-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_1/scaffold_1_3489103-3771845

-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: +)Couldn't classify 74750, 74871
Sorry, prediction pasa_asmbl_1604.p1 fails validation.
(CGC)	 AG	74750-74871	GT	AGG
(CTC)	 AG	75006-75169	GT	AGG
(GCA)	 AG	77559-77818	GT	AGG
(GTG)	 AG	78958-79082	GT	CGG
(GAA)	 AG	79663-79732	GT	AGG
(AAG)	 AG	79970-81059	GT	AAG
(ATT)	 AG	81864-81930	GT	GCG
(GAA)	 AG	82328-82499	GT	AGG
(GAG)	 AG	82703-82747	GT	AAG
(CAT)	 AG	82868-82984	GC	AAG
-recovered pasa_asmbl_1604.p1, terminal, 82868, 82984
-recovered pasa_asmbl_1604.p1, internal, 74750, 74871
-recovered pasa_asmbl_1604.p1, internal, 75006, 75169
-recovered pasa_asmbl_1604.p1, internal, 77559, 77818
-recovered pasa_asmbl_1604.p1, internal, 78958, 79082
-recovered pasa_asmbl_1604.p1, internal, 79663, 79732
-recovered pasa_asmbl_1604.p1, internal, 79970, 81059
-recovered pasa_asmbl_1604.p1, internal, 81864, 81930
-recovered pasa_asmbl_1604.p1, internal, 82328, 82499
-recovered pasa_asmbl_1604.p1, internal, 82703, 82747
-recovered pasa_asmbl_1604.p1, internal, 82868, 82984
Couldn't classify 206034, 206623
Couldn't classify 207154, 207298
Sorry, prediction pasa_asmbl_2706.p1 fails validation.
(GTT)	 AG	206034-206623	GT	AGG
(GTT)	 AG	206895-206990	GT	AGG
(TGA)	 AG	207154-207298	TA	GGT
-recovered pasa_asmbl_2706.p1, internal, 206034, 206623
-recovered pasa_asmbl_2706.p1, internal, 206895, 206990
Valid prediction for GlimmerHMM_glimmerT_415-T1
Valid prediction for GlimmerHMM_glimmerT_416-T1
Valid prediction for snap_scaffold_1-snap.549-T1
Valid prediction for snap_scaffold_1-snap.524-T1
Valid prediction for Augustus_model.g355.t1
Valid prediction for GlimmerHMM_glimmerT_427-T1
Valid prediction for Augustus_model.g350.t1
Couldn't classify 152758, 152817
Couldn't classify 154219, 154350
Sorry, prediction pasa_asmbl_1620.p1 fails validation.
(GTA)	 CA	152758-152817	GT	GTG
(CTC)	 AG	153003-153073	GT	AGG
(TGT)	 AG	153732-153918	GT	TGG
(TCC)	 AG	154219-154350	CC	CAC
-recovered pasa_asmbl_1620.p1, internal, 153003, 153073
-recovered pasa_asmbl_1620.p1, internal, 153732, 153918
Valid prediction for GlimmerHMM_glimmerT_412-T1
Valid prediction for GlimmerHMM_glimmerT_429-T1
Valid prediction for GlimmerHMM_glimmerT_413-T1
Valid prediction for snap_scaffold_1-snap.527-T1
Valid prediction for Augustus_model.g344.t1
Valid prediction for snap_scaffold_1-snap.540-T1
Valid prediction for HiQ_model.g351.t1
Valid prediction for CodingQuarry_transcript_2576-T1
Valid prediction for CodingQuarry_transcript_2570-T1
Valid prediction for Augustus_model.g345.t1
Valid prediction for GlimmerHMM_glimmerT_417-T1
Valid prediction for HiQ_model.g352.t1
Valid prediction for snap_scaffold_1-snap.550-T1
Valid prediction for Augustus_model.g341.t1
Valid prediction for GlimmerHMM_glimmerT_425-T1
Couldn't classify 154447, 154471
Sorry, prediction pasa_asmbl_1623.p1 fails validation.
(GAG)	 CG	154447-154471	GT	CCG
(GGG)	 AG	154926-155239	GT	AGG
(ATC)	 AG	155397-155602	GT	AGG
(CGA)	 AG	155907-156156	GT	TGG
(AAT)	 AG	156416-156455	GT	CAG
(CCC)	 AG	156862-157018	GT	AGG
(CCA)	 AG	157123-157177	GT	CGG
(TAC)	 AG	157293-157527	GT	TGG
(GGA)	 AG	158075-158166	GT	CAG
(CAG)	 AG	158517-158567	GT	TGG
(CCC)	 AG	158724-158814	GT	GGG
(GTG)	 AG	159259-159663	GT	AGG
(GGT)	 AG	159992-160096	GT	AGG
(GTG)	 AG	160485-160552	GT	AGG
(TCC)	 AG	160903-161097	GT	AGG
(GGT)	 AG	161246-161341	GA	AAG
-recovered pasa_asmbl_1623.p1, terminal, 161246, 161341
-recovered pasa_asmbl_1623.p1, internal, 154926, 155239
-recovered pasa_asmbl_1623.p1, internal, 155397, 155602
-recovered pasa_asmbl_1623.p1, internal, 155907, 156156
-recovered pasa_asmbl_1623.p1, internal, 156416, 156455
-recovered pasa_asmbl_1623.p1, internal, 156862, 157018
-recovered pasa_asmbl_1623.p1, internal, 157123, 157177
-recovered pasa_asmbl_1623.p1, internal, 157293, 157527
-recovered pasa_asmbl_1623.p1, internal, 158075, 158166
-recovered pasa_asmbl_1623.p1, internal, 158517, 158567
-recovered pasa_asmbl_1623.p1, internal, 158724, 158814
-recovered pasa_asmbl_1623.p1, internal, 159259, 159663
-recovered pasa_asmbl_1623.p1, internal, 159992, 160096
-recovered pasa_asmbl_1623.p1, internal, 160485, 160552
-recovered pasa_asmbl_1623.p1, internal, 160903, 161097
Valid prediction for CodingQuarry_transcript_2568-T1
Valid prediction for Augustus_model.g362.t1
Valid prediction for HiQ_model.g348.t1
Valid prediction for snap_scaffold_1-snap.526-T1
Valid prediction for snap_scaffold_1-snap.522-T1
Valid prediction for GlimmerHMM_glimmerT_422-T1
Valid prediction for Augustus_model.g343.t1
Valid prediction for GlimmerHMM_glimmerT_423-T1
Valid prediction for snap_scaffold_1-snap.552-T1
Valid prediction for snap_scaffold_1-snap.536-T1
Valid prediction for CodingQuarry_transcript_2575-T1
Valid prediction for pasa_asmbl_1613.p1
Valid prediction for snap_scaffold_1-snap.529-T1
Valid prediction for CodingQuarry_transcript_2574-T1
Valid prediction for Augustus_model.g359.t1
Valid prediction for CodingQuarry_transcript_2572-T1
Valid prediction for snap_scaffold_1-snap.523-T1
Valid prediction for snap_scaffold_1-snap.528-T1
Couldn't classify 147665, 147694
Couldn't classify 152305, 152369
Sorry, prediction pasa_asmbl_2713.p1 fails validation.
(GTT)	 CA	147665-147694	GT	GTG
(ATT)	 AG	148527-148664	GT	AGG
(GCA)	 AG	149153-149230	GT	AGG
(TTG)	 AG	150066-150176	GT	CGG
(ACC)	 AG	151709-151871	GT	AGG
(GGC)	 AG	152058-152144	GT	AGG
(GAT)	 AG	152305-152369	TA	GGT
-recovered pasa_asmbl_2713.p1, internal, 148527, 148664
-recovered pasa_asmbl_2713.p1, internal, 149153, 149230
-recovered pasa_asmbl_2713.p1, internal, 150066, 150176
-recovered pasa_asmbl_2713.p1, internal, 151709, 151871
-recovered pasa_asmbl_2713.p1, internal, 152058, 152144
Valid prediction for Augustus_model.g363.t1
Valid prediction for snap_scaffold_1-snap.557-T1
Valid prediction for GlimmerHMM_glimmerT_420-T1
Valid prediction for GlimmerHMM_glimmerT_426-T1
Valid prediction for pasa_asmbl_1618.p1
Valid prediction for Augustus_model.g361.t1
Valid prediction for GlimmerHMM_glimmerT_431-T1
Valid prediction for snap_scaffold_1-snap.556-T1
Valid prediction for snap_scaffold_1-snap.542-T1
Valid prediction for snap_scaffold_1-snap.521-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_424-T1
Valid prediction for pasa_asmbl_1626.p1
Valid prediction for Augustus_model.g356.t1
Valid prediction for GlimmerHMM_glimmerT_414-T1
Valid prediction for snap_scaffold_1-snap.539-T1
Valid prediction for pasa_asmbl_1611.p2
Valid prediction for GlimmerHMM_glimmerT_410-T1
Valid prediction for snap_scaffold_1-snap.541-T1
Valid prediction for pasa_asmbl_1624.p1
Valid prediction for CodingQuarry_transcript_2578-T1
Valid prediction for GlimmerHMM_glimmerT_433-T1
Valid prediction for GlimmerHMM_glimmerT_436-T1
Valid prediction for pasa_asmbl_1606.p1
Valid prediction for snap_scaffold_1-snap.530-T1
Valid prediction for snap_scaffold_1-snap.520-T1
Valid prediction for HiQ_model.g353.t1
Valid prediction for snap_scaffold_1-snap.544-T1
Valid prediction for CodingQuarry_transcript_2573-T1
Valid prediction for CodingQuarry_transcript_2579-T1
Valid prediction for snap_scaffold_1-snap.545-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 GlimmerHMM_glimmerT_439-T1
Valid prediction for Augustus_model.g360.t1
Valid prediction for Augustus_model.g340.t1
Valid prediction for GlimmerHMM_glimmerT_437-T1
Valid prediction for snap_scaffold_1-snap.548-T1
Couldn't classify 87885, 88009
Sorry, prediction pasa_asmbl_173.p1 fails validation.
(ATG)	 AA	86662-86737	GT	TGG
(AGA)	 AG	86912-86991	GT	AGG
(AAC)	 AG	87603-87690	GT	CAG
(ATG)	 AG	87885-88009	GA	AGG
-recovered pasa_asmbl_173.p1, initial, 86662, 86737
-recovered pasa_asmbl_173.p1, internal, 86912, 86991
-recovered pasa_asmbl_173.p1, internal, 87603, 87690
Valid prediction for Augustus_model.g364.t1
Valid prediction for snap_scaffold_1-snap.543-T1
Valid prediction for GlimmerHMM_glimmerT_432-T1
Valid prediction for snap_scaffold_1-snap.558-T1
Valid prediction for pasa_asmbl_168.p1
Valid prediction for snap_scaffold_1-snap.538-T1
Valid prediction for snap_scaffold_1-snap.533-T1
Valid prediction for GlimmerHMM_glimmerT_419-T1
Valid prediction for Augustus_model.g347.t1
Valid prediction for snap_scaffold_1-snap.532-T1
Valid prediction for snap_scaffold_1-snap.535-T1
Valid prediction for GlimmerHMM_glimmerT_430-T1
Valid prediction for pasa_asmbl_165.p2
Valid prediction for GlimmerHMM_glimmerT_435-T1
Valid prediction for GlimmerHMM_glimmerT_434-T1
Valid prediction for GlimmerHMM_glimmerT_438-T1
Couldn't classify 267899, 267940
Sorry, prediction pasa_asmbl_151.p1 fails validation.
(CAG)	 TA	267899-267940	GT	AGG
(GGA)	 AG	269633-269674	GT	CGG
(AAA)	 AG	270529-270612	GT	AAG
(AAA)	 AG	270743-270841	GT	AGG
(AAA)	 AG	271214-271291	GT	AGG
(AAA)	 AG	271770-271847	GT	AGG
(GAT)	 AG	272143-272247	GT	CGG
(GAG)	 AG	272395-272511	GT	AGG
(CCC)	 AG	272856-272951	GT	CGG
(CCT)	 AG	273115-273192	GT	AGG
(AAA)	 AG	273305-273397	GT	AGG
(GAT)	 AG	274053-274157	GT	CGG
(GAA)	 AG	274398-274514	GT	AGG
(CCA)	 AG	274985-275179	GT	AGG
(CTC)	 AG	275303-275407	GT	AGG
(GAG)	 AG	275578-275670	GT	AGG
(GCC)	 AG	276097-276135	GT	AGG
(AAA)	 AG	276324-276452	GT	AGG
(ACT)	 AG	276581-276667	GT	AGG
(GGC)	 AG	277036-277065	GT	AAG
(AAA)	 AG	277246-277344	AC	AGA
-recovered pasa_asmbl_151.p1, terminal, 277246, 277344
-recovered pasa_asmbl_151.p1, internal, 269633, 269674
-recovered pasa_asmbl_151.p1, internal, 270529, 270612
-recovered pasa_asmbl_151.p1, internal, 270743, 270841
-recovered pasa_asmbl_151.p1, internal, 271214, 271291
-recovered pasa_asmbl_151.p1, internal, 271770, 271847
-recovered pasa_asmbl_151.p1, internal, 272143, 272247
-recovered pasa_asmbl_151.p1, internal, 272395, 272511
-recovered pasa_asmbl_151.p1, internal, 272856, 272951
-recovered pasa_asmbl_151.p1, internal, 273115, 273192
-recovered pasa_asmbl_151.p1, internal, 273305, 273397
-recovered pasa_asmbl_151.p1, internal, 274053, 274157
-recovered pasa_asmbl_151.p1, internal, 274398, 274514
-recovered pasa_asmbl_151.p1, internal, 274985, 275179
-recovered pasa_asmbl_151.p1, internal, 275303, 275407
-recovered pasa_asmbl_151.p1, internal, 275578, 275670
-recovered pasa_asmbl_151.p1, internal, 276097, 276135
-recovered pasa_asmbl_151.p1, internal, 276324, 276452
-recovered pasa_asmbl_151.p1, internal, 276581, 276667
-recovered pasa_asmbl_151.p1, internal, 277036, 277065
Valid prediction for Augustus_model.g342.t1
Valid prediction for snap_scaffold_1-snap.531-T1
Valid prediction for snap_scaffold_1-snap.537-T1
Valid prediction for snap_scaffold_1-snap.554-T1
Valid prediction for pasa_asmbl_163.p1
Valid prediction for HiQ_model.g357.t1
Valid prediction for Augustus_model.g346.t1
Valid prediction for snap_scaffold_1-snap.559-T1
Valid prediction for HiQ_model.g354.t1
Valid prediction for GlimmerHMM_glimmerT_418-T1
Valid prediction for GlimmerHMM_glimmerT_428-T1
Valid prediction for snap_scaffold_1-snap.519-T1
Valid prediction for snap_scaffold_1-snap.551-T1
Valid prediction for HiQ_model.g358.t1
Valid prediction for CodingQuarry_transcript_2577-T1
Valid prediction for CodingQuarry_transcript_2571-T1
Valid prediction for snap_scaffold_1-snap.546-T1
Valid prediction for Augustus_model.g365.t1
Valid prediction for GlimmerHMM_glimmerT_421-T1
Valid prediction for GlimmerHMM_glimmerT_411-T1
Valid prediction for snap_scaffold_1-snap.553-T1
Couldn't classify 100352, 100539
Sorry, prediction pasa_asmbl_1263.p1 fails validation.
(ATG)	 CT	95849-96011	GT	TGG
(GTA)	 AG	97000-97239	GT	AGG
(GCT)	 AG	98477-98566	GT	AGG
(ACC)	 AG	100352-100539	GG	GTG
-recovered pasa_asmbl_1263.p1, initial, 95849, 96011
-recovered pasa_asmbl_1263.p1, terminal, 98477, 98566
-recovered pasa_asmbl_1263.p1, internal, 97000, 97239
-recovered pasa_asmbl_1263.p1, internal, 98477, 98566
Valid prediction for CodingQuarry_transcript_2566-T1
Valid prediction for snap_scaffold_1-snap.518-T1
Valid prediction for CodingQuarry_transcript_2569-T1
Valid prediction for HiQ_model.g349.t1
Valid prediction for snap_scaffold_1-snap.534-T1
Valid prediction for GlimmerHMM_glimmerT_409-T1
Valid prediction for snap_scaffold_1-snap.555-T1
Valid prediction for snap_scaffold_1-snap.525-T1
Valid prediction for snap_scaffold_1-snap.547-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 207301, rend_intergenic: 204846  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 242440, rend_intergenic: 240025  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 260369, rend_intergenic: 257625  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 282743
-exon list size: 433


building trellis

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91.7    
92.0    
92.2    
92.4    
92.6    
92.9    
93.1    
93.3    
93.6    
93.8    
94.0    
94.3    
94.5    
94.7    
94.9    
95.2    
95.4    
95.6    
95.9    
96.1    
96.3    
96.6    
96.8    
97.0    
97.2    
97.5    
97.7    
97.9    
98.2    
98.4    
98.6    
98.9    
99.1    
99.3    
99.5    
99.8    
-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 207301, rend_intergenic: 204846  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 242440, rend_intergenic: 240025  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 260369, rend_intergenic: 257625  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 29 predictions persist after filtering for low support