-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_23/scaffold_23_10880571-10998502

-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.92239_t
Couldn't classify 10507, 10701
Sorry, prediction pasa_asmbl_31177.p1 fails validation.
(GGA)	 GG	10507-10701	GT	ATG
(AGA)	 AG	10923-11098	GT	AGG
(GAT)	 AG	12070-12142	AG	AGA
-recovered pasa_asmbl_31177.p1, terminal, 10923, 11098
-recovered pasa_asmbl_31177.p1, terminal, 12070, 12142
-recovered pasa_asmbl_31177.p1, internal, 10923, 11098
Valid prediction for GeneMark_model.92233_t
Valid prediction for snap_scaffold_23-snap.2136-T1
Valid prediction for GlimmerHMM_glimmerT_53070-T1
Valid prediction for GeneMark_model.92229_t
Valid prediction for GeneMark_model.92246_t
Valid prediction for snap_scaffold_23-snap.2135-T1
Valid prediction for CodingQuarry_transcript_35743-T1
Valid prediction for pasa_asmbl_31175.p1
Valid prediction for GlimmerHMM_glimmerT_53064-T1
Valid prediction for GeneMark_model.92244_t
Valid prediction for GlimmerHMM_glimmerT_53072-T1
Valid prediction for snap_scaffold_23-snap.2134-T1
Valid prediction for snap_scaffold_23-snap.2150-T1
Valid prediction for GlimmerHMM_glimmerT_53073-T1
Valid prediction for GlimmerHMM_glimmerT_53060-T1
Valid prediction for snap_scaffold_23-snap.2143-T1
Valid prediction for CodingQuarry_transcript_35750-T1
Valid prediction for snap_scaffold_23-snap.2147-T1
Valid prediction for snap_scaffold_23-snap.2131-T1
Valid prediction for GlimmerHMM_glimmerT_53062-T1
Valid prediction for CodingQuarry_transcript_35751-T1
Valid prediction for GeneMark_model.92248_t
Valid prediction for GeneMark_model.92227_t
Valid prediction for CodingQuarry_transcript_35745-T1
Valid prediction for GlimmerHMM_glimmerT_53067-T1
Valid prediction for snap_scaffold_23-snap.2139-T1
Valid prediction for GeneMark_model.92236_t
Valid prediction for snap_scaffold_23-snap.2152-T1
Valid prediction for GlimmerHMM_glimmerT_53063-T1
Valid prediction for pasa_asmbl_31185.p1
Valid prediction for snap_scaffold_23-snap.2151-T1
Valid prediction for snap_scaffold_23-snap.2132-T1
Couldn't classify 20128, 20147
Couldn't classify 21965, 22007
Sorry, prediction pasa_asmbl_31183.p1 fails validation.
(CCC)	 AT	20128-20147	GT	AAG
(AAG)	 AG	20528-20669	GT	ATG
(GGG)	 AG	20958-21094	GT	AGG
(ATT)	 AG	21965-22007	AC	GAA
add_exon() Sorry, pasa_asmbl_31183.p1 20958-21094-terminal-2 is invalid.
-recovered pasa_asmbl_31183.p1, terminal, 20958, 21094
-recovered pasa_asmbl_31183.p1, internal, 20528, 20669
-recovered pasa_asmbl_31183.p1, internal, 20958, 21094
Valid prediction for snap_scaffold_23-snap.2145-T1
Valid prediction for GlimmerHMM_glimmerT_53059-T1
Valid prediction for pasa_asmbl_31186.p1
Couldn't classify 16683, 16835
Sorry, prediction pasa_asmbl_31180.p1 fails validation.
(AGC)	 GC	16683-16835	GT	AGG
(CTC)	 AG	17037-17213	GT	AGG
(CCG)	 AG	17299-17496	GA	GAG
-recovered pasa_asmbl_31180.p1, terminal, 17299, 17496
-recovered pasa_asmbl_31180.p1, internal, 17037, 17213
Valid prediction for GeneMark_model.92230_t
Valid prediction for CodingQuarry_transcript_35742-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_23-snap.2146-T1
Valid prediction for GeneMark_model.92243_t
Couldn't classify 56459, 56501
Sorry, prediction pasa_asmbl_31889.p1 fails validation.
(GCA)	 CT	56459-56501	GT	TGG
(GCC)	 AG	57635-57739	GT	AGG
(GTT)	 AG	57915-58107	GT	AGG
(GAG)	 AG	58180-58301	GT	AGG
(ACA)	 AG	58438-58507	GT	AGG
(GGT)	 AG	58611-58656	CA	AAC
-recovered pasa_asmbl_31889.p1, terminal, 58611, 58656
-recovered pasa_asmbl_31889.p1, internal, 57635, 57739
-recovered pasa_asmbl_31889.p1, internal, 57915, 58107
-recovered pasa_asmbl_31889.p1, internal, 58180, 58301
-recovered pasa_asmbl_31889.p1, internal, 58438, 58507
Valid prediction for CodingQuarry_transcript_35749-T1
Couldn't classify 14975, 15256
Sorry, prediction pasa_asmbl_31917.p1 fails validation.
(GTA)	 TG	14975-15256	GT	TGG
(TCC)	 AG	15436-15639	GT	CAG
(CAA)	 AG	15727-15782	GT	AGG
(AGG)	 AG	15888-16040	GT	AAG
(GGA)	 AG	16545-16745	GT	TGG
(GTA)	 AG	17054-17171	GT	TGG
(GAT)	 AG	17270-17401	AG	GAA
-recovered pasa_asmbl_31917.p1, terminal, 17270, 17401
-recovered pasa_asmbl_31917.p1, internal, 15436, 15639
-recovered pasa_asmbl_31917.p1, internal, 15727, 15782
-recovered pasa_asmbl_31917.p1, internal, 15888, 16040
-recovered pasa_asmbl_31917.p1, internal, 16545, 16745
-recovered pasa_asmbl_31917.p1, internal, 17054, 17171
Valid prediction for GeneMark_model.92226_t
Valid prediction for GlimmerHMM_glimmerT_53074-T1
Valid prediction for snap_scaffold_23-snap.2141-T1
Valid prediction for GlimmerHMM_glimmerT_53066-T1
Valid prediction for snap_scaffold_23-snap.2140-T1
Valid prediction for GeneMark_model.92247_t
Valid prediction for GeneMark_model.92238_t
Valid prediction for GeneMark_model.92237_t
Valid prediction for snap_scaffold_23-snap.2138-T1
Valid prediction for GeneMark_model.92245_t
Valid prediction for GeneMark_model.92241_t
Valid prediction for pasa_asmbl_31879.p1
Valid prediction for snap_scaffold_23-snap.2153-T1
Couldn't classify 7583, 7624
Sorry, prediction pasa_asmbl_31898.p3 fails validation.
(ACA)	 AG	7583-7624	GT	TGG
(TGT)	 AG	8293-8412	GT	AGG
(GAG)	 AG	9637-9752	GT	AGG
(GCC)	 AG	10166-10205	AC	GAA
-recovered pasa_asmbl_31898.p3, terminal, 10166, 10205
-recovered pasa_asmbl_31898.p3, internal, 7583, 7624
-recovered pasa_asmbl_31898.p3, internal, 8293, 8412
-recovered pasa_asmbl_31898.p3, internal, 9637, 9752
Valid prediction for snap_scaffold_23-snap.2137-T1
Valid prediction for CodingQuarry_transcript_35753-T1
Couldn't classify 77932, 78033
Sorry, prediction pasa_asmbl_31886.p1 fails validation.
(ATG)	 AG	75299-75361	GT	AGG
(TTC)	 AG	76075-76216	GT	GAG
(GTG)	 AG	77145-77273	GT	TGG
(GCA)	 AG	77471-77604	GT	CAG
(AAA)	 AG	77932-78033	CC	TTC
-recovered pasa_asmbl_31886.p1, initial, 75299, 75361
-recovered pasa_asmbl_31886.p1, internal, 75299, 75361
-recovered pasa_asmbl_31886.p1, internal, 76075, 76216
-recovered pasa_asmbl_31886.p1, internal, 77145, 77273
-recovered pasa_asmbl_31886.p1, internal, 77471, 77604
Valid prediction for GlimmerHMM_glimmerT_53061-T1
Valid prediction for CodingQuarry_transcript_35747-T1
Valid prediction for GlimmerHMM_glimmerT_53075-T1
Valid prediction for snap_scaffold_23-snap.2149-T1
Valid prediction for GlimmerHMM_glimmerT_53065-T1
Valid prediction for CodingQuarry_transcript_35748-T1
Valid prediction for GeneMark_model.92249_t
Valid prediction for GeneMark_model.92250_t
Valid prediction for snap_scaffold_23-snap.2144-T1
Valid prediction for GlimmerHMM_glimmerT_53069-T1
Valid prediction for GeneMark_model.92240_t
Valid prediction for snap_scaffold_23-snap.2155-T1
Valid prediction for GeneMark_model.92235_t
Valid prediction for GeneMark_model.92232_t
Valid prediction for CodingQuarry_transcript_35752-T1
Valid prediction for snap_scaffold_23-snap.2133-T1
Valid prediction for GeneMark_model.92234_t
Couldn't classify 42263, 42281
Couldn't classify 42466, 42890
Sorry, prediction pasa_asmbl_31895.p1 fails validation.
(GAA)	 AA	42263-42281	GT	TGG
(CAG)	 AG	42466-42890	CT	GCC
Valid prediction for snap_scaffold_23-snap.2154-T1
Valid prediction for GlimmerHMM_glimmerT_53068-T1
Valid prediction for GeneMark_model.92231_t
Valid prediction for GeneMark_model.92228_t
Valid prediction for CodingQuarry_transcript_35746-T1
Valid prediction for snap_scaffold_23-snap.2148-T1
Valid prediction for snap_scaffold_23-snap.2142-T1
Valid prediction for GlimmerHMM_glimmerT_53071-T1
Valid prediction for GeneMark_model.92242_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 24202, rend_intergenic: 23836  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38201, rend_intergenic: 32290  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42333, rend_intergenic: 39693  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50603, rend_intergenic: 46324  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63864, rend_intergenic: 59277  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71487, rend_intergenic: 66366  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 117932
-exon list size: 312


building trellis

0.3    
0.6    
1.0    
1.3    
1.6    
1.9    
2.2    
2.5    
2.9    
3.2    
3.5    
3.8    
4.1    
4.5    
4.8    
5.1    
5.4    
5.7    
6.1    
6.4    
6.7    
7.0    
7.3    
7.6    
8.0    
8.3    
8.6    
8.9    
9.2    
9.6    
9.9    
10.2    
10.5    
10.8    
11.1    
11.5    
11.8    
12.1    
12.4    
12.7    
13.1    
13.4    
13.7    
14.0    
14.3    
14.6    
15.0    
15.3    
15.6    
15.9    
16.2    
16.6    
16.9    
17.2    
17.5    
17.8    
18.2    
18.5    
18.8    
19.1    
19.4    
19.7    
20.1    
20.4    
20.7    
21.0    
21.3    
21.7    
22.0    
22.3    
22.6    
22.9    
23.2    
23.6    
23.9    
24.2    
24.5    
24.8    
25.2    
25.5    
25.8    
26.1    
26.4    
26.8    
27.1    
27.4    
27.7    
28.0    
28.3    
28.7    
29.0    
29.3    
29.6    
29.9    
30.3    
30.6    
30.9    
31.2    
31.5    
31.8    
32.2    
32.5    
32.8    
33.1    
33.4    
33.8    
34.1    
34.4    
34.7    
35.0    
35.4    
35.7    
36.0    
36.3    
36.6    
36.9    
37.3    
37.6    
37.9    
38.2    
38.5    
38.9    
39.2    
39.5    
39.8    
40.1    
40.4    
40.8    
41.1    
41.4    
41.7    
42.0    
42.4    
42.7    
43.0    
43.3    
43.6    
43.9    
44.3    
44.6    
44.9    
45.2    
45.5    
45.9    
46.2    
46.5    
46.8    
47.1    
47.5    
47.8    
48.1    
48.4    
48.7    
49.0    
49.4    
49.7    
50.0    
50.3    
50.6    
51.0    
51.3    
51.6    
51.9    
52.2    
52.5    
52.9    
53.2    
53.5    
53.8    
54.1    
54.5    
54.8    
55.1    
55.4    
55.7    
56.1    
56.4    
56.7    
57.0    
57.3    
57.6    
58.0    
58.3    
58.6    
58.9    
59.2    
59.6    
59.9    
60.2    
60.5    
60.8    
61.1    
61.5    
61.8    
62.1    
62.4    
62.7    
63.1    
63.4    
63.7    
64.0    
64.3    
64.6    
65.0    
65.3    
65.6    
65.9    
66.2    
66.6    
66.9    
67.2    
67.5    
67.8    
68.2    
68.5    
68.8    
69.1    
69.4    
69.7    
70.1    
70.4    
70.7    
71.0    
71.3    
71.7    
72.0    
72.3    
72.6    
72.9    
73.2    
73.6    
73.9    
74.2    
74.5    
74.8    
75.2    
75.5    
75.8    
76.1    
76.4    
76.8    
77.1    
77.4    
77.7    
78.0    
78.3    
78.7    
79.0    
79.3    
79.6    
79.9    
80.3    
80.6    
80.9    
81.2    
81.5    
81.8    
82.2    
82.5    
82.8    
83.1    
83.4    
83.8    
84.1    
84.4    
84.7    
85.0    
85.4    
85.7    
86.0    
86.3    
86.6    
86.9    
87.3    
87.6    
87.9    
88.2    
88.5    
88.9    
89.2    
89.5    
89.8    
90.1    
90.4    
90.8    
91.1    
91.4    
91.7    
92.0    
92.4    
92.7    
93.0    
93.3    
93.6    
93.9    
94.3    
94.6    
94.9    
95.2    
95.5    
95.9    
96.2    
96.5    
96.8    
97.1    
97.5    
97.8    
98.1    
98.4    
98.7    
99.0    
99.4    
99.7    
-found 21 predictions from path traversal
Error with prediction: snap lend_intergenic: 24202, rend_intergenic: 23836  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38201, rend_intergenic: 32290  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42333, rend_intergenic: 39693  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50603, rend_intergenic: 46324  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63864, rend_intergenic: 59277  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71487, rend_intergenic: 66366  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support