-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_17/scaffold_17_3899052-4129760

-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 GlimmerHMM_glimmerT_41020-T1
Valid prediction for snap_scaffold_17-snap.862-T1
Valid prediction for Augustus_model.g27478.t1
Valid prediction for snap_scaffold_17-snap.837-T1
Valid prediction for GeneMark_model.70649_t
Valid prediction for GlimmerHMM_glimmerT_41028-T1
Valid prediction for GlimmerHMM_glimmerT_41012-T1
Couldn't classify 186570, 186761
Sorry, prediction pasa_asmbl_17897.p2 fails validation.
(CCT)	 CC	186570-186761	GT	AGG
(GAT)	 AG	187215-187430	GG	GAG
-recovered pasa_asmbl_17897.p2, terminal, 187215, 187430
Valid prediction for Augustus_model.g27463.t1
Valid prediction for GeneMark_model.70670_t
Valid prediction for snap_scaffold_17-snap.845-T1
Valid prediction for pasa_asmbl_17888.p1
Valid prediction for GeneMark_model.70644_t
Valid prediction for snap_scaffold_17-snap.827-T1
Valid prediction for CodingQuarry_transcript_21898-T1
Valid prediction for snap_scaffold_17-snap.836-T1
Couldn't classify 41578, 41698
Couldn't classify 42990, 43040
Sorry, prediction pasa_asmbl_17874.p1 fails validation.
(GAG)	 GT	41578-41698	GT	AGG
(CTG)	 AG	41793-41871	GT	AGG
(GGG)	 AG	42342-42542	GT	ATG
(GGT)	 AG	42638-42776	GT	AGG
(CCT)	 AG	42990-43040	CT	AGC
-recovered pasa_asmbl_17874.p1, internal, 41793, 41871
-recovered pasa_asmbl_17874.p1, internal, 42342, 42542
-recovered pasa_asmbl_17874.p1, internal, 42638, 42776
Valid prediction for GeneMark_model.70694_t
Valid prediction for snap_scaffold_17-snap.861-T1
Valid prediction for GeneMark_model.70665_t
Valid prediction for GeneMark_model.70680_t
Valid prediction for GlimmerHMM_glimmerT_41022-T1
Valid prediction for Augustus_model.g27474.t1
Valid prediction for GeneMark_model.70655_t
Valid prediction for snap_scaffold_17-snap.856-T1
Valid prediction for snap_scaffold_17-snap.854-T1
Valid prediction for GeneMark_model.70664_t
Valid prediction for GeneMark_model.70636_t
Valid prediction for GeneMark_model.70659_t
Valid prediction for GlimmerHMM_glimmerT_41011-T1
Valid prediction for GeneMark_model.70682_t
Valid prediction for GeneMark_model.70642_t
Valid prediction for GeneMark_model.70638_t
Valid prediction for Augustus_model.g27483.t1
Valid prediction for GeneMark_model.70647_t
Valid prediction for GlimmerHMM_glimmerT_41024-T1
Valid prediction for GeneMark_model.70653_t
Valid prediction for GeneMark_model.70688_t
Valid prediction for GeneMark_model.70657_t
Valid prediction for snap_scaffold_17-snap.857-T1
Valid prediction for GeneMark_model.70666_t
Valid prediction for GeneMark_model.70679_t
Valid prediction for GlimmerHMM_glimmerT_41017-T1
Valid prediction for Augustus_model.g27480.t1
Valid prediction for Augustus_model.g27475.t1
Valid prediction for CodingQuarry_transcript_21897-T1
Couldn't classify 170880, 171215
Sorry, prediction pasa_asmbl_17894.p1 fails validation.
(ATG)	 AG	170880-171215	GG	GCG
Valid prediction for GeneMark_model.70651_t
Valid prediction for GeneMark_model.70640_t
Valid prediction for GeneMark_model.70686_t
Valid prediction for GeneMark_model.70676_t
Valid prediction for snap_scaffold_17-snap.843-T1
Valid prediction for GlimmerHMM_glimmerT_41033-T1
Valid prediction for snap_scaffold_17-snap.844-T1
Valid prediction for HiQ_model.g27471.t1
Valid prediction for snap_scaffold_17-snap.865-T1
Valid prediction for snap_scaffold_17-snap.848-T1
Couldn't classify 171912, 175001
Sorry, prediction pasa_asmbl_17895.p1 fails validation.
(GCT)	 TA	171912-175001	TT	GAT
Valid prediction for GlimmerHMM_glimmerT_41031-T1
Valid prediction for GlimmerHMM_glimmerT_41027-T1
Valid prediction for snap_scaffold_17-snap.842-T1
Valid prediction for GeneMark_model.70690_t
Valid prediction for snap_scaffold_17-snap.829-T1
Valid prediction for GlimmerHMM_glimmerT_41030-T1
Valid prediction for Augustus_model.g27467.t1
Valid prediction for GeneMark_model.70677_t
Valid prediction for GlimmerHMM_glimmerT_41013-T1
Valid prediction for GlimmerHMM_glimmerT_41014-T1
Valid prediction for GeneMark_model.70661_t
Valid prediction for Augustus_model.g27464.t1
Valid prediction for Augustus_model.g27482.t1
Valid prediction for CodingQuarry_transcript_21896-T1
Valid prediction for GeneMark_model.70687_t
Valid prediction for snap_scaffold_17-snap.849-T1
Couldn't classify 147504, 147687
Sorry, prediction pasa_asmbl_17893.p1 fails validation.
(CTG)	 CC	147504-147687	GT	TAG
(GTT)	 AG	147825-147930	GT	CCG
(GAA)	 AG	148097-148238	GT	AGG
(CCT)	 AG	148350-148446	GT	TGG
(ACA)	 AG	148608-148806	GT	AGG
(GCA)	 AG	148927-149059	GT	AGG
(GGT)	 AG	149191-149316	GT	AGG
(GGC)	 AG	149498-149596	TG	GAT
-recovered pasa_asmbl_17893.p1, terminal, 149498, 149596
-recovered pasa_asmbl_17893.p1, internal, 147825, 147930
-recovered pasa_asmbl_17893.p1, internal, 148097, 148238
-recovered pasa_asmbl_17893.p1, internal, 148350, 148446
-recovered pasa_asmbl_17893.p1, internal, 148608, 148806
-recovered pasa_asmbl_17893.p1, internal, 148927, 149059
-recovered pasa_asmbl_17893.p1, internal, 149191, 149316
Valid prediction for GeneMark_model.70650_t
Valid prediction for HiQ_model.g27472.t1
Valid prediction for Augustus_model.g27481.t1
Valid prediction for snap_scaffold_17-snap.855-T1
Valid prediction for snap_scaffold_17-snap.846-T1
Valid prediction for GlimmerHMM_glimmerT_41010-T1
Valid prediction for snap_scaffold_17-snap.858-T1
Valid prediction for Augustus_model.g27462.t1
Valid prediction for snap_scaffold_17-snap.859-T1
Valid prediction for Augustus_model.g27479.t1
Valid prediction for snap_scaffold_17-snap.860-T1
Valid prediction for GeneMark_model.70692_t
Valid prediction for GeneMark_model.70668_t
Couldn't classify 98607, 99036
Sorry, prediction pasa_asmbl_17885.p1 fails validation.
(GTG)	 GT	98607-99036	GT	AGG
(ACA)	 AG	99224-99546	AT	AGA
-recovered pasa_asmbl_17885.p1, terminal, 99224, 99546
Valid prediction for GeneMark_model.70672_t
Couldn't classify 144426, 144554
Couldn't classify 145812, 145957
Sorry, prediction pasa_asmbl_17892.p1 fails validation.
(CAA)	 AG	144426-144554	GT	CGG
(AAC)	 AG	144650-144745	GT	AGG
(GAT)	 AG	145405-145618	GT	CCG
(CTA)	 AG	145812-145957	CC	CCC
-recovered pasa_asmbl_17892.p1, internal, 144426, 144554
-recovered pasa_asmbl_17892.p1, internal, 144650, 144745
-recovered pasa_asmbl_17892.p1, internal, 145405, 145618
Valid prediction for HiQ_model.g27470.t1
Valid prediction for GlimmerHMM_glimmerT_41018-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_17-snap.835-T1
Valid prediction for GeneMark_model.70691_t
Valid prediction for snap_scaffold_17-snap.841-T1
Valid prediction for GeneMark_model.70646_t
Valid prediction for snap_scaffold_17-snap.834-T1
Valid prediction for HiQ_model.g27468.t1
Couldn't classify 133297, 133344
Couldn't classify 135087, 135398
Sorry, prediction pasa_asmbl_19551.p1 fails validation.
(TGG)	 AA	133297-133344	GT	AGG
(AAA)	 AG	135087-135398	TT	AGT
Valid prediction for GeneMark_model.70689_t
Valid prediction for GeneMark_model.70641_t
Valid prediction for GlimmerHMM_glimmerT_41026-T1
Valid prediction for Augustus_model.g27466.t1
Valid prediction for GeneMark_model.70658_t
Valid prediction for GeneMark_model.70674_t
Valid prediction for snap_scaffold_17-snap.840-T1
Valid prediction for snap_scaffold_17-snap.830-T1
Valid prediction for snap_scaffold_17-snap.838-T1
Valid prediction for GeneMark_model.70637_t
Valid prediction for GeneMark_model.70685_t
Valid prediction for GeneMark_model.70662_t
Valid prediction for GeneMark_model.70652_t
Valid prediction for GeneMark_model.70656_t
Valid prediction for pasa_asmbl_18871.p1
Valid prediction for GeneMark_model.70660_t
Valid prediction for snap_scaffold_17-snap.831-T1
Valid prediction for CodingQuarry_transcript_21894-T1
Valid prediction for GlimmerHMM_glimmerT_41032-T1
Valid prediction for snap_scaffold_17-snap.832-T1
Valid prediction for GlimmerHMM_glimmerT_41015-T1
Valid prediction for snap_scaffold_17-snap.853-T1
Valid prediction for GeneMark_model.70673_t
Valid prediction for GeneMark_model.70645_t
Valid prediction for GeneMark_model.70643_t
Couldn't classify 142174, 142197
Sorry, prediction pasa_asmbl_18880.p1 fails validation.
(TCT)	 TT	142174-142197	GT	TGG
(GTG)	 AG	142929-142948	GT	AGG
(GGC)	 AG	143138-143240	GT	AGG
(ATA)	 AG	143436-143636	GT	TGG
(GTT)	 AG	143761-144399	GG	AGG
-recovered pasa_asmbl_18880.p1, terminal, 143761, 144399
-recovered pasa_asmbl_18880.p1, internal, 142929, 142948
-recovered pasa_asmbl_18880.p1, internal, 143138, 143240
-recovered pasa_asmbl_18880.p1, internal, 143436, 143636
Valid prediction for Augustus_model.g27476.t1
Valid prediction for Augustus_model.g27473.t1
Valid prediction for GeneMark_model.70671_t
Valid prediction for GeneMark_model.70648_t
Valid prediction for pasa_asmbl_18882.p1
Valid prediction for GeneMark_model.70639_t
Valid prediction for CodingQuarry_transcript_21895-T1
Valid prediction for Augustus_model.g27465.t1
Valid prediction for snap_scaffold_17-snap.828-T1
Valid prediction for snap_scaffold_17-snap.826-T1
Valid prediction for snap_scaffold_17-snap.863-T1
Valid prediction for GlimmerHMM_glimmerT_41023-T1
Valid prediction for GeneMark_model.70669_t
Valid prediction for snap_scaffold_17-snap.852-T1
Couldn't classify 168911, 168988
Couldn't classify 170549, 170794
Sorry, prediction pasa_asmbl_18873.p2 fails validation.
(CTG)	 CT	168911-168988	GT	AGG
(ATA)	 AG	170549-170794	AG	AGA
Valid prediction for GlimmerHMM_glimmerT_41019-T1
Valid prediction for GlimmerHMM_glimmerT_41016-T1
Valid prediction for GeneMark_model.70693_t
Valid prediction for GeneMark_model.70683_t
Valid prediction for GlimmerHMM_glimmerT_41025-T1
Valid prediction for snap_scaffold_17-snap.833-T1
Valid prediction for GeneMark_model.70681_t
Valid prediction for snap_scaffold_17-snap.839-T1
Couldn't classify 135558, 136163
Sorry, prediction pasa_asmbl_18885.p1 fails validation.
(GCA)	 CA	135558-136163	GG	GAG
Valid prediction for GlimmerHMM_glimmerT_41029-T1
Valid prediction for snap_scaffold_17-snap.850-T1
Valid prediction for GeneMark_model.70667_t
Valid prediction for snap_scaffold_17-snap.847-T1
Valid prediction for GlimmerHMM_glimmerT_41021-T1
Valid prediction for GeneMark_model.70654_t
Valid prediction for GeneMark_model.70678_t
Valid prediction for GeneMark_model.70684_t
Valid prediction for snap_scaffold_17-snap.864-T1
Valid prediction for snap_scaffold_17-snap.851-T1
Valid prediction for Augustus_model.g27469.t1
Valid prediction for Augustus_model.g27477.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12718, rend_intergenic: 10457  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13331, rend_intergenic: 13155  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18187, rend_intergenic: 13663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43714, rend_intergenic: 18238  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74692, rend_intergenic: 55915  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126392, rend_intergenic: 125933  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 230709
-exon list size: 752


building trellis

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78.4    
78.5    
78.6    
78.8    
78.9    
79.0    
79.2    
79.3    
79.4    
79.6    
79.7    
79.8    
80.0    
80.1    
80.2    
80.4    
80.5    
80.6    
80.8    
80.9    
81.0    
81.2    
81.3    
81.4    
81.6    
81.7    
81.8    
82.0    
82.1    
82.2    
82.4    
82.5    
82.6    
82.8    
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    
84.6    
84.7    
84.9    
85.0    
85.1    
85.3    
85.4    
85.5    
85.7    
85.8    
85.9    
86.1    
86.2    
86.3    
86.5    
86.6    
86.7    
86.9    
87.0    
87.1    
87.3    
87.4    
87.5    
87.7    
87.8    
87.9    
88.1    
88.2    
88.3    
88.5    
88.6    
88.7    
88.9    
89.0    
89.1    
89.3    
89.4    
89.5    
89.7    
89.8    
89.9    
90.1    
90.2    
90.3    
90.5    
90.6    
90.7    
90.8    
91.0    
91.1    
91.2    
91.4    
91.5    
91.6    
91.8    
91.9    
92.0    
92.2    
92.3    
92.4    
92.6    
92.7    
92.8    
93.0    
93.1    
93.2    
93.4    
93.5    
93.6    
93.8    
93.9    
94.0    
94.2    
94.3    
94.4    
94.6    
94.7    
94.8    
95.0    
95.1    
95.2    
95.4    
95.5    
95.6    
95.8    
95.9    
96.0    
96.2    
96.3    
96.4    
96.6    
96.7    
96.8    
96.9    
97.1    
97.2    
97.3    
97.5    
97.6    
97.7    
97.9    
98.0    
98.1    
98.3    
98.4    
98.5    
98.7    
98.8    
98.9    
99.1    
99.2    
99.3    
99.5    
99.6    
99.7    
99.9    
-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 12718, rend_intergenic: 10457  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13331, rend_intergenic: 13155  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18187, rend_intergenic: 13663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43714, rend_intergenic: 18238  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74692, rend_intergenic: 55915  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126392, rend_intergenic: 125933  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 11480
-exon list size: 7


building trellis

11.1    
22.2    
33.3    
44.4    
55.6    
66.7    
77.8    
88.9    
-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

-building DP trellis

-building trellis in range 1 - 11274
-exon list size: 5


building trellis

14.3    
28.6    
42.9    
57.1    
71.4    
85.7    
-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 - 11244
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-found 1 predictions from path traversal

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

-building DP trellis

-building trellis in range 1 - 11148
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support
	-no exons in range 1 - 10456