-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_17/scaffold_17_10312067-10485688

-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_17-snap.2094-T1
Valid prediction for GlimmerHMM_glimmerT_40947-T1
Valid prediction for snap_scaffold_17-snap.2076-T1
Valid prediction for snap_scaffold_17-snap.2085-T1
Valid prediction for snap_scaffold_17-snap.2084-T1
Valid prediction for snap_scaffold_17-snap.2078-T1
Valid prediction for Augustus_model.g27337.t1
Valid prediction for GlimmerHMM_glimmerT_40949-T1
Valid prediction for GlimmerHMM_glimmerT_40945-T1
Valid prediction for snap_scaffold_17-snap.2087-T1
Valid prediction for snap_scaffold_17-snap.2067-T1
Valid prediction for snap_scaffold_17-snap.2092-T1
Valid prediction for snap_scaffold_17-snap.2098-T1
Valid prediction for snap_scaffold_17-snap.2080-T1
Valid prediction for snap_scaffold_17-snap.2096-T1
Valid prediction for snap_scaffold_17-snap.2081-T1
Valid prediction for snap_scaffold_17-snap.2073-T1
Valid prediction for snap_scaffold_17-snap.2070-T1
Valid prediction for snap_scaffold_17-snap.2064-T1
Valid prediction for GlimmerHMM_glimmerT_40942-T1
Valid prediction for snap_scaffold_17-snap.2069-T1
Valid prediction for snap_scaffold_17-snap.2075-T1
Valid prediction for snap_scaffold_17-snap.2091-T1
Valid prediction for snap_scaffold_17-snap.2088-T1
Valid prediction for snap_scaffold_17-snap.2083-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 CodingQuarry_transcript_22161-T1
Valid prediction for GlimmerHMM_glimmerT_40948-T1
Valid prediction for snap_scaffold_17-snap.2095-T1
Couldn't classify 166747, 166788
Couldn't classify 167999, 168065
Sorry, prediction pasa_asmbl_18243.p1 fails validation.
(AGC)	 AG	166747-166788	GT	TGG
(GCT)	 AG	167048-167170	GT	AGG
(CAA)	 AG	167696-167874	GT	CAG
(CTG)	 AG	167999-168065	AG	TCA
-recovered pasa_asmbl_18243.p1, internal, 166747, 166788
-recovered pasa_asmbl_18243.p1, internal, 167048, 167170
-recovered pasa_asmbl_18243.p1, internal, 167696, 167874
Valid prediction for snap_scaffold_17-snap.2063-T1
Valid prediction for snap_scaffold_17-snap.2077-T1
Valid prediction for snap_scaffold_17-snap.2065-T1
Valid prediction for Augustus_model.g27334.t1
Valid prediction for GlimmerHMM_glimmerT_40946-T1
Valid prediction for snap_scaffold_17-snap.2090-T1
Valid prediction for Augustus_model.g27338.t1
Valid prediction for GlimmerHMM_glimmerT_40953-T1
Valid prediction for snap_scaffold_17-snap.2086-T1
Valid prediction for GlimmerHMM_glimmerT_40943-T1
Valid prediction for snap_scaffold_17-snap.2068-T1
Valid prediction for Augustus_model.g27340.t1
Valid prediction for snap_scaffold_17-snap.2074-T1
Valid prediction for snap_scaffold_17-snap.2072-T1
Couldn't classify 117044, 117097
Sorry, prediction pasa_asmbl_18244.p1 fails validation.
(GGT)	 AG	117044-117097	GT	ATG
(GGG)	 AG	117207-117260	GT	CTG
(GGT)	 AG	117454-117507	GT	CGG
(GGT)	 AG	117665-117709	GT	CGG
(GGA)	 AG	117806-117859	GT	AGG
(GGA)	 AG	117958-117993	GT	AGG
(GGA)	 AG	118108-118170	GT	AGG
(GGT)	 AG	118330-118401	GT	TGG
(GGA)	 AG	118676-118729	GT	CGG
(GGC)	 AG	118915-118959	GT	CAG
(GGT)	 AG	119592-119636	GT	AGG
(GGA)	 AG	120036-120089	GT	AGG
(GGT)	 AG	120220-120273	GT	CGG
(GGA)	 AG	120389-120439	GT	AGG
(GGT)	 AG	120700-120789	GT	TGG
(GGA)	 AG	120941-120976	GT	ATG
(GGG)	 AG	121090-121134	GT	AAG
(GGC)	 AG	122040-122231	GT	ACG
(GCG)	 AG	122364-122427	GT	CGG
(AGA)	 AG	122519-122692	GT	AGG
(GTC)	 AG	122829-122906	GT	GGG
(GAG)	 AG	123103-123296	AA	AGA
add_exon() Sorry, pasa_asmbl_18244.p1 122519-122692-terminal-1 is invalid.
-recovered pasa_asmbl_18244.p1, terminal, 122519, 122692
-recovered pasa_asmbl_18244.p1, terminal, 123103, 123296
-recovered pasa_asmbl_18244.p1, internal, 117044, 117097
-recovered pasa_asmbl_18244.p1, internal, 117207, 117260
-recovered pasa_asmbl_18244.p1, internal, 117454, 117507
-recovered pasa_asmbl_18244.p1, internal, 117665, 117709
-recovered pasa_asmbl_18244.p1, internal, 117806, 117859
-recovered pasa_asmbl_18244.p1, internal, 117958, 117993
-recovered pasa_asmbl_18244.p1, internal, 118108, 118170
-recovered pasa_asmbl_18244.p1, internal, 118330, 118401
-recovered pasa_asmbl_18244.p1, internal, 118676, 118729
-recovered pasa_asmbl_18244.p1, internal, 118915, 118959
-recovered pasa_asmbl_18244.p1, internal, 119592, 119636
-recovered pasa_asmbl_18244.p1, internal, 120036, 120089
-recovered pasa_asmbl_18244.p1, internal, 120220, 120273
-recovered pasa_asmbl_18244.p1, internal, 120389, 120439
-recovered pasa_asmbl_18244.p1, internal, 120700, 120789
-recovered pasa_asmbl_18244.p1, internal, 120941, 120976
-recovered pasa_asmbl_18244.p1, internal, 121090, 121134
-recovered pasa_asmbl_18244.p1, internal, 122040, 122231
-recovered pasa_asmbl_18244.p1, internal, 122364, 122427
-recovered pasa_asmbl_18244.p1, internal, 122519, 122692
-recovered pasa_asmbl_18244.p1, internal, 122829, 122906
Valid prediction for snap_scaffold_17-snap.2071-T1
Valid prediction for GlimmerHMM_glimmerT_40950-T1
Valid prediction for GlimmerHMM_glimmerT_40951-T1
Valid prediction for snap_scaffold_17-snap.2093-T1
Valid prediction for Augustus_model.g27339.t1
Valid prediction for snap_scaffold_17-snap.2079-T1
Valid prediction for Augustus_model.g27335.t1
Couldn't classify 94415, 94468
Couldn't classify 107350, 107364
Sorry, prediction pasa_asmbl_18247.p1 fails validation.
(GGA)	 AA	94415-94468	GT	ATG
(GGT)	 AG	95308-95352	GT	AGG
(GGG)	 AG	95585-95680	GT	CTG
(GGT)	 AG	95989-96021	GT	CGG
(GGG)	 AG	96359-96403	GT	CTG
(GGG)	 AG	96563-96598	GT	AGG
(GGA)	 AG	96789-96908	GT	CAG
(GGA)	 AG	97956-97991	GT	AGG
(GGA)	 AG	98585-98620	GT	AGG
(GGC)	 AG	98765-98893	GT	AGG
(GGG)	 AG	99160-99204	GT	AGG
(GGC)	 AG	100242-100277	GT	CAG
(GGC)	 AG	100380-100433	GT	AGG
(GGA)	 AG	100551-100601	GT	AGG
(GGT)	 AG	101102-101245	GT	AGG
(GGT)	 AG	101814-101849	GT	AAG
(GGA)	 AG	102910-103017	GT	AGG
(GGA)	 AG	103319-103441	GT	CGG
(GGG)	 AG	103689-103742	GT	AGG
(GGT)	 AG	103857-103898	GT	AGG
(GGT)	 AG	104352-104387	GT	CAG
(GGA)	 AG	104554-104607	GT	AGG
(GGT)	 AG	105233-105301	GT	AGG
(GGT)	 AG	105377-105430	GT	CTG
(GGG)	 AG	106035-106061	GT	AGG
(GGA)	 AG	106870-106926	GT	CTG
(GGA)	 AG	107350-107364	GC	CAG
-recovered pasa_asmbl_18247.p1, internal, 95308, 95352
-recovered pasa_asmbl_18247.p1, internal, 95585, 95680
-recovered pasa_asmbl_18247.p1, internal, 95989, 96021
-recovered pasa_asmbl_18247.p1, internal, 96359, 96403
-recovered pasa_asmbl_18247.p1, internal, 96563, 96598
-recovered pasa_asmbl_18247.p1, internal, 96789, 96908
-recovered pasa_asmbl_18247.p1, internal, 97956, 97991
-recovered pasa_asmbl_18247.p1, internal, 98585, 98620
-recovered pasa_asmbl_18247.p1, internal, 98765, 98893
-recovered pasa_asmbl_18247.p1, internal, 99160, 99204
-recovered pasa_asmbl_18247.p1, internal, 100242, 100277
-recovered pasa_asmbl_18247.p1, internal, 100380, 100433
-recovered pasa_asmbl_18247.p1, internal, 100551, 100601
-recovered pasa_asmbl_18247.p1, internal, 101102, 101245
-recovered pasa_asmbl_18247.p1, internal, 101814, 101849
-recovered pasa_asmbl_18247.p1, internal, 102910, 103017
-recovered pasa_asmbl_18247.p1, internal, 103319, 103441
-recovered pasa_asmbl_18247.p1, internal, 103689, 103742
-recovered pasa_asmbl_18247.p1, internal, 103857, 103898
-recovered pasa_asmbl_18247.p1, internal, 104352, 104387
-recovered pasa_asmbl_18247.p1, internal, 104554, 104607
-recovered pasa_asmbl_18247.p1, internal, 105233, 105301
-recovered pasa_asmbl_18247.p1, internal, 105377, 105430
-recovered pasa_asmbl_18247.p1, internal, 106035, 106061
-recovered pasa_asmbl_18247.p1, internal, 106870, 106926
-recovered pasa_asmbl_18247.p1, internal, 107350, 107364
Valid prediction for CodingQuarry_transcript_22162-T1
Valid prediction for snap_scaffold_17-snap.2066-T1
Valid prediction for Augustus_model.g27342.t1
Valid prediction for snap_scaffold_17-snap.2082-T1
Valid prediction for GlimmerHMM_glimmerT_40954-T1
Valid prediction for snap_scaffold_17-snap.2089-T1
Valid prediction for GlimmerHMM_glimmerT_40941-T1
Couldn't classify 82860, 82982
Couldn't classify 86448, 86519
Sorry, prediction pasa_asmbl_18248.p1 fails validation.
(CAG)	 GT	82860-82982	GT	AGG
(CTC)	 AG	83745-84026	GT	AGG
(ATG)	 AG	84749-84829	GT	GGG
(TGC)	 AG	86448-86519	GT	AGG
-recovered pasa_asmbl_18248.p1, initial, 84749, 84829
-recovered pasa_asmbl_18248.p1, internal, 83745, 84026
-recovered pasa_asmbl_18248.p1, internal, 84749, 84829
-recovered pasa_asmbl_18248.p1, internal, 86448, 86519
Valid prediction for snap_scaffold_17-snap.2062-T1
Couldn't classify 94467, 94468
Sorry, prediction CodingQuarry_transcript_22163-T1 fails validation.
(ATG)	 GG	94467-94468	GT	ATG
(GGT)	 AG	95308-95352	GT	AGG
(GGG)	 AG	95585-95680	GT	CTG
(GGT)	 AG	95989-96021	GT	CGG
(GGG)	 AG	96359-96403	GT	CTG
(GGG)	 AG	96563-96598	GT	AGG
(GGA)	 AG	96789-96908	GT	CAG
(GGA)	 AG	97956-97962	CG	GAC
-recovered CodingQuarry_transcript_22163-T1, terminal, 97956, 97962
-recovered CodingQuarry_transcript_22163-T1, internal, 95308, 95352
-recovered CodingQuarry_transcript_22163-T1, internal, 95585, 95680
-recovered CodingQuarry_transcript_22163-T1, internal, 95989, 96021
-recovered CodingQuarry_transcript_22163-T1, internal, 96359, 96403
-recovered CodingQuarry_transcript_22163-T1, internal, 96563, 96598
-recovered CodingQuarry_transcript_22163-T1, internal, 96789, 96908
Valid prediction for GlimmerHMM_glimmerT_40940-T1
Valid prediction for Augustus_model.g27336.t1
Valid prediction for GlimmerHMM_glimmerT_40944-T1
Valid prediction for Augustus_model.g27341.t1
Couldn't classify 112254, 112313
Couldn't classify 114131, 114175
Sorry, prediction pasa_asmbl_18245.p1 fails validation.
(TTT)	 AC	112254-112313	GT	AGG
(GAG)	 AG	112453-112569	GT	GGG
(TGT)	 AG	113397-113438	GT	CGG
(ACC)	 AG	113540-113617	GT	AGG
(GGC)	 AG	114131-114175	GT	TGG
-recovered pasa_asmbl_18245.p1, internal, 112453, 112569
-recovered pasa_asmbl_18245.p1, internal, 113397, 113438
-recovered pasa_asmbl_18245.p1, internal, 113540, 113617
-recovered pasa_asmbl_18245.p1, internal, 114131, 114175
Valid prediction for Augustus_model.g27343.t1
Valid prediction for GlimmerHMM_glimmerT_40952-T1
Valid prediction for GlimmerHMM_glimmerT_40939-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9116, rend_intergenic: 4726  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12268, rend_intergenic: 9187  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26790, rend_intergenic: 12871  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30283, rend_intergenic: 26906  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41039, rend_intergenic: 38198  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45301, rend_intergenic: 41160  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65003, rend_intergenic: 53930  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75963, rend_intergenic: 65923  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84471, rend_intergenic: 76473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103012, rend_intergenic: 85424  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109937, rend_intergenic: 106133  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119832, rend_intergenic: 115407  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125400, rend_intergenic: 123440  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133734, rend_intergenic: 127325  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141745, rend_intergenic: 134452  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153620, rend_intergenic: 147799  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159095, rend_intergenic: 158156  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 173622
-exon list size: 457


building trellis

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89.8    
90.0    
90.2    
90.4    
90.6    
90.8    
91.1    
91.3    
91.5    
91.7    
91.9    
92.2    
92.4    
92.6    
92.8    
93.0    
93.2    
93.5    
93.7    
93.9    
94.1    
94.3    
94.6    
94.8    
95.0    
95.2    
95.4    
95.6    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
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 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 9116, rend_intergenic: 4726  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12268, rend_intergenic: 9187  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26790, rend_intergenic: 12871  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30283, rend_intergenic: 26906  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41039, rend_intergenic: 38198  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45301, rend_intergenic: 41160  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65003, rend_intergenic: 53930  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75963, rend_intergenic: 65923  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84471, rend_intergenic: 76473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103012, rend_intergenic: 85424  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109937, rend_intergenic: 106133  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119832, rend_intergenic: 115407  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125400, rend_intergenic: 123440  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133734, rend_intergenic: 127325  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141745, rend_intergenic: 134452  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153620, rend_intergenic: 147799  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159095, rend_intergenic: 158156  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 10 predictions persist after filtering for low support