-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_12/scaffold_12_5264420-5681436

-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_29362-T1
Valid prediction for Augustus_model.g19373.t1
Valid prediction for CodingQuarry_transcript_10227-T1
Couldn't classify 394118, 394236
Sorry, prediction pasa_asmbl_7666.p1 fails validation.
(CTT)	 CA	394118-394236	GT	AAG
(CAT)	 AG	394939-395177	GT	TGG
(GGG)	 AG	395421-395644	GT	TTG
(CTG)	 AG	396062-396253	GT	AGG
(ATC)	 AG	396591-396774	GT	AAG
(ATA)	 AG	398049-398227	CT	GAC
add_exon() Sorry, pasa_asmbl_7666.p1 396591-396774-terminal-3 is invalid.
-recovered pasa_asmbl_7666.p1, terminal, 396591, 396774
-recovered pasa_asmbl_7666.p1, terminal, 398049, 398227
-recovered pasa_asmbl_7666.p1, internal, 394939, 395177
-recovered pasa_asmbl_7666.p1, internal, 395421, 395644
-recovered pasa_asmbl_7666.p1, internal, 396062, 396253
-recovered pasa_asmbl_7666.p1, internal, 396591, 396774
Couldn't classify 83685, 83731
Couldn't classify 88552, 88581
Sorry, prediction pasa_asmbl_7653.p1 fails validation.
(TCC)	 TC	83685-83731	GT	AAG
(CAT)	 AG	84561-84647	GT	GGG
(GGC)	 AG	84914-85016	GT	AGG
(GGT)	 AG	85605-85681	GT	AGG
(GCA)	 AG	86508-86559	GT	GGG
(GAG)	 AG	86733-86859	GT	AGG
(ACC)	 AG	87856-88066	GT	AGG
(GCC)	 AG	88260-88398	GT	AGG
(CCG)	 AG	88552-88581	CC	CCC
-recovered pasa_asmbl_7653.p1, internal, 84561, 84647
-recovered pasa_asmbl_7653.p1, internal, 84914, 85016
-recovered pasa_asmbl_7653.p1, internal, 85605, 85681
-recovered pasa_asmbl_7653.p1, internal, 86508, 86559
-recovered pasa_asmbl_7653.p1, internal, 86733, 86859
-recovered pasa_asmbl_7653.p1, internal, 87856, 88066
-recovered pasa_asmbl_7653.p1, internal, 88260, 88398
Valid prediction for GlimmerHMM_glimmerT_29387-T1
Valid prediction for HiQ_model.g19380.t1
Valid prediction for Augustus_model.g19393.t1
Valid prediction for GlimmerHMM_glimmerT_29374-T1
Couldn't classify 205427, 205621
Sorry, prediction pasa_asmbl_7656.p1 fails validation.
(ACC)	 CG	205427-205621	GT	CGG
(AAT)	 AG	205882-205980	GT	TGG
(GTG)	 AG	206230-206396	GT	TGG
(GAT)	 AG	206502-206671	GT	CTG
(GTG)	 AG	207050-207318	TA	GAT
-recovered pasa_asmbl_7656.p1, terminal, 207050, 207318
-recovered pasa_asmbl_7656.p1, internal, 205882, 205980
-recovered pasa_asmbl_7656.p1, internal, 206230, 206396
-recovered pasa_asmbl_7656.p1, internal, 206502, 206671
Valid prediction for GlimmerHMM_glimmerT_29369-T1
Valid prediction for Augustus_model.g19364.t1
Valid prediction for GlimmerHMM_glimmerT_29377-T1
Valid prediction for snap_scaffold_12-snap.1075-T1
Valid prediction for snap_scaffold_12-snap.1086-T1
Valid prediction for HiQ_model.g19391.t1
Valid prediction for snap_scaffold_12-snap.1091-T1
Valid prediction for CodingQuarry_transcript_10230-T1
Valid prediction for Augustus_model.g19381.t1
Valid prediction for snap_scaffold_12-snap.1090-T1
Valid prediction for HiQ_model.g19367.t1
Valid prediction for GlimmerHMM_glimmerT_29388-T1
Valid prediction for HiQ_model.g19376.t1
Couldn't classify 90352, 90567
Sorry, prediction pasa_asmbl_7654.p1 fails validation.
(GAT)	 CA	90352-90567	GT	AGG
(AAA)	 AG	90752-90931	GT	CCG
(GTG)	 AG	91032-91387	GT	ATG
(GCC)	 AG	91652-91753	GT	AGG
(GAC)	 AG	92718-92841	AC	AGA
-recovered pasa_asmbl_7654.p1, terminal, 92718, 92841
-recovered pasa_asmbl_7654.p1, internal, 90752, 90931
-recovered pasa_asmbl_7654.p1, internal, 91032, 91387
-recovered pasa_asmbl_7654.p1, internal, 91652, 91753
Valid prediction for Augustus_model.g19377.t1
Valid prediction for snap_scaffold_12-snap.1100-T1
Couldn't classify 381293, 381350
Couldn't classify 385130, 385254
Sorry, prediction pasa_asmbl_7663.p1 fails validation.
(CCT)	 AT	381293-381350	GT	AGG
(GCA)	 AG	383977-384131	GT	AGG
(GTT)	 AG	384779-384923	GT	AGG
(GCA)	 AG	385130-385254	GT	GGG
add_exon() Sorry, pasa_asmbl_7663.p1 384779-384923-terminal-3 is invalid.
-recovered pasa_asmbl_7663.p1, terminal, 384779, 384923
-recovered pasa_asmbl_7663.p1, internal, 383977, 384131
-recovered pasa_asmbl_7663.p1, internal, 384779, 384923
-recovered pasa_asmbl_7663.p1, internal, 385130, 385254
Valid prediction for snap_scaffold_12-snap.1110-T1
Valid prediction for snap_scaffold_12-snap.1101-T1
Valid prediction for CodingQuarry_transcript_10229-T1
Valid prediction for CodingQuarry_transcript_10226-T1
Valid prediction for GlimmerHMM_glimmerT_29379-T1
Valid prediction for GlimmerHMM_glimmerT_29370-T1
Valid prediction for GlimmerHMM_glimmerT_29357-T1
Valid prediction for GlimmerHMM_glimmerT_29354-T1
Valid prediction for GlimmerHMM_glimmerT_29364-T1
Valid prediction for CodingQuarry_transcript_10219-T1
Valid prediction for Augustus_model.g19366.t1
Valid prediction for HiQ_model.g19379.t1
Valid prediction for snap_scaffold_12-snap.1082-T1
Valid prediction for snap_scaffold_12-snap.1112-T1
Valid prediction for Augustus_model.g19365.t1
Valid prediction for GlimmerHMM_glimmerT_29359-T1
Valid prediction for snap_scaffold_12-snap.1067-T1
Valid prediction for CodingQuarry_transcript_10228-T1
Valid prediction for snap_scaffold_12-snap.1078-T1
Valid prediction for snap_scaffold_12-snap.1066-T1
Valid prediction for Augustus_model.g19369.t1
Valid prediction for Augustus_model.g19363.t1
Valid prediction for pasa_asmbl_7657.p1
Valid prediction for snap_scaffold_12-snap.1076-T1
Valid prediction for GlimmerHMM_glimmerT_29353-T1
Valid prediction for snap_scaffold_12-snap.1073-T1
Valid prediction for GlimmerHMM_glimmerT_29373-T1
Couldn't classify 385577, 385741
Couldn't classify 386166, 386208
Sorry, prediction pasa_asmbl_7664.p1 fails validation.
(GTG)	 AC	385577-385741	GT	AGG
(ATG)	 AG	385860-385990	GT	AGG
(CTT)	 AG	386166-386208	AC	GCA
-recovered pasa_asmbl_7664.p1, initial, 385860, 385990
-recovered pasa_asmbl_7664.p1, internal, 385860, 385990
Valid prediction for snap_scaffold_12-snap.1111-T1
Valid prediction for Augustus_model.g19368.t1
Valid prediction for GlimmerHMM_glimmerT_29355-T1
Valid prediction for GlimmerHMM_glimmerT_29368-T1
Couldn't classify 41580, 41754
Sorry, prediction pasa_asmbl_7644.p1 fails validation.
(TCC)	 AC	41580-41754	GT	AGG
(AGC)	 AG	41986-42227	CA	AAC
-recovered pasa_asmbl_7644.p1, terminal, 41986, 42227
Valid prediction for snap_scaffold_12-snap.1079-T1
Valid prediction for snap_scaffold_12-snap.1094-T1
Valid prediction for GlimmerHMM_glimmerT_29389-T1
Valid prediction for CodingQuarry_transcript_10220-T1
Couldn't classify 73431, 73551
Couldn't classify 76472, 76537
Sorry, prediction pasa_asmbl_7650.p1 fails validation.
(GAC)	 TG	73431-73551	GT	AGG
(ATT)	 AG	74004-74181	GT	CAG
(TCT)	 AG	75158-75302	GT	AGG
(ATC)	 AG	76472-76537	CC	ACC
-recovered pasa_asmbl_7650.p1, internal, 74004, 74181
-recovered pasa_asmbl_7650.p1, internal, 75158, 75302
Valid prediction for snap_scaffold_12-snap.1099-T1
Valid prediction for snap_scaffold_12-snap.1113-T1
Valid prediction for Augustus_model.g19392.t1
Valid prediction for pasa_asmbl_7648.p2
Valid prediction for pasa_asmbl_7659.p1

-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 HiQ_model.g19375.t1
Valid prediction for Augustus_model.g19382.t1
Valid prediction for GlimmerHMM_glimmerT_29385-T1
Valid prediction for CodingQuarry_transcript_10224-T1
Valid prediction for GlimmerHMM_glimmerT_29372-T1
Valid prediction for HiQ_model.g19390.t1
Valid prediction for Augustus_model.g19389.t1
Valid prediction for snap_scaffold_12-snap.1114-T1
Valid prediction for snap_scaffold_12-snap.1108-T1
Valid prediction for snap_scaffold_12-snap.1097-T1
Valid prediction for snap_scaffold_12-snap.1083-T1
Valid prediction for snap_scaffold_12-snap.1081-T1
Valid prediction for GlimmerHMM_glimmerT_29384-T1
Valid prediction for snap_scaffold_12-snap.1071-T1
Valid prediction for HiQ_model.g19384.t1
Valid prediction for snap_scaffold_12-snap.1104-T1
Valid prediction for snap_scaffold_12-snap.1116-T1
Valid prediction for GlimmerHMM_glimmerT_29361-T1
Valid prediction for CodingQuarry_transcript_10225-T1
Valid prediction for GlimmerHMM_glimmerT_29375-T1
Valid prediction for snap_scaffold_12-snap.1095-T1
Valid prediction for Augustus_model.g19388.t1
Valid prediction for pasa_asmbl_8494.p1
Valid prediction for CodingQuarry_transcript_10222-T1
Valid prediction for GlimmerHMM_glimmerT_29383-T1
Valid prediction for snap_scaffold_12-snap.1088-T1
Valid prediction for Augustus_model.g19394.t1
Couldn't classify 52204, 52658
Sorry, prediction pasa_asmbl_8514.p1 fails validation.
(CTC)	 GA	52204-52658	GT	AAG
(GTG)	 AG	52888-53677	AT	GAA
-recovered pasa_asmbl_8514.p1, terminal, 52888, 53677
Valid prediction for snap_scaffold_12-snap.1089-T1
Couldn't classify 113273, 113477
Sorry, prediction pasa_asmbl_8505.p1 fails validation.
(CGG)	 AA	113273-113477	GT	AGG
(GTA)	 AG	114143-114261	GT	TGG
(CCC)	 AG	114491-114608	GT	AGG
(GCC)	 AG	114718-114800	GT	ATG
(CGA)	 AG	115378-115539	GT	CTG
(GTG)	 AG	116576-116690	GT	AGG
(ACC)	 AG	116848-116967	GT	AGG
(ACA)	 AG	117238-117398	AT	GAA
-recovered pasa_asmbl_8505.p1, terminal, 117238, 117398
-recovered pasa_asmbl_8505.p1, internal, 114143, 114261
-recovered pasa_asmbl_8505.p1, internal, 114491, 114608
-recovered pasa_asmbl_8505.p1, internal, 114718, 114800
-recovered pasa_asmbl_8505.p1, internal, 115378, 115539
-recovered pasa_asmbl_8505.p1, internal, 116576, 116690
-recovered pasa_asmbl_8505.p1, internal, 116848, 116967
Valid prediction for GlimmerHMM_glimmerT_29365-T1
Valid prediction for pasa_asmbl_8504.p1
Valid prediction for pasa_asmbl_9151.p1
Valid prediction for GlimmerHMM_glimmerT_29378-T1
Valid prediction for Augustus_model.g19378.t1
Valid prediction for snap_scaffold_12-snap.1069-T1
Valid prediction for snap_scaffold_12-snap.1092-T1
Valid prediction for snap_scaffold_12-snap.1098-T1
Valid prediction for GlimmerHMM_glimmerT_29381-T1
Valid prediction for snap_scaffold_12-snap.1105-T1
Valid prediction for HiQ_model.g19371.t1
Valid prediction for snap_scaffold_12-snap.1087-T1
Valid prediction for Augustus_model.g19370.t1
Valid prediction for Augustus_model.g19386.t1
Valid prediction for GlimmerHMM_glimmerT_29371-T1
Valid prediction for snap_scaffold_12-snap.1072-T1
Valid prediction for snap_scaffold_12-snap.1107-T1
Valid prediction for snap_scaffold_12-snap.1106-T1
Valid prediction for Augustus_model.g19387.t1
Valid prediction for CodingQuarry_transcript_10231-T1
Valid prediction for GlimmerHMM_glimmerT_29358-T1
Valid prediction for snap_scaffold_12-snap.1115-T1
Valid prediction for snap_scaffold_12-snap.1109-T1
Valid prediction for GlimmerHMM_glimmerT_29356-T1
Valid prediction for GlimmerHMM_glimmerT_29390-T1
Valid prediction for GlimmerHMM_glimmerT_29360-T1
Valid prediction for HiQ_model.g19374.t1
Valid prediction for pasa_asmbl_8519.p1
Valid prediction for snap_scaffold_12-snap.1103-T1
Couldn't classify 3870, 3948
Sorry, prediction pasa_asmbl_8521.p1 fails validation.
(GAT)	 CA	3870-3948	GT	GGG
(TCC)	 AG	4939-5250	GT	ACG
(AAC)	 AG	6260-6613	GT	AGG
(ACC)	 AG	6896-7308	CA	AGC
-recovered pasa_asmbl_8521.p1, terminal, 6896, 7308
-recovered pasa_asmbl_8521.p1, internal, 4939, 5250
-recovered pasa_asmbl_8521.p1, internal, 6260, 6613
Valid prediction for GlimmerHMM_glimmerT_29376-T1
Valid prediction for snap_scaffold_12-snap.1093-T1
Valid prediction for snap_scaffold_12-snap.1068-T1
Valid prediction for Augustus_model.g19372.t1
Valid prediction for GlimmerHMM_glimmerT_29366-T1
Valid prediction for snap_scaffold_12-snap.1096-T1
Valid prediction for CodingQuarry_transcript_10223-T1
Valid prediction for GlimmerHMM_glimmerT_29386-T1
Valid prediction for CodingQuarry_transcript_10232-T1
Valid prediction for GlimmerHMM_glimmerT_29380-T1
Valid prediction for snap_scaffold_12-snap.1074-T1
Valid prediction for GlimmerHMM_glimmerT_29367-T1
Valid prediction for snap_scaffold_12-snap.1080-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_12-snap.1077-T1
Valid prediction for snap_scaffold_12-snap.1102-T1
Valid prediction for snap_scaffold_12-snap.1070-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_29391-T1
Valid prediction for snap_scaffold_12-snap.1085-T1
Couldn't classify 224933, 225001
Sorry, prediction pasa_asmbl_8495.p1 fails validation.
(AAG)	 GA	224933-225001	GT	CTG
(ACG)	 AG	225092-225190	GT	AGG
(GAA)	 AG	225793-225880	GT	GAG
(GTC)	 AG	226413-226534	GT	ATG
(GTT)	 AG	226881-227001	GT	ACG
(TCA)	 AG	227759-227892	GT	GAG
(GTG)	 AG	228016-228164	GT	GGG
(GTA)	 AG	228314-228462	GT	ACG
(AGG)	 AG	228593-228621	GC	AAG
-recovered pasa_asmbl_8495.p1, terminal, 228593, 228621
-recovered pasa_asmbl_8495.p1, internal, 225092, 225190
-recovered pasa_asmbl_8495.p1, internal, 225793, 225880
-recovered pasa_asmbl_8495.p1, internal, 226413, 226534
-recovered pasa_asmbl_8495.p1, internal, 226881, 227001
-recovered pasa_asmbl_8495.p1, internal, 227759, 227892
-recovered pasa_asmbl_8495.p1, internal, 228016, 228164
-recovered pasa_asmbl_8495.p1, internal, 228314, 228462
-recovered pasa_asmbl_8495.p1, internal, 228593, 228621
Valid prediction for Augustus_model.g19385.t1
Couldn't classify 315273, 315390
Couldn't classify 316134, 316153
Sorry, prediction pasa_asmbl_9220.p1 fails validation.
(GTG)	 AG	315273-315390	GT	TGG
(GTG)	 AG	315806-316003	GT	TGG
(GTC)	 AG	316134-316153	TT	CGT
-recovered pasa_asmbl_9220.p1, internal, 315273, 315390
-recovered pasa_asmbl_9220.p1, internal, 315806, 316003
Valid prediction for pasa_asmbl_8503.p1
Valid prediction for snap_scaffold_12-snap.1084-T1
Valid prediction for GlimmerHMM_glimmerT_29382-T1
Valid prediction for Augustus_model.g19383.t1
Valid prediction for GlimmerHMM_glimmerT_29363-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 38386, rend_intergenic: 8085  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42642, rend_intergenic: 40264  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49597, rend_intergenic: 47238  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85759, rend_intergenic: 79411  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92841, rend_intergenic: 85815  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102657, rend_intergenic: 100194  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104997, rend_intergenic: 103110  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 417017
-exon list size: 571


building trellis

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52.0    
52.2    
52.4    
52.5    
52.7    
52.9    
53.1    
53.2    
53.4    
53.6    
53.8    
53.9    
54.1    
54.3    
54.5    
54.6    
54.8    
55.0    
55.1    
55.3    
55.5    
55.7    
55.8    
56.0    
56.2    
56.4    
56.5    
56.7    
56.9    
57.1    
57.2    
57.4    
57.6    
57.8    
57.9    
58.1    
58.3    
58.5    
58.6    
58.8    
59.0    
59.2    
59.3    
59.5    
59.7    
59.9    
60.0    
60.2    
60.4    
60.6    
60.7    
60.9    
61.1    
61.3    
61.4    
61.6    
61.8    
62.0    
62.1    
62.3    
62.5    
62.7    
62.8    
63.0    
63.2    
63.4    
63.5    
63.7    
63.9    
64.0    
64.2    
64.4    
64.6    
64.7    
64.9    
65.1    
65.3    
65.4    
65.6    
65.8    
66.0    
66.1    
66.3    
66.5    
66.7    
66.8    
67.0    
67.2    
67.4    
67.5    
67.7    
67.9    
68.1    
68.2    
68.4    
68.6    
68.8    
68.9    
69.1    
69.3    
69.5    
69.6    
69.8    
70.0    
70.2    
70.3    
70.5    
70.7    
70.9    
71.0    
71.2    
71.4    
71.6    
71.7    
71.9    
72.1    
72.3    
72.4    
72.6    
72.8    
72.9    
73.1    
73.3    
73.5    
73.6    
73.8    
74.0    
74.2    
74.3    
74.5    
74.7    
74.9    
75.0    
75.2    
75.4    
75.6    
75.7    
75.9    
76.1    
76.3    
76.4    
76.6    
76.8    
77.0    
77.1    
77.3    
77.5    
77.7    
77.8    
78.0    
78.2    
78.4    
78.5    
78.7    
78.9    
79.1    
79.2    
79.4    
79.6    
79.8    
79.9    
80.1    
80.3    
80.5    
80.6    
80.8    
81.0    
81.2    
81.3    
81.5    
81.7    
81.8    
82.0    
82.2    
82.4    
82.5    
82.7    
82.9    
83.1    
83.2    
83.4    
83.6    
83.8    
83.9    
84.1    
84.3    
84.5    
84.6    
84.8    
85.0    
85.2    
85.3    
85.5    
85.7    
85.9    
86.0    
86.2    
86.4    
86.6    
86.7    
86.9    
87.1    
87.3    
87.4    
87.6    
87.8    
88.0    
88.1    
88.3    
88.5    
88.7    
88.8    
89.0    
89.2    
89.4    
89.5    
89.7    
89.9    
90.1    
90.2    
90.4    
90.6    
90.8    
90.9    
91.1    
91.3    
91.4    
91.6    
91.8    
92.0    
92.1    
92.3    
92.5    
92.7    
92.8    
93.0    
93.2    
93.4    
93.5    
93.7    
93.9    
94.1    
94.2    
94.4    
94.6    
94.8    
94.9    
95.1    
95.3    
95.5    
95.6    
95.8    
96.0    
96.2    
96.3    
96.5    
96.7    
96.9    
97.0    
97.2    
97.4    
97.6    
97.7    
97.9    
98.1    
98.3    
98.4    
98.6    
98.8    
99.0    
99.1    
99.3    
99.5    
99.7    
99.8    
-found 43 predictions from path traversal
Error with prediction: snap lend_intergenic: 38386, rend_intergenic: 8085  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42642, rend_intergenic: 40264  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49597, rend_intergenic: 47238  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85759, rend_intergenic: 79411  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92841, rend_intergenic: 85815  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102657, rend_intergenic: 100194  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104997, rend_intergenic: 103110  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 40 predictions persist after filtering for low support