-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_19/scaffold_19_5382214-5550919

-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_44138-T1
Valid prediction for GlimmerHMM_glimmerT_44140-T1
Valid prediction for snap_scaffold_19-snap.1130-T1
Valid prediction for Augustus_model.g29251.t1
Valid prediction for Augustus_model.g29267.t1
Valid prediction for snap_scaffold_19-snap.1148-T1
Valid prediction for GlimmerHMM_glimmerT_44125-T1
Valid prediction for GlimmerHMM_glimmerT_44150-T1
Valid prediction for GlimmerHMM_glimmerT_44131-T1
Couldn't classify 2700, 2882
Couldn't classify 3251, 3381
Sorry, prediction CodingQuarry_transcript_25654-T1 fails validation.
(ATG)	 AG	2360-2519	GT	TGG
(GGG)	 AG	2700-2882	AT	CCA
(CAT)	 TG	3251-3381	GT	AGG
(GTT)	 AG	3511-3582	GT	AAG
(CCA)	 AG	3908-4003	GT	AGG
(GTC)	 AG	4160-4238	GT	AGG
(ACA)	 AG	4790-4824	GT	AGG
(GAT)	 AG	5013-5039	GT	TGG
(GGT)	 AG	5282-5367	GT	AGG
(GGC)	 AG	5504-5615	GT	CTG
(GGA)	 AG	5698-5772	GT	AGG
(ACT)	 AG	5987-6029	GT	AGG
(GAG)	 AG	6178-6280	GT	CGG
(CGG)	 AG	6375-6444	GT	AGG
(CTG)	 AG	6577-6657	GT	TGG
(ATT)	 AG	6748-6806	GT	AAG
(ACC)	 AG	7022-7106	AC	GAA
-recovered CodingQuarry_transcript_25654-T1, initial, 2360, 2519
-recovered CodingQuarry_transcript_25654-T1, terminal, 7022, 7106
-recovered CodingQuarry_transcript_25654-T1, internal, 2360, 2519
-recovered CodingQuarry_transcript_25654-T1, internal, 3511, 3582
-recovered CodingQuarry_transcript_25654-T1, internal, 3908, 4003
-recovered CodingQuarry_transcript_25654-T1, internal, 4160, 4238
-recovered CodingQuarry_transcript_25654-T1, internal, 4790, 4824
-recovered CodingQuarry_transcript_25654-T1, internal, 5013, 5039
-recovered CodingQuarry_transcript_25654-T1, internal, 5282, 5367
-recovered CodingQuarry_transcript_25654-T1, internal, 5504, 5615
-recovered CodingQuarry_transcript_25654-T1, internal, 5698, 5772
-recovered CodingQuarry_transcript_25654-T1, internal, 5987, 6029
-recovered CodingQuarry_transcript_25654-T1, internal, 6178, 6280
-recovered CodingQuarry_transcript_25654-T1, internal, 6375, 6444
-recovered CodingQuarry_transcript_25654-T1, internal, 6577, 6657
-recovered CodingQuarry_transcript_25654-T1, internal, 6748, 6806
Valid prediction for snap_scaffold_19-snap.1145-T1
Valid prediction for Augustus_model.g29268.t1
Couldn't classify 134005, 134040
Couldn't classify 136626, 136796
Sorry, prediction pasa_asmbl_21954.p1 fails validation.
(AAG)	 CC	134005-134040	GT	AGG
(ACA)	 AG	135365-135526	GT	AGG
(ATC)	 AG	136626-136796	TG	AGT
-recovered pasa_asmbl_21954.p1, internal, 135365, 135526
Couldn't classify 81767, 81879
Sorry, prediction CodingQuarry_transcript_25658-T1 fails validation.
(ATG)	 AG	79348-79404	GT	AGG
(GCG)	 AG	80651-80760	GT	AGG
(GAA)	 AG	81334-81459	GT	AAG
(GTT)	 TG	81767-81879	GT	AGG
(TGT)	 AG	81966-82147	GT	AGG
(GTG)	 AG	82432-82596	GA	GAG
-recovered CodingQuarry_transcript_25658-T1, initial, 79348, 79404
-recovered CodingQuarry_transcript_25658-T1, terminal, 82432, 82596
-recovered CodingQuarry_transcript_25658-T1, internal, 79348, 79404
-recovered CodingQuarry_transcript_25658-T1, internal, 80651, 80760
-recovered CodingQuarry_transcript_25658-T1, internal, 81334, 81459
-recovered CodingQuarry_transcript_25658-T1, internal, 81966, 82147
Valid prediction for GlimmerHMM_glimmerT_44148-T1
Valid prediction for snap_scaffold_19-snap.1140-T1
Valid prediction for Augustus_model.g29259.t1
Valid prediction for Augustus_model.g29253.t1
Valid prediction for snap_scaffold_19-snap.1149-T1
Valid prediction for Augustus_model.g29263.t1
Valid prediction for snap_scaffold_19-snap.1135-T1
Valid prediction for GlimmerHMM_glimmerT_44134-T1
Valid prediction for snap_scaffold_19-snap.1132-T1
Valid prediction for GlimmerHMM_glimmerT_44124-T1
Valid prediction for Augustus_model.g29255.t1
Valid prediction for snap_scaffold_19-snap.1139-T1
Valid prediction for pasa_asmbl_21892.p2
Valid prediction for Augustus_model.g29261.t1
Valid prediction for GlimmerHMM_glimmerT_44120-T1
Valid prediction for pasa_asmbl_21373.p1
Couldn't classify 157331, 157351
Couldn't classify 159715, 159853
Sorry, prediction pasa_asmbl_21379.p1 fails validation.
(GGC)	 AG	157331-157351	GT	AGG
(CTC)	 AG	157652-157768	GT	AGG
(ATC)	 AG	159053-159127	GT	AGG
(GAC)	 AG	159274-159431	GT	CGG
(GTT)	 AG	159715-159853	AT	GCA
-recovered pasa_asmbl_21379.p1, internal, 157331, 157351
-recovered pasa_asmbl_21379.p1, internal, 157652, 157768
-recovered pasa_asmbl_21379.p1, internal, 159053, 159127
-recovered pasa_asmbl_21379.p1, internal, 159274, 159431
Valid prediction for GlimmerHMM_glimmerT_44143-T1
Valid prediction for Augustus_model.g29264.t1
Valid prediction for GlimmerHMM_glimmerT_44142-T1
Valid prediction for GlimmerHMM_glimmerT_44133-T1
Couldn't classify 81767, 81879
Sorry, prediction CodingQuarry_transcript_25659-T1 fails validation.
(ATG)	 AG	79545-79556	GT	CAG
(GCG)	 AG	80651-80760	GT	AGG
(GAA)	 AG	81334-81459	GT	AAG
(GTT)	 TG	81767-81879	GT	AGG
(TGT)	 AG	81966-82147	GT	AGG
(GTG)	 AG	82432-82596	GA	GAG
-recovered CodingQuarry_transcript_25659-T1, initial, 79545, 79556
-recovered CodingQuarry_transcript_25659-T1, terminal, 82432, 82596
-recovered CodingQuarry_transcript_25659-T1, internal, 79545, 79556
-recovered CodingQuarry_transcript_25659-T1, internal, 80651, 80760
-recovered CodingQuarry_transcript_25659-T1, internal, 81334, 81459
-recovered CodingQuarry_transcript_25659-T1, internal, 81966, 82147
Valid prediction for Augustus_model.g29266.t1
Valid prediction for snap_scaffold_19-snap.1155-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for Augustus_model.g29262.t1
Valid prediction for snap_scaffold_19-snap.1163-T1
Valid prediction for Augustus_model.g29250.t1
Valid prediction for Augustus_model.g29260.t1
Valid prediction for snap_scaffold_19-snap.1151-T1
Valid prediction for snap_scaffold_19-snap.1137-T1
Valid prediction for GlimmerHMM_glimmerT_44130-T1
Valid prediction for snap_scaffold_19-snap.1141-T1
Valid prediction for snap_scaffold_19-snap.1154-T1
Valid prediction for GlimmerHMM_glimmerT_44149-T1
Valid prediction for HiQ_model.g29246.t1
Valid prediction for HiQ_model.g29257.t1
Valid prediction for CodingQuarry_transcript_25657-T1
Valid prediction for GlimmerHMM_glimmerT_44145-T1
Valid prediction for GlimmerHMM_glimmerT_44127-T1
Valid prediction for GlimmerHMM_glimmerT_44129-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 snap_scaffold_19-snap.1158-T1
Valid prediction for snap_scaffold_19-snap.1159-T1
Valid prediction for GlimmerHMM_glimmerT_44121-T1
Valid prediction for snap_scaffold_19-snap.1131-T1
Valid prediction for GlimmerHMM_glimmerT_44122-T1
Valid prediction for GlimmerHMM_glimmerT_44136-T1
Valid prediction for GlimmerHMM_glimmerT_44135-T1
Valid prediction for GlimmerHMM_glimmerT_44123-T1
Valid prediction for GlimmerHMM_glimmerT_44128-T1
Valid prediction for snap_scaffold_19-snap.1138-T1
Valid prediction for snap_scaffold_19-snap.1152-T1
Valid prediction for HiQ_model.g29256.t1
Valid prediction for GlimmerHMM_glimmerT_44146-T1
Valid prediction for snap_scaffold_19-snap.1150-T1
Valid prediction for CodingQuarry_transcript_25656-T1
Valid prediction for Augustus_model.g29265.t1
Valid prediction for snap_scaffold_19-snap.1164-T1
Valid prediction for snap_scaffold_19-snap.1133-T1
Valid prediction for HiQ_model.g29248.t1
Valid prediction for snap_scaffold_19-snap.1153-T1
Valid prediction for CodingQuarry_transcript_25655-T1
Valid prediction for snap_scaffold_19-snap.1147-T1
Valid prediction for snap_scaffold_19-snap.1161-T1
Valid prediction for Augustus_model.g29247.t1
Valid prediction for pasa_asmbl_22164.p1
Couldn't classify 109941, 110012
Sorry, prediction pasa_asmbl_22160.p1 fails validation.
(CCT)	 CC	109941-110012	GT	AGG
(TAC)	 AG	110120-110210	GT	AGG
(ACT)	 AG	110394-110663	GT	AGG
(CGG)	 AG	110871-111010	GA	AAG
add_exon() Sorry, pasa_asmbl_22160.p1 110394-110663-terminal-1 is invalid.
-recovered pasa_asmbl_22160.p1, terminal, 110394, 110663
-recovered pasa_asmbl_22160.p1, terminal, 110871, 111010
-recovered pasa_asmbl_22160.p1, internal, 110120, 110210
-recovered pasa_asmbl_22160.p1, internal, 110394, 110663
Valid prediction for Augustus_model.g29254.t1
Valid prediction for snap_scaffold_19-snap.1146-T1
Valid prediction for Augustus_model.g29252.t1
Valid prediction for GlimmerHMM_glimmerT_44132-T1
Valid prediction for snap_scaffold_19-snap.1143-T1
Valid prediction for GlimmerHMM_glimmerT_44151-T1
Valid prediction for Augustus_model.g29258.t1
Couldn't classify 155350, 155791
Sorry, prediction pasa_asmbl_22156.p1 fails validation.
(TCC)	 AC	155350-155791	GT	AGG
(AAG)	 AG	156207-156976	TT	AGT
-recovered pasa_asmbl_22156.p1, terminal, 156207, 156976
Valid prediction for GlimmerHMM_glimmerT_44147-T1
Valid prediction for GlimmerHMM_glimmerT_44126-T1
Valid prediction for snap_scaffold_19-snap.1156-T1
Valid prediction for GlimmerHMM_glimmerT_44141-T1
Valid prediction for GlimmerHMM_glimmerT_44144-T1
Valid prediction for snap_scaffold_19-snap.1157-T1
Valid prediction for GlimmerHMM_glimmerT_44137-T1
Valid prediction for snap_scaffold_19-snap.1136-T1
Valid prediction for Augustus_model.g29249.t1
Valid prediction for snap_scaffold_19-snap.1160-T1
Valid prediction for GlimmerHMM_glimmerT_44139-T1
Valid prediction for snap_scaffold_19-snap.1144-T1
Valid prediction for snap_scaffold_19-snap.1162-T1
Valid prediction for snap_scaffold_19-snap.1134-T1
Valid prediction for snap_scaffold_19-snap.1142-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8379, rend_intergenic: 2293  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14588, rend_intergenic: 9115  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27273, rend_intergenic: 20863  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35888, rend_intergenic: 27984  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54128, rend_intergenic: 40459  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66088, rend_intergenic: 61163  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71218, rend_intergenic: 66117  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88225, rend_intergenic: 88066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156508, rend_intergenic: 125731  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161735, rend_intergenic: 156874  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 168706
-exon list size: 425


building trellis

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33.0    
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39.6    
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40.7    
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41.9    
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42.9    
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98.1    
98.4    
98.6    
98.8    
99.1    
99.3    
99.5    
99.8    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 8379, rend_intergenic: 2293  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14588, rend_intergenic: 9115  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27273, rend_intergenic: 20863  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35888, rend_intergenic: 27984  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54128, rend_intergenic: 40459  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66088, rend_intergenic: 61163  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71218, rend_intergenic: 66117  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88225, rend_intergenic: 88066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156508, rend_intergenic: 125731  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161735, rend_intergenic: 156874  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 27 predictions persist after filtering for low support