-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_3/scaffold_3_16225144-16424433

-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_3-snap.3143-T1
Valid prediction for snap_scaffold_3-snap.3117-T1
Valid prediction for snap_scaffold_3-snap.3141-T1
Valid prediction for GlimmerHMM_glimmerT_7997-T1
Valid prediction for snap_scaffold_3-snap.3128-T1
Valid prediction for pasa_asmbl_40615.p1
Valid prediction for Augustus_model.g5282.t1
Valid prediction for snap_scaffold_3-snap.3145-T1
Valid prediction for GlimmerHMM_glimmerT_8010-T1
Valid prediction for Augustus_model.g5281.t1
Valid prediction for GlimmerHMM_glimmerT_8006-T1
Valid prediction for HiQ_model.g5284.t1
Valid prediction for snap_scaffold_3-snap.3119-T1
Valid prediction for GlimmerHMM_glimmerT_8008-T1
Valid prediction for snap_scaffold_3-snap.3126-T1
Valid prediction for snap_scaffold_3-snap.3111-T1
Valid prediction for GlimmerHMM_glimmerT_7998-T1
Valid prediction for snap_scaffold_3-snap.3142-T1
Valid prediction for snap_scaffold_3-snap.3146-T1
Valid prediction for GlimmerHMM_glimmerT_8000-T1
Valid prediction for snap_scaffold_3-snap.3110-T1
Valid prediction for snap_scaffold_3-snap.3123-T1
Valid prediction for Augustus_model.g5290.t1
Valid prediction for snap_scaffold_3-snap.3115-T1
Valid prediction for snap_scaffold_3-snap.3120-T1
Valid prediction for snap_scaffold_3-snap.3108-T1
Valid prediction for snap_scaffold_3-snap.3138-T1
Valid prediction for GlimmerHMM_glimmerT_8012-T1
Valid prediction for GlimmerHMM_glimmerT_8016-T1
Valid prediction for GlimmerHMM_glimmerT_8014-T1
Valid prediction for GlimmerHMM_glimmerT_7995-T1
Valid prediction for GlimmerHMM_glimmerT_8015-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_8009-T1
Valid prediction for snap_scaffold_3-snap.3135-T1
Valid prediction for snap_scaffold_3-snap.3124-T1
Valid prediction for snap_scaffold_3-snap.3114-T1
Couldn't classify 83576, 83648
Sorry, prediction pasa_asmbl_39493.p1 fails validation.
(GAT)	 CA	83576-83648	GT	GGG
(ATG)	 AG	83940-84189	GT	AGG
(AAC)	 AG	84417-84597	GT	AGG
(GAC)	 AG	84892-85063	GT	AGG
(AGG)	 AG	85301-85363	GT	AGG
(GGT)	 AG	85808-85946	GT	CCG
(TGA)	 AG	86423-86577	GT	AGG
(ATC)	 AG	86767-86910	GT	AGG
(ACA)	 AG	87704-87871	GT	GGG
(CTG)	 AG	88057-88550	AA	GAA
add_exon() Sorry, pasa_asmbl_39493.p1 83940-84189-initial-1 is invalid.
-recovered pasa_asmbl_39493.p1, initial, 83940, 84189
add_exon() Sorry, pasa_asmbl_39493.p1 85301-85363-terminal-1 is invalid.
-recovered pasa_asmbl_39493.p1, terminal, 85301, 85363
-recovered pasa_asmbl_39493.p1, terminal, 88057, 88550
-recovered pasa_asmbl_39493.p1, internal, 83940, 84189
-recovered pasa_asmbl_39493.p1, internal, 84417, 84597
-recovered pasa_asmbl_39493.p1, internal, 84892, 85063
-recovered pasa_asmbl_39493.p1, internal, 85301, 85363
-recovered pasa_asmbl_39493.p1, internal, 85808, 85946
-recovered pasa_asmbl_39493.p1, internal, 86423, 86577
-recovered pasa_asmbl_39493.p1, internal, 86767, 86910
-recovered pasa_asmbl_39493.p1, internal, 87704, 87871
Valid prediction for snap_scaffold_3-snap.3131-T1
Valid prediction for snap_scaffold_3-snap.3118-T1
Valid prediction for snap_scaffold_3-snap.3139-T1
Valid prediction for snap_scaffold_3-snap.3113-T1
Valid prediction for CodingQuarry_transcript_46412-T1
Valid prediction for snap_scaffold_3-snap.3112-T1
Valid prediction for snap_scaffold_3-snap.3134-T1
Valid prediction for snap_scaffold_3-snap.3122-T1
Valid prediction for snap_scaffold_3-snap.3106-T1
Valid prediction for GlimmerHMM_glimmerT_7994-T1
Couldn't classify 68143, 68188
Sorry, prediction pasa_asmbl_39503.p1 fails validation.
(AGG)	 CA	68143-68188	GT	TGG
(GTG)	 AG	68363-68498	GT	AGG
(GAC)	 AG	68741-68886	GT	CGG
(ACT)	 AG	69022-69161	CT	AGC
-recovered pasa_asmbl_39503.p1, terminal, 69022, 69161
-recovered pasa_asmbl_39503.p1, internal, 68363, 68498
-recovered pasa_asmbl_39503.p1, internal, 68741, 68886
Valid prediction for snap_scaffold_3-snap.3107-T1
Couldn't classify 52616, 52732
Sorry, prediction pasa_asmbl_39505.p1 fails validation.
(ATG)	 CC	50033-50107	GT	AGG
(AGT)	 AG	50667-51035	GT	AGG
(AGC)	 AG	52616-52732	GG	TGG
-recovered pasa_asmbl_39505.p1, initial, 50033, 50107
-recovered pasa_asmbl_39505.p1, internal, 50667, 51035
Valid prediction for Augustus_model.g5285.t1
Valid prediction for snap_scaffold_3-snap.3136-T1
Valid prediction for GlimmerHMM_glimmerT_7999-T1
Valid prediction for Augustus_model.g5292.t1
Valid prediction for GlimmerHMM_glimmerT_8002-T1
Valid prediction for GlimmerHMM_glimmerT_8003-T1
Valid prediction for GlimmerHMM_glimmerT_8001-T1
Couldn't classify 53177, 53252
Sorry, prediction pasa_asmbl_39504.p1 fails validation.
(CCT)	 GC	53177-53252	GT	GGG
(GAG)	 AG	53711-53854	GT	AGG
(GCA)	 AG	55665-55799	GT	TGG
(TTA)	 AG	56474-56574	GT	AGG
(TCG)	 AG	56994-57143	GT	ACG
(ATC)	 AG	57342-57501	GT	GGG
(CCT)	 AG	57930-58069	GT	AGG
(GTG)	 AG	58506-58589	AG	AGA
-recovered pasa_asmbl_39504.p1, terminal, 58506, 58589
-recovered pasa_asmbl_39504.p1, internal, 53711, 53854
-recovered pasa_asmbl_39504.p1, internal, 55665, 55799
-recovered pasa_asmbl_39504.p1, internal, 56474, 56574
-recovered pasa_asmbl_39504.p1, internal, 56994, 57143
-recovered pasa_asmbl_39504.p1, internal, 57342, 57501
-recovered pasa_asmbl_39504.p1, internal, 57930, 58069
Valid prediction for HiQ_model.g5291.t1
Valid prediction for snap_scaffold_3-snap.3137-T1
Valid prediction for snap_scaffold_3-snap.3129-T1
Valid prediction for GlimmerHMM_glimmerT_7996-T1
Couldn't classify 40947, 40976
Sorry, prediction pasa_asmbl_39506.p1 fails validation.
(ATG)	 AG	37090-37108	GT	TCG
(CGC)	 AG	37249-37327	GT	TGG
(GTC)	 AG	37555-37730	GT	AGG
(ATG)	 AG	37901-37973	GT	AGG
(CTC)	 AG	38524-38734	GT	AGG
(CAA)	 AG	40434-40595	GT	AGG
(GAG)	 AG	40947-40976	CA	AGC
-recovered pasa_asmbl_39506.p1, initial, 37090, 37108
-recovered pasa_asmbl_39506.p1, initial, 37901, 37973
-recovered pasa_asmbl_39506.p1, internal, 37090, 37108
-recovered pasa_asmbl_39506.p1, internal, 37249, 37327
-recovered pasa_asmbl_39506.p1, internal, 37555, 37730
-recovered pasa_asmbl_39506.p1, internal, 37901, 37973
-recovered pasa_asmbl_39506.p1, internal, 38524, 38734
-recovered pasa_asmbl_39506.p1, internal, 40434, 40595
Valid prediction for Augustus_model.g5283.t1
Valid prediction for Augustus_model.g5287.t1
Valid prediction for snap_scaffold_3-snap.3144-T1
Valid prediction for GlimmerHMM_glimmerT_8007-T1
Valid prediction for snap_scaffold_3-snap.3125-T1
Valid prediction for Augustus_model.g5288.t1
Valid prediction for Augustus_model.g5286.t1
Valid prediction for snap_scaffold_3-snap.3127-T1
Valid prediction for GlimmerHMM_glimmerT_8013-T1
Valid prediction for HiQ_model.g5289.t1
Valid prediction for snap_scaffold_3-snap.3116-T1
Valid prediction for GlimmerHMM_glimmerT_8011-T1
Valid prediction for snap_scaffold_3-snap.3140-T1
Valid prediction for GlimmerHMM_glimmerT_8005-T1
Valid prediction for snap_scaffold_3-snap.3132-T1
Valid prediction for CodingQuarry_transcript_46411-T1
Valid prediction for GlimmerHMM_glimmerT_8004-T1
Valid prediction for snap_scaffold_3-snap.3147-T1
Valid prediction for Augustus_model.g5293.t1
Couldn't classify 73432, 73531
Sorry, prediction pasa_asmbl_39499.p1 fails validation.
(AGA)	 GA	73432-73531	GT	CGG
(ACA)	 AG	74638-74709	GT	GGG
(ATG)	 AG	74984-75233	GT	AGG
(AAC)	 AG	75660-75852	GT	AGG
(GGC)	 AG	76194-76365	GT	AGG
(AGG)	 AG	76607-76669	GT	AGG
(GCT)	 AG	76897-77035	GT	CCG
(GGA)	 AG	78181-78335	GT	AGG
(ATC)	 AG	78499-78642	GT	AGG
(ACA)	 AG	79173-79340	GT	GGG
(CTG)	 AG	80515-80969	AT	AAA
add_exon() Sorry, pasa_asmbl_39499.p1 74984-75233-initial-1 is invalid.
-recovered pasa_asmbl_39499.p1, initial, 74984, 75233
add_exon() Sorry, pasa_asmbl_39499.p1 76607-76669-terminal-1 is invalid.
-recovered pasa_asmbl_39499.p1, terminal, 76607, 76669
-recovered pasa_asmbl_39499.p1, terminal, 80515, 80969
-recovered pasa_asmbl_39499.p1, internal, 74638, 74709
-recovered pasa_asmbl_39499.p1, internal, 74984, 75233
-recovered pasa_asmbl_39499.p1, internal, 75660, 75852
-recovered pasa_asmbl_39499.p1, internal, 76194, 76365
-recovered pasa_asmbl_39499.p1, internal, 76607, 76669
-recovered pasa_asmbl_39499.p1, internal, 76897, 77035
-recovered pasa_asmbl_39499.p1, internal, 78181, 78335
-recovered pasa_asmbl_39499.p1, internal, 78499, 78642
-recovered pasa_asmbl_39499.p1, internal, 79173, 79340
Valid prediction for snap_scaffold_3-snap.3109-T1
Valid prediction for snap_scaffold_3-snap.3121-T1
Valid prediction for snap_scaffold_3-snap.3133-T1
Valid prediction for Augustus_model.g5294.t1
Valid prediction for snap_scaffold_3-snap.3130-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9279, rend_intergenic: 7333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15281, rend_intergenic: 9326  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37529, rend_intergenic: 19366  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45830, rend_intergenic: 43649  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49973, rend_intergenic: 46324  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60840, rend_intergenic: 57589  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72952, rend_intergenic: 65975  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75908, rend_intergenic: 73612  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91976, rend_intergenic: 90107  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100171, rend_intergenic: 92661  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175151, rend_intergenic: 162103  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 199290
-exon list size: 384


building trellis

0.3    
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1.0    
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8.0    
8.3    
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9.1    
9.3    
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9.8    
10.1    
10.4    
10.6    
10.9    
11.1    
11.4    
11.7    
11.9    
12.2    
12.4    
12.7    
13.0    
13.2    
13.5    
13.7    
14.0    
14.2    
14.5    
14.8    
15.0    
15.3    
15.5    
15.8    
16.1    
16.3    
16.6    
16.8    
17.1    
17.4    
17.6    
17.9    
18.1    
18.4    
18.7    
18.9    
19.2    
19.4    
19.7    
19.9    
20.2    
20.5    
20.7    
21.0    
21.2    
21.5    
21.8    
22.0    
22.3    
22.5    
22.8    
23.1    
23.3    
23.6    
23.8    
24.1    
24.4    
24.6    
24.9    
25.1    
25.4    
25.6    
25.9    
26.2    
26.4    
26.7    
26.9    
27.2    
27.5    
27.7    
28.0    
28.2    
28.5    
28.8    
29.0    
29.3    
29.5    
29.8    
30.1    
30.3    
30.6    
30.8    
31.1    
31.3    
31.6    
31.9    
32.1    
32.4    
32.6    
32.9    
33.2    
33.4    
33.7    
33.9    
34.2    
34.5    
34.7    
35.0    
35.2    
35.5    
35.8    
36.0    
36.3    
36.5    
36.8    
37.0    
37.3    
37.6    
37.8    
38.1    
38.3    
38.6    
38.9    
39.1    
39.4    
39.6    
39.9    
40.2    
40.4    
40.7    
40.9    
41.2    
41.5    
41.7    
42.0    
42.2    
42.5    
42.7    
43.0    
43.3    
43.5    
43.8    
44.0    
44.3    
44.6    
44.8    
45.1    
45.3    
45.6    
45.9    
46.1    
46.4    
46.6    
46.9    
47.2    
47.4    
47.7    
47.9    
48.2    
48.4    
48.7    
49.0    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.0    
51.3    
51.6    
51.8    
52.1    
52.3    
52.6    
52.8    
53.1    
53.4    
53.6    
53.9    
54.1    
54.4    
54.7    
54.9    
55.2    
55.4    
55.7    
56.0    
56.2    
56.5    
56.7    
57.0    
57.3    
57.5    
57.8    
58.0    
58.3    
58.5    
58.8    
59.1    
59.3    
59.6    
59.8    
60.1    
60.4    
60.6    
60.9    
61.1    
61.4    
61.7    
61.9    
62.2    
62.4    
62.7    
63.0    
63.2    
63.5    
63.7    
64.0    
64.2    
64.5    
64.8    
65.0    
65.3    
65.5    
65.8    
66.1    
66.3    
66.6    
66.8    
67.1    
67.4    
67.6    
67.9    
68.1    
68.4    
68.7    
68.9    
69.2    
69.4    
69.7    
69.9    
70.2    
70.5    
70.7    
71.0    
71.2    
71.5    
71.8    
72.0    
72.3    
72.5    
72.8    
73.1    
73.3    
73.6    
73.8    
74.1    
74.4    
74.6    
74.9    
75.1    
75.4    
75.6    
75.9    
76.2    
76.4    
76.7    
76.9    
77.2    
77.5    
77.7    
78.0    
78.2    
78.5    
78.8    
79.0    
79.3    
79.5    
79.8    
80.1    
80.3    
80.6    
80.8    
81.1    
81.3    
81.6    
81.9    
82.1    
82.4    
82.6    
82.9    
83.2    
83.4    
83.7    
83.9    
84.2    
84.5    
84.7    
85.0    
85.2    
85.5    
85.8    
86.0    
86.3    
86.5    
86.8    
87.0    
87.3    
87.6    
87.8    
88.1    
88.3    
88.6    
88.9    
89.1    
89.4    
89.6    
89.9    
90.2    
90.4    
90.7    
90.9    
91.2    
91.5    
91.7    
92.0    
92.2    
92.5    
92.7    
93.0    
93.3    
93.5    
93.8    
94.0    
94.3    
94.6    
94.8    
95.1    
95.3    
95.6    
95.9    
96.1    
96.4    
96.6    
96.9    
97.2    
97.4    
97.7    
97.9    
98.2    
98.4    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 9279, rend_intergenic: 7333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15281, rend_intergenic: 9326  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37529, rend_intergenic: 19366  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45830, rend_intergenic: 43649  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49973, rend_intergenic: 46324  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60840, rend_intergenic: 57589  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72952, rend_intergenic: 65975  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75908, rend_intergenic: 73612  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91976, rend_intergenic: 90107  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100171, rend_intergenic: 92661  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175151, rend_intergenic: 162103  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

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

-building DP trellis

-building trellis in range 189144 - 199290
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support