-T1
Valid prediction for Augustus_model.g34491.t1
Valid prediction for GlimmerHMM_glimmerT_51569-T1
Valid prediction for snap_scaffold_23-snap.1804-T1
Valid prediction for GlimmerHMM_glimmerT_51589-T1
Valid prediction for snap_scaffold_23-snap.1801-T1
Valid prediction for GlimmerHMM_glimmerT_51586-T1
Valid prediction for snap_scaffold_23-snap.1787-T1
Valid prediction for GlimmerHMM_glimmerT_51575-T1
Valid prediction for Augustus_model.g34482.t1
Valid prediction for Augustus_model.g34487.t1
Valid prediction for Augustus_model.g34485.t1
Valid prediction for snap_scaffold_23-snap.1778-T1
Valid prediction for snap_scaffold_23-snap.1785-T1
Valid prediction for Augustus_model.g34489.t1
Valid prediction for GlimmerHMM_glimmerT_51576-T1
Valid prediction for GlimmerHMM_glimmerT_51592-T1
Valid prediction for snap_scaffold_23-snap.1806-T1
Valid prediction for GlimmerHMM_glimmerT_51574-T1
Valid prediction for GlimmerHMM_glimmerT_51579-T1
Valid prediction for snap_scaffold_23-snap.1818-T1
Valid prediction for GlimmerHMM_glimmerT_51570-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8738, rend_intergenic: 7027  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13793, rend_intergenic: 11612  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20435, rend_intergenic: 14794  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33000, rend_intergenic: 23681  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34945, rend_intergenic: 33413  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38531, rend_intergenic: 35148  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55837, rend_intergenic: 46495  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57205, rend_intergenic: 56469  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62579, rend_intergenic: 62267  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67343, rend_intergenic: 62826  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86943, rend_intergenic: 79264  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89410, rend_intergenic: 87119  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99092, rend_intergenic: 89625  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120948, rend_intergenic: 111980  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132083, rend_intergenic: 121471  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135832, rend_intergenic: 135200  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137427, rend_intergenic: 136063  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141923, rend_intergenic: 138634  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150448, rend_intergenic: 146710  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172035, rend_intergenic: 158334  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173226, rend_intergenic: 172038  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178570, rend_intergenic: 173311  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 179806
-exon list size: 323


building trellis

0.3    
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2.2    
2.5    
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3.7    
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4.3    
4.6    
4.9    
5.2    
5.5    
5.8    
6.2    
6.5    
6.8    
7.1    
7.4    
7.7    
8.0    
8.3    
8.6    
8.9    
9.2    
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10.5    
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11.1    
11.4    
11.7    
12.0    
12.3    
12.6    
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13.2    
13.5    
13.8    
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14.5    
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15.1    
15.4    
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16.0    
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17.8    
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19.1    
19.4    
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20.0    
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20.6    
20.9    
21.2    
21.5    
21.8    
22.2    
22.5    
22.8    
23.1    
23.4    
23.7    
24.0    
24.3    
24.6    
24.9    
25.2    
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25.8    
26.2    
26.5    
26.8    
27.1    
27.4    
27.7    
28.0    
28.3    
28.6    
28.9    
29.2    
29.5    
29.8    
30.2    
30.5    
30.8    
31.1    
31.4    
31.7    
32.0    
32.3    
32.6    
32.9    
33.2    
33.5    
33.8    
34.2    
34.5    
34.8    
35.1    
35.4    
35.7    
36.0    
36.3    
36.6    
36.9    
37.2    
37.5    
37.8    
38.2    
38.5    
38.8    
39.1    
39.4    
39.7    
40.0    
40.3    
40.6    
40.9    
41.2    
41.5    
41.8    
42.2    
42.5    
42.8    
43.1    
43.4    
43.7    
44.0    
44.3    
44.6    
44.9    
45.2    
45.5    
45.8    
46.2    
46.5    
46.8    
47.1    
47.4    
47.7    
48.0    
48.3    
48.6    
48.9    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.1    
51.4    
51.7    
52.0    
52.3    
52.6    
52.9    
53.2    
53.5    
53.8    
54.2    
54.5    
54.8    
55.1    
55.4    
55.7    
56.0    
56.3    
56.6    
56.9    
57.2    
57.5    
57.8    
58.2    
58.5    
58.8    
59.1    
59.4    
59.7    
60.0    
60.3    
60.6    
60.9    
61.2    
61.5    
61.8    
62.2    
62.5    
62.8    
63.1    
63.4    
63.7    
64.0    
64.3    
64.6    
64.9    
65.2    
65.5    
65.8    
66.2    
66.5    
66.8    
67.1    
67.4    
67.7    
68.0    
68.3    
68.6    
68.9    
69.2    
69.5    
69.8    
70.2    
70.5    
70.8    
71.1    
71.4    
71.7    
72.0    
72.3    
72.6    
72.9    
73.2    
73.5    
73.8    
74.2    
74.5    
74.8    
75.1    
75.4    
75.7    
76.0    
76.3    
76.6    
76.9    
77.2    
77.5    
77.8    
78.2    
78.5    
78.8    
79.1    
79.4    
79.7    
80.0    
80.3    
80.6    
80.9    
81.2    
81.5    
81.8    
82.2    
82.5    
82.8    
83.1    
83.4    
83.7    
84.0    
84.3    
84.6    
84.9    
85.2    
85.5    
85.8    
86.2    
86.5    
86.8    
87.1    
87.4    
87.7    
88.0    
88.3    
88.6    
88.9    
89.2    
89.5    
89.8    
90.2    
90.5    
90.8    
91.1    
91.4    
91.7    
92.0    
92.3    
92.6    
92.9    
93.2    
93.5    
93.8    
94.2    
94.5    
94.8    
95.1    
95.4    
95.7    
96.0    
96.3    
96.6    
96.9    
97.2    
97.5    
97.8    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 8738, rend_intergenic: 7027  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13793, rend_intergenic: 11612  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20435, rend_intergenic: 14794  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33000, rend_intergenic: 23681  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34945, rend_intergenic: 33413  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38531, rend_intergenic: 35148  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55837, rend_intergenic: 46495  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57205, rend_intergenic: 56469  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62579, rend_intergenic: 62267  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67343, rend_intergenic: 62826  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86943, rend_intergenic: 79264  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89410, rend_intergenic: 87119  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99092, rend_intergenic: 89625  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120948, rend_intergenic: 111980  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132083, rend_intergenic: 121471  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135832, rend_intergenic: 135200  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137427, rend_intergenic: 136063  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141923, rend_intergenic: 138634  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150448, rend_intergenic: 146710  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172035, rend_intergenic: 158334  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173226, rend_intergenic: 172038  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178570, rend_intergenic: 173311  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support