-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_20/scaffold_20_4114009-4372131

-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_45839-T1
Valid prediction for pasa_asmbl_26572.p1
Valid prediction for GlimmerHMM_glimmerT_45862-T1
Valid prediction for snap_scaffold_20-snap.869-T1
Valid prediction for Augustus_model.g30431.t1
Valid prediction for snap_scaffold_20-snap.878-T1
Valid prediction for snap_scaffold_20-snap.895-T1
Valid prediction for snap_scaffold_20-snap.885-T1
Valid prediction for snap_scaffold_20-snap.914-T1
Valid prediction for GlimmerHMM_glimmerT_45859-T1
Valid prediction for snap_scaffold_20-snap.893-T1
Valid prediction for GlimmerHMM_glimmerT_45856-T1
Couldn't classify 148128, 148248
Couldn't classify 148347, 148420
Sorry, prediction CodingQuarry_transcript_30490-T1 fails validation.
(ATG)	 AA	148128-148248	CT	CCC
(CCC)	 AC	148347-148420	AA	AAA
Couldn't classify 66762, 66894
Couldn't classify 68869, 68916
Sorry, prediction pasa_asmbl_26561.p1 fails validation.
(AAG)	 TT	66762-66894	GT	CAG
(GTC)	 AG	68625-68776	GT	CAG
(GTC)	 AG	68869-68916	CT	GCC
-recovered pasa_asmbl_26561.p1, internal, 68625, 68776
Valid prediction for GlimmerHMM_glimmerT_45836-T1
Valid prediction for GlimmerHMM_glimmerT_45841-T1
Couldn't classify 202185, 202265
Sorry, prediction pasa_asmbl_27133.p1 fails validation.
(GGG)	 AA	202185-202265	GT	GGG
(GTG)	 AG	202584-202761	GT	TGG
(ACA)	 AG	203346-203452	GT	AGG
(GTG)	 AG	204232-204303	GA	AAG
-recovered pasa_asmbl_27133.p1, terminal, 204232, 204303
-recovered pasa_asmbl_27133.p1, internal, 202584, 202761
-recovered pasa_asmbl_27133.p1, internal, 203346, 203452
Valid prediction for Augustus_model.g30442.t1
Valid prediction for Augustus_model.g30437.t1
Valid prediction for Augustus_model.g30439.t1
Valid prediction for GlimmerHMM_glimmerT_45846-T1
Valid prediction for GlimmerHMM_glimmerT_45832-T1
Valid prediction for snap_scaffold_20-snap.871-T1
Valid prediction for HiQ_model.g30441.t1
Couldn't classify 148128, 148248
Couldn't classify 148270, 148397
Sorry, prediction CodingQuarry_transcript_30491-T1 fails validation.
(ATG)	 AA	148128-148248	CT	CCC
(CCC)	 AC	148270-148397	AA	AGA
Valid prediction for snap_scaffold_20-snap.902-T1
Valid prediction for snap_scaffold_20-snap.910-T1
Valid prediction for snap_scaffold_20-snap.865-T1
Valid prediction for GlimmerHMM_glimmerT_45863-T1
Valid prediction for GlimmerHMM_glimmerT_45857-T1
Valid prediction for snap_scaffold_20-snap.900-T1
Valid prediction for HiQ_model.g30436.t1
Valid prediction for GlimmerHMM_glimmerT_45845-T1
Valid prediction for Augustus_model.g30440.t1
Valid prediction for snap_scaffold_20-snap.879-T1
Valid prediction for snap_scaffold_20-snap.890-T1
Valid prediction for snap_scaffold_20-snap.903-T1
Valid prediction for snap_scaffold_20-snap.897-T1
Valid prediction for GlimmerHMM_glimmerT_45833-T1
Valid prediction for snap_scaffold_20-snap.911-T1
Valid prediction for Augustus_model.g30435.t1
Valid prediction for GlimmerHMM_glimmerT_45852-T1
Couldn't classify 118933, 119036
Sorry, prediction pasa_asmbl_26566.p1 fails validation.
(ATG)	 AA	116143-116368	GT	AAG
(AAT)	 AG	118933-119036	TA	GGT
-recovered pasa_asmbl_26566.p1, initial, 116143, 116368
Valid prediction for Augustus_model.g30443.t1
Valid prediction for snap_scaffold_20-snap.889-T1
Valid prediction for CodingQuarry_transcript_30492-T1
Valid prediction for GlimmerHMM_glimmerT_45830-T1
Valid prediction for GlimmerHMM_glimmerT_45860-T1
Valid prediction for snap_scaffold_20-snap.909-T1
Valid prediction for snap_scaffold_20-snap.904-T1
Valid prediction for snap_scaffold_20-snap.873-T1
Valid prediction for GlimmerHMM_glimmerT_45854-T1
Valid prediction for snap_scaffold_20-snap.877-T1
Valid prediction for GlimmerHMM_glimmerT_45843-T1
Valid prediction for snap_scaffold_20-snap.882-T1
Valid prediction for snap_scaffold_20-snap.912-T1
Valid prediction for GlimmerHMM_glimmerT_45838-T1
Couldn't classify 191635, 191731
Couldn't classify 192433, 192596
Couldn't classify 193590, 193742
Couldn't classify 196001, 196152
Sorry, prediction CodingQuarry_transcript_30493-T1 fails validation.
(ATG)	 CC	181070-181084	GT	AGG
(GTC)	 AG	181588-181663	GT	CGG
(TTG)	 AG	181857-181895	GT	CGG
(CCA)	 AG	182007-182074	GT	ATG
(GAG)	 AG	182197-182268	GT	CGG
(ATT)	 AG	182366-182445	GT	ACG
(GAA)	 AG	182578-182656	GT	AGG
(ATC)	 AG	183380-183497	GT	CGG
(AGG)	 AG	183856-184031	GT	AGG
(CTG)	 AG	184324-184404	GT	AGG
(GAG)	 AG	184831-184995	GT	GGG
(AAA)	 AG	186595-186716	GT	AGG
(ACT)	 AG	188850-189063	GT	GTG
(AAA)	 AG	189390-189493	GT	AAG
(CTA)	 AG	191635-191731	GA	GCG
(CAG)	 GA	192433-192596	GT	AGG
(GCT)	 AG	192820-192961	GT	ACG
(GAT)	 AG	193185-193335	GT	GGG
(GTG)	 AG	193590-193742	AT	ACA
(GCA)	 AC	196001-196152	GT	AGG
(CAA)	 AG	196490-196648	GT	AGG
(GAC)	 AG	198534-198641	GT	AGG
(GAG)	 AG	198894-199002	GT	GGG
(ACC)	 AG	199216-199463	GT	AGG
(TTG)	 AG	200921-201133	GT	AGG
(GTG)	 AG	202074-202265	GT	GGG
(GTG)	 AG	202584-202761	GT	TGG
(ACA)	 AG	203346-203452	GT	AGG
(GTG)	 AG	204232-204303	GA	AAG
-recovered CodingQuarry_transcript_30493-T1, initial, 181070, 181084
-recovered CodingQuarry_transcript_30493-T1, terminal, 204232, 204303
-recovered CodingQuarry_transcript_30493-T1, internal, 181588, 181663
-recovered CodingQuarry_transcript_30493-T1, internal, 181857, 181895
-recovered CodingQuarry_transcript_30493-T1, internal, 182007, 182074
-recovered CodingQuarry_transcript_30493-T1, internal, 182197, 182268
-recovered CodingQuarry_transcript_30493-T1, internal, 182366, 182445
-recovered CodingQuarry_transcript_30493-T1, internal, 182578, 182656
-recovered CodingQuarry_transcript_30493-T1, internal, 183380, 183497
-recovered CodingQuarry_transcript_30493-T1, internal, 183856, 184031
-recovered CodingQuarry_transcript_30493-T1, internal, 184324, 184404
-recovered CodingQuarry_transcript_30493-T1, internal, 184831, 184995
-recovered CodingQuarry_transcript_30493-T1, internal, 186595, 186716
-recovered CodingQuarry_transcript_30493-T1, internal, 188850, 189063
-recovered CodingQuarry_transcript_30493-T1, internal, 189390, 189493
-recovered CodingQuarry_transcript_30493-T1, internal, 192820, 192961
-recovered CodingQuarry_transcript_30493-T1, internal, 193185, 193335
-recovered CodingQuarry_transcript_30493-T1, internal, 196490, 196648
-recovered CodingQuarry_transcript_30493-T1, internal, 198534, 198641
-recovered CodingQuarry_transcript_30493-T1, internal, 198894, 199002
-recovered CodingQuarry_transcript_30493-T1, internal, 199216, 199463
-recovered CodingQuarry_transcript_30493-T1, internal, 200921, 201133
-recovered CodingQuarry_transcript_30493-T1, internal, 202074, 202265
-recovered CodingQuarry_transcript_30493-T1, internal, 202584, 202761
-recovered CodingQuarry_transcript_30493-T1, internal, 203346, 203452
Valid prediction for GlimmerHMM_glimmerT_45849-T1
Valid prediction for Augustus_model.g30434.t1
Valid prediction for GlimmerHMM_glimmerT_45851-T1
Valid prediction for snap_scaffold_20-snap.898-T1
Valid prediction for snap_scaffold_20-snap.888-T1
Couldn't classify 241644, 241732
Couldn't classify 242922, 243022
Sorry, prediction pasa_asmbl_26576.p1 fails validation.
(GTG)	 AG	241644-241732	GT	AGG
(TCT)	 AG	242169-242278	GT	AGG
(ATG)	 AG	242922-243022	GT	AGG
add_exon() Sorry, pasa_asmbl_26576.p1 242922-243022-initial-1 is invalid.
-recovered pasa_asmbl_26576.p1, initial, 242922, 243022
-recovered pasa_asmbl_26576.p1, internal, 241644, 241732
-recovered pasa_asmbl_26576.p1, internal, 242169, 242278
-recovered pasa_asmbl_26576.p1, internal, 242922, 243022

-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_45842-T1
Valid prediction for snap_scaffold_20-snap.901-T1
Valid prediction for snap_scaffold_20-snap.886-T1
Valid prediction for GlimmerHMM_glimmerT_45844-T1
Valid prediction for snap_scaffold_20-snap.872-T1
Valid prediction for snap_scaffold_20-snap.908-T1
Valid prediction for snap_scaffold_20-snap.881-T1
Valid prediction for snap_scaffold_20-snap.894-T1
Valid prediction for snap_scaffold_20-snap.896-T1
Valid prediction for GlimmerHMM_glimmerT_45864-T1
Valid prediction for snap_scaffold_20-snap.866-T1
Valid prediction for Augustus_model.g30438.t1
Valid prediction for snap_scaffold_20-snap.906-T1
Valid prediction for GlimmerHMM_glimmerT_45858-T1
Valid prediction for GlimmerHMM_glimmerT_45835-T1
Valid prediction for Augustus_model.g30433.t1
Valid prediction for snap_scaffold_20-snap.899-T1
Valid prediction for snap_scaffold_20-snap.864-T1
Valid prediction for snap_scaffold_20-snap.870-T1
Valid prediction for snap_scaffold_20-snap.883-T1
Valid prediction for snap_scaffold_20-snap.884-T1
Valid prediction for snap_scaffold_20-snap.876-T1
Valid prediction for GlimmerHMM_glimmerT_45831-T1
Valid prediction for GlimmerHMM_glimmerT_45847-T1
Valid prediction for GlimmerHMM_glimmerT_45848-T1
Valid prediction for snap_scaffold_20-snap.891-T1
Couldn't classify 202503, 202916
Sorry, prediction pasa_asmbl_26559.p1 fails validation.
(CCT)	 AA	202503-202916	TG	ACT
Valid prediction for GlimmerHMM_glimmerT_45837-T1
Valid prediction for snap_scaffold_20-snap.880-T1
Valid prediction for GlimmerHMM_glimmerT_45855-T1
Valid prediction for GlimmerHMM_glimmerT_45861-T1
Valid prediction for snap_scaffold_20-snap.867-T1
Valid prediction for snap_scaffold_20-snap.887-T1
Valid prediction for snap_scaffold_20-snap.913-T1
Valid prediction for snap_scaffold_20-snap.916-T1
Valid prediction for snap_scaffold_20-snap.892-T1
Valid prediction for snap_scaffold_20-snap.905-T1
Valid prediction for snap_scaffold_20-snap.907-T1
Valid prediction for GlimmerHMM_glimmerT_45840-T1
Valid prediction for Augustus_model.g30432.t1
Valid prediction for GlimmerHMM_glimmerT_45853-T1
Valid prediction for snap_scaffold_20-snap.874-T1
Valid prediction for snap_scaffold_20-snap.868-T1
Valid prediction for GlimmerHMM_glimmerT_45850-T1
Valid prediction for snap_scaffold_20-snap.875-T1
Valid prediction for GlimmerHMM_glimmerT_45834-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 24731, rend_intergenic: 6647  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39216, rend_intergenic: 30684  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40970, rend_intergenic: 39452  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45304, rend_intergenic: 41009  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58095, rend_intergenic: 48753  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76127, rend_intergenic: 59168  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80989, rend_intergenic: 76269  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81788, rend_intergenic: 81562  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85740, rend_intergenic: 82108  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100444, rend_intergenic: 92572  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105883, rend_intergenic: 100784  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114268, rend_intergenic: 107618  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124948, rend_intergenic: 120201  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136961, rend_intergenic: 126805  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146858, rend_intergenic: 146087  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160533, rend_intergenic: 151339  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163334, rend_intergenic: 160839  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167997, rend_intergenic: 164811  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173227, rend_intergenic: 168532  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 210823, rend_intergenic: 182518  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211686, rend_intergenic: 211119  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 230073, rend_intergenic: 224734  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 258123
-exon list size: 474


building trellis

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92.9    
93.1    
93.3    
93.5    
93.7    
93.9    
94.1    
94.3    
94.5    
94.7    
95.0    
95.2    
95.4    
95.6    
95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
97.1    
97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.2    
99.4    
99.6    
99.8    
-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 24731, rend_intergenic: 6647  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39216, rend_intergenic: 30684  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40970, rend_intergenic: 39452  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45304, rend_intergenic: 41009  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58095, rend_intergenic: 48753  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76127, rend_intergenic: 59168  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80989, rend_intergenic: 76269  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81788, rend_intergenic: 81562  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85740, rend_intergenic: 82108  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100444, rend_intergenic: 92572  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105883, rend_intergenic: 100784  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114268, rend_intergenic: 107618  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124948, rend_intergenic: 120201  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136961, rend_intergenic: 126805  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146858, rend_intergenic: 146087  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160533, rend_intergenic: 151339  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163334, rend_intergenic: 160839  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167997, rend_intergenic: 164811  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173227, rend_intergenic: 168532  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 210823, rend_intergenic: 182518  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211686, rend_intergenic: 211119  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 230073, rend_intergenic: 224734  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

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

-building DP trellis

-building trellis in range 243788 - 258123
-exon list size: 11


building trellis

7.7    
15.4    
23.1    
30.8    
38.5    
46.2    
53.8    
61.5    
69.2    
76.9    
84.6    
92.3    
-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