-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_15533558-15805447

-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_37535-T1
Valid prediction for snap_scaffold_15-snap.3084-T1
Valid prediction for snap_scaffold_15-snap.3098-T1
Valid prediction for GlimmerHMM_glimmerT_37546-T1
Valid prediction for GlimmerHMM_glimmerT_37541-T1
Valid prediction for Augustus_model.g25038.t1
Valid prediction for snap_scaffold_15-snap.3103-T1
Valid prediction for snap_scaffold_15-snap.3116-T1
Valid prediction for GlimmerHMM_glimmerT_37539-T1
Valid prediction for GlimmerHMM_glimmerT_37532-T1
Valid prediction for snap_scaffold_15-snap.3087-T1
Valid prediction for snap_scaffold_15-snap.3090-T1
Valid prediction for Augustus_model.g25027.t1
Valid prediction for GlimmerHMM_glimmerT_37548-T1
Valid prediction for GlimmerHMM_glimmerT_37526-T1
Valid prediction for snap_scaffold_15-snap.3099-T1
Valid prediction for Augustus_model.g25042.t1
Valid prediction for Augustus_model.g25029.t1
Valid prediction for snap_scaffold_15-snap.3092-T1
Valid prediction for Augustus_model.g25025.t1
Valid prediction for snap_scaffold_15-snap.3077-T1
Valid prediction for snap_scaffold_15-snap.3097-T1
Valid prediction for Augustus_model.g25039.t1
Valid prediction for snap_scaffold_15-snap.3102-T1
Valid prediction for snap_scaffold_15-snap.3119-T1
Valid prediction for CodingQuarry_transcript_18267-T1
Valid prediction for snap_scaffold_15-snap.3117-T1
Valid prediction for Augustus_model.g25031.t1
Valid prediction for CodingQuarry_transcript_18265-T1
Valid prediction for GlimmerHMM_glimmerT_37537-T1
Valid prediction for GlimmerHMM_glimmerT_37522-T1
Valid prediction for GlimmerHMM_glimmerT_37533-T1
Couldn't classify 136018, 136068
Couldn't classify 141372, 141410
Sorry, prediction pasa_asmbl_15814.p1 fails validation.
(TCC)	 TC	136018-136068	GT	CGG
(GAC)	 AG	136938-137101	GT	AGG
(AGC)	 AG	137919-138049	GT	AGG
(AGC)	 AG	138766-138926	GT	TGG
(GCT)	 AG	139344-139436	GT	GGG
(GCC)	 AG	141372-141410	GA	AGG
-recovered pasa_asmbl_15814.p1, internal, 136938, 137101
-recovered pasa_asmbl_15814.p1, internal, 137919, 138049
-recovered pasa_asmbl_15814.p1, internal, 138766, 138926
-recovered pasa_asmbl_15814.p1, internal, 139344, 139436
Valid prediction for snap_scaffold_15-snap.3085-T1
Valid prediction for Augustus_model.g25035.t1
Valid prediction for snap_scaffold_15-snap.3118-T1
Valid prediction for GlimmerHMM_glimmerT_37540-T1
Valid prediction for Augustus_model.g25037.t1
Valid prediction for snap_scaffold_15-snap.3104-T1
Couldn't classify 76793, 76926
Sorry, prediction pasa_asmbl_15810.p1 fails validation.
(CAG)	 TG	76793-76926	GT	CGG
(GTT)	 AG	79169-79228	GT	AGG
(CAT)	 AG	79602-79710	GT	AGG
(CTG)	 AG	79947-80000	GT	CGG
(GTG)	 AG	80207-80257	GT	AGG
(GTA)	 AG	80393-80512	GT	AGG
(GTA)	 AG	80663-80790	GT	CCG
(GAC)	 AG	81536-81637	GT	CGG
(GGA)	 AG	81816-82059	CA	GAC
-recovered pasa_asmbl_15810.p1, terminal, 81816, 82059
-recovered pasa_asmbl_15810.p1, internal, 79169, 79228
-recovered pasa_asmbl_15810.p1, internal, 79602, 79710
-recovered pasa_asmbl_15810.p1, internal, 79947, 80000
-recovered pasa_asmbl_15810.p1, internal, 80207, 80257
-recovered pasa_asmbl_15810.p1, internal, 80393, 80512
-recovered pasa_asmbl_15810.p1, internal, 80663, 80790
-recovered pasa_asmbl_15810.p1, internal, 81536, 81637
Valid prediction for snap_scaffold_15-snap.3095-T1
Valid prediction for HiQ_model.g25043.t1
Valid prediction for GlimmerHMM_glimmerT_37547-T1
Valid prediction for GlimmerHMM_glimmerT_37528-T1
Couldn't classify 132190, 132446
Couldn't classify 133057, 133201
Sorry, prediction pasa_asmbl_15813.p1 fails validation.
(AAG)	 TA	132190-132446	GT	AGG
(GGT)	 AG	132670-132753	GT	AAG
(AGA)	 AG	133057-133201	AA	ACA
-recovered pasa_asmbl_15813.p1, internal, 132670, 132753
Valid prediction for GlimmerHMM_glimmerT_37551-T1
Valid prediction for snap_scaffold_15-snap.3114-T1
Valid prediction for CodingQuarry_transcript_18264-T1
Couldn't classify 35550, 35972
Sorry, prediction pasa_asmbl_15805.p1 fails validation.
(CCT)	 CT	35550-35972	GT	TGG
(TCA)	 AG	36232-36294	CA	GAC
-recovered pasa_asmbl_15805.p1, terminal, 36232, 36294
Valid prediction for snap_scaffold_15-snap.3105-T1
Valid prediction for GlimmerHMM_glimmerT_37531-T1
Valid prediction for GlimmerHMM_glimmerT_37549-T1
Valid prediction for pasa_asmbl_15818.p1
Valid prediction for CodingQuarry_transcript_18268-T1
Couldn't classify 116229, 116240
Sorry, prediction pasa_asmbl_15811.p1 fails validation.
(ATC)	 AC	116229-116240	GT	TTG
(ACT)	 AG	116337-116478	GT	AGG
(AAC)	 AG	116623-116768	GT	AGG
(CTG)	 AG	116886-117089	GT	AGG
(GAG)	 AG	117414-117576	GT	AGG
(ATA)	 AG	118000-118086	GT	CAG
(TGC)	 AG	118361-118449	AT	AGA
-recovered pasa_asmbl_15811.p1, terminal, 118361, 118449
-recovered pasa_asmbl_15811.p1, internal, 116337, 116478
-recovered pasa_asmbl_15811.p1, internal, 116623, 116768
-recovered pasa_asmbl_15811.p1, internal, 116886, 117089
-recovered pasa_asmbl_15811.p1, internal, 117414, 117576
-recovered pasa_asmbl_15811.p1, internal, 118000, 118086
Valid prediction for snap_scaffold_15-snap.3083-T1
Valid prediction for snap_scaffold_15-snap.3093-T1
Valid prediction for snap_scaffold_15-snap.3100-T1
Valid prediction for Augustus_model.g25034.t1
Couldn't classify 141474, 141614
Sorry, prediction pasa_asmbl_15815.p1 fails validation.
(CTG)	 TG	141474-141614	GT	TGG
(GCC)	 AG	141738-141902	GA	AAG
-recovered pasa_asmbl_15815.p1, terminal, 141738, 141902
Valid prediction for GlimmerHMM_glimmerT_37536-T1
Valid prediction for snap_scaffold_15-snap.3091-T1
Valid prediction for Augustus_model.g25020.t1
Valid prediction for GlimmerHMM_glimmerT_37542-T1
Valid prediction for pasa_asmbl_15816.p1
Valid prediction for snap_scaffold_15-snap.3089-T1
Valid prediction for Augustus_model.g25028.t1
Valid prediction for HiQ_model.g25044.t1
Valid prediction for Augustus_model.g25023.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_15-snap.3078-T1
Valid prediction for Augustus_model.g25026.t1
Valid prediction for GlimmerHMM_glimmerT_37552-T1
Valid prediction for snap_scaffold_15-snap.3110-T1
Valid prediction for Augustus_model.g25032.t1
Valid prediction for GlimmerHMM_glimmerT_37527-T1
Valid prediction for Augustus_model.g25040.t1
Valid prediction for Augustus_model.g25033.t1
Valid prediction for GlimmerHMM_glimmerT_37523-T1
Valid prediction for snap_scaffold_15-snap.3106-T1
Valid prediction for GlimmerHMM_glimmerT_37529-T1
Valid prediction for snap_scaffold_15-snap.3079-T1
Valid prediction for snap_scaffold_15-snap.3096-T1
Valid prediction for Augustus_model.g25036.t1
Valid prediction for GlimmerHMM_glimmerT_37534-T1
Valid prediction for snap_scaffold_15-snap.3101-T1
Valid prediction for snap_scaffold_15-snap.3109-T1
Valid prediction for GlimmerHMM_glimmerT_37530-T1
Valid prediction for snap_scaffold_15-snap.3115-T1
Valid prediction for snap_scaffold_15-snap.3111-T1
Valid prediction for GlimmerHMM_glimmerT_37544-T1
Valid prediction for snap_scaffold_15-snap.3107-T1
Valid prediction for snap_scaffold_15-snap.3112-T1
Valid prediction for Augustus_model.g25030.t1
Valid prediction for Augustus_model.g25021.t1
Valid prediction for snap_scaffold_15-snap.3082-T1
Valid prediction for GlimmerHMM_glimmerT_37521-T1
Valid prediction for snap_scaffold_15-snap.3113-T1
Valid prediction for snap_scaffold_15-snap.3081-T1
Valid prediction for GlimmerHMM_glimmerT_37538-T1
Valid prediction for snap_scaffold_15-snap.3086-T1
Valid prediction for GlimmerHMM_glimmerT_37550-T1
Valid prediction for Augustus_model.g25045.t1
Valid prediction for snap_scaffold_15-snap.3108-T1
Valid prediction for GlimmerHMM_glimmerT_37525-T1
Valid prediction for GlimmerHMM_glimmerT_37545-T1
Valid prediction for Augustus_model.g25022.t1
Valid prediction for Augustus_model.g25041.t1
Valid prediction for CodingQuarry_transcript_18266-T1
Valid prediction for Augustus_model.g25024.t1
Valid prediction for GlimmerHMM_glimmerT_37543-T1
Couldn't classify 112211, 112411
Sorry, prediction pasa_asmbl_14797.p1 fails validation.
(TCA)	 CT	112211-112411	GT	AGG
(GAG)	 AG	114108-114147	GT	TAG
(GTT)	 AG	114275-114432	GT	TGG
(GAC)	 AG	114876-115011	GT	CAG
(ATC)	 AG	115300-115374	GT	AAG
(ATG)	 AG	116645-116777	GT	ATG
(GAA)	 AG	116905-117040	GT	CTG
(AAT)	 AG	117365-117517	GA	AGG
add_exon() Sorry, pasa_asmbl_14797.p1 116645-116777-initial-1 is invalid.
-recovered pasa_asmbl_14797.p1, initial, 116645, 116777
-recovered pasa_asmbl_14797.p1, terminal, 117365, 117517
-recovered pasa_asmbl_14797.p1, internal, 114108, 114147
-recovered pasa_asmbl_14797.p1, internal, 114275, 114432
-recovered pasa_asmbl_14797.p1, internal, 114876, 115011
-recovered pasa_asmbl_14797.p1, internal, 115300, 115374
-recovered pasa_asmbl_14797.p1, internal, 116645, 116777
-recovered pasa_asmbl_14797.p1, internal, 116905, 117040
Couldn't classify 245805, 245842
Sorry, prediction pasa_asmbl_14796.p1 fails validation.
(GTG)	 AT	245805-245842	GT	AGG
(TTT)	 AG	246842-246974	GT	AGG
(CAT)	 AG	247094-247192	GT	AGG
(CTT)	 AG	247323-247508	GT	AGG
(ATT)	 AG	247646-247948	TT	AAT
-recovered pasa_asmbl_14796.p1, terminal, 247646, 247948
-recovered pasa_asmbl_14796.p1, internal, 246842, 246974
-recovered pasa_asmbl_14796.p1, internal, 247094, 247192
-recovered pasa_asmbl_14796.p1, internal, 247323, 247508
Valid prediction for snap_scaffold_15-snap.3088-T1
Couldn't classify 255264, 255323
Couldn't classify 260116, 260300
Sorry, prediction pasa_asmbl_14794.p1 fails validation.
(AAC)	 TG	255264-255323	GT	CGG
(GTG)	 AG	256703-256798	GT	AGG
(GGT)	 AG	257276-257555	GT	AGG
(GTA)	 AG	260116-260300	TG	TGT
-recovered pasa_asmbl_14794.p1, internal, 256703, 256798
-recovered pasa_asmbl_14794.p1, internal, 257276, 257555
Couldn't classify 198761, 199177
Sorry, prediction pasa_asmbl_15809.p1 fails validation.
(ATG)	 GT	198761-199177	CA	CTC
Valid prediction for snap_scaffold_15-snap.3080-T1
Valid prediction for GlimmerHMM_glimmerT_37524-T1
Valid prediction for snap_scaffold_15-snap.3094-T1
Valid prediction for snap_scaffold_15-snap.3120-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 194937, rend_intergenic: 193702  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 271890
-exon list size: 357


building trellis

0.3    
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10.9    
11.1    
11.4    
11.7    
12.0    
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13.1    
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13.6    
13.9    
14.2    
14.5    
14.8    
15.0    
15.3    
15.6    
15.9    
16.2    
16.4    
16.7    
17.0    
17.3    
17.5    
17.8    
18.1    
18.4    
18.7    
18.9    
19.2    
19.5    
19.8    
20.1    
20.3    
20.6    
20.9    
21.2    
21.4    
21.7    
22.0    
22.3    
22.6    
22.8    
23.1    
23.4    
23.7    
24.0    
24.2    
24.5    
24.8    
25.1    
25.3    
25.6    
25.9    
26.2    
26.5    
26.7    
27.0    
27.3    
27.6    
27.9    
28.1    
28.4    
28.7    
29.0    
29.2    
29.5    
29.8    
30.1    
30.4    
30.6    
30.9    
31.2    
31.5    
31.8    
32.0    
32.3    
32.6    
32.9    
33.1    
33.4    
33.7    
34.0    
34.3    
34.5    
34.8    
35.1    
35.4    
35.7    
35.9    
36.2    
36.5    
36.8    
37.0    
37.3    
37.6    
37.9    
38.2    
38.4    
38.7    
39.0    
39.3    
39.6    
39.8    
40.1    
40.4    
40.7    
40.9    
41.2    
41.5    
41.8    
42.1    
42.3    
42.6    
42.9    
43.2    
43.5    
43.7    
44.0    
44.3    
44.6    
44.8    
45.1    
45.4    
45.7    
46.0    
46.2    
46.5    
46.8    
47.1    
47.4    
47.6    
47.9    
48.2    
48.5    
48.7    
49.0    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
51.0    
51.3    
51.5    
51.8    
52.1    
52.4    
52.6    
52.9    
53.2    
53.5    
53.8    
54.0    
54.3    
54.6    
54.9    
55.2    
55.4    
55.7    
56.0    
56.3    
56.5    
56.8    
57.1    
57.4    
57.7    
57.9    
58.2    
58.5    
58.8    
59.1    
59.3    
59.6    
59.9    
60.2    
60.4    
60.7    
61.0    
61.3    
61.6    
61.8    
62.1    
62.4    
62.7    
63.0    
63.2    
63.5    
63.8    
64.1    
64.3    
64.6    
64.9    
65.2    
65.5    
65.7    
66.0    
66.3    
66.6    
66.9    
67.1    
67.4    
67.7    
68.0    
68.2    
68.5    
68.8    
69.1    
69.4    
69.6    
69.9    
70.2    
70.5    
70.8    
71.0    
71.3    
71.6    
71.9    
72.1    
72.4    
72.7    
73.0    
73.3    
73.5    
73.8    
74.1    
74.4    
74.7    
74.9    
75.2    
75.5    
75.8    
76.0    
76.3    
76.6    
76.9    
77.2    
77.4    
77.7    
78.0    
78.3    
78.6    
78.8    
79.1    
79.4    
79.7    
79.9    
80.2    
80.5    
80.8    
81.1    
81.3    
81.6    
81.9    
82.2    
82.5    
82.7    
83.0    
83.3    
83.6    
83.8    
84.1    
84.4    
84.7    
85.0    
85.2    
85.5    
85.8    
86.1    
86.4    
86.6    
86.9    
87.2    
87.5    
87.7    
88.0    
88.3    
88.6    
88.9    
89.1    
89.4    
89.7    
90.0    
90.3    
90.5    
90.8    
91.1    
91.4    
91.6    
91.9    
92.2    
92.5    
92.8    
93.0    
93.3    
93.6    
93.9    
94.2    
94.4    
94.7    
95.0    
95.3    
95.5    
95.8    
96.1    
96.4    
96.7    
96.9    
97.2    
97.5    
97.8    
98.1    
98.3    
98.6    
98.9    
99.2    
99.4    
99.7    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 194937, rend_intergenic: 193702  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 30 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 255594 - 271890
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-found 1 predictions from path traversal

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

-building DP trellis

-building trellis in range 255594 - 269363
-exon list size: 1


building trellis

33.3    
66.7    
-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