-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_10/scaffold_10_16899310-17109793

-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 CodingQuarry_transcript_5669-T1
Valid prediction for GeneMark_model.46103_t
Valid prediction for GeneMark_model.46074_t
Valid prediction for GlimmerHMM_glimmerT_26710-T1
Valid prediction for GeneMark_model.46112_t
Valid prediction for GlimmerHMM_glimmerT_26711-T1
Valid prediction for snap_scaffold_10-snap.3440-T1
Valid prediction for GeneMark_model.46130_t
Valid prediction for GeneMark_model.46101_t
Valid prediction for GlimmerHMM_glimmerT_26707-T1
Valid prediction for GlimmerHMM_glimmerT_26716-T1
Valid prediction for GeneMark_model.46120_t
Valid prediction for GeneMark_model.46075_t
Valid prediction for pasa_asmbl_5010.p1
Valid prediction for GeneMark_model.46104_t
Valid prediction for GeneMark_model.46091_t
Valid prediction for HiQ_model.g17900.t1
Valid prediction for GeneMark_model.46108_t
Valid prediction for snap_scaffold_10-snap.3457-T1
Valid prediction for GeneMark_model.46110_t
Valid prediction for GeneMark_model.46118_t
Valid prediction for snap_scaffold_10-snap.3469-T1
Valid prediction for GeneMark_model.46126_t
Valid prediction for Augustus_model.g17906.t1
Valid prediction for GlimmerHMM_glimmerT_26723-T1
Valid prediction for GeneMark_model.46076_t
Valid prediction for CodingQuarry_transcript_5668-T1
Valid prediction for snap_scaffold_10-snap.3461-T1
Valid prediction for GeneMark_model.46117_t
Valid prediction for snap_scaffold_10-snap.3474-T1
Valid prediction for snap_scaffold_10-snap.3450-T1
Valid prediction for GeneMark_model.46080_t
Valid prediction for GlimmerHMM_glimmerT_26704-T1
Valid prediction for GeneMark_model.46119_t
Valid prediction for GeneMark_model.46131_t
Valid prediction for GeneMark_model.46123_t
Valid prediction for Augustus_model.g17893.t1
Valid prediction for GeneMark_model.46132_t
Valid prediction for GeneMark_model.46095_t
Valid prediction for snap_scaffold_10-snap.3473-T1
Valid prediction for snap_scaffold_10-snap.3458-T1
Valid prediction for snap_scaffold_10-snap.3472-T1
Valid prediction for GeneMark_model.46090_t
Valid prediction for snap_scaffold_10-snap.3470-T1
Valid prediction for GeneMark_model.46124_t
Valid prediction for Augustus_model.g17895.t1
Valid prediction for GeneMark_model.46106_t
Couldn't classify 70480, 70908
Couldn't classify 71030, 71503
Sorry, prediction pasa_asmbl_5009.p1 fails validation.
(AAG)	 TG	70480-70908	GT	AGG
(GGC)	 AG	71030-71503	CG	CAC
Valid prediction for snap_scaffold_10-snap.3441-T1
Valid prediction for snap_scaffold_10-snap.3452-T1
Valid prediction for snap_scaffold_10-snap.3446-T1
Valid prediction for GlimmerHMM_glimmerT_26712-T1
Valid prediction for GeneMark_model.46114_t
Valid prediction for Augustus_model.g17890.t1
Valid prediction for snap_scaffold_10-snap.3468-T1
Valid prediction for GeneMark_model.46086_t
Valid prediction for GeneMark_model.46073_t
Valid prediction for GeneMark_model.46071_t
Valid prediction for GeneMark_model.46093_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 GlimmerHMM_glimmerT_26706-T1
Valid prediction for GeneMark_model.46083_t
Couldn't classify 49726, 49906
Couldn't classify 50905, 51045
Sorry, prediction pasa_asmbl_3927.p1 fails validation.
(GAG)	 GG	49726-49906	GT	GGG
(GTG)	 AG	50279-50400	GT	AGG
(GAC)	 AG	50905-51045	AG	GTA
-recovered pasa_asmbl_3927.p1, internal, 50279, 50400
Valid prediction for GeneMark_model.46129_t
Valid prediction for Augustus_model.g17902.t1
Valid prediction for Augustus_model.g17897.t1
Valid prediction for snap_scaffold_10-snap.3460-T1
Valid prediction for GeneMark_model.46084_t
Valid prediction for GeneMark_model.46107_t
Valid prediction for GeneMark_model.46094_t
Valid prediction for Augustus_model.g17907.t1
Valid prediction for GlimmerHMM_glimmerT_26717-T1
Couldn't classify 58227, 58340
Couldn't classify 58383, 58502
Sorry, prediction CodingQuarry_transcript_5671-T1 fails validation.
(ATG)	 AG	58227-58340	AC	ACA
(GCC)	 AT	58383-58502	TT	AGT
Valid prediction for GeneMark_model.46100_t
Valid prediction for Augustus_model.g17894.t1
Valid prediction for GlimmerHMM_glimmerT_26722-T1
Valid prediction for pasa_asmbl_4072.p1
Valid prediction for snap_scaffold_10-snap.3466-T1
Valid prediction for Augustus_model.g17892.t1
Couldn't classify 176488, 176700
Couldn't classify 176822, 176983
Sorry, prediction pasa_asmbl_4067.p1 fails validation.
(CCC)	 TG	176488-176700	GT	AGG
(GGC)	 AG	176822-176983	AA	CGA
Valid prediction for Augustus_model.g17904.t1
Valid prediction for GlimmerHMM_glimmerT_26713-T1
Valid prediction for pasa_asmbl_3920.p1
Valid prediction for snap_scaffold_10-snap.3455-T1
Valid prediction for GeneMark_model.46128_t
Valid prediction for GlimmerHMM_glimmerT_26714-T1
Valid prediction for GeneMark_model.46082_t
Valid prediction for GlimmerHMM_glimmerT_26720-T1
Valid prediction for GeneMark_model.46089_t
Valid prediction for snap_scaffold_10-snap.3456-T1
Valid prediction for GeneMark_model.46078_t
Valid prediction for snap_scaffold_10-snap.3467-T1
Valid prediction for GeneMark_model.46070_t
Valid prediction for GeneMark_model.46113_t
Valid prediction for CodingQuarry_transcript_5666-T1
Valid prediction for Augustus_model.g17891.t1
Valid prediction for Augustus_model.g17899.t1
Valid prediction for GlimmerHMM_glimmerT_26718-T1
Valid prediction for GeneMark_model.46092_t
Valid prediction for snap_scaffold_10-snap.3442-T1
Valid prediction for GeneMark_model.46081_t
Valid prediction for GlimmerHMM_glimmerT_26705-T1
Valid prediction for snap_scaffold_10-snap.3448-T1
Valid prediction for Augustus_model.g17903.t1
Valid prediction for GlimmerHMM_glimmerT_26715-T1
Valid prediction for snap_scaffold_10-snap.3475-T1
Valid prediction for snap_scaffold_10-snap.3449-T1
Valid prediction for Augustus_model.g17905.t1
Valid prediction for GeneMark_model.46077_t
Valid prediction for snap_scaffold_10-snap.3444-T1
Couldn't classify 113967, 114210
Sorry, prediction pasa_asmbl_3921.p1 fails validation.
(GCC)	 TT	113967-114210	GT	AGG
(GAC)	 AG	114510-114622	TC	GAT
-recovered pasa_asmbl_3921.p1, terminal, 114510, 114622
Valid prediction for snap_scaffold_10-snap.3465-T1
Valid prediction for Augustus_model.g17896.t1
Valid prediction for GeneMark_model.46115_t
Couldn't classify 37863, 37968
Couldn't classify 40726, 40876
Sorry, prediction pasa_asmbl_3986.p1 fails validation.
(CAG)	 TA	37863-37968	GT	AGG
(GTA)	 AG	38804-38982	GT	AGG
(CTG)	 AG	39833-39973	GT	AGG
(ACC)	 AG	40404-40492	GT	AGG
(GCC)	 AG	40726-40876	TC	TCT
-recovered pasa_asmbl_3986.p1, internal, 38804, 38982
-recovered pasa_asmbl_3986.p1, internal, 39833, 39973
-recovered pasa_asmbl_3986.p1, internal, 40404, 40492
Valid prediction for GeneMark_model.46116_t
Valid prediction for GlimmerHMM_glimmerT_26724-T1
Couldn't classify 57080, 57169
Sorry, prediction pasa_asmbl_3926.p1 fails validation.
(GCC)	 AG	57080-57169	GT	AGG
(GAG)	 AG	57255-57470	GT	CGG
(ATC)	 AG	57932-57994	AG	AGA
-recovered pasa_asmbl_3926.p1, terminal, 57932, 57994
-recovered pasa_asmbl_3926.p1, internal, 57080, 57169
-recovered pasa_asmbl_3926.p1, internal, 57255, 57470
Valid prediction for GeneMark_model.46098_t
Valid prediction for GeneMark_model.46111_t
Valid prediction for GeneMark_model.46125_t
Couldn't classify 10399, 10508
Sorry, prediction pasa_asmbl_3933.p1 fails validation.
(TTG)	 TA	10399-10508	GT	AGG
(GTT)	 AG	11449-11530	GT	CGG
(GAG)	 AG	11805-11978	GT	AGG
(GGA)	 AG	12457-12547	GT	GGG
(AGT)	 AG	12860-12965	GT	TCG
(TAA)	 AG	13097-13262	GT	AGG
(ACG)	 AG	13605-13706	GT	AGG
(CAG)	 AG	14301-14397	GT	TGG
(ATG)	 AG	14673-14732	GT	AGG
(GGC)	 AG	14987-15115	GT	GAG
(CGT)	 AG	15289-15407	GT	AGG
(CCC)	 AG	15853-16146	GG	GAG
-recovered pasa_asmbl_3933.p1, initial, 14673, 14732
add_exon() Sorry, pasa_asmbl_3933.p1 14987-15115-terminal-1 is invalid.
-recovered pasa_asmbl_3933.p1, terminal, 14987, 15115
-recovered pasa_asmbl_3933.p1, terminal, 15853, 16146
-recovered pasa_asmbl_3933.p1, internal, 11449, 11530
-recovered pasa_asmbl_3933.p1, internal, 11805, 11978
-recovered pasa_asmbl_3933.p1, internal, 12457, 12547
-recovered pasa_asmbl_3933.p1, internal, 12860, 12965
-recovered pasa_asmbl_3933.p1, internal, 13097, 13262
-recovered pasa_asmbl_3933.p1, internal, 13605, 13706
-recovered pasa_asmbl_3933.p1, internal, 14301, 14397
-recovered pasa_asmbl_3933.p1, internal, 14673, 14732
-recovered pasa_asmbl_3933.p1, internal, 14987, 15115
-recovered pasa_asmbl_3933.p1, internal, 15289, 15407
Couldn't classify 117506, 117627
Sorry, prediction pasa_asmbl_4037.p1 fails validation.
(ATG)	 AG	115187-115275	GT	CGG
(GCA)	 AG	115376-115521	GT	AGG
(GGT)	 AG	115809-115983	GT	TGG
(GGT)	 AG	116350-116507	GT	TGG
(GTG)	 AG	117506-117627	CC	ACC
-recovered pasa_asmbl_4037.p1, initial, 115187, 115275
-recovered pasa_asmbl_4037.p1, internal, 115187, 115275
-recovered pasa_asmbl_4037.p1, internal, 115376, 115521
-recovered pasa_asmbl_4037.p1, internal, 115809, 115983
-recovered pasa_asmbl_4037.p1, internal, 116350, 116507
Valid prediction for GeneMark_model.46102_t
Valid prediction for GeneMark_model.46099_t
Valid prediction for HiQ_model.g17898.t1
Valid prediction for snap_scaffold_10-snap.3463-T1
Valid prediction for GlimmerHMM_glimmerT_26708-T1
Valid prediction for snap_scaffold_10-snap.3459-T1
Valid prediction for GeneMark_model.46072_t
Valid prediction for GeneMark_model.46121_t
Couldn't classify 117506, 117749
Couldn't classify 117822, 118462
Sorry, prediction CodingQuarry_transcript_5667-T1 fails validation.
(ATG)	 TC	115250-115275	GT	CGG
(GCA)	 AG	115376-115521	GT	AGG
(GGT)	 AG	115809-115983	GT	TGG
(GGT)	 AG	116350-116507	GT	TGG
(GTG)	 AG	117506-117749	CT	ACC
(CTA)	 AC	117822-118462	GT	AGG
(AAC)	 AG	118733-118953	CA	AAC
-recovered CodingQuarry_transcript_5667-T1, initial, 115250, 115275
-recovered CodingQuarry_transcript_5667-T1, terminal, 118733, 118953
-recovered CodingQuarry_transcript_5667-T1, internal, 115376, 115521
-recovered CodingQuarry_transcript_5667-T1, internal, 115809, 115983
-recovered CodingQuarry_transcript_5667-T1, internal, 116350, 116507
Valid prediction for GeneMark_model.46087_t
Valid prediction for snap_scaffold_10-snap.3445-T1
Valid prediction for snap_scaffold_10-snap.3443-T1
Valid prediction for GeneMark_model.46079_t
Valid prediction for snap_scaffold_10-snap.3439-T1
Valid prediction for GeneMark_model.46109_t
Valid prediction for snap_scaffold_10-snap.3464-T1
Valid prediction for Augustus_model.g17901.t1
Valid prediction for snap_scaffold_10-snap.3462-T1
Valid prediction for GlimmerHMM_glimmerT_26709-T1
Valid prediction for snap_scaffold_10-snap.3478-T1
Couldn't classify 172269, 172769
Sorry, prediction pasa_asmbl_3919.p1 fails validation.
(CTC)	 AC	172269-172769	CA	GAC
Valid prediction for snap_scaffold_10-snap.3454-T1
Valid prediction for snap_scaffold_10-snap.3471-T1
Valid prediction for GeneMark_model.46096_t
Valid prediction for snap_scaffold_10-snap.3447-T1
Couldn't classify 177170, 177967
Sorry, prediction pasa_asmbl_3918.p1 fails validation.
(CAA)	 AT	177170-177967	CG	GAC
Valid prediction for snap_scaffold_10-snap.3451-T1
Couldn't classify 110854, 110923
Couldn't classify 113462, 113720
Sorry, prediction pasa_asmbl_3923.p1 fails validation.
(TCA)	 AC	110854-110923	GT	AGG
(GTG)	 AG	111796-111874	GT	CAG
(GAT)	 AG	113462-113720	CC	CCC
-recovered pasa_asmbl_3923.p1, internal, 111796, 111874
Valid prediction for snap_scaffold_10-snap.3476-T1
Valid prediction for GlimmerHMM_glimmerT_26719-T1
Valid prediction for GeneMark_model.46105_t
Valid prediction for GlimmerHMM_glimmerT_26721-T1
Valid prediction for GeneMark_model.46122_t
Valid prediction for snap_scaffold_10-snap.3453-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 20389, rend_intergenic: 3364  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29186, rend_intergenic: 20885  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63574, rend_intergenic: 61601  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77021, rend_intergenic: 73615  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83436, rend_intergenic: 77769  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104878, rend_intergenic: 98529  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119372, rend_intergenic: 117818  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135459, rend_intergenic: 119723  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177940, rend_intergenic: 156897  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183280, rend_intergenic: 178419  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197394, rend_intergenic: 194339  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 210484
-exon list size: 728


building trellis

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62.3    
62.5    
62.6    
62.7    
62.9    
63.0    
63.2    
63.3    
63.4    
63.6    
63.7    
63.8    
64.0    
64.1    
64.2    
64.4    
64.5    
64.7    
64.8    
64.9    
65.1    
65.2    
65.3    
65.5    
65.6    
65.8    
65.9    
66.0    
66.2    
66.3    
66.4    
66.6    
66.7    
66.8    
67.0    
67.1    
67.3    
67.4    
67.5    
67.7    
67.8    
67.9    
68.1    
68.2    
68.4    
68.5    
68.6    
68.8    
68.9    
69.0    
69.2    
69.3    
69.5    
69.6    
69.7    
69.9    
70.0    
70.1    
70.3    
70.4    
70.5    
70.7    
70.8    
71.0    
71.1    
71.2    
71.4    
71.5    
71.6    
71.8    
71.9    
72.1    
72.2    
72.3    
72.5    
72.6    
72.7    
72.9    
73.0    
73.2    
73.3    
73.4    
73.6    
73.7    
73.8    
74.0    
74.1    
74.2    
74.4    
74.5    
74.7    
74.8    
74.9    
75.1    
75.2    
75.3    
75.5    
75.6    
75.8    
75.9    
76.0    
76.2    
76.3    
76.4    
76.6    
76.7    
76.8    
77.0    
77.1    
77.3    
77.4    
77.5    
77.7    
77.8    
77.9    
78.1    
78.2    
78.4    
78.5    
78.6    
78.8    
78.9    
79.0    
79.2    
79.3    
79.5    
79.6    
79.7    
79.9    
80.0    
80.1    
80.3    
80.4    
80.5    
80.7    
80.8    
81.0    
81.1    
81.2    
81.4    
81.5    
81.6    
81.8    
81.9    
82.1    
82.2    
82.3    
82.5    
82.6    
82.7    
82.9    
83.0    
83.2    
83.3    
83.4    
83.6    
83.7    
83.8    
84.0    
84.1    
84.2    
84.4    
84.5    
84.7    
84.8    
84.9    
85.1    
85.2    
85.3    
85.5    
85.6    
85.8    
85.9    
86.0    
86.2    
86.3    
86.4    
86.6    
86.7    
86.8    
87.0    
87.1    
87.3    
87.4    
87.5    
87.7    
87.8    
87.9    
88.1    
88.2    
88.4    
88.5    
88.6    
88.8    
88.9    
89.0    
89.2    
89.3    
89.5    
89.6    
89.7    
89.9    
90.0    
90.1    
90.3    
90.4    
90.5    
90.7    
90.8    
91.0    
91.1    
91.2    
91.4    
91.5    
91.6    
91.8    
91.9    
92.1    
92.2    
92.3    
92.5    
92.6    
92.7    
92.9    
93.0    
93.2    
93.3    
93.4    
93.6    
93.7    
93.8    
94.0    
94.1    
94.2    
94.4    
94.5    
94.7    
94.8    
94.9    
95.1    
95.2    
95.3    
95.5    
95.6    
95.8    
95.9    
96.0    
96.2    
96.3    
96.4    
96.6    
96.7    
96.8    
97.0    
97.1    
97.3    
97.4    
97.5    
97.7    
97.8    
97.9    
98.1    
98.2    
98.4    
98.5    
98.6    
98.8    
98.9    
99.0    
99.2    
99.3    
99.5    
99.6    
99.7    
99.9    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 20389, rend_intergenic: 3364  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29186, rend_intergenic: 20885  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63574, rend_intergenic: 61601  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77021, rend_intergenic: 73615  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83436, rend_intergenic: 77769  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104878, rend_intergenic: 98529  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119372, rend_intergenic: 117818  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135459, rend_intergenic: 119723  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177940, rend_intergenic: 156897  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183280, rend_intergenic: 178419  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197394, rend_intergenic: 194339  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 16187
-exon list size: 50


building trellis

1.9    
3.8    
5.8    
7.7    
9.6    
11.5    
13.5    
15.4    
17.3    
19.2    
21.2    
23.1    
25.0    
26.9    
28.8    
30.8    
32.7    
34.6    
36.5    
38.5    
40.4    
42.3    
44.2    
46.2    
48.1    
50.0    
51.9    
53.8    
55.8    
57.7    
59.6    
61.5    
63.5    
65.4    
67.3    
69.2    
71.2    
73.1    
75.0    
76.9    
78.8    
80.8    
82.7    
84.6    
86.5    
88.5    
90.4    
92.3    
94.2    
96.2    
98.1    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 11717
-exon list size: 30


building trellis

3.1    
6.2    
9.4    
12.5    
15.6    
18.8    
21.9    
25.0    
28.1    
31.2    
34.4    
37.5    
40.6    
43.8    
46.9    
50.0    
53.1    
56.2    
59.4    
62.5    
65.6    
68.8    
71.9    
75.0    
78.1    
81.2    
84.4    
87.5    
90.6    
93.8    
96.9    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support