-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_16/scaffold_16_4320611-4512249

-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_38222-T1
Valid prediction for snap_scaffold_16-snap.881-T1
Valid prediction for snap_scaffold_16-snap.844-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_38230-T1
Valid prediction for GlimmerHMM_glimmerT_38242-T1
Valid prediction for snap_scaffold_16-snap.847-T1
Valid prediction for snap_scaffold_16-snap.872-T1
Couldn't classify 97455, 97865
Sorry, prediction pasa_asmbl_16183.p1 fails validation.
(CAG)	 TA	97455-97865	AC	AAA
Valid prediction for GlimmerHMM_glimmerT_38236-T1
Valid prediction for snap_scaffold_16-snap.868-T1
Valid prediction for snap_scaffold_16-snap.871-T1
Valid prediction for snap_scaffold_16-snap.865-T1
Valid prediction for HiQ_model.g25520.t1
Valid prediction for GlimmerHMM_glimmerT_38212-T1
Valid prediction for snap_scaffold_16-snap.849-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for Augustus_model.g25499.t1
Valid prediction for GlimmerHMM_glimmerT_38241-T1
Valid prediction for GlimmerHMM_glimmerT_38240-T1
Valid prediction for snap_scaffold_16-snap.866-T1
Valid prediction for snap_scaffold_16-snap.867-T1
Valid prediction for GlimmerHMM_glimmerT_38226-T1
Valid prediction for snap_scaffold_16-snap.863-T1
Valid prediction for snap_scaffold_16-snap.850-T1
Valid prediction for Augustus_model.g25500.t1
Valid prediction for Augustus_model.g25516.t1
Valid prediction for Augustus_model.g25515.t1
Valid prediction for Augustus_model.g25517.t1
Couldn't classify 165672, 165773
Sorry, prediction pasa_asmbl_16184.p1 fails validation.
(CTG)	 CT	165672-165773	GT	AAG
(CCC)	 AG	166590-166665	GT	CGG
(GAA)	 AG	166861-166955	GT	ATG
(GAG)	 AG	167278-167448	GT	CTG
(GAT)	 AG	168016-168049	GT	GGG
(TGC)	 AG	168405-168484	GT	AAG
(GGC)	 AG	169065-169133	GT	AGG
(GCT)	 AG	169235-169336	GT	AGG
(CTT)	 AG	169518-169593	GT	GGG
(TGA)	 AG	169810-169922	GT	AGG
(ATC)	 AG	170099-170218	GG	GAG
-recovered pasa_asmbl_16184.p1, terminal, 170099, 170218
-recovered pasa_asmbl_16184.p1, internal, 166590, 166665
-recovered pasa_asmbl_16184.p1, internal, 166861, 166955
-recovered pasa_asmbl_16184.p1, internal, 167278, 167448
-recovered pasa_asmbl_16184.p1, internal, 168016, 168049
-recovered pasa_asmbl_16184.p1, internal, 168405, 168484
-recovered pasa_asmbl_16184.p1, internal, 169065, 169133
-recovered pasa_asmbl_16184.p1, internal, 169235, 169336
-recovered pasa_asmbl_16184.p1, internal, 169518, 169593
-recovered pasa_asmbl_16184.p1, internal, 169810, 169922
Valid prediction for snap_scaffold_16-snap.852-T1
Valid prediction for snap_scaffold_16-snap.878-T1
Valid prediction for Augustus_model.g25518.t1
Valid prediction for snap_scaffold_16-snap.879-T1
Valid prediction for Augustus_model.g25521.t1
Valid prediction for Augustus_model.g25519.t1
Valid prediction for GlimmerHMM_glimmerT_38239-T1
Valid prediction for snap_scaffold_16-snap.882-T1
Valid prediction for GlimmerHMM_glimmerT_38225-T1
Valid prediction for snap_scaffold_16-snap.877-T1
Valid prediction for Augustus_model.g25512.t1
Valid prediction for GlimmerHMM_glimmerT_38232-T1
Valid prediction for Augustus_model.g25513.t1
Valid prediction for snap_scaffold_16-snap.880-T1
Valid prediction for Augustus_model.g25508.t1
Valid prediction for GlimmerHMM_glimmerT_38243-T1
Valid prediction for snap_scaffold_16-snap.846-T1
Valid prediction for GlimmerHMM_glimmerT_38234-T1
Valid prediction for snap_scaffold_16-snap.876-T1
Valid prediction for snap_scaffold_16-snap.861-T1
Valid prediction for GlimmerHMM_glimmerT_38233-T1
Valid prediction for GlimmerHMM_glimmerT_38216-T1
Valid prediction for snap_scaffold_16-snap.854-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_38221-T1
Valid prediction for Augustus_model.g25503.t1
Valid prediction for GlimmerHMM_glimmerT_38228-T1
Valid prediction for GlimmerHMM_glimmerT_38229-T1
Valid prediction for Augustus_model.g25514.t1
Valid prediction for Augustus_model.g25511.t1
Valid prediction for GlimmerHMM_glimmerT_38220-T1
Couldn't classify 101435, 101497
Sorry, prediction pasa_asmbl_17062.p1 fails validation.
(ATG)	 CA	99086-99151	GT	TGG
(ATA)	 AG	99291-99397	GT	AGG
(GAT)	 AG	100035-100218	GT	TGG
(AAT)	 AG	101435-101497	AA	GGA
-recovered pasa_asmbl_17062.p1, initial, 99086, 99151
-recovered pasa_asmbl_17062.p1, internal, 99291, 99397
-recovered pasa_asmbl_17062.p1, internal, 100035, 100218
Valid prediction for Augustus_model.g25509.t1
Valid prediction for GlimmerHMM_glimmerT_38238-T1
Couldn't classify 159125, 159263
Couldn't classify 160861, 161034
Sorry, prediction pasa_asmbl_17059.p1 fails validation.
(TCT)	 CG	159125-159263	GT	CGG
(ACT)	 AG	159366-159468	GT	GGG
(AAG)	 AG	159592-159634	GT	AGG
(GCG)	 AG	160317-160436	GT	AGG
(CGG)	 AG	160861-161034	AC	ACA
-recovered pasa_asmbl_17059.p1, internal, 159366, 159468
-recovered pasa_asmbl_17059.p1, internal, 159592, 159634
-recovered pasa_asmbl_17059.p1, internal, 160317, 160436
Valid prediction for snap_scaffold_16-snap.843-T1
Valid prediction for Augustus_model.g25510.t1
Valid prediction for snap_scaffold_16-snap.859-T1
Valid prediction for Augustus_model.g25507.t1
Valid prediction for GlimmerHMM_glimmerT_38244-T1
Valid prediction for snap_scaffold_16-snap.860-T1
Valid prediction for snap_scaffold_16-snap.848-T1
Valid prediction for snap_scaffold_16-snap.855-T1
Valid prediction for GlimmerHMM_glimmerT_38215-T1
Valid prediction for CodingQuarry_transcript_19948-T1
Valid prediction for snap_scaffold_16-snap.873-T1
Valid prediction for pasa_asmbl_17056.p1
Valid prediction for GlimmerHMM_glimmerT_38227-T1
Valid prediction for snap_scaffold_16-snap.851-T1
Valid prediction for GlimmerHMM_glimmerT_38219-T1
Valid prediction for snap_scaffold_16-snap.870-T1
Valid prediction for GlimmerHMM_glimmerT_38224-T1
Valid prediction for snap_scaffold_16-snap.858-T1
Valid prediction for GlimmerHMM_glimmerT_38214-T1
Valid prediction for GlimmerHMM_glimmerT_38235-T1
Valid prediction for HiQ_model.g25501.t1
Couldn't classify 167018, 168298
Sorry, prediction pasa_asmbl_17058.p1 fails validation.
(CCC)	 CC	167018-168298	AA	GAA
Valid prediction for snap_scaffold_16-snap.875-T1
Valid prediction for GlimmerHMM_glimmerT_38237-T1
Valid prediction for snap_scaffold_16-snap.869-T1
Valid prediction for GlimmerHMM_glimmerT_38223-T1
Valid prediction for snap_scaffold_16-snap.864-T1
Valid prediction for GlimmerHMM_glimmerT_38218-T1
Valid prediction for snap_scaffold_16-snap.857-T1
Valid prediction for Augustus_model.g25505.t1
Valid prediction for GlimmerHMM_glimmerT_38231-T1
Valid prediction for snap_scaffold_16-snap.862-T1
Valid prediction for snap_scaffold_16-snap.842-T1
Valid prediction for snap_scaffold_16-snap.883-T1
Valid prediction for HiQ_model.g25502.t1
Valid prediction for Augustus_model.g25504.t1
Valid prediction for GlimmerHMM_glimmerT_38217-T1
Valid prediction for snap_scaffold_16-snap.856-T1
Valid prediction for snap_scaffold_16-snap.853-T1
Valid prediction for GlimmerHMM_glimmerT_38213-T1
Valid prediction for Augustus_model.g25506.t1
Valid prediction for GlimmerHMM_glimmerT_38245-T1
Valid prediction for CodingQuarry_transcript_19949-T1
Couldn't classify 161128, 161160
Couldn't classify 166658, 166960
Sorry, prediction pasa_asmbl_17534.p1 fails validation.
(GTC)	 GG	161128-161160	GT	AGG
(AAC)	 AG	161261-161325	GT	AGG
(TCC)	 AG	161426-161562	GT	AGG
(ATG)	 AG	161722-161864	GT	AGG
(TTT)	 AG	162032-162190	GT	ACG
(AAA)	 AG	162298-162376	GT	CGG
(ATA)	 AG	162514-162587	GT	TGG
(CTT)	 AG	162704-162793	GT	AGG
(ATG)	 AG	162978-163103	GT	ACG
(TAC)	 AG	163335-163376	GT	TGG
(ACG)	 AG	163505-163610	GT	AGG
(ATT)	 AG	165697-165728	GT	AGG
(GGT)	 AG	166658-166960	CC	GGC
add_exon() Sorry, pasa_asmbl_17534.p1 161722-161864-initial-1 is invalid.
-recovered pasa_asmbl_17534.p1, initial, 161722, 161864
-recovered pasa_asmbl_17534.p1, initial, 162978, 163103
-recovered pasa_asmbl_17534.p1, internal, 161261, 161325
-recovered pasa_asmbl_17534.p1, internal, 161426, 161562
-recovered pasa_asmbl_17534.p1, internal, 161722, 161864
-recovered pasa_asmbl_17534.p1, internal, 162032, 162190
-recovered pasa_asmbl_17534.p1, internal, 162298, 162376
-recovered pasa_asmbl_17534.p1, internal, 162514, 162587
-recovered pasa_asmbl_17534.p1, internal, 162704, 162793
-recovered pasa_asmbl_17534.p1, internal, 162978, 163103
-recovered pasa_asmbl_17534.p1, internal, 163335, 163376
-recovered pasa_asmbl_17534.p1, internal, 163505, 163610
-recovered pasa_asmbl_17534.p1, internal, 165697, 165728
Valid prediction for snap_scaffold_16-snap.840-T1
Valid prediction for snap_scaffold_16-snap.845-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_16-snap.874-T1
Valid prediction for snap_scaffold_16-snap.841-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 38815, rend_intergenic: 29377  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49804, rend_intergenic: 40179  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52288, rend_intergenic: 52148  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60799, rend_intergenic: 52297  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63768, rend_intergenic: 61430  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64808, rend_intergenic: 64367  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71607, rend_intergenic: 65097  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73008, rend_intergenic: 72360  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78770, rend_intergenic: 73345  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125409, rend_intergenic: 122321  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129165, rend_intergenic: 127364  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 70456, rend_intergenic: 70453  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 191639
-exon list size: 425


building trellis

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2.8    
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3.7    
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13.6    
13.8    
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14.8    
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15.2    
15.5    
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16.4    
16.6    
16.9    
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17.3    
17.6    
17.8    
18.0    
18.3    
18.5    
18.7    
19.0    
19.2    
19.4    
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19.9    
20.1    
20.4    
20.6    
20.8    
21.1    
21.3    
21.5    
21.8    
22.0    
22.2    
22.5    
22.7    
23.0    
23.2    
23.4    
23.7    
23.9    
24.1    
24.4    
24.6    
24.8    
25.1    
25.3    
25.5    
25.8    
26.0    
26.2    
26.5    
26.7    
26.9    
27.2    
27.4    
27.6    
27.9    
28.1    
28.3    
28.6    
28.8    
29.0    
29.3    
29.5    
29.7    
30.0    
30.2    
30.4    
30.7    
30.9    
31.1    
31.4    
31.6    
31.9    
32.1    
32.3    
32.6    
32.8    
33.0    
33.3    
33.5    
33.7    
34.0    
34.2    
34.4    
34.7    
34.9    
35.1    
35.4    
35.6    
35.8    
36.1    
36.3    
36.5    
36.8    
37.0    
37.2    
37.5    
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    
40.7    
41.0    
41.2    
41.5    
41.7    
41.9    
42.2    
42.4    
42.6    
42.9    
43.1    
43.3    
43.6    
43.8    
44.0    
44.3    
44.5    
44.7    
45.0    
45.2    
45.4    
45.7    
45.9    
46.1    
46.4    
46.6    
46.8    
47.1    
47.3    
47.5    
47.8    
48.0    
48.2    
48.5    
48.7    
48.9    
49.2    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.8    
51.1    
51.3    
51.5    
51.8    
52.0    
52.2    
52.5    
52.7    
52.9    
53.2    
53.4    
53.6    
53.9    
54.1    
54.3    
54.6    
54.8    
55.0    
55.3    
55.5    
55.7    
56.0    
56.2    
56.4    
56.7    
56.9    
57.1    
57.4    
57.6    
57.8    
58.1    
58.3    
58.5    
58.8    
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59.3    
59.5    
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60.0    
60.2    
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60.9    
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61.4    
61.6    
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64.6    
64.9    
65.1    
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65.6    
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66.0    
66.3    
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66.7    
67.0    
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68.1    
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69.3    
69.6    
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70.3    
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70.7    
71.0    
71.2    
71.4    
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72.1    
72.4    
72.6    
72.8    
73.1    
73.3    
73.5    
73.8    
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74.5    
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74.9    
75.2    
75.4    
75.6    
75.9    
76.1    
76.3    
76.6    
76.8    
77.0    
77.3    
77.5    
77.8    
78.0    
78.2    
78.5    
78.7    
78.9    
79.2    
79.4    
79.6    
79.9    
80.1    
80.3    
80.6    
80.8    
81.0    
81.3    
81.5    
81.7    
82.0    
82.2    
82.4    
82.7    
82.9    
83.1    
83.4    
83.6    
83.8    
84.1    
84.3    
84.5    
84.8    
85.0    
85.2    
85.5    
85.7    
85.9    
86.2    
86.4    
86.7    
86.9    
87.1    
87.4    
87.6    
87.8    
88.1    
88.3    
88.5    
88.8    
89.0    
89.2    
89.5    
89.7    
89.9    
90.2    
90.4    
90.6    
90.9    
91.1    
91.3    
91.6    
91.8    
92.0    
92.3    
92.5    
92.7    
93.0    
93.2    
93.4    
93.7    
93.9    
94.1    
94.4    
94.6    
94.8    
95.1    
95.3    
95.6    
95.8    
96.0    
96.3    
96.5    
96.7    
97.0    
97.2    
97.4    
97.7    
97.9    
98.1    
98.4    
98.6    
98.8    
99.1    
99.3    
99.5    
99.8    
-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 38815, rend_intergenic: 29377  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49804, rend_intergenic: 40179  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52288, rend_intergenic: 52148  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60799, rend_intergenic: 52297  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63768, rend_intergenic: 61430  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64808, rend_intergenic: 64367  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71607, rend_intergenic: 65097  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73008, rend_intergenic: 72360  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78770, rend_intergenic: 73345  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125409, rend_intergenic: 122321  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129165, rend_intergenic: 127364  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 70456, rend_intergenic: 70453  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 31 predictions persist after filtering for low support