-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_20/scaffold_20_2567069-2818436

-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_45620-T1
Valid prediction for GlimmerHMM_glimmerT_45631-T1
Valid prediction for Augustus_model.g30321.t1
Valid prediction for GlimmerHMM_glimmerT_45636-T1
Valid prediction for snap_scaffold_20-snap.549-T1
Valid prediction for HiQ_model.g30319.t1
Valid prediction for snap_scaffold_20-snap.551-T1
Valid prediction for Augustus_model.g30314.t1
Valid prediction for snap_scaffold_20-snap.587-T1
Couldn't classify 113736, 113918
Couldn't classify 114724, 114833
Sorry, prediction pasa_asmbl_27141.p1 fails validation.
(GCC)	 CA	113736-113918	GT	GGG
(GTG)	 AG	114197-114320	GT	GGG
(AGA)	 AG	114724-114833	GA	TGG
-recovered pasa_asmbl_27141.p1, internal, 114197, 114320
Valid prediction for pasa_asmbl_26507.p2
Valid prediction for GlimmerHMM_glimmerT_45642-T1
Valid prediction for Augustus_model.g30320.t1
Valid prediction for GlimmerHMM_glimmerT_45641-T1
Valid prediction for snap_scaffold_20-snap.561-T1
Valid prediction for GlimmerHMM_glimmerT_45615-T1
Valid prediction for GlimmerHMM_glimmerT_45625-T1
Valid prediction for Augustus_model.g30310.t1
Valid prediction for GlimmerHMM_glimmerT_45630-T1
Valid prediction for snap_scaffold_20-snap.576-T1
Valid prediction for snap_scaffold_20-snap.555-T1
Valid prediction for GlimmerHMM_glimmerT_45623-T1
Valid prediction for HiQ_model.g30324.t1
Valid prediction for snap_scaffold_20-snap.575-T1
Valid prediction for snap_scaffold_20-snap.554-T1
Couldn't classify 135414, 135640
Couldn't classify 136473, 136611
Sorry, prediction pasa_asmbl_26499.p1 fails validation.
(AGA)	 CC	135414-135640	GT	AGG
(GTT)	 AG	135794-136003	GT	AGG
(TCA)	 AG	136473-136611	AT	CCA
-recovered pasa_asmbl_26499.p1, internal, 135794, 136003
Valid prediction for snap_scaffold_20-snap.571-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_45640-T1
Valid prediction for snap_scaffold_20-snap.567-T1
Valid prediction for GlimmerHMM_glimmerT_45639-T1
Valid prediction for GlimmerHMM_glimmerT_45638-T1
Valid prediction for GlimmerHMM_glimmerT_45646-T1
Valid prediction for snap_scaffold_20-snap.586-T1
Valid prediction for GlimmerHMM_glimmerT_45645-T1
Couldn't classify 137163, 137314
Couldn't classify 137907, 138032
Sorry, prediction pasa_asmbl_26500.p1 fails validation.
(CTG)	 AC	137163-137314	GT	AGG
(CTG)	 AG	137535-137631	GT	AGG
(ATG)	 AG	137907-138032	GG	GGG
-recovered pasa_asmbl_26500.p1, internal, 137535, 137631
Valid prediction for snap_scaffold_20-snap.565-T1
Valid prediction for snap_scaffold_20-snap.563-T1
Couldn't classify 57210, 57379
Couldn't classify 59269, 59440
Sorry, prediction pasa_asmbl_26495.p1 fails validation.
(CAG)	 TG	57210-57379	GT	AGG
(GCT)	 AG	57514-57715	GT	AGG
(GCT)	 AG	57931-58050	GT	AGG
(GAG)	 AG	58269-58354	GT	AAG
(GTA)	 AG	58563-58724	GT	AGG
(AGA)	 AG	59269-59440	CT	CCC
-recovered pasa_asmbl_26495.p1, internal, 57514, 57715
-recovered pasa_asmbl_26495.p1, internal, 57931, 58050
-recovered pasa_asmbl_26495.p1, internal, 58269, 58354
-recovered pasa_asmbl_26495.p1, internal, 58563, 58724
Couldn't classify 87271, 87597
Sorry, prediction pasa_asmbl_25665.p1 fails validation.
(GGC)	 GG	87271-87597	CT	AAC
Valid prediction for Augustus_model.g30317.t1
Valid prediction for CodingQuarry_transcript_30463-T1
Valid prediction for GlimmerHMM_glimmerT_45628-T1
Valid prediction for pasa_asmbl_26497.p2
Valid prediction for snap_scaffold_20-snap.556-T1
Valid prediction for snap_scaffold_20-snap.559-T1
Valid prediction for Augustus_model.g30318.t1
Valid prediction for snap_scaffold_20-snap.585-T1
Valid prediction for snap_scaffold_20-snap.584-T1
Valid prediction for snap_scaffold_20-snap.589-T1
Valid prediction for snap_scaffold_20-snap.568-T1
Valid prediction for Augustus_model.g30315.t1
Valid prediction for Augustus_model.g30307.t1
Valid prediction for Augustus_model.g30313.t1
Valid prediction for snap_scaffold_20-snap.547-T1
Valid prediction for Augustus_model.g30323.t1
Valid prediction for GlimmerHMM_glimmerT_45637-T1
Valid prediction for Augustus_model.g30305.t1
Valid prediction for GlimmerHMM_glimmerT_45624-T1
Valid prediction for snap_scaffold_20-snap.580-T1
Valid prediction for snap_scaffold_20-snap.590-T1
Valid prediction for HiQ_model.g30312.t1
Valid prediction for Augustus_model.g30309.t1
Valid prediction for snap_scaffold_20-snap.550-T1
Valid prediction for GlimmerHMM_glimmerT_45632-T1
Valid prediction for snap_scaffold_20-snap.564-T1
Valid prediction for snap_scaffold_20-snap.577-T1
Valid prediction for GlimmerHMM_glimmerT_45616-T1
Valid prediction for snap_scaffold_20-snap.581-T1
Couldn't classify 103906, 103995
Couldn't classify 104553, 104658
Sorry, prediction CodingQuarry_transcript_30462-T1 fails validation.
(ATG)	 TG	103514-103516	GT	TGG
(AGG)	 AG	103906-103995	AG	GAA
(CTC)	 TC	104553-104658	GT	AGG
(TGT)	 AG	105931-105967	GT	GGG
(GGG)	 AG	106177-106254	GT	ACG
(GTG)	 AG	106583-106685	GT	AGG
(GGT)	 AG	107877-107989	GT	GGG
(GCG)	 AG	109872-110022	GA	AGG
-recovered CodingQuarry_transcript_30462-T1, initial, 103514, 103516
-recovered CodingQuarry_transcript_30462-T1, terminal, 109872, 110022
-recovered CodingQuarry_transcript_30462-T1, internal, 105931, 105967
-recovered CodingQuarry_transcript_30462-T1, internal, 106177, 106254
-recovered CodingQuarry_transcript_30462-T1, internal, 106583, 106685
-recovered CodingQuarry_transcript_30462-T1, internal, 107877, 107989
Valid prediction for snap_scaffold_20-snap.579-T1
Valid prediction for CodingQuarry_transcript_30461-T1
Valid prediction for snap_scaffold_20-snap.560-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_20-snap.572-T1
Couldn't classify 52873, 52963
Sorry, prediction pasa_asmbl_25670.p2 fails validation.
(AAC)	 AA	52873-52963	GT	AGG
(CTG)	 AG	55265-55333	GT	AGG
(TGG)	 AG	55577-55653	GT	AGG
(GTG)	 AG	58488-58543	GT	AAG
(GTT)	 AG	59326-59435	GT	CGG
(AGT)	 AG	60226-60251	AG	AGA
-recovered pasa_asmbl_25670.p2, terminal, 60226, 60251
-recovered pasa_asmbl_25670.p2, internal, 55265, 55333
-recovered pasa_asmbl_25670.p2, internal, 55577, 55653
-recovered pasa_asmbl_25670.p2, internal, 58488, 58543
-recovered pasa_asmbl_25670.p2, internal, 59326, 59435
Couldn't classify 173083, 173202
Couldn't classify 173548, 173739
Sorry, prediction pasa_asmbl_25662.p1 fails validation.
(CAG)	 TG	173083-173202	GT	AGG
(AGC)	 AG	173548-173739	GC	ACG
-recovered pasa_asmbl_25662.p1, internal, 173548, 173739
Valid prediction for snap_scaffold_20-snap.574-T1
Valid prediction for GlimmerHMM_glimmerT_45622-T1
Valid prediction for Augustus_model.g30308.t1
Couldn't classify 105044, 105126
Sorry, prediction pasa_asmbl_25667.p1 fails validation.
(GAC)	 AG	105044-105126	GT	AAG
(GAT)	 AG	105281-105444	GT	CGG
(GTA)	 AG	105685-105835	GT	AGG
(GGT)	 AG	106146-106282	GT	AGG
(AGC)	 AG	106972-107126	GT	AGG
(GGG)	 AG	107451-107502	GT	AGG
(GTA)	 AG	108002-108117	GT	GTG
(TGT)	 AG	109273-109346	GT	AGG
(ACT)	 AG	109641-109785	GG	GAG
-recovered pasa_asmbl_25667.p1, terminal, 109641, 109785
-recovered pasa_asmbl_25667.p1, internal, 105044, 105126
-recovered pasa_asmbl_25667.p1, internal, 105281, 105444
-recovered pasa_asmbl_25667.p1, internal, 105685, 105835
-recovered pasa_asmbl_25667.p1, internal, 106146, 106282
-recovered pasa_asmbl_25667.p1, internal, 106972, 107126
-recovered pasa_asmbl_25667.p1, internal, 107451, 107502
-recovered pasa_asmbl_25667.p1, internal, 108002, 108117
-recovered pasa_asmbl_25667.p1, internal, 109273, 109346
Valid prediction for GlimmerHMM_glimmerT_45619-T1
Couldn't classify 174181, 174352
Sorry, prediction pasa_asmbl_25660.p1 fails validation.
(AGG)	 GG	174181-174352	GT	CGG
(AGG)	 AG	175943-176110	GT	GGG
(GTA)	 AG	176517-176706	GT	AGG
(AGC)	 AG	178363-178436	GT	TGG
(ATA)	 AG	180491-180619	GT	TGG
(GCC)	 AG	181114-181226	AC	AAA
-recovered pasa_asmbl_25660.p1, terminal, 181114, 181226
-recovered pasa_asmbl_25660.p1, internal, 175943, 176110
-recovered pasa_asmbl_25660.p1, internal, 176517, 176706
-recovered pasa_asmbl_25660.p1, internal, 178363, 178436
-recovered pasa_asmbl_25660.p1, internal, 180491, 180619
Valid prediction for GlimmerHMM_glimmerT_45643-T1
Valid prediction for snap_scaffold_20-snap.553-T1
Couldn't classify 235384, 235497
Couldn't classify 236945, 237111
Sorry, prediction pasa_asmbl_26236.p1 fails validation.
(GAG)	 TA	235384-235497	GT	AGG
(AAA)	 AG	235608-235712	GT	AGG
(AGG)	 AG	236173-236323	GT	CAG
(ACG)	 AG	236945-237111	TA	GGT
-recovered pasa_asmbl_26236.p1, internal, 235608, 235712
-recovered pasa_asmbl_26236.p1, internal, 236173, 236323
Valid prediction for GlimmerHMM_glimmerT_45644-T1
Valid prediction for pasa_asmbl_25654.p1
Valid prediction for snap_scaffold_20-snap.557-T1
Valid prediction for CodingQuarry_transcript_30459-T1
Valid prediction for snap_scaffold_20-snap.548-T1
Valid prediction for GlimmerHMM_glimmerT_45629-T1
Valid prediction for snap_scaffold_20-snap.578-T1
Valid prediction for snap_scaffold_20-snap.594-T1
Valid prediction for snap_scaffold_20-snap.588-T1
Valid prediction for snap_scaffold_20-snap.562-T1
Valid prediction for snap_scaffold_20-snap.569-T1
Valid prediction for GlimmerHMM_glimmerT_45617-T1
Valid prediction for GlimmerHMM_glimmerT_45621-T1
Couldn't classify 203589, 203820
Couldn't classify 204779, 205080
Sorry, prediction pasa_asmbl_25652.p1 fails validation.
(CAG)	 TC	203589-203820	GT	CGG
(GAA)	 AG	204214-204270	GT	AGG
(TGG)	 AG	204779-205080	GC	AAG
-recovered pasa_asmbl_25652.p1, internal, 204214, 204270
-recovered pasa_asmbl_25652.p1, internal, 204779, 205080
Valid prediction for CodingQuarry_transcript_30464-T1
Valid prediction for snap_scaffold_20-snap.582-T1
Valid prediction for snap_scaffold_20-snap.570-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for snap_scaffold_20-snap.552-T1
Valid prediction for Augustus_model.g30316.t1
Valid prediction for snap_scaffold_20-snap.591-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for snap_scaffold_20-snap.566-T1
Valid prediction for Augustus_model.g30306.t1
Valid prediction for Augustus_model.g30322.t1
Valid prediction for GlimmerHMM_glimmerT_45634-T1
Valid prediction for Augustus_model.g30311.t1
Valid prediction for GlimmerHMM_glimmerT_45633-T1
Valid prediction for GlimmerHMM_glimmerT_45618-T1
Valid prediction for GlimmerHMM_glimmerT_45635-T1
Valid prediction for GlimmerHMM_glimmerT_45627-T1
Valid prediction for snap_scaffold_20-snap.593-T1
Valid prediction for snap_scaffold_20-snap.583-T1
Valid prediction for snap_scaffold_20-snap.558-T1
Couldn't classify 238746, 239225
Sorry, prediction pasa_asmbl_25649.p1 fails validation.
(CAT)	 TT	238746-239225	AG	GAA
Valid prediction for GlimmerHMM_glimmerT_45626-T1
Valid prediction for snap_scaffold_20-snap.573-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6200, rend_intergenic: 2379  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11365, rend_intergenic: 6284  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17939, rend_intergenic: 12686  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27099, rend_intergenic: 19322  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52136, rend_intergenic: 48566  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59485, rend_intergenic: 56303  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63502, rend_intergenic: 59957  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73045, rend_intergenic: 69170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81209, rend_intergenic: 74149  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104396, rend_intergenic: 95131  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146403, rend_intergenic: 104399  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152974, rend_intergenic: 146991  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159422, rend_intergenic: 155159  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182974, rend_intergenic: 168646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 205278, rend_intergenic: 184512  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 208436, rend_intergenic: 206939  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 232511, rend_intergenic: 209827  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 235572, rend_intergenic: 233198  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 251368
-exon list size: 459


building trellis

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88.7    
88.9    
89.2    
89.4    
89.6    
89.8    
90.0    
90.2    
90.5    
90.7    
90.9    
91.1    
91.3    
91.5    
91.8    
92.0    
92.2    
92.4    
92.6    
92.8    
93.1    
93.3    
93.5    
93.7    
93.9    
94.1    
94.4    
94.6    
94.8    
95.0    
95.2    
95.4    
95.7    
95.9    
96.1    
96.3    
96.5    
96.7    
97.0    
97.2    
97.4    
97.6    
97.8    
98.0    
98.3    
98.5    
98.7    
98.9    
99.1    
99.3    
99.6    
99.8    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 6200, rend_intergenic: 2379  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11365, rend_intergenic: 6284  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17939, rend_intergenic: 12686  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27099, rend_intergenic: 19322  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52136, rend_intergenic: 48566  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59485, rend_intergenic: 56303  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63502, rend_intergenic: 59957  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73045, rend_intergenic: 69170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81209, rend_intergenic: 74149  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104396, rend_intergenic: 95131  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146403, rend_intergenic: 104399  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152974, rend_intergenic: 146991  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159422, rend_intergenic: 155159  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182974, rend_intergenic: 168646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 205278, rend_intergenic: 184512  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 208436, rend_intergenic: 206939  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 232511, rend_intergenic: 209827  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 235572, rend_intergenic: 233198  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 239592 - 251368
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-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 240305 - 251368
-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