-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_5/scaffold_5_14265038-14555582

-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_5-snap.2645-T1
Valid prediction for Augustus_model.g8697.t1
Valid prediction for Augustus_model.g8698.t1
Valid prediction for Augustus_model.g8685.t1
Couldn't classify 175643, 176205
Couldn't classify 179247, 179286
Sorry, prediction pasa_asmbl_45934.p1 fails validation.
(AGT)	 CC	175643-176205	GT	AGG
(CAT)	 AG	176312-176480	GT	AGG
(TTG)	 AG	178930-179132	GT	ATG
(CAT)	 AG	179247-179286	AT	ACA
-recovered pasa_asmbl_45934.p1, internal, 176312, 176480
-recovered pasa_asmbl_45934.p1, internal, 178930, 179132
Valid prediction for Augustus_model.g8696.t1
Couldn't classify 179380, 179419
Couldn't classify 184424, 185145
Sorry, prediction pasa_asmbl_45935.p1 fails validation.
(CAT)	 AA	179380-179419	GT	CTG
(CCC)	 AG	181233-181373	GT	GGG
(ATG)	 AG	183941-183996	GT	CTG
(AGC)	 AG	184089-184221	GT	AGG
(TAC)	 AG	184424-185145	GA	AGG
-recovered pasa_asmbl_45935.p1, initial, 183941, 183996
-recovered pasa_asmbl_45935.p1, internal, 181233, 181373
-recovered pasa_asmbl_45935.p1, internal, 183941, 183996
-recovered pasa_asmbl_45935.p1, internal, 184089, 184221
Valid prediction for snap_scaffold_5-snap.2648-T1
Valid prediction for Augustus_model.g8692.t1
Couldn't classify 285210, 285252
Couldn't classify 286083, 286107
Sorry, prediction pasa_asmbl_45945.p1 fails validation.
(GAC)	 GT	285210-285252	GT	CGG
(GTC)	 AG	285492-285626	GT	AAG
(ATC)	 AG	285734-285932	GT	GAG
(CTA)	 AG	286083-286107	AC	AGA
add_exon() Sorry, pasa_asmbl_45945.p1 285734-285932-terminal-3 is invalid.
-recovered pasa_asmbl_45945.p1, terminal, 285734, 285932
-recovered pasa_asmbl_45945.p1, internal, 285492, 285626
-recovered pasa_asmbl_45945.p1, internal, 285734, 285932
Valid prediction for GlimmerHMM_glimmerT_13078-T1
Valid prediction for Augustus_model.g8689.t1
Valid prediction for Augustus_model.g8690.t1
Valid prediction for snap_scaffold_5-snap.2650-T1
Valid prediction for GlimmerHMM_glimmerT_13084-T1
Valid prediction for GlimmerHMM_glimmerT_13058-T1
Valid prediction for snap_scaffold_5-snap.2630-T1
Valid prediction for snap_scaffold_5-snap.2641-T1
Valid prediction for GlimmerHMM_glimmerT_13067-T1
Valid prediction for GlimmerHMM_glimmerT_13065-T1
Valid prediction for snap_scaffold_5-snap.2633-T1
Valid prediction for HiQ_model.g8691.t1
Valid prediction for snap_scaffold_5-snap.2649-T1
Valid prediction for Augustus_model.g8699.t1
Couldn't classify 238849, 238855
Sorry, prediction pasa_asmbl_45938.p1 fails validation.
(AGA)	 CA	238849-238855	GT	GGG
(GAG)	 AG	239077-239208	GT	AGG
(GCA)	 AG	239341-239549	GC	AGG
-recovered pasa_asmbl_45938.p1, terminal, 239341, 239549
-recovered pasa_asmbl_45938.p1, internal, 239077, 239208
-recovered pasa_asmbl_45938.p1, internal, 239341, 239549
Valid prediction for snap_scaffold_5-snap.2638-T1
Valid prediction for snap_scaffold_5-snap.2646-T1
Valid prediction for snap_scaffold_5-snap.2661-T1
Couldn't classify 254811, 254832
Couldn't classify 255511, 255603
Sorry, prediction pasa_asmbl_45939.p2 fails validation.
(AGT)	 TC	254811-254832	GT	AGG
(AAA)	 AG	255039-255154	GT	AGG
(TTC)	 AG	255238-255351	GT	AGG
(TCC)	 AG	255511-255603	GG	CAG
-recovered pasa_asmbl_45939.p2, internal, 255039, 255154
-recovered pasa_asmbl_45939.p2, internal, 255238, 255351
Valid prediction for GlimmerHMM_glimmerT_13061-T1
Valid prediction for GlimmerHMM_glimmerT_13081-T1
Valid prediction for GlimmerHMM_glimmerT_13063-T1
Valid prediction for GlimmerHMM_glimmerT_13074-T1
Valid prediction for snap_scaffold_5-snap.2644-T1
Valid prediction for GlimmerHMM_glimmerT_13077-T1
Valid prediction for snap_scaffold_5-snap.2652-T1
Valid prediction for snap_scaffold_5-snap.2640-T1
Valid prediction for GlimmerHMM_glimmerT_13070-T1
Couldn't classify 150420, 150471
Sorry, prediction pasa_asmbl_45931.p1 fails validation.
(AAC)	 AG	150420-150471	GT	TGG
(GGT)	 AG	151808-151902	GT	CTG
(GAT)	 AG	152216-152296	GT	GGG
(GAG)	 AG	152462-152537	GT	TGG
(GGA)	 AG	152989-153065	GT	AGG
(GTG)	 AG	153250-153410	GT	AGG
(TTT)	 AG	153495-153637	GT	AGG
(GGA)	 AG	154428-154540	GT	AGG
(CCC)	 AG	155303-155512	GT	AGG
(GTG)	 AG	157697-157858	GT	GAG
(GAT)	 AG	158374-158466	GT	AGG
(TGT)	 AG	158579-158662	GT	AGG
(GCC)	 AG	159620-159790	GT	AGG
(GTG)	 AG	159907-160005	GT	CTG
(GTG)	 AG	161120-161209	GT	AGG
(GTG)	 AG	161493-161637	GT	GGG
(GGG)	 AG	161918-161982	GT	AAG
(GAA)	 AG	162507-162662	GT	AGG
(GTT)	 AG	163201-163265	GT	GGG
(ATA)	 AG	163623-163731	GT	AGG
(GGT)	 AG	163890-163947	GT	AGG
(GCA)	 AG	165140-165343	GT	CGG
(ATG)	 AG	166304-166440	AC	AGA
-recovered pasa_asmbl_45931.p1, terminal, 166304, 166440
-recovered pasa_asmbl_45931.p1, internal, 150420, 150471
-recovered pasa_asmbl_45931.p1, internal, 151808, 151902
-recovered pasa_asmbl_45931.p1, internal, 152216, 152296
-recovered pasa_asmbl_45931.p1, internal, 152462, 152537
-recovered pasa_asmbl_45931.p1, internal, 152989, 153065
-recovered pasa_asmbl_45931.p1, internal, 153250, 153410
-recovered pasa_asmbl_45931.p1, internal, 153495, 153637
-recovered pasa_asmbl_45931.p1, internal, 154428, 154540
-recovered pasa_asmbl_45931.p1, internal, 155303, 155512
-recovered pasa_asmbl_45931.p1, internal, 157697, 157858
-recovered pasa_asmbl_45931.p1, internal, 158374, 158466
-recovered pasa_asmbl_45931.p1, internal, 158579, 158662
-recovered pasa_asmbl_45931.p1, internal, 159620, 159790
-recovered pasa_asmbl_45931.p1, internal, 159907, 160005
-recovered pasa_asmbl_45931.p1, internal, 161120, 161209
-recovered pasa_asmbl_45931.p1, internal, 161493, 161637
-recovered pasa_asmbl_45931.p1, internal, 161918, 161982
-recovered pasa_asmbl_45931.p1, internal, 162507, 162662
-recovered pasa_asmbl_45931.p1, internal, 163201, 163265
-recovered pasa_asmbl_45931.p1, internal, 163623, 163731
-recovered pasa_asmbl_45931.p1, internal, 163890, 163947
-recovered pasa_asmbl_45931.p1, internal, 165140, 165343
Valid prediction for snap_scaffold_5-snap.2647-T1
Valid prediction for GlimmerHMM_glimmerT_13079-T1
Valid prediction for Augustus_model.g8694.t1
Valid prediction for snap_scaffold_5-snap.2662-T1
Valid prediction for snap_scaffold_5-snap.2658-T1
Couldn't classify 10613, 11119
Sorry, prediction pasa_asmbl_45924.p1 fails validation.
(AGC)	 CC	10613-11119	TA	GCT
Couldn't classify 112321, 112435
Couldn't classify 112662, 112966
Sorry, prediction pasa_asmbl_45926.p1 fails validation.
(AGT)	 GC	112321-112435	GT	TGG
(GGG)	 AG	112662-112966	GC	GAG
-recovered pasa_asmbl_45926.p1, internal, 112662, 112966
Valid prediction for snap_scaffold_5-snap.2665-T1
Valid prediction for GlimmerHMM_glimmerT_13068-T1
Valid prediction for snap_scaffold_5-snap.2663-T1
Valid prediction for GlimmerHMM_glimmerT_13075-T1
Valid prediction for GlimmerHMM_glimmerT_13080-T1
Valid prediction for snap_scaffold_5-snap.2642-T1
Couldn't classify 113099, 114094
Sorry, prediction pasa_asmbl_45927.p1 fails validation.
(GGC)	 AA	113099-114094	CA	GAC
Valid prediction for GlimmerHMM_glimmerT_13066-T1
Valid prediction for snap_scaffold_5-snap.2659-T1
Valid prediction for HiQ_model.g8701.t1
Valid prediction for Augustus_model.g8693.t1
Couldn't classify 287158, 287297
Sorry, prediction pasa_asmbl_45946.p2 fails validation.
(TAC)	 TC	287158-287297	GT	AAG
(GTT)	 AG	287426-287480	GT	AGG
(ATC)	 AG	287574-287726	GA	AGG
-recovered pasa_asmbl_45946.p2, terminal, 287574, 287726
-recovered pasa_asmbl_45946.p2, internal, 287426, 287480
Couldn't classify 233581, 233746
Couldn't classify 238110, 238252
Sorry, prediction pasa_asmbl_45937.p1 fails validation.
(CAC)	 GG	233581-233746	GT	AGG
(TGG)	 AG	233844-233943	GT	ACG
(GGA)	 AG	235859-235957	GT	GAG
(GTG)	 AG	236527-236630	GT	AGG
(GTG)	 AG	237512-237661	GT	GAG
(AGC)	 AG	237766-237921	GT	GGG
(GAA)	 AG	238110-238252	GA	AGG
-recovered pasa_asmbl_45937.p1, internal, 233844, 233943
-recovered pasa_asmbl_45937.p1, internal, 235859, 235957
-recovered pasa_asmbl_45937.p1, internal, 236527, 236630
-recovered pasa_asmbl_45937.p1, internal, 237512, 237661
-recovered pasa_asmbl_45937.p1, internal, 237766, 237921
Couldn't classify 272598, 272700
Sorry, prediction pasa_asmbl_45941.p2 fails validation.
(TCG)	 CA	272598-272700	GT	TTG
(TGA)	 AG	272811-273151	AA	GAA
-recovered pasa_asmbl_45941.p2, terminal, 272811, 273151
Valid prediction for GlimmerHMM_glimmerT_13072-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_13083-T1
Valid prediction for snap_scaffold_5-snap.2664-T1
Valid prediction for snap_scaffold_5-snap.2660-T1
Valid prediction for snap_scaffold_5-snap.2631-T1
Valid prediction for GlimmerHMM_glimmerT_13071-T1
Valid prediction for snap_scaffold_5-snap.2655-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_13059-T1
Valid prediction for Augustus_model.g8700.t1
Valid prediction for snap_scaffold_5-snap.2639-T1
Valid prediction for snap_scaffold_5-snap.2637-T1
Valid prediction for pasa_asmbl_44596.p1
Valid prediction for snap_scaffold_5-snap.2651-T1
Valid prediction for GlimmerHMM_glimmerT_13064-T1
Valid prediction for Augustus_model.g8687.t1
Valid prediction for GlimmerHMM_glimmerT_13076-T1
Valid prediction for GlimmerHMM_glimmerT_13069-T1
Valid prediction for snap_scaffold_5-snap.2654-T1
Valid prediction for snap_scaffold_5-snap.2636-T1
Valid prediction for GlimmerHMM_glimmerT_13060-T1
Valid prediction for Augustus_model.g8695.t1
Valid prediction for snap_scaffold_5-snap.2656-T1
Valid prediction for snap_scaffold_5-snap.2643-T1
Valid prediction for snap_scaffold_5-snap.2634-T1
Valid prediction for Augustus_model.g8686.t1
Valid prediction for GlimmerHMM_glimmerT_13082-T1
Valid prediction for snap_scaffold_5-snap.2632-T1
Valid prediction for snap_scaffold_5-snap.2653-T1
Valid prediction for snap_scaffold_5-snap.2657-T1
Valid prediction for GlimmerHMM_glimmerT_13062-T1
Valid prediction for GlimmerHMM_glimmerT_13073-T1
Valid prediction for Augustus_model.g8688.t1
Valid prediction for snap_scaffold_5-snap.2635-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 153398, rend_intergenic: 151144  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188424, rend_intergenic: 182380  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 256732, rend_intergenic: 246159  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 290545
-exon list size: 355


building trellis

0.3    
0.6    
0.8    
1.1    
1.4    
1.7    
2.0    
2.2    
2.5    
2.8    
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3.4    
3.6    
3.9    
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4.5    
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5.0    
5.3    
5.6    
5.9    
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7.0    
7.3    
7.6    
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8.1    
8.4    
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10.1    
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10.6    
10.9    
11.2    
11.5    
11.8    
12.0    
12.3    
12.6    
12.9    
13.2    
13.4    
13.7    
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14.3    
14.6    
14.8    
15.1    
15.4    
15.7    
16.0    
16.2    
16.5    
16.8    
17.1    
17.4    
17.6    
17.9    
18.2    
18.5    
18.8    
19.0    
19.3    
19.6    
19.9    
20.2    
20.4    
20.7    
21.0    
21.3    
21.6    
21.8    
22.1    
22.4    
22.7    
23.0    
23.2    
23.5    
23.8    
24.1    
24.4    
24.6    
24.9    
25.2    
25.5    
25.8    
26.1    
26.3    
26.6    
26.9    
27.2    
27.5    
27.7    
28.0    
28.3    
28.6    
28.9    
29.1    
29.4    
29.7    
30.0    
30.3    
30.5    
30.8    
31.1    
31.4    
31.7    
31.9    
32.2    
32.5    
32.8    
33.1    
33.3    
33.6    
33.9    
34.2    
34.5    
34.7    
35.0    
35.3    
35.6    
35.9    
36.1    
36.4    
36.7    
37.0    
37.3    
37.5    
37.8    
38.1    
38.4    
38.7    
38.9    
39.2    
39.5    
39.8    
40.1    
40.3    
40.6    
40.9    
41.2    
41.5    
41.7    
42.0    
42.3    
42.6    
42.9    
43.1    
43.4    
43.7    
44.0    
44.3    
44.5    
44.8    
45.1    
45.4    
45.7    
45.9    
46.2    
46.5    
46.8    
47.1    
47.3    
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    
52.7    
52.9    
53.2    
53.5    
53.8    
54.1    
54.3    
54.6    
54.9    
55.2    
55.5    
55.7    
56.0    
56.3    
56.6    
56.9    
57.1    
57.4    
57.7    
58.0    
58.3    
58.5    
58.8    
59.1    
59.4    
59.7    
59.9    
60.2    
60.5    
60.8    
61.1    
61.3    
61.6    
61.9    
62.2    
62.5    
62.7    
63.0    
63.3    
63.6    
63.9    
64.1    
64.4    
64.7    
65.0    
65.3    
65.5    
65.8    
66.1    
66.4    
66.7    
66.9    
67.2    
67.5    
67.8    
68.1    
68.3    
68.6    
68.9    
69.2    
69.5    
69.7    
70.0    
70.3    
70.6    
70.9    
71.1    
71.4    
71.7    
72.0    
72.3    
72.5    
72.8    
73.1    
73.4    
73.7    
73.9    
74.2    
74.5    
74.8    
75.1    
75.4    
75.6    
75.9    
76.2    
76.5    
76.8    
77.0    
77.3    
77.6    
77.9    
78.2    
78.4    
78.7    
79.0    
79.3    
79.6    
79.8    
80.1    
80.4    
80.7    
81.0    
81.2    
81.5    
81.8    
82.1    
82.4    
82.6    
82.9    
83.2    
83.5    
83.8    
84.0    
84.3    
84.6    
84.9    
85.2    
85.4    
85.7    
86.0    
86.3    
86.6    
86.8    
87.1    
87.4    
87.7    
88.0    
88.2    
88.5    
88.8    
89.1    
89.4    
89.6    
89.9    
90.2    
90.5    
90.8    
91.0    
91.3    
91.6    
91.9    
92.2    
92.4    
92.7    
93.0    
93.3    
93.6    
93.8    
94.1    
94.4    
94.7    
95.0    
95.2    
95.5    
95.8    
96.1    
96.4    
96.6    
96.9    
97.2    
97.5    
97.8    
98.0    
98.3    
98.6    
98.9    
99.2    
99.4    
99.7    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 153398, rend_intergenic: 151144  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188424, rend_intergenic: 182380  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 256732, rend_intergenic: 246159  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support