-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_24/scaffold_24_10624862-10845424

-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 GeneMark_model.95256_t
Couldn't classify 216561, 216687
Sorry, prediction GlimmerHMM_glimmerT_54706-T1 fails validation.
(ATG)	 AA	211069-211278	GT	AGG
(GCC)	 AG	211819-212142	GT	AGG
(TTT)	 AG	216561-216687	GT	AGG
-recovered GlimmerHMM_glimmerT_54706-T1, initial, 211069, 211278
-recovered GlimmerHMM_glimmerT_54706-T1, internal, 211819, 212142
-recovered GlimmerHMM_glimmerT_54706-T1, internal, 216561, 216687
Valid prediction for snap_scaffold_24-snap.2281-T1
Valid prediction for snap_scaffold_24-snap.2302-T1
Couldn't classify 43188, 43281
Sorry, prediction pasa_asmbl_32587.p1 fails validation.
(AGG)	 CC	43188-43281	GT	TGG
(TAC)	 AG	43405-43561	GT	CTG
(GAG)	 AG	43893-44108	GT	TCG
(AAT)	 AG	44277-44420	GT	CAG
(GAT)	 AG	44574-44687	GT	CTG
(CAT)	 AG	44822-44996	GT	AGG
(GTG)	 AG	45334-45430	GT	AGG
(GTG)	 AG	45674-45972	GG	GAG
add_exon() Sorry, pasa_asmbl_32587.p1 45334-45430-terminal-3 is invalid.
-recovered pasa_asmbl_32587.p1, terminal, 45334, 45430
-recovered pasa_asmbl_32587.p1, terminal, 45674, 45972
-recovered pasa_asmbl_32587.p1, internal, 43405, 43561
-recovered pasa_asmbl_32587.p1, internal, 43893, 44108
-recovered pasa_asmbl_32587.p1, internal, 44277, 44420
-recovered pasa_asmbl_32587.p1, internal, 44574, 44687
-recovered pasa_asmbl_32587.p1, internal, 44822, 44996
-recovered pasa_asmbl_32587.p1, internal, 45334, 45430
Valid prediction for snap_scaffold_24-snap.2292-T1
Valid prediction for GlimmerHMM_glimmerT_54691-T1
Valid prediction for snap_scaffold_24-snap.2287-T1
Valid prediction for snap_scaffold_24-snap.2294-T1
Valid prediction for GeneMark_model.95278_t
Valid prediction for GeneMark_model.95275_t
Valid prediction for GeneMark_model.95266_t
Valid prediction for GeneMark_model.95268_t
Valid prediction for GlimmerHMM_glimmerT_54693-T1
Couldn't classify 203787, 203999
Sorry, prediction pasa_asmbl_32591.p1 fails validation.
(ATG)	 GT	202408-202559	GT	AGG
(GAT)	 AG	202654-202799	GT	AGG
(GTG)	 AG	202984-203056	GT	AAG
(GTA)	 AG	203150-203301	GT	AGG
(GTC)	 AG	203522-203649	GT	AGG
(TCC)	 AG	203787-203999	GC	GGG
-recovered pasa_asmbl_32591.p1, initial, 202408, 202559
-recovered pasa_asmbl_32591.p1, internal, 202654, 202799
-recovered pasa_asmbl_32591.p1, internal, 202984, 203056
-recovered pasa_asmbl_32591.p1, internal, 203150, 203301
-recovered pasa_asmbl_32591.p1, internal, 203522, 203649
-recovered pasa_asmbl_32591.p1, internal, 203787, 203999
Valid prediction for GlimmerHMM_glimmerT_54677-T1
Valid prediction for GlimmerHMM_glimmerT_54678-T1
Valid prediction for GeneMark_model.95273_t
Valid prediction for snap_scaffold_24-snap.2279-T1
Valid prediction for GeneMark_model.95280_t
Valid prediction for GlimmerHMM_glimmerT_54694-T1
Valid prediction for snap_scaffold_24-snap.2299-T1
Valid prediction for CodingQuarry_transcript_37367-T1
Valid prediction for GlimmerHMM_glimmerT_54704-T1
Valid prediction for GlimmerHMM_glimmerT_54699-T1
Valid prediction for snap_scaffold_24-snap.2305-T1
Valid prediction for GlimmerHMM_glimmerT_54692-T1
Valid prediction for GeneMark_model.95282_t
Valid prediction for GlimmerHMM_glimmerT_54701-T1
Valid prediction for GeneMark_model.95274_t
Valid prediction for GlimmerHMM_glimmerT_54687-T1
Valid prediction for GlimmerHMM_glimmerT_54695-T1
Valid prediction for snap_scaffold_24-snap.2277-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_54686-T1
Valid prediction for GeneMark_model.95262_t
Valid prediction for snap_scaffold_24-snap.2284-T1
Valid prediction for GlimmerHMM_glimmerT_54696-T1
Valid prediction for snap_scaffold_24-snap.2308-T1
Valid prediction for snap_scaffold_24-snap.2285-T1
Valid prediction for snap_scaffold_24-snap.2298-T1
Valid prediction for snap_scaffold_24-snap.2309-T1
Valid prediction for GlimmerHMM_glimmerT_54683-T1
Valid prediction for GlimmerHMM_glimmerT_54684-T1
Valid prediction for snap_scaffold_24-snap.2293-T1
Valid prediction for GlimmerHMM_glimmerT_54703-T1
Valid prediction for snap_scaffold_24-snap.2307-T1
Valid prediction for GlimmerHMM_glimmerT_54698-T1
Valid prediction for GeneMark_model.95261_t
Valid prediction for GeneMark_model.95277_t
Valid prediction for snap_scaffold_24-snap.2310-T1
Valid prediction for GeneMark_model.95258_t
Couldn't classify 211819, 212142
Sorry, prediction pasa_asmbl_32594.p1 fails validation.
(ATG)	 AA	211069-211278	GT	AGG
(GCC)	 AG	211819-212142	GT	AGG
-recovered pasa_asmbl_32594.p1, initial, 211069, 211278
-recovered pasa_asmbl_32594.p1, internal, 211819, 212142
Couldn't classify 144024, 144146
Sorry, prediction pasa_asmbl_32590.p1 fails validation.
(GAT)	 AT	144024-144146	GT	AGG
(TTT)	 AG	144227-144325	GT	TGG
(ATG)	 AG	144426-144545	GT	TGG
(GCG)	 AG	144655-144844	GT	TGG
(CAA)	 AG	144933-145020	GT	GGG
(AGG)	 AG	145124-145309	GT	AAG
(CTT)	 AG	145430-145571	GT	TTG
(ATT)	 AG	145744-145912	GT	AGG
(TGC)	 AG	146003-146067	GT	CAG
(GAA)	 AG	146151-146219	GT	AAG
(GTT)	 AG	146342-146551	GT	AGG
(ATG)	 AG	146712-146857	GT	AGG
(AAT)	 AG	147177-147315	GT	AGG
(CTG)	 AG	147397-147489	GA	AAG
-recovered pasa_asmbl_32590.p1, initial, 144426, 144545
-recovered pasa_asmbl_32590.p1, initial, 146712, 146857
-recovered pasa_asmbl_32590.p1, terminal, 147397, 147489
-recovered pasa_asmbl_32590.p1, internal, 144227, 144325
-recovered pasa_asmbl_32590.p1, internal, 144426, 144545
-recovered pasa_asmbl_32590.p1, internal, 144655, 144844
-recovered pasa_asmbl_32590.p1, internal, 144933, 145020
-recovered pasa_asmbl_32590.p1, internal, 145124, 145309
-recovered pasa_asmbl_32590.p1, internal, 145430, 145571
-recovered pasa_asmbl_32590.p1, internal, 145744, 145912
-recovered pasa_asmbl_32590.p1, internal, 146003, 146067
-recovered pasa_asmbl_32590.p1, internal, 146151, 146219
-recovered pasa_asmbl_32590.p1, internal, 146342, 146551
-recovered pasa_asmbl_32590.p1, internal, 146712, 146857
-recovered pasa_asmbl_32590.p1, internal, 147177, 147315
Valid prediction for snap_scaffold_24-snap.2295-T1
Valid prediction for GeneMark_model.95281_t
Valid prediction for snap_scaffold_24-snap.2280-T1
Couldn't classify 200027, 200068
Couldn't classify 202984, 203057
Sorry, prediction pasa_asmbl_32592.p1 fails validation.
(CAC)	 CA	200027-200068	GT	AGG
(GTG)	 AG	202447-202559	GT	AGG
(GAT)	 AG	202654-202799	GT	AGG
(GTG)	 AG	202984-203057	TG	AGT
-recovered pasa_asmbl_32592.p1, internal, 202447, 202559
-recovered pasa_asmbl_32592.p1, internal, 202654, 202799
Valid prediction for GeneMark_model.95264_t
Valid prediction for GlimmerHMM_glimmerT_54672-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_54676-T1
Valid prediction for GlimmerHMM_glimmerT_54682-T1
Valid prediction for CodingQuarry_transcript_37368-T1
Valid prediction for snap_scaffold_24-snap.2296-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_54679-T1
Valid prediction for snap_scaffold_24-snap.2306-T1
Valid prediction for GlimmerHMM_glimmerT_54681-T1
Valid prediction for snap_scaffold_24-snap.2283-T1
Valid prediction for GeneMark_model.95279_t
Valid prediction for snap_scaffold_24-snap.2289-T1
Valid prediction for snap_scaffold_24-snap.2288-T1
Valid prediction for GeneMark_model.95265_t
Valid prediction for GeneMark_model.95267_t
Valid prediction for snap_scaffold_24-snap.2301-T1
Valid prediction for GeneMark_model.95276_t
Valid prediction for GlimmerHMM_glimmerT_54702-T1
Valid prediction for GlimmerHMM_glimmerT_54688-T1
Valid prediction for GlimmerHMM_glimmerT_54705-T1
Valid prediction for pasa_asmbl_33215.p1
Valid prediction for snap_scaffold_24-snap.2278-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for snap_scaffold_24-snap.2290-T1
Valid prediction for GlimmerHMM_glimmerT_54697-T1
Valid prediction for snap_scaffold_24-snap.2297-T1
Valid prediction for GeneMark_model.95270_t
Valid prediction for GlimmerHMM_glimmerT_54685-T1
Valid prediction for snap_scaffold_24-snap.2291-T1
Valid prediction for GlimmerHMM_glimmerT_54675-T1
Valid prediction for GeneMark_model.95257_t
Valid prediction for GlimmerHMM_glimmerT_54674-T1
Valid prediction for snap_scaffold_24-snap.2304-T1
Valid prediction for GeneMark_model.95259_t
Valid prediction for snap_scaffold_24-snap.2300-T1
Valid prediction for pasa_asmbl_33210.p1
Valid prediction for snap_scaffold_24-snap.2286-T1
Valid prediction for GlimmerHMM_glimmerT_54689-T1
Valid prediction for snap_scaffold_24-snap.2303-T1
Valid prediction for GeneMark_model.95271_t
Valid prediction for GeneMark_model.95260_t
Valid prediction for GeneMark_model.95269_t
Valid prediction for GlimmerHMM_glimmerT_54673-T1
Valid prediction for GeneMark_model.95272_t
Valid prediction for snap_scaffold_24-snap.2282-T1
Valid prediction for GlimmerHMM_glimmerT_54700-T1
Valid prediction for GlimmerHMM_glimmerT_54690-T1
Valid prediction for GlimmerHMM_glimmerT_54680-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 72254, rend_intergenic: 72251  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 6806, rend_intergenic: 2948  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19715, rend_intergenic: 8315  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55184, rend_intergenic: 51059  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 220563
-exon list size: 449


building trellis

0.2    
0.4    
0.7    
0.9    
1.1    
1.3    
1.6    
1.8    
2.0    
2.2    
2.4    
2.7    
2.9    
3.1    
3.3    
3.5    
3.8    
4.0    
4.2    
4.4    
4.7    
4.9    
5.1    
5.3    
5.5    
5.8    
6.0    
6.2    
6.4    
6.7    
6.9    
7.1    
7.3    
7.5    
7.8    
8.0    
8.2    
8.4    
8.6    
8.9    
9.1    
9.3    
9.5    
9.8    
10.0    
10.2    
10.4    
10.6    
10.9    
11.1    
11.3    
11.5    
11.8    
12.0    
12.2    
12.4    
12.6    
12.9    
13.1    
13.3    
13.5    
13.7    
14.0    
14.2    
14.4    
14.6    
14.9    
15.1    
15.3    
15.5    
15.7    
16.0    
16.2    
16.4    
16.6    
16.9    
17.1    
17.3    
17.5    
17.7    
18.0    
18.2    
18.4    
18.6    
18.8    
19.1    
19.3    
19.5    
19.7    
20.0    
20.2    
20.4    
20.6    
20.8    
21.1    
21.3    
21.5    
21.7    
22.0    
22.2    
22.4    
22.6    
22.8    
23.1    
23.3    
23.5    
23.7    
23.9    
24.2    
24.4    
24.6    
24.8    
25.1    
25.3    
25.5    
25.7    
25.9    
26.2    
26.4    
26.6    
26.8    
27.1    
27.3    
27.5    
27.7    
27.9    
28.2    
28.4    
28.6    
28.8    
29.0    
29.3    
29.5    
29.7    
29.9    
30.2    
30.4    
30.6    
30.8    
31.0    
31.3    
31.5    
31.7    
31.9    
32.2    
32.4    
32.6    
32.8    
33.0    
33.3    
33.5    
33.7    
33.9    
34.1    
34.4    
34.6    
34.8    
35.0    
35.3    
35.5    
35.7    
35.9    
36.1    
36.4    
36.6    
36.8    
37.0    
37.3    
37.5    
37.7    
37.9    
38.1    
38.4    
38.6    
38.8    
39.0    
39.2    
39.5    
39.7    
39.9    
40.1    
40.4    
40.6    
40.8    
41.0    
41.2    
41.5    
41.7    
41.9    
42.1    
42.4    
42.6    
42.8    
43.0    
43.2    
43.5    
43.7    
43.9    
44.1    
44.3    
44.6    
44.8    
45.0    
45.2    
45.5    
45.7    
45.9    
46.1    
46.3    
46.6    
46.8    
47.0    
47.2    
47.5    
47.7    
47.9    
48.1    
48.3    
48.6    
48.8    
49.0    
49.2    
49.4    
49.7    
49.9    
50.1    
50.3    
50.6    
50.8    
51.0    
51.2    
51.4    
51.7    
51.9    
52.1    
52.3    
52.5    
52.8    
53.0    
53.2    
53.4    
53.7    
53.9    
54.1    
54.3    
54.5    
54.8    
55.0    
55.2    
55.4    
55.7    
55.9    
56.1    
56.3    
56.5    
56.8    
57.0    
57.2    
57.4    
57.6    
57.9    
58.1    
58.3    
58.5    
58.8    
59.0    
59.2    
59.4    
59.6    
59.9    
60.1    
60.3    
60.5    
60.8    
61.0    
61.2    
61.4    
61.6    
61.9    
62.1    
62.3    
62.5    
62.7    
63.0    
63.2    
63.4    
63.6    
63.9    
64.1    
64.3    
64.5    
64.7    
65.0    
65.2    
65.4    
65.6    
65.9    
66.1    
66.3    
66.5    
66.7    
67.0    
67.2    
67.4    
67.6    
67.8    
68.1    
68.3    
68.5    
68.7    
69.0    
69.2    
69.4    
69.6    
69.8    
70.1    
70.3    
70.5    
70.7    
71.0    
71.2    
71.4    
71.6    
71.8    
72.1    
72.3    
72.5    
72.7    
72.9    
73.2    
73.4    
73.6    
73.8    
74.1    
74.3    
74.5    
74.7    
74.9    
75.2    
75.4    
75.6    
75.8    
76.1    
76.3    
76.5    
76.7    
76.9    
77.2    
77.4    
77.6    
77.8    
78.0    
78.3    
78.5    
78.7    
78.9    
79.2    
79.4    
79.6    
79.8    
80.0    
80.3    
80.5    
80.7    
80.9    
81.2    
81.4    
81.6    
81.8    
82.0    
82.3    
82.5    
82.7    
82.9    
83.1    
83.4    
83.6    
83.8    
84.0    
84.3    
84.5    
84.7    
84.9    
85.1    
85.4    
85.6    
85.8    
86.0    
86.3    
86.5    
86.7    
86.9    
87.1    
87.4    
87.6    
87.8    
88.0    
88.2    
88.5    
88.7    
88.9    
89.1    
89.4    
89.6    
89.8    
90.0    
90.2    
90.5    
90.7    
90.9    
91.1    
91.4    
91.6    
91.8    
92.0    
92.2    
92.5    
92.7    
92.9    
93.1    
93.3    
93.6    
93.8    
94.0    
94.2    
94.5    
94.7    
94.9    
95.1    
95.3    
95.6    
95.8    
96.0    
96.2    
96.5    
96.7    
96.9    
97.1    
97.3    
97.6    
97.8    
98.0    
98.2    
98.4    
98.7    
98.9    
99.1    
99.3    
99.6    
99.8    
-found 35 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 72254, rend_intergenic: 72251  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 6806, rend_intergenic: 2948  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19715, rend_intergenic: 8315  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55184, rend_intergenic: 51059  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 28 predictions persist after filtering for low support