-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_28/scaffold_28_4023778-4252681

-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.104658_t
Valid prediction for GlimmerHMM_glimmerT_60036-T1
Valid prediction for snap_scaffold_28-snap.993-T1
Valid prediction for GeneMark_model.104655_t
Valid prediction for Augustus_model.g39964.t1
Valid prediction for Augustus_model.g39959.t1
Valid prediction for snap_scaffold_28-snap.1008-T1
Valid prediction for GeneMark_model.104650_t
Valid prediction for GeneMark_model.104633_t
Valid prediction for snap_scaffold_28-snap.981-T1
Valid prediction for GeneMark_model.104637_t
Valid prediction for GeneMark_model.104639_t
Valid prediction for snap_scaffold_28-snap.979-T1
Valid prediction for GeneMark_model.104657_t
Valid prediction for snap_scaffold_28-snap.1009-T1
Valid prediction for GeneMark_model.104668_t
Couldn't classify 221708, 221815
Couldn't classify 224264, 224371
Sorry, prediction pasa_asmbl_38225.p1 fails validation.
(GGT)	 AG	221708-221815	GT	TGG
(GGA)	 AG	221906-221959	GT	AGG
(GGT)	 AG	222207-222260	GT	AGG
(GGT)	 AG	222846-222902	GT	GAG
(GGT)	 AG	223139-223192	GT	AGG
(GGT)	 AG	223338-223391	GT	CTG
(GGA)	 AG	223484-223537	GT	AAG
(GGT)	 AG	223632-223685	GT	CAG
(GGT)	 AG	223851-223958	GT	AGG
(GGG)	 AG	224069-224176	GT	AGG
(GGG)	 AG	224264-224371	GT	TGG
-recovered pasa_asmbl_38225.p1, internal, 221708, 221815
-recovered pasa_asmbl_38225.p1, internal, 221906, 221959
-recovered pasa_asmbl_38225.p1, internal, 222207, 222260
-recovered pasa_asmbl_38225.p1, internal, 222846, 222902
-recovered pasa_asmbl_38225.p1, internal, 223139, 223192
-recovered pasa_asmbl_38225.p1, internal, 223338, 223391
-recovered pasa_asmbl_38225.p1, internal, 223484, 223537
-recovered pasa_asmbl_38225.p1, internal, 223632, 223685
-recovered pasa_asmbl_38225.p1, internal, 223851, 223958
-recovered pasa_asmbl_38225.p1, internal, 224069, 224176
-recovered pasa_asmbl_38225.p1, internal, 224264, 224371
Valid prediction for Augustus_model.g39961.t1
Valid prediction for snap_scaffold_28-snap.998-T1
Valid prediction for CodingQuarry_transcript_43528-T1
Valid prediction for HiQ_model.g39970.t1
Valid prediction for CodingQuarry_transcript_43534-T1
Valid prediction for Augustus_model.g39971.t1
Valid prediction for GlimmerHMM_glimmerT_60035-T1
Valid prediction for snap_scaffold_28-snap.1004-T1
Valid prediction for GlimmerHMM_glimmerT_60042-T1
Couldn't classify 86990, 87005
Couldn't classify 89462, 89576
Sorry, prediction pasa_asmbl_38545.p1 fails validation.
(TGC)	 CC	86990-87005	GT	AGG
(GCT)	 AG	87138-87371	GT	AGG
(GGG)	 AG	87716-87826	GT	TGG
(GCA)	 AG	89127-89319	GT	GGG
(GTA)	 AG	89462-89576	TA	GAT
add_exon() Sorry, pasa_asmbl_38545.p1 87138-87371-terminal-1 is invalid.
-recovered pasa_asmbl_38545.p1, terminal, 87138, 87371
-recovered pasa_asmbl_38545.p1, internal, 87138, 87371
-recovered pasa_asmbl_38545.p1, internal, 87716, 87826
-recovered pasa_asmbl_38545.p1, internal, 89127, 89319
Valid prediction for HiQ_model.g39962.t1
Couldn't classify 122652, 123692
Sorry, prediction pasa_asmbl_38210.p1 fails validation.
(CAG)	 AT	122652-123692	AA	AGA
Valid prediction for snap_scaffold_28-snap.983-T1
Valid prediction for snap_scaffold_28-snap.1003-T1
Valid prediction for GeneMark_model.104675_t
Valid prediction for GlimmerHMM_glimmerT_60037-T1
Valid prediction for snap_scaffold_28-snap.1007-T1
Valid prediction for Augustus_model.g39960.t1
Couldn't classify 183914, 184148
Sorry, prediction pasa_asmbl_38221.p1 fails validation.
(TCC)	 AT	183914-184148	GT	CAG
(TCC)	 AG	184392-184564	GT	AGG
(CTG)	 AG	185696-185905	GT	AGG
(CTT)	 AG	186072-186272	CG	GAC
-recovered pasa_asmbl_38221.p1, terminal, 186072, 186272
-recovered pasa_asmbl_38221.p1, internal, 184392, 184564
-recovered pasa_asmbl_38221.p1, internal, 185696, 185905
Valid prediction for GeneMark_model.104651_t
Valid prediction for GeneMark_model.104640_t
Valid prediction for CodingQuarry_transcript_43529-T1
Valid prediction for GlimmerHMM_glimmerT_60033-T1
Valid prediction for GlimmerHMM_glimmerT_60038-T1
Valid prediction for Augustus_model.g39965.t1
Valid prediction for GlimmerHMM_glimmerT_60049-T1
Valid prediction for GeneMark_model.104636_t
Valid prediction for snap_scaffold_28-snap.977-T1
Valid prediction for snap_scaffold_28-snap.988-T1
Couldn't classify 96155, 96537
Sorry, prediction pasa_asmbl_38206.p1 fails validation.
(TGC)	 CC	96155-96537	GT	AAG
(CCC)	 AG	96830-97255	GT	GGG
(GTC)	 AG	97596-97744	GT	CAG
(GCG)	 AG	98806-99016	GT	AAG
(ACC)	 AG	99436-99526	GT	GGG
(CAG)	 AG	99723-99888	GT	AGG
(ATG)	 AG	101168-101466	GT	AGG
(ATT)	 AG	101795-101942	GT	TGG
(GTA)	 AG	102249-102346	GT	AAG
(GAG)	 AG	102724-104025	GG	AGG
add_exon() Sorry, pasa_asmbl_38206.p1 101168-101466-initial-1 is invalid.
-recovered pasa_asmbl_38206.p1, initial, 101168, 101466
-recovered pasa_asmbl_38206.p1, terminal, 102724, 104025
-recovered pasa_asmbl_38206.p1, internal, 96830, 97255
-recovered pasa_asmbl_38206.p1, internal, 97596, 97744
-recovered pasa_asmbl_38206.p1, internal, 98806, 99016
-recovered pasa_asmbl_38206.p1, internal, 99436, 99526
-recovered pasa_asmbl_38206.p1, internal, 99723, 99888
-recovered pasa_asmbl_38206.p1, internal, 101168, 101466
-recovered pasa_asmbl_38206.p1, internal, 101795, 101942
-recovered pasa_asmbl_38206.p1, internal, 102249, 102346
Valid prediction for GeneMark_model.104632_t
Valid prediction for snap_scaffold_28-snap.989-T1
Valid prediction for snap_scaffold_28-snap.990-T1
Valid prediction for GeneMark_model.104630_t
Valid prediction for GlimmerHMM_glimmerT_60044-T1
Valid prediction for GlimmerHMM_glimmerT_60034-T1
Valid prediction for snap_scaffold_28-snap.978-T1
Valid prediction for GlimmerHMM_glimmerT_60032-T1
Valid prediction for snap_scaffold_28-snap.991-T1
Valid prediction for CodingQuarry_transcript_43527-T1
Valid prediction for GeneMark_model.104662_t
Valid prediction for snap_scaffold_28-snap.1001-T1
Valid prediction for GeneMark_model.104666_t
Valid prediction for snap_scaffold_28-snap.1002-T1
Valid prediction for snap_scaffold_28-snap.1005-T1
Valid prediction for GlimmerHMM_glimmerT_60046-T1
Valid prediction for CodingQuarry_transcript_43536-T1
Valid prediction for pasa_asmbl_38207.p1
Valid prediction for GeneMark_model.104673_t
Valid prediction for CodingQuarry_transcript_43533-T1
Valid prediction for GeneMark_model.104648_t
Valid prediction for snap_scaffold_28-snap.1006-T1
Valid prediction for GeneMark_model.104643_t
Valid prediction for GlimmerHMM_glimmerT_60045-T1
Valid prediction for GlimmerHMM_glimmerT_60048-T1
Valid prediction for snap_scaffold_28-snap.975-T1
Valid prediction for GeneMark_model.104653_t
Valid prediction for GeneMark_model.104664_t
Valid prediction for GeneMark_model.104646_t
Valid prediction for CodingQuarry_transcript_43531-T1
Valid prediction for GeneMark_model.104663_t
Valid prediction for snap_scaffold_28-snap.985-T1
Valid prediction for GeneMark_model.104644_t
Couldn't classify 93064, 93214
Couldn't classify 93685, 93830
Sorry, prediction pasa_asmbl_38205.p1 fails validation.
(CTG)	 AT	93064-93214	GT	AGG
(GCG)	 AG	93685-93830	GC	GGG
-recovered pasa_asmbl_38205.p1, internal, 93685, 93830
Valid prediction for CodingQuarry_transcript_43535-T1
Valid prediction for GeneMark_model.104670_t
Valid prediction for GeneMark_model.104671_t
Valid prediction for GlimmerHMM_glimmerT_60047-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 Augustus_model.g39967.t1
Valid prediction for GeneMark_model.104654_t
Valid prediction for snap_scaffold_28-snap.996-T1
Valid prediction for GeneMark_model.104659_t
Valid prediction for Augustus_model.g39968.t1
Valid prediction for snap_scaffold_28-snap.1000-T1
Valid prediction for GeneMark_model.104631_t
Valid prediction for snap_scaffold_28-snap.976-T1
Valid prediction for GeneMark_model.104652_t
Valid prediction for GeneMark_model.104635_t
Valid prediction for Augustus_model.g39954.t1
Valid prediction for snap_scaffold_28-snap.972-T1
Valid prediction for GeneMark_model.104656_t
Valid prediction for GeneMark_model.104667_t
Valid prediction for Augustus_model.g39963.t1
Valid prediction for snap_scaffold_28-snap.995-T1
Valid prediction for GlimmerHMM_glimmerT_60043-T1
Valid prediction for snap_scaffold_28-snap.974-T1
Valid prediction for GlimmerHMM_glimmerT_60029-T1
Valid prediction for snap_scaffold_28-snap.980-T1
Valid prediction for GeneMark_model.104665_t
Valid prediction for snap_scaffold_28-snap.970-T1
Valid prediction for GeneMark_model.104645_t
Valid prediction for snap_scaffold_28-snap.973-T1
Valid prediction for Augustus_model.g39957.t1
Valid prediction for GlimmerHMM_glimmerT_60031-T1
Valid prediction for snap_scaffold_28-snap.987-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.104661_t
Valid prediction for snap_scaffold_28-snap.986-T1
Valid prediction for GeneMark_model.104638_t
Valid prediction for snap_scaffold_28-snap.982-T1
Valid prediction for GeneMark_model.104649_t
Valid prediction for GeneMark_model.104672_t
Valid prediction for GeneMark_model.104634_t
Valid prediction for GeneMark_model.104674_t
Valid prediction for snap_scaffold_28-snap.999-T1
Valid prediction for GlimmerHMM_glimmerT_60030-T1
Valid prediction for GlimmerHMM_glimmerT_60039-T1
Valid prediction for GeneMark_model.104660_t
Valid prediction for snap_scaffold_28-snap.997-T1
Valid prediction for GeneMark_model.104629_t
Valid prediction for HiQ_model.g39969.t1
Valid prediction for Augustus_model.g39958.t1
Valid prediction for snap_scaffold_28-snap.994-T1
Valid prediction for GeneMark_model.104647_t
Valid prediction for snap_scaffold_28-snap.984-T1
Valid prediction for CodingQuarry_transcript_43530-T1
Valid prediction for GeneMark_model.104642_t
Valid prediction for GeneMark_model.104641_t
Valid prediction for GlimmerHMM_glimmerT_60040-T1
Valid prediction for GlimmerHMM_glimmerT_60028-T1
Valid prediction for GeneMark_model.104669_t
Valid prediction for pasa_asmbl_37522.p1
Valid prediction for Augustus_model.g39956.t1
Valid prediction for snap_scaffold_28-snap.971-T1
Valid prediction for Augustus_model.g39966.t1
Couldn't classify 89095, 89202
Couldn't classify 89939, 90265
Sorry, prediction pasa_asmbl_37519.p1 fails validation.
(CTG)	 AC	89095-89202	GT	AGG
(TTC)	 AG	89705-89725	GT	AGG
(TCT)	 AG	89939-90265	GG	GGG
-recovered pasa_asmbl_37519.p1, internal, 89705, 89725
Valid prediction for Augustus_model.g39955.t1
Valid prediction for snap_scaffold_28-snap.992-T1
Valid prediction for GlimmerHMM_glimmerT_60041-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 40877, rend_intergenic: 38804  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43821, rend_intergenic: 42239  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83499, rend_intergenic: 79633  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85205, rend_intergenic: 85001  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104025, rend_intergenic: 92086  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144195, rend_intergenic: 140575  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148812, rend_intergenic: 144948  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163238, rend_intergenic: 162840  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 228904
-exon list size: 656


building trellis

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83.9    
84.0    
84.2    
84.3    
84.5    
84.7    
84.8    
85.0    
85.1    
85.3    
85.4    
85.6    
85.7    
85.9    
86.0    
86.2    
86.3    
86.5    
86.6    
86.8    
86.9    
87.1    
87.2    
87.4    
87.5    
87.7    
87.8    
88.0    
88.1    
88.3    
88.4    
88.6    
88.8    
88.9    
89.1    
89.2    
89.4    
89.5    
89.7    
89.8    
90.0    
90.1    
90.3    
90.4    
90.6    
90.7    
90.9    
91.0    
91.2    
91.3    
91.5    
91.6    
91.8    
91.9    
92.1    
92.2    
92.4    
92.6    
92.7    
92.9    
93.0    
93.2    
93.3    
93.5    
93.6    
93.8    
93.9    
94.1    
94.2    
94.4    
94.5    
94.7    
94.8    
95.0    
95.1    
95.3    
95.4    
95.6    
95.7    
95.9    
96.0    
96.2    
96.4    
96.5    
96.7    
96.8    
97.0    
97.1    
97.3    
97.4    
97.6    
97.7    
97.9    
98.0    
98.2    
98.3    
98.5    
98.6    
98.8    
98.9    
99.1    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 40877, rend_intergenic: 38804  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43821, rend_intergenic: 42239  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83499, rend_intergenic: 79633  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85205, rend_intergenic: 85001  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104025, rend_intergenic: 92086  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144195, rend_intergenic: 140575  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148812, rend_intergenic: 144948  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163238, rend_intergenic: 162840  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 26 predictions persist after filtering for low support