-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_7/scaffold_7_2370401-2561006

-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 snap_scaffold_7-snap.578-T1
Valid prediction for snap_scaffold_7-snap.563-T1
Valid prediction for snap_scaffold_7-snap.597-T1
Valid prediction for GlimmerHMM_glimmerT_17036-T1
Valid prediction for Augustus_model.g11354.t1
Valid prediction for GlimmerHMM_glimmerT_17028-T1
Valid prediction for GlimmerHMM_glimmerT_17024-T1
Couldn't classify 145208, 145516
Sorry, prediction pasa_asmbl_49652.p2 fails validation.
(GCT)	 CA	145208-145516	TC	CTT
Valid prediction for snap_scaffold_7-snap.586-T1
Valid prediction for snap_scaffold_7-snap.601-T1
Valid prediction for snap_scaffold_7-snap.571-T1
Valid prediction for snap_scaffold_7-snap.566-T1
Valid prediction for GlimmerHMM_glimmerT_17045-T1
Valid prediction for Augustus_model.g11356.t1
Valid prediction for Augustus_model.g11353.t1
Valid prediction for Augustus_model.g11367.t1
Valid prediction for GlimmerHMM_glimmerT_17025-T1
Valid prediction for GlimmerHMM_glimmerT_17042-T1
Valid prediction for snap_scaffold_7-snap.576-T1
Valid prediction for Augustus_model.g11363.t1
Valid prediction for snap_scaffold_7-snap.599-T1
Valid prediction for GlimmerHMM_glimmerT_17046-T1
Valid prediction for snap_scaffold_7-snap.594-T1
Valid prediction for GlimmerHMM_glimmerT_17026-T1
Valid prediction for snap_scaffold_7-snap.583-T1
Valid prediction for GlimmerHMM_glimmerT_17033-T1
Valid prediction for pasa_asmbl_49649.p1
Valid prediction for snap_scaffold_7-snap.575-T1
Valid prediction for snap_scaffold_7-snap.568-T1
Valid prediction for snap_scaffold_7-snap.561-T1
Valid prediction for snap_scaffold_7-snap.589-T1
Valid prediction for GlimmerHMM_glimmerT_17032-T1
Valid prediction for GlimmerHMM_glimmerT_17041-T1
Couldn't classify 114795, 114844
Sorry, prediction pasa_asmbl_49648.p1 fails validation.
(CCC)	 AC	114795-114844	GT	AGG
(GGG)	 AG	116148-116248	GT	AGG
(AGC)	 AG	116413-116493	GT	AGG
(ACA)	 AG	116617-116808	GT	AGG
(GTG)	 AG	117030-117100	GT	AGG
(ATC)	 AG	117335-117451	GT	GGG
(GAG)	 AG	117562-117721	GT	AGG
(GAG)	 AG	118175-118297	GT	AGG
(CAT)	 AG	118653-118759	GT	AGG
(AGG)	 AG	118998-119177	GT	AGG
(GTG)	 AG	119677-119697	GG	GAG
add_exon() Sorry, pasa_asmbl_49648.p1 116617-116808-terminal-1 is invalid.
-recovered pasa_asmbl_49648.p1, terminal, 116617, 116808
-recovered pasa_asmbl_49648.p1, terminal, 119677, 119697
-recovered pasa_asmbl_49648.p1, internal, 116148, 116248
-recovered pasa_asmbl_49648.p1, internal, 116413, 116493
-recovered pasa_asmbl_49648.p1, internal, 116617, 116808
-recovered pasa_asmbl_49648.p1, internal, 117030, 117100
-recovered pasa_asmbl_49648.p1, internal, 117335, 117451
-recovered pasa_asmbl_49648.p1, internal, 117562, 117721
-recovered pasa_asmbl_49648.p1, internal, 118175, 118297
-recovered pasa_asmbl_49648.p1, internal, 118653, 118759
-recovered pasa_asmbl_49648.p1, internal, 118998, 119177
Valid prediction for Augustus_model.g11355.t1
Valid prediction for snap_scaffold_7-snap.582-T1
Valid prediction for GlimmerHMM_glimmerT_17048-T1
Valid prediction for snap_scaffold_7-snap.592-T1
Valid prediction for HiQ_model.g11360.t1
Couldn't classify 100915, 101068
Couldn't classify 101213, 101982
Sorry, prediction pasa_asmbl_49643.p1 fails validation.
(CGG)	 CC	100915-101068	GT	GGG
(ACA)	 AG	101213-101982	GC	TGG
-recovered pasa_asmbl_49643.p1, internal, 101213, 101982
Couldn't classify 147464, 147809
Sorry, prediction pasa_asmbl_49654.p1 fails validation.
(CCA)	 CA	147464-147809	GT	CGG
(GAA)	 AG	148169-148302	GT	AGG
(AAT)	 AG	149081-149101	GG	GAG
-recovered pasa_asmbl_49654.p1, terminal, 149081, 149101
-recovered pasa_asmbl_49654.p1, internal, 148169, 148302
Valid prediction for snap_scaffold_7-snap.569-T1
Valid prediction for snap_scaffold_7-snap.590-T1
Valid prediction for Augustus_model.g11364.t1
Couldn't classify 145208, 145369
Couldn't classify 146940, 147457
Sorry, prediction pasa_asmbl_49653.p1 fails validation.
(GCT)	 CA	145208-145369	GT	AGG
(GTC)	 AG	145484-145649	GT	AGG
(ACT)	 AG	146940-147457	GC	AGG
-recovered pasa_asmbl_49653.p1, internal, 145484, 145649
-recovered pasa_asmbl_49653.p1, internal, 146940, 147457
Valid prediction for GlimmerHMM_glimmerT_17030-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.g11352.t1
Couldn't classify 21064, 21107
Sorry, prediction pasa_asmbl_51547.p1 fails validation.
(ATG)	 GG	17552-17715	GT	AGG
(AGC)	 AG	17823-18018	GT	AGG
(GTG)	 AG	18746-18908	GT	AAG
(ACC)	 AG	21064-21107	GT	AGG
-recovered pasa_asmbl_51547.p1, initial, 17552, 17715
-recovered pasa_asmbl_51547.p1, internal, 17823, 18018
-recovered pasa_asmbl_51547.p1, internal, 18746, 18908
-recovered pasa_asmbl_51547.p1, internal, 21064, 21107
Valid prediction for GlimmerHMM_glimmerT_17027-T1
Couldn't classify 66382, 66485
Couldn't classify 68234, 68431
Sorry, prediction pasa_asmbl_50751.p1 fails validation.
(GTC)	 TA	66382-66485	GT	AGG
(GAG)	 AG	66711-66786	GT	AGG
(GAC)	 AG	68234-68431	GG	TGG
-recovered pasa_asmbl_50751.p1, internal, 66711, 66786
Valid prediction for GlimmerHMM_glimmerT_17035-T1
Valid prediction for snap_scaffold_7-snap.581-T1
Valid prediction for Augustus_model.g11359.t1
Valid prediction for snap_scaffold_7-snap.588-T1
Valid prediction for snap_scaffold_7-snap.562-T1
Couldn't classify 63830, 63896
Couldn't classify 65431, 65481
Sorry, prediction pasa_asmbl_50752.p1 fails validation.
(CTC)	 CG	63830-63896	GT	CCG
(AGA)	 AG	64333-64502	GT	GGG
(AGC)	 AG	64712-64873	GT	GGG
(TTC)	 AG	65431-65481	AG	CCA
-recovered pasa_asmbl_50752.p1, internal, 64333, 64502
-recovered pasa_asmbl_50752.p1, internal, 64712, 64873
Valid prediction for snap_scaffold_7-snap.572-T1
Valid prediction for snap_scaffold_7-snap.565-T1
Valid prediction for GlimmerHMM_glimmerT_17040-T1
Valid prediction for GlimmerHMM_glimmerT_17037-T1
Valid prediction for GlimmerHMM_glimmerT_17023-T1
Valid prediction for GlimmerHMM_glimmerT_17022-T1
Valid prediction for GlimmerHMM_glimmerT_17021-T1
Valid prediction for Augustus_model.g11357.t1
Valid prediction for snap_scaffold_7-snap.600-T1
Valid prediction for snap_scaffold_7-snap.579-T1
Valid prediction for snap_scaffold_7-snap.580-T1
Sorry, intron length (7) is less than minimum required (10)
Couldn't classify 32702, 32819
Sorry, prediction pasa_asmbl_50760.p1 fails validation.
(CAG)	 TG	32702-32819	GT	TAG
(CCC)	 AG	33122-33204	GT	AGG
(GTC)	 AG	33355-33555	GT	AGG
(TTT)	 AG	34032-34169	GT	AGG
(GGC)	 AG	35458-35566	GT	AGG
(CCA)	 AG	37195-37284	GT	CGG
(GTA)	 AG	37408-37571	GG	AGG
-recovered pasa_asmbl_50760.p1, terminal, 37408, 37571
-recovered pasa_asmbl_50760.p1, internal, 33122, 33204
-recovered pasa_asmbl_50760.p1, internal, 33355, 33555
-recovered pasa_asmbl_50760.p1, internal, 34032, 34169
-recovered pasa_asmbl_50760.p1, internal, 35458, 35566
-recovered pasa_asmbl_50760.p1, internal, 37195, 37284
Valid prediction for snap_scaffold_7-snap.567-T1
Valid prediction for GlimmerHMM_glimmerT_17038-T1
Valid prediction for Augustus_model.g11361.t1
Valid prediction for snap_scaffold_7-snap.587-T1
Valid prediction for GlimmerHMM_glimmerT_17031-T1
Valid prediction for GlimmerHMM_glimmerT_17039-T1
Valid prediction for snap_scaffold_7-snap.570-T1
Valid prediction for snap_scaffold_7-snap.573-T1
Valid prediction for snap_scaffold_7-snap.564-T1
Valid prediction for Augustus_model.g11368.t1
Valid prediction for snap_scaffold_7-snap.591-T1
Valid prediction for GlimmerHMM_glimmerT_17043-T1
Valid prediction for GlimmerHMM_glimmerT_17049-T1
Valid prediction for GlimmerHMM_glimmerT_17047-T1
Valid prediction for snap_scaffold_7-snap.598-T1
Valid prediction for GlimmerHMM_glimmerT_17029-T1
Valid prediction for GlimmerHMM_glimmerT_17051-T1
Valid prediction for snap_scaffold_7-snap.596-T1
Valid prediction for snap_scaffold_7-snap.595-T1
Valid prediction for Augustus_model.g11366.t1
Couldn't classify 55059, 55196
Sorry, prediction pasa_asmbl_50753.p1 fails validation.
(TCA)	 TC	55059-55196	GT	TGG
(AAA)	 AG	55282-55356	GT	AGG
(TCT)	 AG	55598-55723	GT	TGG
(GAG)	 AG	56646-56867	GT	AGG
(GAG)	 AG	56956-57099	GT	TGG
(TGT)	 AG	57277-57333	GT	TGG
(CAA)	 AG	58266-58409	GT	AGG
(AAC)	 AG	58751-58843	GT	AGG
(GCT)	 AG	58965-59148	GT	CCG
(CGG)	 AG	59307-59470	GT	AGG
(TGT)	 AG	59576-59656	GT	TGG
(AAG)	 AG	59854-59961	GT	ACG
(GCG)	 AG	60320-60355	AG	AGA
-recovered pasa_asmbl_50753.p1, terminal, 60320, 60355
-recovered pasa_asmbl_50753.p1, internal, 55282, 55356
-recovered pasa_asmbl_50753.p1, internal, 55598, 55723
-recovered pasa_asmbl_50753.p1, internal, 56646, 56867
-recovered pasa_asmbl_50753.p1, internal, 56956, 57099
-recovered pasa_asmbl_50753.p1, internal, 57277, 57333
-recovered pasa_asmbl_50753.p1, internal, 58266, 58409
-recovered pasa_asmbl_50753.p1, internal, 58751, 58843
-recovered pasa_asmbl_50753.p1, internal, 58965, 59148
-recovered pasa_asmbl_50753.p1, internal, 59307, 59470
-recovered pasa_asmbl_50753.p1, internal, 59576, 59656
-recovered pasa_asmbl_50753.p1, internal, 59854, 59961
Valid prediction for Augustus_model.g11365.t1
Valid prediction for snap_scaffold_7-snap.577-T1
Valid prediction for snap_scaffold_7-snap.574-T1
Valid prediction for GlimmerHMM_glimmerT_17044-T1
Valid prediction for GlimmerHMM_glimmerT_17034-T1
Valid prediction for Augustus_model.g11369.t1
Valid prediction for Augustus_model.g11358.t1
Valid prediction for snap_scaffold_7-snap.584-T1
Valid prediction for snap_scaffold_7-snap.593-T1
Valid prediction for Augustus_model.g11362.t1
Valid prediction for snap_scaffold_7-snap.585-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_17050-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 5549, rend_intergenic: 3351  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 8183, rend_intergenic: 5833  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25027, rend_intergenic: 8510  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31065, rend_intergenic: 25056  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32176, rend_intergenic: 31840  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38399, rend_intergenic: 34641  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47714, rend_intergenic: 43944  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61687, rend_intergenic: 49077  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72985, rend_intergenic: 62649  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78127, rend_intergenic: 73976  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82996, rend_intergenic: 80492  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115410, rend_intergenic: 95134  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135904, rend_intergenic: 131415  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147843, rend_intergenic: 144893  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153210, rend_intergenic: 151627  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162510, rend_intergenic: 153445  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166337, rend_intergenic: 162997  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172241, rend_intergenic: 166524  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175205, rend_intergenic: 172379  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183849, rend_intergenic: 181208  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 190606
-exon list size: 419


building trellis

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29.9    
30.2    
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30.9    
31.1    
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33.3    
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34.9    
35.2    
35.4    
35.6    
35.9    
36.1    
36.3    
36.6    
36.8    
37.1    
37.3    
37.5    
37.8    
38.0    
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38.7    
39.0    
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39.9    
40.1    
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40.9    
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42.0    
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42.8    
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45.6    
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97.6    
97.9    
98.1    
98.3    
98.6    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 5549, rend_intergenic: 3351  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 8183, rend_intergenic: 5833  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25027, rend_intergenic: 8510  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31065, rend_intergenic: 25056  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32176, rend_intergenic: 31840  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38399, rend_intergenic: 34641  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47714, rend_intergenic: 43944  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61687, rend_intergenic: 49077  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72985, rend_intergenic: 62649  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78127, rend_intergenic: 73976  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82996, rend_intergenic: 80492  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115410, rend_intergenic: 95134  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135904, rend_intergenic: 131415  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147843, rend_intergenic: 144893  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153210, rend_intergenic: 151627  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162510, rend_intergenic: 153445  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166337, rend_intergenic: 162997  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172241, rend_intergenic: 166524  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175205, rend_intergenic: 172379  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183849, rend_intergenic: 181208  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support