-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_17/scaffold_17_3474822-3672238

-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.70531_t
Valid prediction for GeneMark_model.70563_t
Valid prediction for GeneMark_model.70529_t
Valid prediction for GeneMark_model.70536_t
Valid prediction for snap_scaffold_17-snap.751-T1
Valid prediction for GlimmerHMM_glimmerT_40960-T1
Valid prediction for Augustus_model.g27436.t1
Valid prediction for snap_scaffold_17-snap.736-T1
Valid prediction for snap_scaffold_17-snap.750-T1
Valid prediction for snap_scaffold_17-snap.770-T1
Valid prediction for snap_scaffold_17-snap.773-T1
Valid prediction for GeneMark_model.70550_t
Valid prediction for GeneMark_model.70534_t
Valid prediction for GeneMark_model.70528_t
Valid prediction for snap_scaffold_17-snap.748-T1
Valid prediction for snap_scaffold_17-snap.755-T1
Valid prediction for GeneMark_model.70546_t
Valid prediction for GlimmerHMM_glimmerT_40964-T1
Couldn't classify 182035, 182139
Couldn't classify 182812, 182919
Sorry, prediction CodingQuarry_transcript_21890-T1 fails validation.
(ATG)	 TC	180966-180994	GT	AGG
(GGA)	 AG	181446-181680	GT	AGG
(GTA)	 AG	181785-181853	GT	GGG
(GAG)	 AG	182035-182139	TC	TAT
(CAG)	 TT	182812-182919	GT	AGG
(AAG)	 AG	183303-183416	GT	AGG
(CAG)	 AG	185696-185827	AT	GAA
-recovered CodingQuarry_transcript_21890-T1, initial, 180966, 180994
-recovered CodingQuarry_transcript_21890-T1, terminal, 185696, 185827
-recovered CodingQuarry_transcript_21890-T1, internal, 181446, 181680
-recovered CodingQuarry_transcript_21890-T1, internal, 181785, 181853
-recovered CodingQuarry_transcript_21890-T1, internal, 183303, 183416
Valid prediction for GlimmerHMM_glimmerT_40972-T1
Valid prediction for GlimmerHMM_glimmerT_40959-T1
Valid prediction for GeneMark_model.70559_t
Valid prediction for GeneMark_model.70551_t
Valid prediction for GlimmerHMM_glimmerT_40961-T1
Valid prediction for GeneMark_model.70552_t
Valid prediction for snap_scaffold_17-snap.776-T1
Couldn't classify 182035, 182139
Couldn't classify 182812, 182919
Sorry, prediction CodingQuarry_transcript_21891-T1 fails validation.
(ATG)	 TC	180966-180994	GT	AGG
(GGA)	 AG	181446-181680	GT	AGG
(GTA)	 AG	181785-181853	GT	GGG
(GAG)	 AG	182035-182139	TC	TAT
(CAG)	 TT	182812-182919	GT	AGG
(AAG)	 AG	183303-183416	GT	AGG
(GTG)	 AG	184697-184816	GT	AGG
(CAG)	 AG	185699-185827	AT	GAA
-recovered CodingQuarry_transcript_21891-T1, initial, 180966, 180994
-recovered CodingQuarry_transcript_21891-T1, terminal, 185699, 185827
-recovered CodingQuarry_transcript_21891-T1, internal, 181446, 181680
-recovered CodingQuarry_transcript_21891-T1, internal, 181785, 181853
-recovered CodingQuarry_transcript_21891-T1, internal, 183303, 183416
-recovered CodingQuarry_transcript_21891-T1, internal, 184697, 184816
Valid prediction for GeneMark_model.70544_t
Valid prediction for snap_scaffold_17-snap.744-T1
Valid prediction for GlimmerHMM_glimmerT_40962-T1
Valid prediction for snap_scaffold_17-snap.756-T1
Valid prediction for GlimmerHMM_glimmerT_40968-T1
Valid prediction for GeneMark_model.70555_t
Valid prediction for GeneMark_model.70541_t
Valid prediction for GlimmerHMM_glimmerT_40956-T1
Valid prediction for snap_scaffold_17-snap.767-T1
Valid prediction for snap_scaffold_17-snap.759-T1
Valid prediction for GeneMark_model.70562_t
Valid prediction for snap_scaffold_17-snap.761-T1
Valid prediction for GeneMark_model.70535_t
Valid prediction for GeneMark_model.70524_t
Valid prediction for snap_scaffold_17-snap.765-T1
Valid prediction for snap_scaffold_17-snap.746-T1
Valid prediction for GeneMark_model.70545_t
Valid prediction for GeneMark_model.70521_t
Valid prediction for GeneMark_model.70548_t
Valid prediction for Augustus_model.g27431.t1
Valid prediction for GeneMark_model.70526_t
Valid prediction for GeneMark_model.70557_t
Valid prediction for GeneMark_model.70553_t
Valid prediction for GeneMark_model.70516_t
Valid prediction for GeneMark_model.70519_t
Valid prediction for GlimmerHMM_glimmerT_40967-T1
Valid prediction for GeneMark_model.70538_t
Valid prediction for GeneMark_model.70523_t
Couldn't classify 185696, 185722
Sorry, prediction pasa_asmbl_17857.p1 fails validation.
(ATG)	 CA	182842-182919	GT	AGG
(AAG)	 AG	183303-183416	GT	AGG
(GTG)	 AG	184697-184816	GT	AGG
(CAG)	 AG	185696-185722	AG	GGA
-recovered pasa_asmbl_17857.p1, initial, 182842, 182919
-recovered pasa_asmbl_17857.p1, internal, 183303, 183416
-recovered pasa_asmbl_17857.p1, internal, 184697, 184816
Valid prediction for GlimmerHMM_glimmerT_40975-T1
Valid prediction for Augustus_model.g27428.t1
Valid prediction for snap_scaffold_17-snap.758-T1
Valid prediction for GlimmerHMM_glimmerT_40976-T1
Valid prediction for snap_scaffold_17-snap.743-T1
Valid prediction for snap_scaffold_17-snap.738-T1
Valid prediction for GlimmerHMM_glimmerT_40974-T1
Valid prediction for GlimmerHMM_glimmerT_40965-T1
Valid prediction for snap_scaffold_17-snap.768-T1
Valid prediction for Augustus_model.g27427.t1
Valid prediction for snap_scaffold_17-snap.763-T1
Valid prediction for GeneMark_model.70518_t
Valid prediction for snap_scaffold_17-snap.740-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.g27433.t1
Valid prediction for GlimmerHMM_glimmerT_40963-T1
Valid prediction for GeneMark_model.70543_t
Valid prediction for snap_scaffold_17-snap.772-T1
Valid prediction for GlimmerHMM_glimmerT_40957-T1
Valid prediction for GlimmerHMM_glimmerT_40971-T1
Valid prediction for GeneMark_model.70527_t
Valid prediction for GlimmerHMM_glimmerT_40969-T1
Valid prediction for GeneMark_model.70537_t
Valid prediction for snap_scaffold_17-snap.762-T1
Valid prediction for snap_scaffold_17-snap.766-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for snap_scaffold_17-snap.747-T1
Valid prediction for Augustus_model.g27434.t1
Valid prediction for snap_scaffold_17-snap.741-T1
Valid prediction for Augustus_model.g27430.t1
Valid prediction for snap_scaffold_17-snap.774-T1
Valid prediction for GeneMark_model.70522_t
Valid prediction for snap_scaffold_17-snap.753-T1
Valid prediction for snap_scaffold_17-snap.754-T1
Valid prediction for GeneMark_model.70520_t
Valid prediction for snap_scaffold_17-snap.760-T1
Valid prediction for GeneMark_model.70558_t
Valid prediction for Augustus_model.g27435.t1
Couldn't classify 184939, 184969
Couldn't classify 189006, 189095
Sorry, prediction pasa_asmbl_19547.p1 fails validation.
(CCC)	 CG	184939-184969	GT	ACG
(TAA)	 AG	186142-186383	GT	TGG
(AAT)	 AG	189006-189095	GT	AGG
-recovered pasa_asmbl_19547.p1, internal, 186142, 186383
-recovered pasa_asmbl_19547.p1, internal, 189006, 189095
Valid prediction for GlimmerHMM_glimmerT_40958-T1
Valid prediction for GeneMark_model.70533_t
Valid prediction for GeneMark_model.70549_t
Valid prediction for GlimmerHMM_glimmerT_40973-T1
Valid prediction for GeneMark_model.70517_t
Valid prediction for GlimmerHMM_glimmerT_40977-T1
Valid prediction for GeneMark_model.70532_t
Valid prediction for GeneMark_model.70530_t
Valid prediction for snap_scaffold_17-snap.739-T1
Valid prediction for snap_scaffold_17-snap.769-T1
Valid prediction for GlimmerHMM_glimmerT_40954-T1
Valid prediction for GeneMark_model.70515_t
Valid prediction for snap_scaffold_17-snap.775-T1
Valid prediction for GeneMark_model.70560_t
Valid prediction for GeneMark_model.70547_t
Valid prediction for snap_scaffold_17-snap.777-T1
Valid prediction for snap_scaffold_17-snap.771-T1
Valid prediction for snap_scaffold_17-snap.742-T1
Valid prediction for GeneMark_model.70539_t
Valid prediction for GeneMark_model.70561_t
Valid prediction for snap_scaffold_17-snap.745-T1
Valid prediction for GlimmerHMM_glimmerT_40970-T1
Valid prediction for snap_scaffold_17-snap.764-T1
Valid prediction for Augustus_model.g27432.t1
Valid prediction for snap_scaffold_17-snap.737-T1
Valid prediction for GlimmerHMM_glimmerT_40955-T1
Valid prediction for GeneMark_model.70554_t
Valid prediction for snap_scaffold_17-snap.752-T1
Valid prediction for GlimmerHMM_glimmerT_40966-T1
Valid prediction for Augustus_model.g27429.t1
Valid prediction for GeneMark_model.70542_t
Valid prediction for GeneMark_model.70556_t
Valid prediction for snap_scaffold_17-snap.757-T1
Valid prediction for Augustus_model.g27426.t1
Valid prediction for GeneMark_model.70540_t
Valid prediction for GeneMark_model.70525_t
Valid prediction for snap_scaffold_17-snap.749-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8403, rend_intergenic: 5321  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13893, rend_intergenic: 11669  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19413, rend_intergenic: 17585  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26160, rend_intergenic: 19764  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35755, rend_intergenic: 26555  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41999, rend_intergenic: 38881  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48182, rend_intergenic: 46278  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55208, rend_intergenic: 50693  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69373, rend_intergenic: 58802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75493, rend_intergenic: 69707  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120821, rend_intergenic: 118650  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152827, rend_intergenic: 151815  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185827, rend_intergenic: 185039  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 197417
-exon list size: 579


building trellis

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90.9    
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91.7    
91.9    
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98.3    
98.5    
98.6    
98.8    
99.0    
99.1    
99.3    
99.5    
99.7    
99.8    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 8403, rend_intergenic: 5321  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13893, rend_intergenic: 11669  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19413, rend_intergenic: 17585  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26160, rend_intergenic: 19764  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35755, rend_intergenic: 26555  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41999, rend_intergenic: 38881  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48182, rend_intergenic: 46278  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55208, rend_intergenic: 50693  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69373, rend_intergenic: 58802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75493, rend_intergenic: 69707  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120821, rend_intergenic: 118650  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152827, rend_intergenic: 151815  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185827, rend_intergenic: 185039  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 12 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 185828 - 197417
-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 186575 - 197417
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-found 1 predictions from path traversal

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