-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_13353585-13605640

-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 Augustus_model.g12400.t1
Valid prediction for Augustus_model.g12395.t1
Valid prediction for Augustus_model.g12406.t1
Valid prediction for Augustus_model.g12410.t1
Valid prediction for CodingQuarry_transcript_57704-T1
Valid prediction for snap_scaffold_7-snap.2538-T1
Valid prediction for GlimmerHMM_glimmerT_18415-T1
Valid prediction for GlimmerHMM_glimmerT_18413-T1
Valid prediction for Augustus_model.g12398.t1
Valid prediction for GlimmerHMM_glimmerT_18401-T1
Valid prediction for GlimmerHMM_glimmerT_18410-T1
Valid prediction for GlimmerHMM_glimmerT_18395-T1
Valid prediction for GlimmerHMM_glimmerT_18400-T1
Valid prediction for snap_scaffold_7-snap.2513-T1
Valid prediction for Augustus_model.g12396.t1
Valid prediction for Augustus_model.g12393.t1
Valid prediction for HiQ_model.g12409.t1
Valid prediction for GlimmerHMM_glimmerT_18412-T1
Valid prediction for snap_scaffold_7-snap.2525-T1
Valid prediction for snap_scaffold_7-snap.2510-T1
Valid prediction for Augustus_model.g12405.t1
Couldn't classify 115151, 115191
Couldn't classify 122323, 122374
Sorry, prediction pasa_asmbl_50344.p1 fails validation.
(ACG)	 CT	115151-115191	GT	TGG
(GAT)	 AG	115485-115616	GT	AGG
(GGC)	 AG	115713-115775	GT	TGG
(GAC)	 AG	115894-115975	GT	AGG
(CAC)	 AG	116082-116198	GT	AGG
(TCT)	 AG	117182-117260	GT	CTG
(TTG)	 AG	117636-117694	GT	CTG
(GAC)	 AG	119444-119496	GT	AAG
(GAG)	 AG	120156-120194	GT	AGG
(CAA)	 AG	122323-122374	GT	AGG
-recovered pasa_asmbl_50344.p1, internal, 115485, 115616
-recovered pasa_asmbl_50344.p1, internal, 115713, 115775
-recovered pasa_asmbl_50344.p1, internal, 115894, 115975
-recovered pasa_asmbl_50344.p1, internal, 116082, 116198
-recovered pasa_asmbl_50344.p1, internal, 117182, 117260
-recovered pasa_asmbl_50344.p1, internal, 117636, 117694
-recovered pasa_asmbl_50344.p1, internal, 119444, 119496
-recovered pasa_asmbl_50344.p1, internal, 120156, 120194
-recovered pasa_asmbl_50344.p1, internal, 122323, 122374
Valid prediction for GlimmerHMM_glimmerT_18388-T1
Valid prediction for snap_scaffold_7-snap.2541-T1
Valid prediction for GlimmerHMM_glimmerT_18394-T1
Valid prediction for GlimmerHMM_glimmerT_18405-T1
Valid prediction for snap_scaffold_7-snap.2527-T1
Valid prediction for pasa_asmbl_50358.p1
Valid prediction for snap_scaffold_7-snap.2508-T1
Valid prediction for pasa_asmbl_50364.p1
Valid prediction for GlimmerHMM_glimmerT_18406-T1
Valid prediction for CodingQuarry_transcript_57703-T1
Valid prediction for GlimmerHMM_glimmerT_18398-T1
Couldn't classify 100608, 100671
Sorry, prediction pasa_asmbl_50341.p1 fails validation.
(AGA)	 CC	100608-100671	GT	GGG
(AGC)	 AG	100821-100941	GT	AGG
(GGT)	 AG	101036-101330	TG	AAT
-recovered pasa_asmbl_50341.p1, terminal, 101036, 101330
-recovered pasa_asmbl_50341.p1, internal, 100821, 100941
Valid prediction for Augustus_model.g12403.t1
Valid prediction for Augustus_model.g12407.t1
Couldn't classify 111800, 111848
Couldn't classify 114894, 114917
Sorry, prediction pasa_asmbl_50343.p1 fails validation.
(GTC)	 AT	111800-111848	GT	TGG
(GGG)	 AG	114076-114166	GT	AGG
(GAG)	 AG	114294-114358	GT	CGG
(TAA)	 AG	114572-114627	GT	AGG
(GGT)	 AG	114750-114797	GT	AGG
(GGG)	 AG	114894-114917	AA	ACA
-recovered pasa_asmbl_50343.p1, internal, 114076, 114166
-recovered pasa_asmbl_50343.p1, internal, 114294, 114358
-recovered pasa_asmbl_50343.p1, internal, 114572, 114627
-recovered pasa_asmbl_50343.p1, internal, 114750, 114797
Valid prediction for GlimmerHMM_glimmerT_18407-T1
Couldn't classify 123455, 123559
Couldn't classify 125193, 125347
Sorry, prediction pasa_asmbl_50346.p1 fails validation.
(GGA)	 CA	123455-123559	GT	CGG
(AAG)	 AG	123767-123808	GT	ATG
(ATG)	 AG	124227-124311	GT	AGG
(ACC)	 AG	124546-124625	GT	AGG
(CTC)	 AG	124863-124923	GT	TGG
(GGA)	 AG	125193-125347	GG	AAG
-recovered pasa_asmbl_50346.p1, initial, 124227, 124311
-recovered pasa_asmbl_50346.p1, internal, 123767, 123808
-recovered pasa_asmbl_50346.p1, internal, 124227, 124311
-recovered pasa_asmbl_50346.p1, internal, 124546, 124625
-recovered pasa_asmbl_50346.p1, internal, 124863, 124923
Valid prediction for snap_scaffold_7-snap.2533-T1
Valid prediction for CodingQuarry_transcript_57701-T1
Valid prediction for pasa_asmbl_50349.p1
Valid prediction for snap_scaffold_7-snap.2535-T1
Valid prediction for GlimmerHMM_glimmerT_18387-T1
Valid prediction for snap_scaffold_7-snap.2517-T1
Couldn't classify 147176, 147327
Sorry, prediction pasa_asmbl_50348.p1 fails validation.
(ATG)	 AT	142085-142271	GT	AGG
(GTT)	 AG	142526-142680	GT	AGG
(GTG)	 AG	143812-144018	GT	AGG
(GGC)	 AG	144597-144678	GT	TGG
(GCG)	 AG	147176-147327	TC	GGT
-recovered pasa_asmbl_50348.p1, initial, 142085, 142271
-recovered pasa_asmbl_50348.p1, internal, 142526, 142680
-recovered pasa_asmbl_50348.p1, internal, 143812, 144018
-recovered pasa_asmbl_50348.p1, internal, 144597, 144678
Valid prediction for GlimmerHMM_glimmerT_18393-T1
Valid prediction for GlimmerHMM_glimmerT_18409-T1
Valid prediction for snap_scaffold_7-snap.2540-T1
Couldn't classify 125819, 125975
Sorry, prediction pasa_asmbl_50347.p1 fails validation.
(CTG)	 CT	125819-125975	GT	CGG
(ACA)	 AG	126083-126151	GT	CCG
(GGT)	 AG	126255-126347	GT	AGG
(TGT)	 AG	126447-126517	GT	AGG
(ATC)	 AG	126634-126689	GT	AGG
(GGT)	 AG	127585-127672	GC	GAG
add_exon() Sorry, pasa_asmbl_50347.p1 126255-126347-terminal-1 is invalid.
-recovered pasa_asmbl_50347.p1, terminal, 126255, 126347
-recovered pasa_asmbl_50347.p1, terminal, 127585, 127672
-recovered pasa_asmbl_50347.p1, internal, 126083, 126151
-recovered pasa_asmbl_50347.p1, internal, 126255, 126347
-recovered pasa_asmbl_50347.p1, internal, 126447, 126517
-recovered pasa_asmbl_50347.p1, internal, 126634, 126689
-recovered pasa_asmbl_50347.p1, internal, 127585, 127672
Valid prediction for snap_scaffold_7-snap.2531-T1
Valid prediction for snap_scaffold_7-snap.2543-T1
Valid prediction for Augustus_model.g12394.t1
Valid prediction for GlimmerHMM_glimmerT_18402-T1
Valid prediction for snap_scaffold_7-snap.2522-T1
Valid prediction for CodingQuarry_transcript_57700-T1
Valid prediction for Augustus_model.g12404.t1
Valid prediction for Augustus_model.g12391.t1
Valid prediction for snap_scaffold_7-snap.2536-T1
Valid prediction for snap_scaffold_7-snap.2534-T1
Valid prediction for snap_scaffold_7-snap.2523-T1
Couldn't classify 98834, 98888
Couldn't classify 99013, 99443
Sorry, prediction pasa_asmbl_50340.p1 fails validation.
(CGA)	 AA	98834-98888	GT	AGG
(CCA)	 AG	99013-99443	CT	GGC
Valid prediction for snap_scaffold_7-snap.2520-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_7-snap.2526-T1
Valid prediction for snap_scaffold_7-snap.2516-T1
Valid prediction for snap_scaffold_7-snap.2539-T1
Valid prediction for pasa_asmbl_51311.p1
Valid prediction for snap_scaffold_7-snap.2524-T1
Valid prediction for snap_scaffold_7-snap.2514-T1
Valid prediction for GlimmerHMM_glimmerT_18384-T1
Valid prediction for snap_scaffold_7-snap.2512-T1
Valid prediction for GlimmerHMM_glimmerT_18386-T1
Valid prediction for GlimmerHMM_glimmerT_18389-T1
Couldn't classify 120541, 120888
Sorry, prediction pasa_asmbl_51306.p1 fails validation.
(TAC)	 CC	120541-120888	GT	AGG
(GAA)	 AG	121047-121189	GT	AAG
(GTC)	 AG	121615-121726	TT	GAT
-recovered pasa_asmbl_51306.p1, terminal, 121615, 121726
-recovered pasa_asmbl_51306.p1, internal, 121047, 121189
Valid prediction for GlimmerHMM_glimmerT_18408-T1
Valid prediction for GlimmerHMM_glimmerT_18382-T1
Valid prediction for snap_scaffold_7-snap.2544-T1
Valid prediction for snap_scaffold_7-snap.2518-T1
Valid prediction for GlimmerHMM_glimmerT_18385-T1
Valid prediction for GlimmerHMM_glimmerT_18390-T1
Valid prediction for snap_scaffold_7-snap.2532-T1
Valid prediction for GlimmerHMM_glimmerT_18414-T1
Valid prediction for CodingQuarry_transcript_57696-T1
Valid prediction for CodingQuarry_transcript_57699-T1
Valid prediction for snap_scaffold_7-snap.2511-T1
Valid prediction for GlimmerHMM_glimmerT_18396-T1
Valid prediction for GlimmerHMM_glimmerT_18383-T1
Valid prediction for GlimmerHMM_glimmerT_18403-T1
Valid prediction for GlimmerHMM_glimmerT_18411-T1
Valid prediction for snap_scaffold_7-snap.2509-T1
Valid prediction for GlimmerHMM_glimmerT_18381-T1
Valid prediction for snap_scaffold_7-snap.2521-T1
Valid prediction for GlimmerHMM_glimmerT_18391-T1
Valid prediction for Augustus_model.g12392.t1
Valid prediction for HiQ_model.g12397.t1
Valid prediction for snap_scaffold_7-snap.2507-T1
Valid prediction for pasa_asmbl_51516.p1
Valid prediction for snap_scaffold_7-snap.2537-T1
Valid prediction for GlimmerHMM_glimmerT_18392-T1
Valid prediction for Augustus_model.g12411.t1
Valid prediction for snap_scaffold_7-snap.2528-T1
Valid prediction for Augustus_model.g12401.t1
Valid prediction for snap_scaffold_7-snap.2529-T1
Valid prediction for GlimmerHMM_glimmerT_18379-T1
Valid prediction for snap_scaffold_7-snap.2519-T1
Valid prediction for snap_scaffold_7-snap.2530-T1
Valid prediction for GlimmerHMM_glimmerT_18399-T1
Valid prediction for Augustus_model.g12402.t1
Valid prediction for Augustus_model.g12399.t1
Couldn't classify 115846, 115893
Couldn't classify 117120, 117247
Sorry, prediction pasa_asmbl_51308.p1 fails validation.
(GTG)	 AT	115846-115893	GT	AGG
(GAG)	 AG	116019-116140	GT	AGG
(GAA)	 AG	116308-116429	GT	GAG
(CCT)	 AG	116618-116746	GT	CAG
(GTA)	 AG	117120-117247	TA	GGT
-recovered pasa_asmbl_51308.p1, internal, 116019, 116140
-recovered pasa_asmbl_51308.p1, internal, 116308, 116429
-recovered pasa_asmbl_51308.p1, internal, 116618, 116746
Valid prediction for GlimmerHMM_glimmerT_18397-T1
Valid prediction for GlimmerHMM_glimmerT_18404-T1
Couldn't classify 166100, 166417
Sorry, prediction pasa_asmbl_50339.p2 fails validation.
(GTG)	 CT	166100-166417	GA	GAG
Valid prediction for GlimmerHMM_glimmerT_18380-T1
Valid prediction for CodingQuarry_transcript_57702-T1
Valid prediction for CodingQuarry_transcript_57698-T1
Valid prediction for HiQ_model.g12408.t1
Valid prediction for snap_scaffold_7-snap.2515-T1
Valid prediction for snap_scaffold_7-snap.2542-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 182851, rend_intergenic: 182848  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 7735, rend_intergenic: 3600  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27737, rend_intergenic: 7739  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31579, rend_intergenic: 28546  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34924, rend_intergenic: 31668  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62006, rend_intergenic: 41487  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71906, rend_intergenic: 65645  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79814, rend_intergenic: 72020  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84646, rend_intergenic: 81574  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87931, rend_intergenic: 85936  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95061, rend_intergenic: 90681  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110259, rend_intergenic: 107454  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115779, rend_intergenic: 113686  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116231, rend_intergenic: 115922  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127672, rend_intergenic: 116285  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137871, rend_intergenic: 131859  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192733, rend_intergenic: 189495  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193071, rend_intergenic: 192796  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 252056
-exon list size: 467


building trellis

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95.9    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.4    
99.6    
99.8    
-found 39 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 182851, rend_intergenic: 182848  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 7735, rend_intergenic: 3600  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27737, rend_intergenic: 7739  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31579, rend_intergenic: 28546  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34924, rend_intergenic: 31668  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62006, rend_intergenic: 41487  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71906, rend_intergenic: 65645  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79814, rend_intergenic: 72020  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84646, rend_intergenic: 81574  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87931, rend_intergenic: 85936  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95061, rend_intergenic: 90681  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110259, rend_intergenic: 107454  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115779, rend_intergenic: 113686  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116231, rend_intergenic: 115922  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127672, rend_intergenic: 116285  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137871, rend_intergenic: 131859  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192733, rend_intergenic: 189495  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193071, rend_intergenic: 192796  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 26 predictions persist after filtering for low support