-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_9/scaffold_9_12705293-12963061

-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_9-snap.2532-T1
Valid prediction for snap_scaffold_9-snap.2520-T1
Valid prediction for GlimmerHMM_glimmerT_23108-T1
Valid prediction for GlimmerHMM_glimmerT_23118-T1
Couldn't classify 98960, 99493
Sorry, prediction pasa_asmbl_54466.p1 fails validation.
(ATG)	 TA	98960-99493	AG	TCA
Valid prediction for snap_scaffold_9-snap.2527-T1
Couldn't classify 123378, 123435
Sorry, prediction pasa_asmbl_54472.p1 fails validation.
(CGT)	 TC	123378-123435	GT	AGG
(AGC)	 AG	123581-123721	GT	CGG
(GCA)	 AG	123820-123918	GT	TGG
(GGA)	 AG	124025-124111	GT	GAG
(GTC)	 AG	124224-124393	GG	GAG
-recovered pasa_asmbl_54472.p1, terminal, 124224, 124393
-recovered pasa_asmbl_54472.p1, internal, 123581, 123721
-recovered pasa_asmbl_54472.p1, internal, 123820, 123918
-recovered pasa_asmbl_54472.p1, internal, 124025, 124111
Valid prediction for snap_scaffold_9-snap.2535-T1
Valid prediction for snap_scaffold_9-snap.2551-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_23111-T1
Valid prediction for GlimmerHMM_glimmerT_23104-T1
Valid prediction for GlimmerHMM_glimmerT_23093-T1
Valid prediction for snap_scaffold_9-snap.2524-T1
Valid prediction for snap_scaffold_9-snap.2553-T1
Valid prediction for GlimmerHMM_glimmerT_23089-T1
Valid prediction for snap_scaffold_9-snap.2514-T1
Valid prediction for Augustus_model.g15404.t1
Valid prediction for snap_scaffold_9-snap.2550-T1
Valid prediction for GlimmerHMM_glimmerT_23087-T1
Valid prediction for Augustus_model.g15413.t1
Valid prediction for pasa_asmbl_54476.p2
Valid prediction for GlimmerHMM_glimmerT_23103-T1
Valid prediction for Augustus_model.g15409.t1
Valid prediction for snap_scaffold_9-snap.2538-T1
Valid prediction for Augustus_model.g15405.t1
Valid prediction for GlimmerHMM_glimmerT_23090-T1
Valid prediction for GlimmerHMM_glimmerT_23105-T1
Valid prediction for pasa_asmbl_54470.p1
Valid prediction for GlimmerHMM_glimmerT_23095-T1
Valid prediction for snap_scaffold_9-snap.2557-T1
Couldn't classify 2509, 3204
Sorry, prediction pasa_asmbl_54463.p1 fails validation.
(GCT)	 CT	2509-3204	GT	AGG
(GTG)	 AG	3307-3858	GT	AGG
(AAA)	 AG	6379-6517	GT	AGG
(GAC)	 AG	8974-9051	GT	GGG
(ACC)	 AG	9836-9967	GT	CAG
(AGA)	 AG	10860-10965	GT	AAG
(GGT)	 AG	11212-11737	AG	GAA
-recovered pasa_asmbl_54463.p1, terminal, 11212, 11737
-recovered pasa_asmbl_54463.p1, internal, 3307, 3858
-recovered pasa_asmbl_54463.p1, internal, 6379, 6517
-recovered pasa_asmbl_54463.p1, internal, 8974, 9051
-recovered pasa_asmbl_54463.p1, internal, 9836, 9967
-recovered pasa_asmbl_54463.p1, internal, 10860, 10965
Valid prediction for Augustus_model.g15402.t1
Valid prediction for snap_scaffold_9-snap.2512-T1
Valid prediction for Augustus_model.g15416.t1
Valid prediction for GlimmerHMM_glimmerT_23099-T1
Valid prediction for snap_scaffold_9-snap.2548-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_9-snap.2528-T1
Valid prediction for snap_scaffold_9-snap.2503-T1
Valid prediction for snap_scaffold_9-snap.2509-T1
Valid prediction for snap_scaffold_9-snap.2554-T1
Valid prediction for snap_scaffold_9-snap.2555-T1
Valid prediction for GlimmerHMM_glimmerT_23094-T1
Couldn't classify 104872, 104916
Sorry, prediction pasa_asmbl_54467.p1 fails validation.
(AGA)	 AC	104872-104916	GT	CTG
(TAT)	 AG	105245-105298	GT	AGG
(ATC)	 AG	105470-105636	GT	TGG
(GTA)	 AG	105842-106075	GT	AGG
(CTC)	 AG	106261-106455	GT	CTG
(AGT)	 AG	106589-106723	GT	GTG
(AGA)	 AG	106811-107039	AG	AGA
-recovered pasa_asmbl_54467.p1, terminal, 106811, 107039
-recovered pasa_asmbl_54467.p1, internal, 105245, 105298
-recovered pasa_asmbl_54467.p1, internal, 105470, 105636
-recovered pasa_asmbl_54467.p1, internal, 105842, 106075
-recovered pasa_asmbl_54467.p1, internal, 106261, 106455
-recovered pasa_asmbl_54467.p1, internal, 106589, 106723
Valid prediction for snap_scaffold_9-snap.2517-T1
Couldn't classify 142089, 142146
Couldn't classify 144234, 144395
Sorry, prediction pasa_asmbl_54475.p1 fails validation.
(AAC)	 TT	142089-142146	GT	AGG
(ACA)	 AG	142368-142385	GT	TGG
(ACA)	 AG	142631-142787	GT	AGG
(TGC)	 AG	142904-143015	GT	TGG
(AGG)	 AG	143824-143901	GT	AGG
(GAG)	 AG	144234-144395	CA	CCC
-recovered pasa_asmbl_54475.p1, internal, 142368, 142385
-recovered pasa_asmbl_54475.p1, internal, 142631, 142787
-recovered pasa_asmbl_54475.p1, internal, 142904, 143015
-recovered pasa_asmbl_54475.p1, internal, 143824, 143901
Valid prediction for snap_scaffold_9-snap.2558-T1
Couldn't classify 122271, 122410
Couldn't classify 122972, 123080
Sorry, prediction pasa_asmbl_54733.p1 fails validation.
(AAC)	 GG	122271-122410	GT	AAG
(GAA)	 AG	122827-122874	GT	AGG
(CGG)	 AG	122972-123080	TA	CCT
add_exon() Sorry, pasa_asmbl_54733.p1 122827-122874-terminal-1 is invalid.
-recovered pasa_asmbl_54733.p1, terminal, 122827, 122874
-recovered pasa_asmbl_54733.p1, internal, 122827, 122874
Valid prediction for snap_scaffold_9-snap.2522-T1
Valid prediction for snap_scaffold_9-snap.2518-T1
Valid prediction for Augustus_model.g15411.t1
Valid prediction for snap_scaffold_9-snap.2510-T1
Valid prediction for HiQ_model.g15397.t1
Valid prediction for snap_scaffold_9-snap.2506-T1
Valid prediction for Augustus_model.g15398.t1
Valid prediction for snap_scaffold_9-snap.2542-T1
Valid prediction for GlimmerHMM_glimmerT_23101-T1
Valid prediction for snap_scaffold_9-snap.2545-T1
Couldn't classify 140268, 140406
Couldn't classify 141528, 141665
Sorry, prediction pasa_asmbl_54474.p1 fails validation.
(TTT)	 AG	140268-140406	GT	AGG
(CGG)	 AG	140863-140994	GT	CGG
(GCT)	 AG	141228-141427	GT	TGG
(CCG)	 AG	141528-141665	AA	GCA
-recovered pasa_asmbl_54474.p1, internal, 140268, 140406
-recovered pasa_asmbl_54474.p1, internal, 140863, 140994
-recovered pasa_asmbl_54474.p1, internal, 141228, 141427
Valid prediction for Augustus_model.g15407.t1
Valid prediction for Augustus_model.g15408.t1
Valid prediction for Augustus_model.g15410.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_23110-T1
Valid prediction for GlimmerHMM_glimmerT_23100-T1
Valid prediction for CodingQuarry_transcript_62383-T1
Valid prediction for GlimmerHMM_glimmerT_23088-T1
Valid prediction for GlimmerHMM_glimmerT_23098-T1
Valid prediction for Augustus_model.g15412.t1
Valid prediction for snap_scaffold_9-snap.2516-T1
Valid prediction for snap_scaffold_9-snap.2541-T1
Valid prediction for snap_scaffold_9-snap.2504-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g15414.t1
Valid prediction for GlimmerHMM_glimmerT_23116-T1
Valid prediction for Augustus_model.g15417.t1
Valid prediction for snap_scaffold_9-snap.2526-T1
Valid prediction for snap_scaffold_9-snap.2511-T1
Valid prediction for GlimmerHMM_glimmerT_23109-T1
Valid prediction for CodingQuarry_transcript_62385-T1
Valid prediction for snap_scaffold_9-snap.2508-T1
Valid prediction for snap_scaffold_9-snap.2543-T1
Valid prediction for Augustus_model.g15401.t1
Valid prediction for GlimmerHMM_glimmerT_23102-T1
Valid prediction for GlimmerHMM_glimmerT_23113-T1
Valid prediction for snap_scaffold_9-snap.2547-T1
Valid prediction for snap_scaffold_9-snap.2515-T1
Valid prediction for GlimmerHMM_glimmerT_23112-T1
Valid prediction for Augustus_model.g15406.t1
Valid prediction for GlimmerHMM_glimmerT_23117-T1
Valid prediction for GlimmerHMM_glimmerT_23107-T1
Valid prediction for snap_scaffold_9-snap.2505-T1
Valid prediction for snap_scaffold_9-snap.2513-T1
Valid prediction for snap_scaffold_9-snap.2521-T1
Valid prediction for GlimmerHMM_glimmerT_23097-T1
Valid prediction for GlimmerHMM_glimmerT_23119-T1
Valid prediction for snap_scaffold_9-snap.2533-T1
Valid prediction for snap_scaffold_9-snap.2534-T1
Valid prediction for GlimmerHMM_glimmerT_23114-T1
Valid prediction for snap_scaffold_9-snap.2507-T1
Valid prediction for snap_scaffold_9-snap.2530-T1
Valid prediction for GlimmerHMM_glimmerT_23092-T1
Valid prediction for HiQ_model.g15399.t1
Valid prediction for GlimmerHMM_glimmerT_23091-T1
Valid prediction for Augustus_model.g15418.t1
Valid prediction for snap_scaffold_9-snap.2519-T1
Valid prediction for GlimmerHMM_glimmerT_23106-T1
Valid prediction for snap_scaffold_9-snap.2531-T1
Valid prediction for GlimmerHMM_glimmerT_23115-T1
Valid prediction for snap_scaffold_9-snap.2546-T1
Valid prediction for GlimmerHMM_glimmerT_23096-T1
Valid prediction for snap_scaffold_9-snap.2552-T1
Valid prediction for CodingQuarry_transcript_62384-T1
Valid prediction for snap_scaffold_9-snap.2536-T1
Valid prediction for snap_scaffold_9-snap.2540-T1
Valid prediction for snap_scaffold_9-snap.2544-T1
Valid prediction for snap_scaffold_9-snap.2529-T1
Valid prediction for Augustus_model.g15403.t1
Valid prediction for pasa_asmbl_55404.p1
Valid prediction for snap_scaffold_9-snap.2537-T1
Valid prediction for Augustus_model.g15415.t1
Valid prediction for snap_scaffold_9-snap.2525-T1
Valid prediction for snap_scaffold_9-snap.2549-T1
Valid prediction for snap_scaffold_9-snap.2539-T1
Valid prediction for snap_scaffold_9-snap.2523-T1
Valid prediction for Augustus_model.g15400.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14511, rend_intergenic: 1579  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22391, rend_intergenic: 20030  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33008, rend_intergenic: 22439  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45327, rend_intergenic: 34230  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54415, rend_intergenic: 45718  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55716, rend_intergenic: 54517  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57857, rend_intergenic: 55756  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62343, rend_intergenic: 57926  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69080, rend_intergenic: 64195  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74909, rend_intergenic: 71833  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79022, rend_intergenic: 76263  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88894, rend_intergenic: 83712  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91389, rend_intergenic: 88917  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97892, rend_intergenic: 92042  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107039, rend_intergenic: 102053  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124393, rend_intergenic: 114624  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129665, rend_intergenic: 128006  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132745, rend_intergenic: 132073  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143698, rend_intergenic: 137180  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152503, rend_intergenic: 145106  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170845, rend_intergenic: 159121  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179335, rend_intergenic: 172472  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182446, rend_intergenic: 179893  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199522, rend_intergenic: 194065  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 205893, rend_intergenic: 201178  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209303, rend_intergenic: 205942  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 231713, rend_intergenic: 210107  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 257769
-exon list size: 529


building trellis

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84.4    
84.6    
84.7    
84.9    
85.1    
85.3    
85.5    
85.7    
85.9    
86.1    
86.3    
86.4    
86.6    
86.8    
87.0    
87.2    
87.4    
87.6    
87.8    
87.9    
88.1    
88.3    
88.5    
88.7    
88.9    
89.1    
89.3    
89.5    
89.6    
89.8    
90.0    
90.2    
90.4    
90.6    
90.8    
91.0    
91.1    
91.3    
91.5    
91.7    
91.9    
92.1    
92.3    
92.5    
92.7    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
94.0    
94.2    
94.4    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.9    
96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.2    
99.4    
99.6    
99.8    
-found 40 predictions from path traversal
Error with prediction: snap lend_intergenic: 14511, rend_intergenic: 1579  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22391, rend_intergenic: 20030  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33008, rend_intergenic: 22439  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45327, rend_intergenic: 34230  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54415, rend_intergenic: 45718  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55716, rend_intergenic: 54517  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57857, rend_intergenic: 55756  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62343, rend_intergenic: 57926  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69080, rend_intergenic: 64195  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74909, rend_intergenic: 71833  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79022, rend_intergenic: 76263  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88894, rend_intergenic: 83712  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91389, rend_intergenic: 88917  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97892, rend_intergenic: 92042  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107039, rend_intergenic: 102053  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124393, rend_intergenic: 114624  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129665, rend_intergenic: 128006  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132745, rend_intergenic: 132073  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143698, rend_intergenic: 137180  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152503, rend_intergenic: 145106  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170845, rend_intergenic: 159121  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179335, rend_intergenic: 172472  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182446, rend_intergenic: 179893  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199522, rend_intergenic: 194065  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 205893, rend_intergenic: 201178  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209303, rend_intergenic: 205942  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 231713, rend_intergenic: 210107  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 28 predictions persist after filtering for low support