-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_26/scaffold_26_9492942-9678483

-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.100594_t
Valid prediction for Augustus_model.g38474.t1
Couldn't classify 115509, 115817
Sorry, prediction pasa_asmbl_35767.p1 fails validation.
(TAT)	 TC	115509-115817	CA	AAC
Valid prediction for snap_scaffold_26-snap.2163-T1
Valid prediction for GlimmerHMM_glimmerT_57738-T1
Valid prediction for GeneMark_model.100609_t
Valid prediction for snap_scaffold_26-snap.2164-T1
Valid prediction for GeneMark_model.100596_t
Valid prediction for GeneMark_model.100584_t
Valid prediction for pasa_asmbl_35765.p1
Valid prediction for snap_scaffold_26-snap.2146-T1
Valid prediction for GeneMark_model.100580_t
Valid prediction for snap_scaffold_26-snap.2148-T1
Valid prediction for Augustus_model.g38466.t1
Valid prediction for GeneMark_model.100607_t
Valid prediction for GeneMark_model.100604_t
Valid prediction for snap_scaffold_26-snap.2149-T1
Valid prediction for GeneMark_model.100605_t
Valid prediction for GlimmerHMM_glimmerT_57743-T1
Valid prediction for pasa_asmbl_35759.p1
Valid prediction for snap_scaffold_26-snap.2171-T1
Valid prediction for GeneMark_model.100598_t
Valid prediction for snap_scaffold_26-snap.2147-T1
Valid prediction for GeneMark_model.100572_t
Valid prediction for snap_scaffold_26-snap.2144-T1
Valid prediction for Augustus_model.g38475.t1
Valid prediction for GlimmerHMM_glimmerT_57733-T1
Couldn't classify 39918, 40073
Sorry, prediction pasa_asmbl_35762.p1 fails validation.
(ATG)	 GG	36026-36283	GT	GGG
(ATT)	 AG	37115-37277	GT	AGG
(GTC)	 AG	38011-38157	GT	AGG
(TGG)	 AG	38241-38366	GT	AGG
(TGA)	 AG	38445-38635	GT	GGG
(GAC)	 AG	39918-40073	TA	GGT
-recovered pasa_asmbl_35762.p1, initial, 36026, 36283
-recovered pasa_asmbl_35762.p1, internal, 37115, 37277
-recovered pasa_asmbl_35762.p1, internal, 38011, 38157
-recovered pasa_asmbl_35762.p1, internal, 38241, 38366
-recovered pasa_asmbl_35762.p1, internal, 38445, 38635
Valid prediction for GlimmerHMM_glimmerT_57745-T1
Valid prediction for HiQ_model.g38472.t1
Valid prediction for GeneMark_model.100613_t
Valid prediction for snap_scaffold_26-snap.2167-T1
Valid prediction for CodingQuarry_transcript_40345-T1
Valid prediction for Augustus_model.g38463.t1
Valid prediction for GlimmerHMM_glimmerT_57734-T1
Valid prediction for GlimmerHMM_glimmerT_57730-T1
Valid prediction for snap_scaffold_26-snap.2145-T1
Valid prediction for Augustus_model.g38470.t1
Valid prediction for GeneMark_model.100592_t
Valid prediction for snap_scaffold_26-snap.2172-T1
Valid prediction for GlimmerHMM_glimmerT_57729-T1
Valid prediction for CodingQuarry_transcript_40346-T1
Valid prediction for snap_scaffold_26-snap.2154-T1
Valid prediction for GlimmerHMM_glimmerT_57736-T1
Valid prediction for GeneMark_model.100578_t
Valid prediction for GlimmerHMM_glimmerT_57739-T1
Valid prediction for GlimmerHMM_glimmerT_57744-T1
Valid prediction for CodingQuarry_transcript_40344-T1
Valid prediction for GeneMark_model.100574_t
Valid prediction for snap_scaffold_26-snap.2160-T1
Couldn't classify 43537, 43696
Sorry, prediction pasa_asmbl_35846.p1 fails validation.
(TTC)	 CT	43537-43696	GT	GGG
(GTT)	 AG	45495-45630	GT	AGG
(GTT)	 AG	46263-46446	GT	AGG
(GGT)	 AG	48774-48911	GT	AGG
(GCG)	 AG	49665-49754	AC	GAA
-recovered pasa_asmbl_35846.p1, terminal, 49665, 49754
-recovered pasa_asmbl_35846.p1, internal, 45495, 45630
-recovered pasa_asmbl_35846.p1, internal, 46263, 46446
-recovered pasa_asmbl_35846.p1, internal, 48774, 48911
Valid prediction for GeneMark_model.100577_t
Valid prediction for snap_scaffold_26-snap.2150-T1
Couldn't classify 21410, 21410
Sorry, prediction CodingQuarry_transcript_40342-T1 fails validation.
(AGT)	 AC	21410-21410	GT	CAG
(TGA)	 AG	21574-21678	GT	CGG
(GAG)	 AG	21985-22071	GT	AGG
(GGA)	 AG	22188-22284	GT	AAG
(GGA)	 AG	22609-22700	GT	AGG
(GTG)	 AG	24446-24505	GT	TGG
(GTA)	 AG	24757-24794	GC	AGG
(TAT)	 AG	25903-25949	GT	AGG
(GCA)	 AG	26867-26953	GT	AGG
(GTC)	 AG	27131-27175	GT	AGG
(GGT)	 AG	27825-27881	GT	AAG
(TCT)	 AG	28436-28487	GT	AGG
(AGT)	 AG	30024-30092	GT	AGG
(GAC)	 AG	30336-30401	GT	AGG
(GGG)	 AG	30547-30673	GT	AGG
(GGA)	 AG	30967-31037	CT	AGC
add_exon() Sorry, CodingQuarry_transcript_40342-T1 25903-25949-terminal-2 is invalid.
-recovered CodingQuarry_transcript_40342-T1, terminal, 25903, 25949
-recovered CodingQuarry_transcript_40342-T1, terminal, 27825, 27881
add_exon() Sorry, CodingQuarry_transcript_40342-T1 30547-30673-terminal-3 is invalid.
-recovered CodingQuarry_transcript_40342-T1, terminal, 30547, 30673
-recovered CodingQuarry_transcript_40342-T1, terminal, 30967, 31037
-recovered CodingQuarry_transcript_40342-T1, internal, 21574, 21678
-recovered CodingQuarry_transcript_40342-T1, internal, 21985, 22071
-recovered CodingQuarry_transcript_40342-T1, internal, 22188, 22284
-recovered CodingQuarry_transcript_40342-T1, internal, 22609, 22700
-recovered CodingQuarry_transcript_40342-T1, internal, 24446, 24505
-recovered CodingQuarry_transcript_40342-T1, internal, 24757, 24794
-recovered CodingQuarry_transcript_40342-T1, internal, 25903, 25949
-recovered CodingQuarry_transcript_40342-T1, internal, 26867, 26953
-recovered CodingQuarry_transcript_40342-T1, internal, 27131, 27175
-recovered CodingQuarry_transcript_40342-T1, internal, 27825, 27881
-recovered CodingQuarry_transcript_40342-T1, internal, 28436, 28487
-recovered CodingQuarry_transcript_40342-T1, internal, 30024, 30092
-recovered CodingQuarry_transcript_40342-T1, internal, 30336, 30401
-recovered CodingQuarry_transcript_40342-T1, internal, 30547, 30673
Valid prediction for GeneMark_model.100601_t
Valid prediction for GlimmerHMM_glimmerT_57731-T1
Valid prediction for GeneMark_model.100603_t
Valid prediction for snap_scaffold_26-snap.2169-T1
Couldn't classify 116211, 116405
Sorry, prediction pasa_asmbl_35771.p1 fails validation.
(TGT)	 TG	116211-116405	GT	TGG
(GTG)	 AG	116563-116760	GT	AGG
(GAG)	 AG	117461-117550	GT	AGG
(GGT)	 AG	118015-118077	TG	GAT
-recovered pasa_asmbl_35771.p1, terminal, 118015, 118077
-recovered pasa_asmbl_35771.p1, internal, 116563, 116760
-recovered pasa_asmbl_35771.p1, internal, 117461, 117550
Valid prediction for snap_scaffold_26-snap.2153-T1
Valid prediction for Augustus_model.g38473.t1
Valid prediction for snap_scaffold_26-snap.2165-T1
Valid prediction for snap_scaffold_26-snap.2158-T1
Valid prediction for GeneMark_model.100608_t
Valid prediction for GlimmerHMM_glimmerT_57740-T1
Couldn't classify 38510, 38635
Sorry, prediction Augustus_model.g38464.t1 fails validation.
(AAC)	 TC	38510-38635	GT	GGG
(GAC)	 AG	39918-40072	GT	AGG
(TGA)	 AG	42726-42906	GT	AGG
(AAT)	 AG	43393-43442	GT	AGG
(GGT)	 AG	43581-43696	GT	GGG
(GTT)	 AG	45495-45630	GT	AGG
(GTT)	 AG	46263-46446	GT	AGG
(GGT)	 AG	48774-48911	GT	AGG
(GCG)	 AG	49665-49754	AC	GAA
-recovered Augustus_model.g38464.t1, terminal, 49665, 49754
-recovered Augustus_model.g38464.t1, internal, 39918, 40072
-recovered Augustus_model.g38464.t1, internal, 42726, 42906
-recovered Augustus_model.g38464.t1, internal, 43393, 43442
-recovered Augustus_model.g38464.t1, internal, 43581, 43696
-recovered Augustus_model.g38464.t1, internal, 45495, 45630
-recovered Augustus_model.g38464.t1, internal, 46263, 46446
-recovered Augustus_model.g38464.t1, internal, 48774, 48911
Valid prediction for GeneMark_model.100591_t
Valid prediction for GeneMark_model.100588_t
Valid prediction for GeneMark_model.100575_t
Valid prediction for HiQ_model.g38462.t1
Valid prediction for GeneMark_model.100582_t

-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_26-snap.2159-T1
Valid prediction for GeneMark_model.100571_t
Valid prediction for GlimmerHMM_glimmerT_57735-T1
Valid prediction for GeneMark_model.100576_t
Valid prediction for Augustus_model.g38469.t1
Valid prediction for GeneMark_model.100579_t
Couldn't classify 82738, 82828
Sorry, prediction pasa_asmbl_35059.p1 fails validation.
(GGA)	 TA	82738-82828	GT	TGG
(CTT)	 AG	83849-83889	GT	AGG
(GAG)	 AG	84928-85170	AC	AGA
-recovered pasa_asmbl_35059.p1, terminal, 84928, 85170
-recovered pasa_asmbl_35059.p1, internal, 83849, 83889
Valid prediction for GeneMark_model.100597_t
Valid prediction for GeneMark_model.100600_t
Couldn't classify 118487, 118900
Sorry, prediction pasa_asmbl_35055.p1 fails validation.
(CAC)	 GC	118487-118900	CT	GAC
Couldn't classify 116881, 116998
Couldn't classify 118035, 118132
Sorry, prediction pasa_asmbl_35056.p1 fails validation.
(TCG)	 TG	116881-116998	GT	AGG
(GTG)	 AG	117231-117394	GT	AGG
(GTG)	 AG	117803-117884	GT	AGG
(GTG)	 AG	118035-118132	AC	GCA
add_exon() Sorry, pasa_asmbl_35056.p1 117803-117884-terminal-3 is invalid.
-recovered pasa_asmbl_35056.p1, terminal, 117803, 117884
-recovered pasa_asmbl_35056.p1, internal, 117231, 117394
-recovered pasa_asmbl_35056.p1, internal, 117803, 117884
Valid prediction for GeneMark_model.100611_t
Valid prediction for Augustus_model.g38461.t1
Valid prediction for GeneMark_model.100581_t
Valid prediction for GeneMark_model.100593_t
Valid prediction for GeneMark_model.100585_t
Couldn't classify 108010, 108193
Couldn't classify 109169, 109228
Sorry, prediction pasa_asmbl_35058.p1 fails validation.
(CGG)	 TA	108010-108193	GT	TGG
(GGG)	 AG	108536-108684	GT	AGG
(GTA)	 AG	109169-109228	GA	CAG
-recovered pasa_asmbl_35058.p1, internal, 108536, 108684
Valid prediction for GlimmerHMM_glimmerT_57732-T1
Valid prediction for GeneMark_model.100602_t
Valid prediction for snap_scaffold_26-snap.2156-T1
Valid prediction for snap_scaffold_26-snap.2162-T1
Valid prediction for GeneMark_model.100587_t
Valid prediction for snap_scaffold_26-snap.2157-T1
Valid prediction for snap_scaffold_26-snap.2170-T1
Couldn't classify 111347, 111398
Couldn't classify 113582, 113618
Sorry, prediction pasa_asmbl_35057.p1 fails validation.
(CTA)	 CG	111347-111398	GT	AGG
(AGC)	 AG	111499-111645	GT	AGG
(ACT)	 AG	111961-112221	GT	GGG
(GTG)	 AG	113207-113342	GT	CGG
(CTG)	 AG	113582-113618	GG	GAG
-recovered pasa_asmbl_35057.p1, internal, 111499, 111645
-recovered pasa_asmbl_35057.p1, internal, 111961, 112221
-recovered pasa_asmbl_35057.p1, internal, 113207, 113342
Valid prediction for snap_scaffold_26-snap.2166-T1
Valid prediction for Augustus_model.g38465.t1
Valid prediction for snap_scaffold_26-snap.2152-T1
Valid prediction for Augustus_model.g38467.t1
Valid prediction for snap_scaffold_26-snap.2151-T1
Valid prediction for GeneMark_model.100583_t
Valid prediction for snap_scaffold_26-snap.2161-T1
Valid prediction for GeneMark_model.100599_t
Valid prediction for snap_scaffold_26-snap.2173-T1
Valid prediction for GeneMark_model.100589_t
Valid prediction for GeneMark_model.100573_t
Valid prediction for GeneMark_model.100610_t
Valid prediction for GeneMark_model.100606_t
Valid prediction for GlimmerHMM_glimmerT_57737-T1
Valid prediction for HiQ_model.g38471.t1
Valid prediction for GlimmerHMM_glimmerT_57742-T1
Valid prediction for snap_scaffold_26-snap.2155-T1
Valid prediction for GeneMark_model.100595_t
Valid prediction for snap_scaffold_26-snap.2168-T1
Valid prediction for Augustus_model.g38468.t1
Valid prediction for GlimmerHMM_glimmerT_57741-T1
Valid prediction for GeneMark_model.100612_t
Valid prediction for GeneMark_model.100590_t
Valid prediction for snap_scaffold_26-snap.2174-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 49754, rend_intergenic: 39849  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60306, rend_intergenic: 57158  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87726, rend_intergenic: 80822  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109893, rend_intergenic: 105013  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151056, rend_intergenic: 149879  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153427, rend_intergenic: 152915  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157294, rend_intergenic: 155471  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 185542
-exon list size: 419


building trellis

0.2    
0.5    
0.7    
1.0    
1.2    
1.4    
1.7    
1.9    
2.1    
2.4    
2.6    
2.9    
3.1    
3.3    
3.6    
3.8    
4.0    
4.3    
4.5    
4.8    
5.0    
5.2    
5.5    
5.7    
5.9    
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6.4    
6.7    
6.9    
7.1    
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7.8    
8.1    
8.3    
8.6    
8.8    
9.0    
9.3    
9.5    
9.7    
10.0    
10.2    
10.5    
10.7    
10.9    
11.2    
11.4    
11.6    
11.9    
12.1    
12.4    
12.6    
12.8    
13.1    
13.3    
13.5    
13.8    
14.0    
14.3    
14.5    
14.7    
15.0    
15.2    
15.4    
15.7    
15.9    
16.2    
16.4    
16.6    
16.9    
17.1    
17.3    
17.6    
17.8    
18.1    
18.3    
18.5    
18.8    
19.0    
19.2    
19.5    
19.7    
20.0    
20.2    
20.4    
20.7    
20.9    
21.1    
21.4    
21.6    
21.9    
22.1    
22.3    
22.6    
22.8    
23.0    
23.3    
23.5    
23.8    
24.0    
24.2    
24.5    
24.7    
24.9    
25.2    
25.4    
25.7    
25.9    
26.1    
26.4    
26.6    
26.8    
27.1    
27.3    
27.6    
27.8    
28.0    
28.3    
28.5    
28.7    
29.0    
29.2    
29.5    
29.7    
29.9    
30.2    
30.4    
30.6    
30.9    
31.1    
31.4    
31.6    
31.8    
32.1    
32.3    
32.5    
32.8    
33.0    
33.3    
33.5    
33.7    
34.0    
34.2    
34.4    
34.7    
34.9    
35.2    
35.4    
35.6    
35.9    
36.1    
36.3    
36.6    
36.8    
37.1    
37.3    
37.5    
37.8    
38.0    
38.2    
38.5    
38.7    
39.0    
39.2    
39.4    
39.7    
39.9    
40.1    
40.4    
40.6    
40.9    
41.1    
41.3    
41.6    
41.8    
42.0    
42.3    
42.5    
42.8    
43.0    
43.2    
43.5    
43.7    
43.9    
44.2    
44.4    
44.7    
44.9    
45.1    
45.4    
45.6    
45.8    
46.1    
46.3    
46.6    
46.8    
47.0    
47.3    
47.5    
47.7    
48.0    
48.2    
48.5    
48.7    
48.9    
49.2    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.8    
51.1    
51.3    
51.5    
51.8    
52.0    
52.3    
52.5    
52.7    
53.0    
53.2    
53.4    
53.7    
53.9    
54.2    
54.4    
54.6    
54.9    
55.1    
55.3    
55.6    
55.8    
56.1    
56.3    
56.5    
56.8    
57.0    
57.2    
57.5    
57.7    
58.0    
58.2    
58.4    
58.7    
58.9    
59.1    
59.4    
59.6    
59.9    
60.1    
60.3    
60.6    
60.8    
61.0    
61.3    
61.5    
61.8    
62.0    
62.2    
62.5    
62.7    
62.9    
63.2    
63.4    
63.7    
63.9    
64.1    
64.4    
64.6    
64.8    
65.1    
65.3    
65.6    
65.8    
66.0    
66.3    
66.5    
66.7    
67.0    
67.2    
67.5    
67.7    
67.9    
68.2    
68.4    
68.6    
68.9    
69.1    
69.4    
69.6    
69.8    
70.1    
70.3    
70.5    
70.8    
71.0    
71.3    
71.5    
71.7    
72.0    
72.2    
72.4    
72.7    
72.9    
73.2    
73.4    
73.6    
73.9    
74.1    
74.3    
74.6    
74.8    
75.1    
75.3    
75.5    
75.8    
76.0    
76.2    
76.5    
76.7    
77.0    
77.2    
77.4    
77.7    
77.9    
78.1    
78.4    
78.6    
78.9    
79.1    
79.3    
79.6    
79.8    
80.0    
80.3    
80.5    
80.8    
81.0    
81.2    
81.5    
81.7    
81.9    
82.2    
82.4    
82.7    
82.9    
83.1    
83.4    
83.6    
83.8    
84.1    
84.3    
84.6    
84.8    
85.0    
85.3    
85.5    
85.7    
86.0    
86.2    
86.5    
86.7    
86.9    
87.2    
87.4    
87.6    
87.9    
88.1    
88.4    
88.6    
88.8    
89.1    
89.3    
89.5    
89.8    
90.0    
90.3    
90.5    
90.7    
91.0    
91.2    
91.4    
91.7    
91.9    
92.2    
92.4    
92.6    
92.9    
93.1    
93.3    
93.6    
93.8    
94.1    
94.3    
94.5    
94.8    
95.0    
95.2    
95.5    
95.7    
96.0    
96.2    
96.4    
96.7    
96.9    
97.1    
97.4    
97.6    
97.9    
98.1    
98.3    
98.6    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 49754, rend_intergenic: 39849  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60306, rend_intergenic: 57158  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87726, rend_intergenic: 80822  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109893, rend_intergenic: 105013  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151056, rend_intergenic: 149879  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153427, rend_intergenic: 152915  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157294, rend_intergenic: 155471  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support