-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_7200828-7359946

-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 CodingQuarry_transcript_10267-T1
Valid prediction for pasa_asmbl_7749.p1
Valid prediction for pasa_asmbl_7744.p1
Valid prediction for CodingQuarry_transcript_10275-T1
Valid prediction for snap_scaffold_12-snap.1307-T1
Valid prediction for Augustus_model.g19479.t1
Valid prediction for HiQ_model.g19495.t1
Valid prediction for GlimmerHMM_glimmerT_29543-T1
Valid prediction for GlimmerHMM_glimmerT_29546-T1
Valid prediction for GlimmerHMM_glimmerT_29527-T1
Valid prediction for GlimmerHMM_glimmerT_29542-T1
Valid prediction for snap_scaffold_12-snap.1314-T1
Valid prediction for snap_scaffold_12-snap.1332-T1
Valid prediction for snap_scaffold_12-snap.1339-T1
Valid prediction for Augustus_model.g19493.t1
Valid prediction for snap_scaffold_12-snap.1320-T1
Couldn't classify 107058, 107157
Sorry, prediction pasa_asmbl_7741.p1 fails validation.
(AGG)	 TC	107058-107157	GT	AGG
(GGT)	 AG	109215-109456	GT	AGG
(GTG)	 AG	109798-109968	GT	AGG
(GTG)	 AG	110287-110451	GT	AGG
(GAG)	 AG	110869-111399	TT	GAT
-recovered pasa_asmbl_7741.p1, terminal, 110869, 111399
-recovered pasa_asmbl_7741.p1, internal, 109215, 109456
-recovered pasa_asmbl_7741.p1, internal, 109798, 109968
-recovered pasa_asmbl_7741.p1, internal, 110287, 110451
Valid prediction for snap_scaffold_12-snap.1337-T1
Valid prediction for Augustus_model.g19490.t1
Valid prediction for snap_scaffold_12-snap.1317-T1
Valid prediction for HiQ_model.g19497.t1
Valid prediction for snap_scaffold_12-snap.1341-T1
Valid prediction for GlimmerHMM_glimmerT_29554-T1
Valid prediction for GlimmerHMM_glimmerT_29528-T1
Valid prediction for HiQ_model.g19488.t1
Valid prediction for Augustus_model.g19487.t1
Couldn't classify 91980, 92034
Couldn't classify 93043, 93168
Sorry, prediction pasa_asmbl_8204.p1 fails validation.
(GCG)	 TG	91980-92034	GT	AGG
(CTC)	 AG	92515-92759	GT	AGG
(AGT)	 AG	93043-93168	GT	AGG
-recovered pasa_asmbl_8204.p1, internal, 92515, 92759
-recovered pasa_asmbl_8204.p1, internal, 93043, 93168
Valid prediction for Augustus_model.g19486.t1
Couldn't classify 18726, 18854
Sorry, prediction pasa_asmbl_7726.p1 fails validation.
(CTC)	 CT	18726-18854	GT	TGG
(GCG)	 AG	19070-19100	GT	CGG
(GAT)	 AG	19691-19764	GT	GTG
(TTG)	 AG	21149-21230	GT	CGG
(CCT)	 AG	21445-21452	CC	GAC
-recovered pasa_asmbl_7726.p1, terminal, 21445, 21452
-recovered pasa_asmbl_7726.p1, internal, 19070, 19100
-recovered pasa_asmbl_7726.p1, internal, 19691, 19764
-recovered pasa_asmbl_7726.p1, internal, 21149, 21230
Couldn't classify 128151, 128165
Couldn't classify 128352, 128491
Sorry, prediction CodingQuarry_transcript_10273-T1 fails validation.
(ATG)	 CC	128151-128165	AG	CGA
(AGC)	 GC	128352-128491	GT	AGG
(CTG)	 AG	128990-129068	GT	AGG
(GTG)	 AG	129443-129637	TA	GAT
-recovered CodingQuarry_transcript_10273-T1, terminal, 129443, 129637
-recovered CodingQuarry_transcript_10273-T1, internal, 128990, 129068
Couldn't classify 84586, 84668
Sorry, prediction pasa_asmbl_7737.p1 fails validation.
(ATC)	 AC	84586-84668	GT	ACG
(TCA)	 AG	85533-85593	GT	ATG
(GGA)	 AG	85728-85809	GT	TGG
(GCC)	 AG	85908-86004	GT	GAG
(TGG)	 AG	86173-86353	GT	AGG
(ACC)	 AG	86567-86720	GT	CGG
(GTA)	 AG	86891-87126	GT	AGG
(ATG)	 AG	87270-87396	GT	TGG
(GTA)	 AG	87521-87600	GT	AGG
(GGA)	 AG	87723-87863	GT	TGG
(CAA)	 AG	88023-88119	GT	CGG
(GTG)	 AG	88207-88308	GT	AGG
(CCG)	 AG	88415-88658	GT	AGG
(AGC)	 AG	88740-88804	GT	TGG
(GGC)	 AG	88944-89020	GT	AGG
(GTT)	 AG	89194-89268	GT	CCG
(ATC)	 AG	89367-89480	GT	AGG
(AGG)	 AG	89613-89725	GT	AGG
(CAA)	 AG	89909-90009	GT	TGG
(ATG)	 AG	90317-90426	CC	AAC
-recovered pasa_asmbl_7737.p1, initial, 87270, 87396
-recovered pasa_asmbl_7737.p1, terminal, 90317, 90426
-recovered pasa_asmbl_7737.p1, internal, 85533, 85593
-recovered pasa_asmbl_7737.p1, internal, 85728, 85809
-recovered pasa_asmbl_7737.p1, internal, 85908, 86004
-recovered pasa_asmbl_7737.p1, internal, 86173, 86353
-recovered pasa_asmbl_7737.p1, internal, 86567, 86720
-recovered pasa_asmbl_7737.p1, internal, 86891, 87126
-recovered pasa_asmbl_7737.p1, internal, 87270, 87396
-recovered pasa_asmbl_7737.p1, internal, 87521, 87600
-recovered pasa_asmbl_7737.p1, internal, 87723, 87863
-recovered pasa_asmbl_7737.p1, internal, 88023, 88119
-recovered pasa_asmbl_7737.p1, internal, 88207, 88308
-recovered pasa_asmbl_7737.p1, internal, 88415, 88658
-recovered pasa_asmbl_7737.p1, internal, 88740, 88804
-recovered pasa_asmbl_7737.p1, internal, 88944, 89020
-recovered pasa_asmbl_7737.p1, internal, 89194, 89268
-recovered pasa_asmbl_7737.p1, internal, 89367, 89480
-recovered pasa_asmbl_7737.p1, internal, 89613, 89725
-recovered pasa_asmbl_7737.p1, internal, 89909, 90009
Valid prediction for Augustus_model.g19492.t1
Valid prediction for snap_scaffold_12-snap.1310-T1
Couldn't classify 66620, 66850
Sorry, prediction pasa_asmbl_7733.p1 fails validation.
(ATG)	 AG	65740-65847	GT	AGG
(ACC)	 AG	66620-66850	AA	TGA
-recovered pasa_asmbl_7733.p1, initial, 65740, 65847
-recovered pasa_asmbl_7733.p1, internal, 65740, 65847
Valid prediction for snap_scaffold_12-snap.1334-T1
Valid prediction for GlimmerHMM_glimmerT_29553-T1
Valid prediction for snap_scaffold_12-snap.1324-T1
Couldn't classify 80912, 81940
Sorry, prediction pasa_asmbl_7736.p1 fails validation.
(GCC)	 CA	80912-81940	GA	GAG
Valid prediction for CodingQuarry_transcript_10274-T1
Valid prediction for Augustus_model.g19478.t1
Valid prediction for pasa_asmbl_7745.p1
Valid prediction for CodingQuarry_transcript_10266-T1
Valid prediction for Augustus_model.g19498.t1
Valid prediction for HiQ_model.g19499.t1
Valid prediction for GlimmerHMM_glimmerT_29549-T1
Valid prediction for snap_scaffold_12-snap.1312-T1
Valid prediction for GlimmerHMM_glimmerT_29544-T1
Valid prediction for GlimmerHMM_glimmerT_29541-T1
Valid prediction for snap_scaffold_12-snap.1328-T1
Valid prediction for snap_scaffold_12-snap.1342-T1
Valid prediction for snap_scaffold_12-snap.1327-T1
Valid prediction for Augustus_model.g19483.t1
Couldn't classify 95669, 95877
Sorry, prediction pasa_asmbl_7738.p2 fails validation.
(TCA)	 CT	95669-95877	GT	AGG
(CGT)	 AG	96010-96081	GT	GGG
(GGA)	 AG	96278-96446	GT	AGG
(CAA)	 AG	96580-96651	AG	AGA
-recovered pasa_asmbl_7738.p2, terminal, 96580, 96651
-recovered pasa_asmbl_7738.p2, internal, 96010, 96081
-recovered pasa_asmbl_7738.p2, internal, 96278, 96446
Valid prediction for snap_scaffold_12-snap.1329-T1
Valid prediction for GlimmerHMM_glimmerT_29538-T1
Valid prediction for GlimmerHMM_glimmerT_29547-T1
Valid prediction for GlimmerHMM_glimmerT_29526-T1
Couldn't classify 68270, 68362
Sorry, prediction pasa_asmbl_7734.p1 fails validation.
(AAC)	 CC	68270-68362	GT	AGG
(ATC)	 AG	68519-68677	GT	AGG
(GTG)	 AG	68900-69007	GT	AGG
(ATG)	 AG	69103-69216	GT	AGG
(TCC)	 AG	69390-69545	GT	GGG
(ACG)	 AG	69670-69858	GT	AGG
(GCA)	 AG	70258-70333	GT	AGG
(AAA)	 AG	70494-70697	GT	AGG
(AGC)	 AG	71011-71159	GT	AGG
(GAA)	 AG	71294-71386	GT	CAG
(GTG)	 AG	71503-71799	GT	CGG
(GCT)	 AG	71886-71964	GT	GGG
(GCC)	 AG	72355-72479	GG	GAG
-recovered pasa_asmbl_7734.p1, initial, 69103, 69216
add_exon() Sorry, pasa_asmbl_7734.p1 70258-70333-terminal-3 is invalid.
-recovered pasa_asmbl_7734.p1, terminal, 70258, 70333
-recovered pasa_asmbl_7734.p1, terminal, 72355, 72479
-recovered pasa_asmbl_7734.p1, internal, 68519, 68677
-recovered pasa_asmbl_7734.p1, internal, 68900, 69007
-recovered pasa_asmbl_7734.p1, internal, 69103, 69216
-recovered pasa_asmbl_7734.p1, internal, 69390, 69545
-recovered pasa_asmbl_7734.p1, internal, 69670, 69858
-recovered pasa_asmbl_7734.p1, internal, 70258, 70333
-recovered pasa_asmbl_7734.p1, internal, 70494, 70697
-recovered pasa_asmbl_7734.p1, internal, 71011, 71159
-recovered pasa_asmbl_7734.p1, internal, 71294, 71386
-recovered pasa_asmbl_7734.p1, internal, 71503, 71799
-recovered pasa_asmbl_7734.p1, internal, 71886, 71964
Valid prediction for GlimmerHMM_glimmerT_29555-T1
Valid prediction for snap_scaffold_12-snap.1315-T1
Valid prediction for CodingQuarry_transcript_10272-T1
Valid prediction for GlimmerHMM_glimmerT_29551-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 HiQ_model.g19485.t1
Valid prediction for snap_scaffold_12-snap.1336-T1
Valid prediction for GlimmerHMM_glimmerT_29536-T1
Valid prediction for snap_scaffold_12-snap.1325-T1
Valid prediction for pasa_asmbl_8564.p1
Valid prediction for snap_scaffold_12-snap.1326-T1
Valid prediction for snap_scaffold_12-snap.1323-T1
Valid prediction for snap_scaffold_12-snap.1319-T1
Valid prediction for Augustus_model.g19481.t1
Valid prediction for GlimmerHMM_glimmerT_29532-T1
Valid prediction for Augustus_model.g19480.t1
Valid prediction for GlimmerHMM_glimmerT_29545-T1
Valid prediction for snap_scaffold_12-snap.1313-T1
Valid prediction for snap_scaffold_12-snap.1330-T1
Valid prediction for CodingQuarry_transcript_10270-T1
Valid prediction for GlimmerHMM_glimmerT_29540-T1
Valid prediction for snap_scaffold_12-snap.1322-T1
Valid prediction for Augustus_model.g19491.t1
Valid prediction for GlimmerHMM_glimmerT_29530-T1
Valid prediction for snap_scaffold_12-snap.1308-T1
Valid prediction for pasa_asmbl_8568.p1
Couldn't classify 123397, 123444
Couldn't classify 123559, 123993
Sorry, prediction pasa_asmbl_8562.p1 fails validation.
(GAC)	 AG	123397-123444	GT	AGG
(TTT)	 AG	123559-123993	GA	GAG
-recovered pasa_asmbl_8562.p1, internal, 123397, 123444
Couldn't classify 121643, 121750
Couldn't classify 122652, 122699
Sorry, prediction pasa_asmbl_9254.p1 fails validation.
(CTG)	 AG	121643-121750	GT	AGG
(GAG)	 AG	122394-122540	GT	GGG
(GAG)	 AG	122652-122699	AT	ACA
-recovered pasa_asmbl_9254.p1, internal, 121643, 121750
-recovered pasa_asmbl_9254.p1, internal, 122394, 122540
Valid prediction for HiQ_model.g19484.t1
Couldn't classify 26505, 27065
Sorry, prediction pasa_asmbl_8573.p1 fails validation.
(GGT)	 GT	26505-27065	GT	AGG
(GCA)	 AG	27200-27319	GT	AGG
(GTG)	 AG	27457-27554	GT	AGG
(ATG)	 AG	27810-27903	GT	TAG
(GAG)	 AG	28093-28242	CA	AGC
add_exon() Sorry, pasa_asmbl_8573.p1 27810-27903-initial-1 is invalid.
-recovered pasa_asmbl_8573.p1, initial, 27810, 27903
-recovered pasa_asmbl_8573.p1, terminal, 28093, 28242
-recovered pasa_asmbl_8573.p1, internal, 27200, 27319
-recovered pasa_asmbl_8573.p1, internal, 27457, 27554
-recovered pasa_asmbl_8573.p1, internal, 27810, 27903
Valid prediction for HiQ_model.g19496.t1
Valid prediction for CodingQuarry_transcript_10268-T1
Valid prediction for snap_scaffold_12-snap.1338-T1
Valid prediction for GlimmerHMM_glimmerT_29537-T1
Valid prediction for snap_scaffold_12-snap.1335-T1
Valid prediction for CodingQuarry_transcript_10271-T1
Valid prediction for GlimmerHMM_glimmerT_29534-T1
Valid prediction for HiQ_model.g19494.t1
Valid prediction for pasa_asmbl_8569.p1
Valid prediction for GlimmerHMM_glimmerT_29539-T1
Valid prediction for GlimmerHMM_glimmerT_29552-T1
Valid prediction for GlimmerHMM_glimmerT_29531-T1
Valid prediction for GlimmerHMM_glimmerT_29556-T1
Valid prediction for snap_scaffold_12-snap.1333-T1
Valid prediction for HiQ_model.g19489.t1
Valid prediction for snap_scaffold_12-snap.1311-T1
Valid prediction for snap_scaffold_12-snap.1340-T1
Valid prediction for GlimmerHMM_glimmerT_29550-T1
Valid prediction for snap_scaffold_12-snap.1309-T1
Couldn't classify 129201, 129254
Sorry, prediction pasa_asmbl_9229.p1 fails validation.
(ATG)	 GG	127433-127578	GT	AGG
(GTA)	 AG	127933-128076	GT	AGG
(GCT)	 AG	128593-128779	GT	AGG
(TTA)	 AG	129201-129254	CA	AGC
-recovered pasa_asmbl_9229.p1, initial, 127433, 127578
-recovered pasa_asmbl_9229.p1, internal, 127933, 128076
-recovered pasa_asmbl_9229.p1, internal, 128593, 128779
Valid prediction for snap_scaffold_12-snap.1316-T1
Valid prediction for pasa_asmbl_8572.p1
Valid prediction for GlimmerHMM_glimmerT_29535-T1
Valid prediction for GlimmerHMM_glimmerT_29529-T1
Valid prediction for snap_scaffold_12-snap.1318-T1
Valid prediction for Augustus_model.g19482.t1
Valid prediction for GlimmerHMM_glimmerT_29548-T1
Valid prediction for GlimmerHMM_glimmerT_29533-T1
Valid prediction for snap_scaffold_12-snap.1331-T1
Valid prediction for snap_scaffold_12-snap.1321-T1
Valid prediction for Augustus_model.g19500.t1
Valid prediction for CodingQuarry_transcript_10269-T1
Valid prediction for snap_scaffold_12-snap.1343-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15988, rend_intergenic: 6987  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17605, rend_intergenic: 16048  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27498, rend_intergenic: 20935  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37726, rend_intergenic: 29257  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39134, rend_intergenic: 37850  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47332, rend_intergenic: 44549  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56414, rend_intergenic: 53286  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101929, rend_intergenic: 98452  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108416, rend_intergenic: 106368  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124561, rend_intergenic: 117780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144795, rend_intergenic: 141137  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 159119
-exon list size: 401


building trellis

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78.9    
79.2    
79.4    
79.7    
79.9    
80.1    
80.4    
80.6    
80.9    
81.1    
81.4    
81.6    
81.9    
82.1    
82.4    
82.6    
82.9    
83.1    
83.4    
83.6    
83.9    
84.1    
84.4    
84.6    
84.9    
85.1    
85.4    
85.6    
85.9    
86.1    
86.4    
86.6    
86.8    
87.1    
87.3    
87.6    
87.8    
88.1    
88.3    
88.6    
88.8    
89.1    
89.3    
89.6    
89.8    
90.1    
90.3    
90.6    
90.8    
91.1    
91.3    
91.6    
91.8    
92.1    
92.3    
92.6    
92.8    
93.1    
93.3    
93.5    
93.8    
94.0    
94.3    
94.5    
94.8    
95.0    
95.3    
95.5    
95.8    
96.0    
96.3    
96.5    
96.8    
97.0    
97.3    
97.5    
97.8    
98.0    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 15988, rend_intergenic: 6987  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17605, rend_intergenic: 16048  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27498, rend_intergenic: 20935  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37726, rend_intergenic: 29257  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39134, rend_intergenic: 37850  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47332, rend_intergenic: 44549  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56414, rend_intergenic: 53286  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101929, rend_intergenic: 98452  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108416, rend_intergenic: 106368  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124561, rend_intergenic: 117780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144795, rend_intergenic: 141137  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 27 predictions persist after filtering for low support