-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_19/scaffold_19_12988395-13139278

-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 pasa_asmbl_22650.p1
Valid prediction for snap_scaffold_19-snap.2571-T1
Valid prediction for Augustus_model.g30852.t1
Valid prediction for snap_scaffold_19-snap.2567-T1
Valid prediction for snap_scaffold_19-snap.2554-T1
Valid prediction for snap_scaffold_19-snap.2562-T1
Valid prediction for snap_scaffold_19-snap.2574-T1
Valid prediction for GeneMark_model.80510_t
Valid prediction for snap_scaffold_19-snap.2563-T1
Valid prediction for snap_scaffold_19-snap.2551-T1
Valid prediction for snap_scaffold_19-snap.2556-T1
Valid prediction for Augustus_model.g30860.t1
Valid prediction for GeneMark_model.80482_t
Valid prediction for GlimmerHMM_glimmerT_46244-T1
Valid prediction for GeneMark_model.80502_t
Valid prediction for GeneMark_model.80500_t
Valid prediction for snap_scaffold_19-snap.2564-T1
Valid prediction for Augustus_model.g30855.t1
Valid prediction for GeneMark_model.80513_t
Couldn't classify 107493, 107870
Sorry, prediction pasa_asmbl_22657.p1 fails validation.
(CTG)	 CC	107493-107870	CA	AAC
Valid prediction for GlimmerHMM_glimmerT_46229-T1
Valid prediction for GeneMark_model.80478_t
Valid prediction for GeneMark_model.80497_t
Valid prediction for snap_scaffold_19-snap.2577-T1
Valid prediction for GlimmerHMM_glimmerT_46233-T1
Valid prediction for Augustus_model.g30862.t1
Valid prediction for GeneMark_model.80486_t
Valid prediction for GlimmerHMM_glimmerT_46230-T1
Valid prediction for snap_scaffold_19-snap.2566-T1
Valid prediction for GlimmerHMM_glimmerT_46236-T1
Valid prediction for GeneMark_model.80504_t
Valid prediction for snap_scaffold_19-snap.2549-T1
Valid prediction for snap_scaffold_19-snap.2580-T1
Valid prediction for GeneMark_model.80484_t
Valid prediction for Augustus_model.g30865.t1
Valid prediction for HiQ_model.g30853.t1
Valid prediction for GeneMark_model.80490_t
Valid prediction for GeneMark_model.80487_t
Valid prediction for GeneMark_model.80498_t
Valid prediction for Augustus_model.g30858.t1
Valid prediction for GlimmerHMM_glimmerT_46227-T1
Valid prediction for GlimmerHMM_glimmerT_46225-T1
Valid prediction for GeneMark_model.80508_t
Valid prediction for GeneMark_model.80499_t
Valid prediction for GeneMark_model.80495_t
Valid prediction for GeneMark_model.80477_t
Valid prediction for snap_scaffold_19-snap.2558-T1
Valid prediction for snap_scaffold_19-snap.2583-T1
Couldn't classify 13839, 14127
Sorry, prediction pasa_asmbl_22644.p1 fails validation.
(GTG)	 AT	13839-14127	GT	AGG
(TGG)	 AG	14375-14553	GT	AGG
(GTG)	 AG	14692-14912	GT	CTG
(GTT)	 AG	15015-15186	GT	TGG
(GTG)	 AG	15366-15521	GT	TGG
(GTG)	 AG	15877-15960	GT	AGG
(TTC)	 AG	16165-16285	GT	AGG
(GCC)	 AG	16401-16485	GT	GGG
(GGT)	 AG	17001-17091	GT	AGG
(ATC)	 AG	17326-17536	GT	AGG
(AGT)	 AG	17650-17733	GT	AGG
(ATC)	 AG	17876-17997	GT	CGG
(AAC)	 AG	18339-18434	GT	AGG
(GGG)	 AG	18633-18697	GT	AGG
(GCT)	 AG	18978-19115	GT	AGG
(TGG)	 AG	19449-19497	TA	GAT
-recovered pasa_asmbl_22644.p1, terminal, 19449, 19497
-recovered pasa_asmbl_22644.p1, internal, 14375, 14553
-recovered pasa_asmbl_22644.p1, internal, 14692, 14912
-recovered pasa_asmbl_22644.p1, internal, 15015, 15186
-recovered pasa_asmbl_22644.p1, internal, 15366, 15521
-recovered pasa_asmbl_22644.p1, internal, 15877, 15960
-recovered pasa_asmbl_22644.p1, internal, 16165, 16285
-recovered pasa_asmbl_22644.p1, internal, 16401, 16485
-recovered pasa_asmbl_22644.p1, internal, 17001, 17091
-recovered pasa_asmbl_22644.p1, internal, 17326, 17536
-recovered pasa_asmbl_22644.p1, internal, 17650, 17733
-recovered pasa_asmbl_22644.p1, internal, 17876, 17997
-recovered pasa_asmbl_22644.p1, internal, 18339, 18434
-recovered pasa_asmbl_22644.p1, internal, 18633, 18697
-recovered pasa_asmbl_22644.p1, internal, 18978, 19115
Valid prediction for snap_scaffold_19-snap.2568-T1
Valid prediction for snap_scaffold_19-snap.2552-T1
Valid prediction for GlimmerHMM_glimmerT_46241-T1
Valid prediction for GeneMark_model.80514_t
Valid prediction for snap_scaffold_19-snap.2560-T1
Valid prediction for Augustus_model.g30861.t1
Valid prediction for GeneMark_model.80493_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 snap_scaffold_19-snap.2573-T1
Valid prediction for GeneMark_model.80506_t
Couldn't classify 11562, 12062
Sorry, prediction pasa_asmbl_21818.p1 fails validation.
(CCC)	 CC	11562-12062	AC	ACA
Valid prediction for Augustus_model.g30867.t1
Valid prediction for pasa_asmbl_21809.p1
Valid prediction for GeneMark_model.80479_t
Valid prediction for HiQ_model.g30866.t1
Valid prediction for CodingQuarry_transcript_25830-T1
Valid prediction for snap_scaffold_19-snap.2570-T1
Valid prediction for snap_scaffold_19-snap.2557-T1
Valid prediction for GeneMark_model.80483_t
Valid prediction for GlimmerHMM_glimmerT_46239-T1
Valid prediction for Augustus_model.g30857.t1
Valid prediction for CodingQuarry_transcript_25834-T1
Valid prediction for snap_scaffold_19-snap.2581-T1
Valid prediction for snap_scaffold_19-snap.2576-T1
Valid prediction for GlimmerHMM_glimmerT_46237-T1
Valid prediction for GeneMark_model.80511_t
Valid prediction for snap_scaffold_19-snap.2555-T1
Valid prediction for snap_scaffold_19-snap.2561-T1
Valid prediction for snap_scaffold_19-snap.2565-T1
Valid prediction for GeneMark_model.80485_t
Valid prediction for snap_scaffold_19-snap.2578-T1
Valid prediction for HiQ_model.g30869.t1
Valid prediction for pasa_asmbl_21794.p1
Valid prediction for Augustus_model.g30864.t1
Valid prediction for GeneMark_model.80494_t
Valid prediction for snap_scaffold_19-snap.2550-T1
Valid prediction for GeneMark_model.80515_t
Valid prediction for Augustus_model.g30859.t1
Couldn't classify 24225, 24313
Sorry, prediction pasa_asmbl_21815.p1 fails validation.
(TGG)	 CC	24225-24313	GT	CTG
(CTT)	 AG	24432-24555	GT	AGG
(TTG)	 AG	24644-24691	GT	TGG
(ATC)	 AG	24870-25115	GT	AGG
(GCT)	 AG	25225-25347	GT	AGG
(ATT)	 AG	25484-25591	CC	AAC
-recovered pasa_asmbl_21815.p1, terminal, 25484, 25591
-recovered pasa_asmbl_21815.p1, internal, 24432, 24555
-recovered pasa_asmbl_21815.p1, internal, 24644, 24691
-recovered pasa_asmbl_21815.p1, internal, 24870, 25115
-recovered pasa_asmbl_21815.p1, internal, 25225, 25347
Valid prediction for GeneMark_model.80507_t
Valid prediction for GeneMark_model.80488_t
Valid prediction for Augustus_model.g30854.t1
Valid prediction for GeneMark_model.80481_t
Valid prediction for snap_scaffold_19-snap.2579-T1
Valid prediction for snap_scaffold_19-snap.2582-T1
Valid prediction for GeneMark_model.80512_t
Valid prediction for GeneMark_model.80503_t
Valid prediction for snap_scaffold_19-snap.2569-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for HiQ_model.g30856.t1
Valid prediction for CodingQuarry_transcript_25831-T1
Valid prediction for GlimmerHMM_glimmerT_46240-T1
Valid prediction for CodingQuarry_transcript_25836-T1
Valid prediction for GeneMark_model.80491_t
Valid prediction for GeneMark_model.80501_t
Valid prediction for GlimmerHMM_glimmerT_46228-T1
Couldn't classify 12186, 12405
Sorry, prediction pasa_asmbl_21817.p1 fails validation.
(CCT)	 CA	12186-12405	GT	AGG
(GCT)	 AG	13274-13333	GT	AGG
(GTG)	 AG	14431-14609	CA	AAC
-recovered pasa_asmbl_21817.p1, terminal, 14431, 14609
-recovered pasa_asmbl_21817.p1, internal, 13274, 13333
Valid prediction for snap_scaffold_19-snap.2553-T1
Valid prediction for snap_scaffold_19-snap.2559-T1
Valid prediction for GlimmerHMM_glimmerT_46242-T1
Valid prediction for GlimmerHMM_glimmerT_46226-T1
Valid prediction for GlimmerHMM_glimmerT_46235-T1
Valid prediction for CodingQuarry_transcript_25832-T1
Valid prediction for snap_scaffold_19-snap.2584-T1
Couldn't classify 2848, 2867
Sorry, prediction pasa_asmbl_21821.p1 fails validation.
(GAG)	 AC	2848-2867	GT	AGG
(AGA)	 AG	3267-3392	GT	AGG
(GAA)	 AG	3542-3640	GT	CAG
(GTT)	 AG	4607-4772	GT	AGG
(GTT)	 AG	4891-5041	GT	AAG
(TTG)	 AG	5218-5308	GT	AGG
(TGT)	 AG	5398-5500	GT	AGG
(TTG)	 AG	7101-7231	GT	AGG
(GTC)	 AG	7478-7562	GT	AGG
(GAG)	 AG	8255-8422	GT	CTG
(ACA)	 AG	8652-8705	GG	AGG
-recovered pasa_asmbl_21821.p1, terminal, 8652, 8705
-recovered pasa_asmbl_21821.p1, internal, 3267, 3392
-recovered pasa_asmbl_21821.p1, internal, 3542, 3640
-recovered pasa_asmbl_21821.p1, internal, 4607, 4772
-recovered pasa_asmbl_21821.p1, internal, 4891, 5041
-recovered pasa_asmbl_21821.p1, internal, 5218, 5308
-recovered pasa_asmbl_21821.p1, internal, 5398, 5500
-recovered pasa_asmbl_21821.p1, internal, 7101, 7231
-recovered pasa_asmbl_21821.p1, internal, 7478, 7562
-recovered pasa_asmbl_21821.p1, internal, 8255, 8422
Valid prediction for pasa_asmbl_21814.p1
Valid prediction for GlimmerHMM_glimmerT_46234-T1
Valid prediction for GlimmerHMM_glimmerT_46238-T1
Valid prediction for GlimmerHMM_glimmerT_46224-T1
Couldn't classify 51543, 51629
Sorry, prediction pasa_asmbl_21810.p1 fails validation.
(ATG)	 AC	49189-49242	GT	GGG
(TTC)	 AG	49904-49978	GT	AGG
(ACC)	 AG	50736-50783	GT	GGG
(GTG)	 AG	50986-51054	GT	CGG
(GTC)	 AG	51543-51629	GT	AAG
-recovered pasa_asmbl_21810.p1, initial, 49189, 49242
-recovered pasa_asmbl_21810.p1, internal, 49904, 49978
-recovered pasa_asmbl_21810.p1, internal, 50736, 50783
-recovered pasa_asmbl_21810.p1, internal, 50986, 51054
-recovered pasa_asmbl_21810.p1, internal, 51543, 51629
Valid prediction for Augustus_model.g30868.t1
Valid prediction for GlimmerHMM_glimmerT_46231-T1
Valid prediction for GlimmerHMM_glimmerT_46232-T1
Valid prediction for pasa_asmbl_21804.p1
Valid prediction for GeneMark_model.80509_t
Valid prediction for HiQ_model.g30863.t1
Valid prediction for snap_scaffold_19-snap.2572-T1
Valid prediction for GeneMark_model.80476_t
Valid prediction for GlimmerHMM_glimmerT_46245-T1
Valid prediction for GeneMark_model.80492_t
Valid prediction for GlimmerHMM_glimmerT_46243-T1
Valid prediction for CodingQuarry_transcript_25828-T1
Valid prediction for GeneMark_model.80505_t
Valid prediction for snap_scaffold_19-snap.2575-T1
Valid prediction for CodingQuarry_transcript_25835-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8303, rend_intergenic: 4356  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25543, rend_intergenic: 22314  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37930, rend_intergenic: 35621  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44679, rend_intergenic: 38994  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57784, rend_intergenic: 47797  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87548, rend_intergenic: 83173  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98376, rend_intergenic: 90143  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100975, rend_intergenic: 99208  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123282, rend_intergenic: 117042  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136231, rend_intergenic: 135857  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139158, rend_intergenic: 136276  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146460, rend_intergenic: 142180  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 150884
-exon list size: 575


building trellis

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92.5    
92.7    
92.9    
93.1    
93.2    
93.4    
93.6    
93.8    
93.9    
94.1    
94.3    
94.5    
94.6    
94.8    
95.0    
95.1    
95.3    
95.5    
95.7    
95.8    
96.0    
96.2    
96.4    
96.5    
96.7    
96.9    
97.1    
97.2    
97.4    
97.6    
97.7    
97.9    
98.1    
98.3    
98.4    
98.6    
98.8    
99.0    
99.1    
99.3    
99.5    
99.7    
99.8    
-found 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 8303, rend_intergenic: 4356  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25543, rend_intergenic: 22314  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37930, rend_intergenic: 35621  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44679, rend_intergenic: 38994  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57784, rend_intergenic: 47797  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87548, rend_intergenic: 83173  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98376, rend_intergenic: 90143  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100975, rend_intergenic: 99208  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123282, rend_intergenic: 117042  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136231, rend_intergenic: 135857  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139158, rend_intergenic: 136276  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146460, rend_intergenic: 142180  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support