-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_21/scaffold_21_782775-1029028

-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_21-snap.165-T1
Valid prediction for snap_scaffold_21-snap.149-T1
Valid prediction for GeneMark_model.83814_t
Valid prediction for CodingQuarry_transcript_32374-T1
Valid prediction for Augustus_model.g32243.t1
Valid prediction for Augustus_model.g32251.t1
Valid prediction for GeneMark_model.83810_t
Valid prediction for snap_scaffold_21-snap.159-T1
Valid prediction for Augustus_model.g32242.t1
Valid prediction for GeneMark_model.83820_t
Valid prediction for HiQ_model.g32245.t1
Valid prediction for snap_scaffold_21-snap.158-T1
Valid prediction for GlimmerHMM_glimmerT_48207-T1
Valid prediction for GlimmerHMM_glimmerT_48224-T1
Valid prediction for GeneMark_model.83803_t
Valid prediction for GeneMark_model.83798_t
Valid prediction for snap_scaffold_21-snap.140-T1
Valid prediction for snap_scaffold_21-snap.144-T1
Valid prediction for Augustus_model.g32241.t1
Valid prediction for GeneMark_model.83818_t
Valid prediction for CodingQuarry_transcript_32377-T1
Couldn't classify 40885, 41034
Sorry, prediction pasa_asmbl_28331.p1 fails validation.
(TGG)	 GC	40885-41034	GT	AGG
(GAT)	 AG	41333-41469	GT	TGG
(CTG)	 AG	42133-42259	GT	GGG
(GGG)	 AG	42567-42602	GT	AGG
(ATT)	 AG	42812-42933	GT	GTG
(ATG)	 AG	43860-43989	GT	CTG
(GAC)	 AG	46317-46465	GT	GTG
(ATG)	 AG	46933-47062	GT	TGG
(GAT)	 AG	47219-47251	GT	TGG
(CTA)	 AG	47605-47714	GT	AGG
(CTG)	 AG	48385-48511	GT	ATG
(AGT)	 AG	48757-48884	GT	ATG
(ATG)	 AG	50507-50630	GT	AGG
(CCC)	 AG	51921-52079	GT	AGG
(GCT)	 AG	52742-52901	GT	AGG
(GCG)	 AG	53084-53172	GG	AGG
add_exon() Sorry, pasa_asmbl_28331.p1 43860-43989-initial-1 is invalid.
-recovered pasa_asmbl_28331.p1, initial, 43860, 43989
add_exon() Sorry, pasa_asmbl_28331.p1 46933-47062-initial-1 is invalid.
-recovered pasa_asmbl_28331.p1, initial, 46933, 47062
add_exon() Sorry, pasa_asmbl_28331.p1 50507-50630-initial-1 is invalid.
-recovered pasa_asmbl_28331.p1, initial, 50507, 50630
-recovered pasa_asmbl_28331.p1, terminal, 53084, 53172
-recovered pasa_asmbl_28331.p1, internal, 41333, 41469
-recovered pasa_asmbl_28331.p1, internal, 42133, 42259
-recovered pasa_asmbl_28331.p1, internal, 42567, 42602
-recovered pasa_asmbl_28331.p1, internal, 42812, 42933
-recovered pasa_asmbl_28331.p1, internal, 43860, 43989
-recovered pasa_asmbl_28331.p1, internal, 46317, 46465
-recovered pasa_asmbl_28331.p1, internal, 46933, 47062
-recovered pasa_asmbl_28331.p1, internal, 47219, 47251
-recovered pasa_asmbl_28331.p1, internal, 47605, 47714
-recovered pasa_asmbl_28331.p1, internal, 48385, 48511
-recovered pasa_asmbl_28331.p1, internal, 48757, 48884
-recovered pasa_asmbl_28331.p1, internal, 50507, 50630
-recovered pasa_asmbl_28331.p1, internal, 51921, 52079
-recovered pasa_asmbl_28331.p1, internal, 52742, 52901
Valid prediction for Augustus_model.g32252.t1
Valid prediction for snap_scaffold_21-snap.143-T1
Couldn't classify 150341, 151261
Sorry, prediction pasa_asmbl_28232.p1 fails validation.
(GGG)	 GG	150341-151261	TC	TCT
Valid prediction for snap_scaffold_21-snap.134-T1
Valid prediction for Augustus_model.g32253.t1
Valid prediction for GlimmerHMM_glimmerT_48222-T1
Valid prediction for snap_scaffold_21-snap.147-T1
Valid prediction for GlimmerHMM_glimmerT_48227-T1
Valid prediction for HiQ_model.g32248.t1
Valid prediction for GeneMark_model.83799_t
Valid prediction for Augustus_model.g32244.t1
Valid prediction for GeneMark_model.83812_t
Valid prediction for snap_scaffold_21-snap.167-T1
Valid prediction for GeneMark_model.83822_t
Valid prediction for GeneMark_model.83817_t
Valid prediction for GeneMark_model.83808_t
Couldn't classify 52598, 52901
Sorry, prediction pasa_asmbl_28337.p1 fails validation.
(TTG)	 GT	52598-52901	GT	AGG
(GCG)	 AG	53084-53172	GG	AGG
-recovered pasa_asmbl_28337.p1, terminal, 53084, 53172
Valid prediction for GlimmerHMM_glimmerT_48223-T1
Valid prediction for GlimmerHMM_glimmerT_48221-T1
Valid prediction for GlimmerHMM_glimmerT_48209-T1
Valid prediction for snap_scaffold_21-snap.161-T1
Valid prediction for GeneMark_model.83800_t
Valid prediction for GeneMark_model.83826_t
Valid prediction for GeneMark_model.83802_t
Valid prediction for GlimmerHMM_glimmerT_48210-T1
Valid prediction for snap_scaffold_21-snap.146-T1
Valid prediction for snap_scaffold_21-snap.150-T1
Couldn't classify 31113, 34604
Sorry, prediction pasa_asmbl_28330.p1 fails validation.
(ACG)	 GA	31113-34604	GT	AGG
(GAA)	 AG	34708-34752	GT	TGG
(ATA)	 AG	36245-36364	GA	AAG
-recovered pasa_asmbl_28330.p1, terminal, 36245, 36364
-recovered pasa_asmbl_28330.p1, internal, 34708, 34752
Valid prediction for GlimmerHMM_glimmerT_48217-T1
Valid prediction for GeneMark_model.83815_t
Valid prediction for GlimmerHMM_glimmerT_48215-T1
Valid prediction for GeneMark_model.83823_t
Valid prediction for GeneMark_model.83801_t
Valid prediction for pasa_asmbl_28329.p1
Valid prediction for GeneMark_model.83825_t
Valid prediction for snap_scaffold_21-snap.138-T1
Valid prediction for snap_scaffold_21-snap.155-T1
Valid prediction for snap_scaffold_21-snap.145-T1
Valid prediction for snap_scaffold_21-snap.152-T1
Valid prediction for CodingQuarry_transcript_32373-T1
Valid prediction for CodingQuarry_transcript_32370-T1
Valid prediction for Augustus_model.g32249.t1
Couldn't classify 200961, 201116
Sorry, prediction pasa_asmbl_28339.p1 fails validation.
(TCT)	 TC	200961-201116	GT	AGG
(GGC)	 AG	202165-202297	GT	CTG
(ACC)	 AG	203212-203324	GT	AGG
(GAC)	 AG	203597-203723	GT	AGG
(GAA)	 AG	203968-204089	GT	ACG
(GAG)	 AG	204881-205010	GT	CTG
(TAT)	 AG	205665-205691	GT	AGG
(GGA)	 AG	206223-206337	GT	AGG
(ACA)	 AG	206421-206511	AG	AGA
-recovered pasa_asmbl_28339.p1, terminal, 206421, 206511
-recovered pasa_asmbl_28339.p1, internal, 202165, 202297
-recovered pasa_asmbl_28339.p1, internal, 203212, 203324
-recovered pasa_asmbl_28339.p1, internal, 203597, 203723
-recovered pasa_asmbl_28339.p1, internal, 203968, 204089
-recovered pasa_asmbl_28339.p1, internal, 204881, 205010
-recovered pasa_asmbl_28339.p1, internal, 205665, 205691
-recovered pasa_asmbl_28339.p1, internal, 206223, 206337
Valid prediction for GlimmerHMM_glimmerT_48208-T1
Valid prediction for snap_scaffold_21-snap.135-T1
Valid prediction for GeneMark_model.83813_t
Valid prediction for GlimmerHMM_glimmerT_48216-T1
Valid prediction for snap_scaffold_21-snap.139-T1
Valid prediction for CodingQuarry_transcript_32372-T1
Valid prediction for GeneMark_model.83807_t
Valid prediction for snap_scaffold_21-snap.137-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_48219-T1
Valid prediction for snap_scaffold_21-snap.160-T1
Valid prediction for snap_scaffold_21-snap.133-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_48214-T1
Valid prediction for GlimmerHMM_glimmerT_48226-T1
Valid prediction for pasa_asmbl_27390.p1
Valid prediction for GeneMark_model.83811_t
Valid prediction for snap_scaffold_21-snap.151-T1
Valid prediction for GlimmerHMM_glimmerT_48218-T1
Valid prediction for Augustus_model.g32250.t1
Valid prediction for GeneMark_model.83816_t
Valid prediction for snap_scaffold_21-snap.142-T1
Valid prediction for CodingQuarry_transcript_32376-T1
Couldn't classify 27861, 28007
Sorry, prediction pasa_asmbl_27394.p1 fails validation.
(GAC)	 CA	27861-28007	GT	GGG
(CCC)	 AG	30293-30384	GT	AAG
(GCA)	 AG	32028-32132	GT	AGG
(GAA)	 AG	32489-32553	GT	AGG
(GTG)	 AG	32667-32777	GT	AGG
(TAG)	 AG	33999-34163	GT	GGG
(ACA)	 AG	34605-34718	GT	AGG
(ACT)	 AG	34947-35191	CT	AGC
add_exon() Sorry, pasa_asmbl_27394.p1 34605-34718-terminal-1 is invalid.
-recovered pasa_asmbl_27394.p1, terminal, 34605, 34718
-recovered pasa_asmbl_27394.p1, terminal, 34947, 35191
-recovered pasa_asmbl_27394.p1, internal, 30293, 30384
-recovered pasa_asmbl_27394.p1, internal, 32028, 32132
-recovered pasa_asmbl_27394.p1, internal, 32489, 32553
-recovered pasa_asmbl_27394.p1, internal, 32667, 32777
-recovered pasa_asmbl_27394.p1, internal, 33999, 34163
-recovered pasa_asmbl_27394.p1, internal, 34605, 34718
Valid prediction for GeneMark_model.83819_t
Valid prediction for snap_scaffold_21-snap.153-T1
Valid prediction for GlimmerHMM_glimmerT_48213-T1
Valid prediction for snap_scaffold_21-snap.132-T1
Valid prediction for snap_scaffold_21-snap.163-T1
Valid prediction for GlimmerHMM_glimmerT_48211-T1
Valid prediction for Augustus_model.g32254.t1
Valid prediction for GeneMark_model.83805_t
Valid prediction for snap_scaffold_21-snap.157-T1
Valid prediction for Augustus_model.g32246.t1
Valid prediction for GeneMark_model.83806_t
Valid prediction for snap_scaffold_21-snap.166-T1
Valid prediction for snap_scaffold_21-snap.164-T1
Valid prediction for GlimmerHMM_glimmerT_48212-T1
Valid prediction for snap_scaffold_21-snap.162-T1
Valid prediction for CodingQuarry_transcript_32375-T1
Valid prediction for GlimmerHMM_glimmerT_48225-T1
Couldn't classify 187994, 188122
Sorry, prediction pasa_asmbl_27389.p1 fails validation.
(GTG)	 AG	187994-188122	GT	AGG
(GCT)	 AG	188462-188565	GT	TCG
(GTC)	 AG	188800-188902	GT	TGG
(GGA)	 AG	189423-189591	GT	AGG
(CTG)	 AG	189684-189772	GT	CAG
(GAC)	 AG	189869-189994	GT	AGG
(CCC)	 AG	190189-190347	CC	GAC
-recovered pasa_asmbl_27389.p1, terminal, 190189, 190347
-recovered pasa_asmbl_27389.p1, internal, 187994, 188122
-recovered pasa_asmbl_27389.p1, internal, 188462, 188565
-recovered pasa_asmbl_27389.p1, internal, 188800, 188902
-recovered pasa_asmbl_27389.p1, internal, 189423, 189591
-recovered pasa_asmbl_27389.p1, internal, 189684, 189772
-recovered pasa_asmbl_27389.p1, internal, 189869, 189994
Valid prediction for snap_scaffold_21-snap.156-T1
Valid prediction for snap_scaffold_21-snap.148-T1
Valid prediction for GeneMark_model.83821_t
Valid prediction for snap_scaffold_21-snap.141-T1
Valid prediction for GlimmerHMM_glimmerT_48228-T1
Valid prediction for snap_scaffold_21-snap.154-T1
Valid prediction for HiQ_model.g32247.t1
Valid prediction for GeneMark_model.83824_t
Valid prediction for GeneMark_model.83804_t
Valid prediction for snap_scaffold_21-snap.136-T1
Valid prediction for GlimmerHMM_glimmerT_48220-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 28639, rend_intergenic: 27267  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152557, rend_intergenic: 150563  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199930, rend_intergenic: 197196  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 230943, rend_intergenic: 220692  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 246254
-exon list size: 436


building trellis

0.2    
0.5    
0.7    
0.9    
1.1    
1.4    
1.6    
1.8    
2.1    
2.3    
2.5    
2.7    
3.0    
3.2    
3.4    
3.7    
3.9    
4.1    
4.3    
4.6    
4.8    
5.0    
5.3    
5.5    
5.7    
5.9    
6.2    
6.4    
6.6    
6.8    
7.1    
7.3    
7.5    
7.8    
8.0    
8.2    
8.4    
8.7    
8.9    
9.1    
9.4    
9.6    
9.8    
10.0    
10.3    
10.5    
10.7    
11.0    
11.2    
11.4    
11.6    
11.9    
12.1    
12.3    
12.6    
12.8    
13.0    
13.2    
13.5    
13.7    
13.9    
14.2    
14.4    
14.6    
14.8    
15.1    
15.3    
15.5    
15.8    
16.0    
16.2    
16.4    
16.7    
16.9    
17.1    
17.4    
17.6    
17.8    
18.0    
18.3    
18.5    
18.7    
18.9    
19.2    
19.4    
19.6    
19.9    
20.1    
20.3    
20.5    
20.8    
21.0    
21.2    
21.5    
21.7    
21.9    
22.1    
22.4    
22.6    
22.8    
23.1    
23.3    
23.5    
23.7    
24.0    
24.2    
24.4    
24.7    
24.9    
25.1    
25.3    
25.6    
25.8    
26.0    
26.3    
26.5    
26.7    
26.9    
27.2    
27.4    
27.6    
27.9    
28.1    
28.3    
28.5    
28.8    
29.0    
29.2    
29.5    
29.7    
29.9    
30.1    
30.4    
30.6    
30.8    
31.1    
31.3    
31.5    
31.7    
32.0    
32.2    
32.4    
32.6    
32.9    
33.1    
33.3    
33.6    
33.8    
34.0    
34.2    
34.5    
34.7    
34.9    
35.2    
35.4    
35.6    
35.8    
36.1    
36.3    
36.5    
36.8    
37.0    
37.2    
37.4    
37.7    
37.9    
38.1    
38.4    
38.6    
38.8    
39.0    
39.3    
39.5    
39.7    
40.0    
40.2    
40.4    
40.6    
40.9    
41.1    
41.3    
41.6    
41.8    
42.0    
42.2    
42.5    
42.7    
42.9    
43.2    
43.4    
43.6    
43.8    
44.1    
44.3    
44.5    
44.7    
45.0    
45.2    
45.4    
45.7    
45.9    
46.1    
46.3    
46.6    
46.8    
47.0    
47.3    
47.5    
47.7    
47.9    
48.2    
48.4    
48.6    
48.9    
49.1    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
50.7    
50.9    
51.1    
51.4    
51.6    
51.8    
52.1    
52.3    
52.5    
52.7    
53.0    
53.2    
53.4    
53.7    
53.9    
54.1    
54.3    
54.6    
54.8    
55.0    
55.3    
55.5    
55.7    
55.9    
56.2    
56.4    
56.6    
56.8    
57.1    
57.3    
57.5    
57.8    
58.0    
58.2    
58.4    
58.7    
58.9    
59.1    
59.4    
59.6    
59.8    
60.0    
60.3    
60.5    
60.7    
61.0    
61.2    
61.4    
61.6    
61.9    
62.1    
62.3    
62.6    
62.8    
63.0    
63.2    
63.5    
63.7    
63.9    
64.2    
64.4    
64.6    
64.8    
65.1    
65.3    
65.5    
65.8    
66.0    
66.2    
66.4    
66.7    
66.9    
67.1    
67.4    
67.6    
67.8    
68.0    
68.3    
68.5    
68.7    
68.9    
69.2    
69.4    
69.6    
69.9    
70.1    
70.3    
70.5    
70.8    
71.0    
71.2    
71.5    
71.7    
71.9    
72.1    
72.4    
72.6    
72.8    
73.1    
73.3    
73.5    
73.7    
74.0    
74.2    
74.4    
74.7    
74.9    
75.1    
75.3    
75.6    
75.8    
76.0    
76.3    
76.5    
76.7    
76.9    
77.2    
77.4    
77.6    
77.9    
78.1    
78.3    
78.5    
78.8    
79.0    
79.2    
79.5    
79.7    
79.9    
80.1    
80.4    
80.6    
80.8    
81.1    
81.3    
81.5    
81.7    
82.0    
82.2    
82.4    
82.6    
82.9    
83.1    
83.3    
83.6    
83.8    
84.0    
84.2    
84.5    
84.7    
84.9    
85.2    
85.4    
85.6    
85.8    
86.1    
86.3    
86.5    
86.8    
87.0    
87.2    
87.4    
87.7    
87.9    
88.1    
88.4    
88.6    
88.8    
89.0    
89.3    
89.5    
89.7    
90.0    
90.2    
90.4    
90.6    
90.9    
91.1    
91.3    
91.6    
91.8    
92.0    
92.2    
92.5    
92.7    
92.9    
93.2    
93.4    
93.6    
93.8    
94.1    
94.3    
94.5    
94.7    
95.0    
95.2    
95.4    
95.7    
95.9    
96.1    
96.3    
96.6    
96.8    
97.0    
97.3    
97.5    
97.7    
97.9    
98.2    
98.4    
98.6    
98.9    
99.1    
99.3    
99.5    
99.8    
-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 28639, rend_intergenic: 27267  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152557, rend_intergenic: 150563  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199930, rend_intergenic: 197196  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 230943, rend_intergenic: 220692  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support