-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_2/scaffold_2_19745907-19927914

-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: +)Couldn't classify 119626, 119703
Sorry, prediction pasa_asmbl_25352.p1 fails validation.
(ATG)	 AG	116344-116409	GT	AGG
(AGA)	 AG	117483-117654	GT	AGG
(GAG)	 AG	119062-119172	GT	CGG
(CTG)	 AG	119411-119541	GT	TGG
(TTT)	 AG	119626-119703	NN	NNN
-recovered pasa_asmbl_25352.p1, initial, 116344, 116409
-recovered pasa_asmbl_25352.p1, internal, 116344, 116409
-recovered pasa_asmbl_25352.p1, internal, 117483, 117654
-recovered pasa_asmbl_25352.p1, internal, 119062, 119172
-recovered pasa_asmbl_25352.p1, internal, 119411, 119541
Valid prediction for Augustus_model.g3797.t1
Valid prediction for GlimmerHMM_glimmerT_5710-T1
Valid prediction for snap_scaffold_2-snap.3849-T1
Valid prediction for snap_scaffold_2-snap.3855-T1
Valid prediction for snap_scaffold_2-snap.3875-T1
Valid prediction for snap_scaffold_2-snap.3858-T1
Valid prediction for snap_scaffold_2-snap.3853-T1
Valid prediction for GlimmerHMM_glimmerT_5708-T1
Valid prediction for snap_scaffold_2-snap.3850-T1
Valid prediction for snap_scaffold_2-snap.3844-T1
Valid prediction for Augustus_model.g3805.t1
Valid prediction for snap_scaffold_2-snap.3856-T1
Valid prediction for snap_scaffold_2-snap.3864-T1
Valid prediction for snap_scaffold_2-snap.3876-T1
Couldn't classify 130394, 130816
Sorry, prediction pasa_asmbl_25296.p1 fails validation.
(CTA)	 TT	130394-130816	CG	AGC
Valid prediction for GlimmerHMM_glimmerT_5718-T1
Valid prediction for snap_scaffold_2-snap.3842-T1
Valid prediction for snap_scaffold_2-snap.3874-T1
Valid prediction for HiQ_model.g3800.t1
Valid prediction for GlimmerHMM_glimmerT_5715-T1
Couldn't classify 82394, 85105
Sorry, prediction pasa_asmbl_25292.p1 fails validation.
(CTG)	 CT	82394-85105	AG	TCA
Valid prediction for snap_scaffold_2-snap.3843-T1
Valid prediction for CodingQuarry_transcript_28871-T1
Valid prediction for pasa_asmbl_25285.p1
Couldn't classify 153860, 153910
Sorry, prediction pasa_asmbl_25299.p1 fails validation.
(AAC)	 AG	153860-153910	GT	AGG
(GGC)	 AG	154573-154661	GT	GGG
(GTA)	 AG	155095-155222	GT	AGG
(TGT)	 AG	155541-155636	GT	TTG
(CCT)	 AG	155721-155880	GT	CGG
(GTC)	 AG	155971-156154	GA	AGG
-recovered pasa_asmbl_25299.p1, terminal, 155971, 156154
-recovered pasa_asmbl_25299.p1, internal, 153860, 153910
-recovered pasa_asmbl_25299.p1, internal, 154573, 154661
-recovered pasa_asmbl_25299.p1, internal, 155095, 155222
-recovered pasa_asmbl_25299.p1, internal, 155541, 155636
-recovered pasa_asmbl_25299.p1, internal, 155721, 155880
Valid prediction for CodingQuarry_transcript_28870-T1
Valid prediction for Augustus_model.g3798.t1
Valid prediction for CodingQuarry_transcript_28869-T1
Valid prediction for GlimmerHMM_glimmerT_5707-T1
Valid prediction for GlimmerHMM_glimmerT_5711-T1
Valid prediction for Augustus_model.g3801.t1
Valid prediction for pasa_asmbl_25294.p1
Couldn't classify 93952, 94563
Sorry, prediction pasa_asmbl_25293.p1 fails validation.
(GCC)	 TC	93952-94563	GT	AGG
(ATC)	 AG	96309-97796	GA	GAG
-recovered pasa_asmbl_25293.p1, terminal, 96309, 97796
Valid prediction for GlimmerHMM_glimmerT_5721-T1
Valid prediction for snap_scaffold_2-snap.3860-T1
Valid prediction for CodingQuarry_transcript_28872-T1
Valid prediction for HiQ_model.g3796.t1
Valid prediction for HiQ_model.g3802.t1
Valid prediction for GlimmerHMM_glimmerT_5716-T1
Valid prediction for snap_scaffold_2-snap.3852-T1
Valid prediction for GlimmerHMM_glimmerT_5717-T1
Valid prediction for snap_scaffold_2-snap.3841-T1
Valid prediction for snap_scaffold_2-snap.3872-T1
Couldn't classify 133515, 133694
Sorry, prediction pasa_asmbl_25297.p1 fails validation.
(CCG)	 CC	133515-133694	GT	AGG
(GTT)	 AG	134358-134471	GT	AGG
(AAA)	 AG	134742-134835	GT	AGG
(GCA)	 AG	135038-135222	GT	TGG
(GAC)	 AG	135566-135688	AA	AGA
-recovered pasa_asmbl_25297.p1, terminal, 135566, 135688
-recovered pasa_asmbl_25297.p1, internal, 134358, 134471
-recovered pasa_asmbl_25297.p1, internal, 134742, 134835
-recovered pasa_asmbl_25297.p1, internal, 135038, 135222
Valid prediction for CodingQuarry_transcript_28868-T1
Valid prediction for snap_scaffold_2-snap.3869-T1
Valid prediction for Augustus_model.g3799.t1
Valid prediction for snap_scaffold_2-snap.3863-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_5720-T1
Valid prediction for snap_scaffold_2-snap.3873-T1
Valid prediction for HiQ_model.g3803.t1
Valid prediction for GlimmerHMM_glimmerT_5719-T1
Valid prediction for snap_scaffold_2-snap.3868-T1
Couldn't classify 32921, 33139
Couldn't classify 33248, 34472
Sorry, prediction CodingQuarry_transcript_28875-T1 fails validation.
(ATG)	 GT	31522-31647	GT	CGG
(ACA)	 AG	32921-33139	AA	CCA
(GCT)	 CC	33248-34472	GT	AGG
(AAG)	 AG	34789-34928	GT	AGG
(TTG)	 AG	35125-35191	GT	GGG
(GTG)	 AG	35433-35476	GT	AGG
(ACG)	 AG	35640-35781	GT	GGG
(GCA)	 AG	35855-35933	GT	AGG
(ATA)	 AG	36458-36533	GT	AGG
(TTG)	 AG	36681-36794	GT	TTG
(TGG)	 AG	37167-37260	GT	AGG
(AGC)	 AG	37478-37683	GT	GGG
(GCA)	 AG	37964-38107	GT	AGG
(TGG)	 AG	38779-38859	GT	AGG
(AAA)	 AG	38975-39046	GT	AGG
(TTG)	 AG	39402-39452	TT	GAT
-recovered CodingQuarry_transcript_28875-T1, initial, 31522, 31647
-recovered CodingQuarry_transcript_28875-T1, terminal, 39402, 39452
-recovered CodingQuarry_transcript_28875-T1, internal, 34789, 34928
-recovered CodingQuarry_transcript_28875-T1, internal, 35125, 35191
-recovered CodingQuarry_transcript_28875-T1, internal, 35433, 35476
-recovered CodingQuarry_transcript_28875-T1, internal, 35640, 35781
-recovered CodingQuarry_transcript_28875-T1, internal, 35855, 35933
-recovered CodingQuarry_transcript_28875-T1, internal, 36458, 36533
-recovered CodingQuarry_transcript_28875-T1, internal, 36681, 36794
-recovered CodingQuarry_transcript_28875-T1, internal, 37167, 37260
-recovered CodingQuarry_transcript_28875-T1, internal, 37478, 37683
-recovered CodingQuarry_transcript_28875-T1, internal, 37964, 38107
-recovered CodingQuarry_transcript_28875-T1, internal, 38779, 38859
-recovered CodingQuarry_transcript_28875-T1, internal, 38975, 39046
Valid prediction for GlimmerHMM_glimmerT_5709-T1
Valid prediction for snap_scaffold_2-snap.3862-T1
Valid prediction for snap_scaffold_2-snap.3861-T1
Valid prediction for snap_scaffold_2-snap.3848-T1
Valid prediction for snap_scaffold_2-snap.3859-T1
Valid prediction for pasa_asmbl_23877.p1
Valid prediction for GlimmerHMM_glimmerT_5706-T1
Valid prediction for snap_scaffold_2-snap.3851-T1
Valid prediction for snap_scaffold_2-snap.3871-T1
Valid prediction for snap_scaffold_2-snap.3846-T1
Valid prediction for snap_scaffold_2-snap.3865-T1
Valid prediction for snap_scaffold_2-snap.3857-T1
Valid prediction for GlimmerHMM_glimmerT_5712-T1
Valid prediction for snap_scaffold_2-snap.3866-T1
Valid prediction for CodingQuarry_transcript_28873-T1
Valid prediction for pasa_asmbl_25291.p1
Valid prediction for snap_scaffold_2-snap.3854-T1
Valid prediction for snap_scaffold_2-snap.3847-T1
Valid prediction for GlimmerHMM_glimmerT_5723-T1
Valid prediction for pasa_asmbl_23875.p1
Valid prediction for GlimmerHMM_glimmerT_5714-T1
Valid prediction for snap_scaffold_2-snap.3867-T1
Valid prediction for Augustus_model.g3806.t1
Valid prediction for GlimmerHMM_glimmerT_5713-T1
Valid prediction for CodingQuarry_transcript_28874-T1
Valid prediction for snap_scaffold_2-snap.3845-T1
Valid prediction for HiQ_model.g3804.t1
Valid prediction for GlimmerHMM_glimmerT_5722-T1
Valid prediction for GlimmerHMM_glimmerT_5705-T1
Valid prediction for snap_scaffold_2-snap.3870-T1
Valid prediction for snap_scaffold_2-snap.3840-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10430, rend_intergenic: 7128  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43839, rend_intergenic: 35602  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75113, rend_intergenic: 72523  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79004, rend_intergenic: 75182  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97796, rend_intergenic: 93772  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114255, rend_intergenic: 105424  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123518, rend_intergenic: 119425  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156154, rend_intergenic: 152796  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162782, rend_intergenic: 157430  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180395, rend_intergenic: 165296  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 182008
-exon list size: 289


building trellis

0.3    
0.7    
1.0    
1.4    
1.7    
2.1    
2.4    
2.7    
3.1    
3.4    
3.8    
4.1    
4.5    
4.8    
5.2    
5.5    
5.8    
6.2    
6.5    
6.9    
7.2    
7.6    
7.9    
8.2    
8.6    
8.9    
9.3    
9.6    
10.0    
10.3    
10.7    
11.0    
11.3    
11.7    
12.0    
12.4    
12.7    
13.1    
13.4    
13.7    
14.1    
14.4    
14.8    
15.1    
15.5    
15.8    
16.2    
16.5    
16.8    
17.2    
17.5    
17.9    
18.2    
18.6    
18.9    
19.2    
19.6    
19.9    
20.3    
20.6    
21.0    
21.3    
21.6    
22.0    
22.3    
22.7    
23.0    
23.4    
23.7    
24.1    
24.4    
24.7    
25.1    
25.4    
25.8    
26.1    
26.5    
26.8    
27.1    
27.5    
27.8    
28.2    
28.5    
28.9    
29.2    
29.6    
29.9    
30.2    
30.6    
30.9    
31.3    
31.6    
32.0    
32.3    
32.6    
33.0    
33.3    
33.7    
34.0    
34.4    
34.7    
35.1    
35.4    
35.7    
36.1    
36.4    
36.8    
37.1    
37.5    
37.8    
38.1    
38.5    
38.8    
39.2    
39.5    
39.9    
40.2    
40.5    
40.9    
41.2    
41.6    
41.9    
42.3    
42.6    
43.0    
43.3    
43.6    
44.0    
44.3    
44.7    
45.0    
45.4    
45.7    
46.0    
46.4    
46.7    
47.1    
47.4    
47.8    
48.1    
48.5    
48.8    
49.1    
49.5    
49.8    
50.2    
50.5    
50.9    
51.2    
51.5    
51.9    
52.2    
52.6    
52.9    
53.3    
53.6    
54.0    
54.3    
54.6    
55.0    
55.3    
55.7    
56.0    
56.4    
56.7    
57.0    
57.4    
57.7    
58.1    
58.4    
58.8    
59.1    
59.5    
59.8    
60.1    
60.5    
60.8    
61.2    
61.5    
61.9    
62.2    
62.5    
62.9    
63.2    
63.6    
63.9    
64.3    
64.6    
64.9    
65.3    
65.6    
66.0    
66.3    
66.7    
67.0    
67.4    
67.7    
68.0    
68.4    
68.7    
69.1    
69.4    
69.8    
70.1    
70.4    
70.8    
71.1    
71.5    
71.8    
72.2    
72.5    
72.9    
73.2    
73.5    
73.9    
74.2    
74.6    
74.9    
75.3    
75.6    
75.9    
76.3    
76.6    
77.0    
77.3    
77.7    
78.0    
78.4    
78.7    
79.0    
79.4    
79.7    
80.1    
80.4    
80.8    
81.1    
81.4    
81.8    
82.1    
82.5    
82.8    
83.2    
83.5    
83.8    
84.2    
84.5    
84.9    
85.2    
85.6    
85.9    
86.3    
86.6    
86.9    
87.3    
87.6    
88.0    
88.3    
88.7    
89.0    
89.3    
89.7    
90.0    
90.4    
90.7    
91.1    
91.4    
91.8    
92.1    
92.4    
92.8    
93.1    
93.5    
93.8    
94.2    
94.5    
94.8    
95.2    
95.5    
95.9    
96.2    
96.6    
96.9    
97.3    
97.6    
97.9    
98.3    
98.6    
99.0    
99.3    
99.7    
-found 18 predictions from path traversal
Error with prediction: snap lend_intergenic: 10430, rend_intergenic: 7128  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43839, rend_intergenic: 35602  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75113, rend_intergenic: 72523  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79004, rend_intergenic: 75182  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97796, rend_intergenic: 93772  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114255, rend_intergenic: 105424  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123518, rend_intergenic: 119425  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156154, rend_intergenic: 152796  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162782, rend_intergenic: 157430  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180395, rend_intergenic: 165296  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 13 predictions persist after filtering for low support