-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_15/scaffold_15_12080482-12226346

-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 Augustus_model.g24697.t1
Couldn't classify 4355, 4999
Couldn't classify 5394, 5522
Sorry, prediction pasa_asmbl_15532.p1 fails validation.
(CTC)	 CC	4355-4999	GT	TGG
(GAG)	 AG	5394-5522	GA	AAG
Valid prediction for Augustus_model.g24693.t1
Valid prediction for GlimmerHMM_glimmerT_37090-T1
Couldn't classify 141380, 141499
Sorry, prediction pasa_asmbl_15548.p1 fails validation.
(TCC)	 GC	141380-141499	GT	TGG
(GGT)	 AG	141609-141740	GT	TAG
(TCG)	 AG	141992-142142	GT	TGG
(ACT)	 AG	142560-143080	AC	AAA
-recovered pasa_asmbl_15548.p1, terminal, 142560, 143080
-recovered pasa_asmbl_15548.p1, internal, 141609, 141740
-recovered pasa_asmbl_15548.p1, internal, 141992, 142142
Valid prediction for snap_scaffold_15-snap.2476-T1
Valid prediction for snap_scaffold_15-snap.2481-T1
Couldn't classify 16835, 16855
Couldn't classify 17812, 17835
Sorry, prediction pasa_asmbl_15902.p1 fails validation.
(CTC)	 AG	16835-16855	GT	AGG
(TGT)	 AG	16996-17196	GT	AGG
(GCA)	 AG	17393-17491	GT	AGG
(TGC)	 AG	17812-17835	AA	GGA
-recovered pasa_asmbl_15902.p1, internal, 16835, 16855
-recovered pasa_asmbl_15902.p1, internal, 16996, 17196
-recovered pasa_asmbl_15902.p1, internal, 17393, 17491
Valid prediction for snap_scaffold_15-snap.2475-T1
Valid prediction for Augustus_model.g24700.t1
Valid prediction for snap_scaffold_15-snap.2496-T1
Valid prediction for snap_scaffold_15-snap.2488-T1
Couldn't classify 3533, 4108
Sorry, prediction pasa_asmbl_15531.p1 fails validation.
(GAC)	 AG	3533-4108	GT	GGG
-recovered pasa_asmbl_15531.p1, internal, 3533, 4108
Valid prediction for GlimmerHMM_glimmerT_37088-T1
Valid prediction for snap_scaffold_15-snap.2491-T1
Valid prediction for GlimmerHMM_glimmerT_37093-T1
Valid prediction for snap_scaffold_15-snap.2479-T1
Valid prediction for pasa_asmbl_15540.p1
Valid prediction for snap_scaffold_15-snap.2480-T1
Valid prediction for snap_scaffold_15-snap.2490-T1
Valid prediction for Augustus_model.g24696.t1
Valid prediction for GlimmerHMM_glimmerT_37089-T1
Couldn't classify 2244, 2390
Couldn't classify 2962, 3001
Sorry, prediction pasa_asmbl_15530.p1 fails validation.
(CAA)	 AC	2244-2390	GT	AGG
(AGC)	 AG	2600-2838	GT	TTG
(AGG)	 AG	2962-3001	CG	TCC
-recovered pasa_asmbl_15530.p1, internal, 2600, 2838
Valid prediction for GlimmerHMM_glimmerT_37095-T1
Valid prediction for snap_scaffold_15-snap.2494-T1
Valid prediction for snap_scaffold_15-snap.2486-T1
Couldn't classify 140150, 140216
Couldn't classify 140961, 141076
Sorry, prediction pasa_asmbl_15948.p1 fails validation.
(GTA)	 GT	140150-140216	GT	CAG
(ATG)	 AG	140744-140857	GT	GTG
(TTA)	 AG	140961-141076	GT	AGG
add_exon() Sorry, pasa_asmbl_15948.p1 140744-140857-initial-1 is invalid.
-recovered pasa_asmbl_15948.p1, initial, 140744, 140857
-recovered pasa_asmbl_15948.p1, internal, 140744, 140857
-recovered pasa_asmbl_15948.p1, internal, 140961, 141076
Couldn't classify 137754, 137871
Couldn't classify 139355, 139380
Sorry, prediction pasa_asmbl_15547.p1 fails validation.
(GGG)	 AG	137754-137871	GT	GAG
(ACG)	 AG	137997-138110	GT	CAG
(ATG)	 AG	138530-138643	GT	TCG
(GCG)	 AG	138797-138910	GT	AGG
(CCA)	 AG	139052-139168	GT	CAG
(ACA)	 AG	139355-139380	TG	CAT
add_exon() Sorry, pasa_asmbl_15547.p1 138530-138643-initial-1 is invalid.
-recovered pasa_asmbl_15547.p1, initial, 138530, 138643
-recovered pasa_asmbl_15547.p1, internal, 137754, 137871
-recovered pasa_asmbl_15547.p1, internal, 137997, 138110
-recovered pasa_asmbl_15547.p1, internal, 138530, 138643
-recovered pasa_asmbl_15547.p1, internal, 138797, 138910
-recovered pasa_asmbl_15547.p1, internal, 139052, 139168
Couldn't classify 7853, 7900
Couldn't classify 12232, 12261
Sorry, prediction pasa_asmbl_15534.p1 fails validation.
(ACC)	 GG	7853-7900	GT	AGG
(GAG)	 AG	10705-10848	GT	AGG
(TTT)	 AG	11374-11514	GT	AGG
(AGA)	 AG	11654-11836	GT	GGG
(GTT)	 AG	12232-12261	AT	ACA
-recovered pasa_asmbl_15534.p1, internal, 10705, 10848
-recovered pasa_asmbl_15534.p1, internal, 11374, 11514
-recovered pasa_asmbl_15534.p1, internal, 11654, 11836
Valid prediction for snap_scaffold_15-snap.2499-T1
Couldn't classify 12319, 12369
Couldn't classify 16700, 16789
Sorry, prediction pasa_asmbl_15536.p1 fails validation.
(TGT)	 CC	12319-12369	GT	AGG
(ATG)	 AG	12701-12886	GT	CTG
(GAG)	 AG	13052-13174	GT	AGG
(ATC)	 AG	13463-13645	GT	AGG
(AGT)	 AG	13916-14044	GT	AGG
(GAC)	 AG	14964-15068	GT	AGG
(AAT)	 AG	15217-15675	GT	TGG
(AGA)	 AG	15903-15985	GT	AGG
(GCT)	 AG	16110-16248	GT	AGG
(GAC)	 AG	16454-16570	GT	GGG
(GGT)	 AG	16700-16789	GA	CCG
-recovered pasa_asmbl_15536.p1, initial, 12701, 12886
-recovered pasa_asmbl_15536.p1, internal, 12701, 12886
-recovered pasa_asmbl_15536.p1, internal, 13052, 13174
-recovered pasa_asmbl_15536.p1, internal, 13463, 13645
-recovered pasa_asmbl_15536.p1, internal, 13916, 14044
-recovered pasa_asmbl_15536.p1, internal, 14964, 15068
-recovered pasa_asmbl_15536.p1, internal, 15217, 15675
-recovered pasa_asmbl_15536.p1, internal, 15903, 15985
-recovered pasa_asmbl_15536.p1, internal, 16110, 16248
-recovered pasa_asmbl_15536.p1, internal, 16454, 16570
Valid prediction for Augustus_model.g24701.t1
Valid prediction for snap_scaffold_15-snap.2482-T1
Couldn't classify 127243, 127414
Couldn't classify 132263, 132366
Sorry, prediction pasa_asmbl_15545.p2 fails validation.
(CCC)	 GC	127243-127414	GT	TGG
(CAA)	 AG	128544-128604	GT	AGG
(TTG)	 AG	131059-131189	GT	AGG
(ATC)	 AG	131987-132106	GT	CGG
(CCG)	 AG	132263-132366	TG	CCT
-recovered pasa_asmbl_15545.p2, internal, 128544, 128604
-recovered pasa_asmbl_15545.p2, internal, 131059, 131189
-recovered pasa_asmbl_15545.p2, internal, 131987, 132106
Valid prediction for CodingQuarry_transcript_18167-T1
Couldn't classify 134962, 134991
Couldn't classify 137285, 137407
Sorry, prediction pasa_asmbl_15546.p1 fails validation.
(GGA)	 AT	134962-134991	GT	AGG
(GAG)	 AG	135367-135540	GT	AGG
(GTG)	 AG	137285-137407	TC	GCT
-recovered pasa_asmbl_15546.p1, internal, 135367, 135540
Valid prediction for snap_scaffold_15-snap.2492-T1
Couldn't classify 6371, 6439
Couldn't classify 6888, 7097
Sorry, prediction pasa_asmbl_15533.p1 fails validation.
(CTC)	 GA	6371-6439	GT	AGG
(GCC)	 AG	6553-6753	GT	GCG
(ATT)	 AG	6888-7097	CG	TCC
-recovered pasa_asmbl_15533.p1, internal, 6553, 6753
Valid prediction for snap_scaffold_15-snap.2498-T1
Valid prediction for Augustus_model.g24695.t1
Valid prediction for snap_scaffold_15-snap.2497-T1
Valid prediction for Augustus_model.g24692.t1
Couldn't classify 17911, 17994
Couldn't classify 34093, 34131
Sorry, prediction pasa_asmbl_15537.p1 fails validation.
(CTG)	 AA	17911-17994	GT	AGG
(AAG)	 AG	18320-18493	GT	AGG
(GAC)	 AG	18666-18800	GT	AGG
(CGA)	 AG	19697-19893	GT	AGG
(GTT)	 AG	20132-20267	GT	TGG
(GAT)	 AG	20684-20866	GT	AGG
(CTC)	 AG	21446-21595	GT	AGG
(GAG)	 AG	21863-22033	GT	AGG
(ATG)	 AG	22282-22437	GT	AGG
(CCC)	 AG	22603-22752	GT	AGG
(GTT)	 AG	22986-23156	GT	AGG
(ATG)	 AG	23354-23487	GT	CGG
(GTG)	 AG	24527-24734	GT	AGG
(AAA)	 AG	25250-25432	GT	AGG
(GAG)	 AG	25722-25835	GT	AGG
(ATG)	 AG	26040-26194	GC	AGG
(GGA)	 AG	26305-26452	GT	AGG
(CGG)	 AG	27327-27421	GT	AGG
(GTC)	 AG	28245-28476	GT	AGG
(CAC)	 AG	28875-29072	GT	AGG
(ACC)	 AG	30731-30856	GT	AGG
(GAG)	 AG	31806-31961	GT	AGG
(GTC)	 AG	34093-34131	CT	CTC
-recovered pasa_asmbl_15537.p1, initial, 22282, 22437
-recovered pasa_asmbl_15537.p1, initial, 23354, 23487
-recovered pasa_asmbl_15537.p1, initial, 26040, 26194
-recovered pasa_asmbl_15537.p1, internal, 18320, 18493
-recovered pasa_asmbl_15537.p1, internal, 18666, 18800
-recovered pasa_asmbl_15537.p1, internal, 19697, 19893
-recovered pasa_asmbl_15537.p1, internal, 20132, 20267
-recovered pasa_asmbl_15537.p1, internal, 20684, 20866
-recovered pasa_asmbl_15537.p1, internal, 21446, 21595
-recovered pasa_asmbl_15537.p1, internal, 21863, 22033
-recovered pasa_asmbl_15537.p1, internal, 22282, 22437
-recovered pasa_asmbl_15537.p1, internal, 22603, 22752
-recovered pasa_asmbl_15537.p1, internal, 22986, 23156
-recovered pasa_asmbl_15537.p1, internal, 23354, 23487
-recovered pasa_asmbl_15537.p1, internal, 24527, 24734
-recovered pasa_asmbl_15537.p1, internal, 25250, 25432
-recovered pasa_asmbl_15537.p1, internal, 25722, 25835
-recovered pasa_asmbl_15537.p1, internal, 26040, 26194
-recovered pasa_asmbl_15537.p1, internal, 26305, 26452
-recovered pasa_asmbl_15537.p1, internal, 27327, 27421
-recovered pasa_asmbl_15537.p1, internal, 28245, 28476
-recovered pasa_asmbl_15537.p1, internal, 28875, 29072
-recovered pasa_asmbl_15537.p1, internal, 30731, 30856
-recovered pasa_asmbl_15537.p1, internal, 31806, 31961

-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_37092-T1
Valid prediction for Augustus_model.g24694.t1
Valid prediction for GlimmerHMM_glimmerT_37091-T1
Valid prediction for pasa_asmbl_14564.p1
Valid prediction for GlimmerHMM_glimmerT_37086-T1
Valid prediction for snap_scaffold_15-snap.2487-T1
Valid prediction for GlimmerHMM_glimmerT_37085-T1
Valid prediction for CodingQuarry_transcript_18165-T1
Valid prediction for CodingQuarry_transcript_18166-T1
Valid prediction for snap_scaffold_15-snap.2489-T1
Valid prediction for snap_scaffold_15-snap.2483-T1
Valid prediction for GlimmerHMM_glimmerT_37094-T1
Valid prediction for HiQ_model.g24691.t1
Valid prediction for snap_scaffold_15-snap.2493-T1
Valid prediction for GlimmerHMM_glimmerT_37087-T1
Valid prediction for snap_scaffold_15-snap.2495-T1
Valid prediction for snap_scaffold_15-snap.2484-T1
Valid prediction for Augustus_model.g24699.t1
Valid prediction for Augustus_model.g24698.t1
Valid prediction for snap_scaffold_15-snap.2477-T1
Valid prediction for snap_scaffold_15-snap.2474-T1
Valid prediction for snap_scaffold_15-snap.2473-T1
Valid prediction for snap_scaffold_15-snap.2485-T1
Valid prediction for snap_scaffold_15-snap.2478-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12852, rend_intergenic: 10417  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29614, rend_intergenic: 18365  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32834, rend_intergenic: 30594  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74403, rend_intergenic: 72035  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123308, rend_intergenic: 121228  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 145865
-exon list size: 273


building trellis

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0.7    
1.1    
1.5    
1.8    
2.2    
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2.9    
3.3    
3.6    
4.0    
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5.8    
6.2    
6.5    
6.9    
7.3    
7.6    
8.0    
8.4    
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10.2    
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10.9    
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11.6    
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12.4    
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14.2    
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14.9    
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15.6    
16.0    
16.4    
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17.1    
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18.2    
18.5    
18.9    
19.3    
19.6    
20.0    
20.4    
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21.1    
21.5    
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22.2    
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24.0    
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25.1    
25.5    
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26.2    
26.5    
26.9    
27.3    
27.6    
28.0    
28.4    
28.7    
29.1    
29.5    
29.8    
30.2    
30.5    
30.9    
31.3    
31.6    
32.0    
32.4    
32.7    
33.1    
33.5    
33.8    
34.2    
34.5    
34.9    
35.3    
35.6    
36.0    
36.4    
36.7    
37.1    
37.5    
37.8    
38.2    
38.5    
38.9    
39.3    
39.6    
40.0    
40.4    
40.7    
41.1    
41.5    
41.8    
42.2    
42.5    
42.9    
43.3    
43.6    
44.0    
44.4    
44.7    
45.1    
45.5    
45.8    
46.2    
46.5    
46.9    
47.3    
47.6    
48.0    
48.4    
48.7    
49.1    
49.5    
49.8    
50.2    
50.5    
50.9    
51.3    
51.6    
52.0    
52.4    
52.7    
53.1    
53.5    
53.8    
54.2    
54.5    
54.9    
55.3    
55.6    
56.0    
56.4    
56.7    
57.1    
57.5    
57.8    
58.2    
58.5    
58.9    
59.3    
59.6    
60.0    
60.4    
60.7    
61.1    
61.5    
61.8    
62.2    
62.5    
62.9    
63.3    
63.6    
64.0    
64.4    
64.7    
65.1    
65.5    
65.8    
66.2    
66.5    
66.9    
67.3    
67.6    
68.0    
68.4    
68.7    
69.1    
69.5    
69.8    
70.2    
70.5    
70.9    
71.3    
71.6    
72.0    
72.4    
72.7    
73.1    
73.5    
73.8    
74.2    
74.5    
74.9    
75.3    
75.6    
76.0    
76.4    
76.7    
77.1    
77.5    
77.8    
78.2    
78.5    
78.9    
79.3    
79.6    
80.0    
80.4    
80.7    
81.1    
81.5    
81.8    
82.2    
82.5    
82.9    
83.3    
83.6    
84.0    
84.4    
84.7    
85.1    
85.5    
85.8    
86.2    
86.5    
86.9    
87.3    
87.6    
88.0    
88.4    
88.7    
89.1    
89.5    
89.8    
90.2    
90.5    
90.9    
91.3    
91.6    
92.0    
92.4    
92.7    
93.1    
93.5    
93.8    
94.2    
94.5    
94.9    
95.3    
95.6    
96.0    
96.4    
96.7    
97.1    
97.5    
97.8    
98.2    
98.5    
98.9    
99.3    
99.6    
-found 15 predictions from path traversal
Error with prediction: snap lend_intergenic: 12852, rend_intergenic: 10417  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29614, rend_intergenic: 18365  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32834, rend_intergenic: 30594  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74403, rend_intergenic: 72035  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123308, rend_intergenic: 121228  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 11 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 10704
-exon list size: 14


building trellis

6.2    
12.5    
18.8    
25.0    
31.2    
37.5    
43.8    
50.0    
56.2    
62.5    
68.8    
75.0    
81.2    
87.5    
93.8    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support