-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_6/scaffold_6_2907572-3051759

-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 GeneMark_model.24722_t
Valid prediction for Augustus_model.g9724.t1
Valid prediction for GeneMark_model.24706_t
Valid prediction for snap_scaffold_6-snap.702-T1
Sorry, intron length (3) is less than minimum required (10)
Sorry, intron length (9) is less than minimum required (10)
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for snap_scaffold_6-snap.689-T1
Valid prediction for snap_scaffold_6-snap.706-T1
Valid prediction for GeneMark_model.24737_t
Valid prediction for snap_scaffold_6-snap.686-T1
Valid prediction for snap_scaffold_6-snap.695-T1
Valid prediction for snap_scaffold_6-snap.676-T1
Valid prediction for GeneMark_model.24715_t
Valid prediction for GeneMark_model.24746_t
Valid prediction for GeneMark_model.24707_t
Valid prediction for GeneMark_model.24728_t
Valid prediction for GlimmerHMM_glimmerT_14583-T1
Valid prediction for GlimmerHMM_glimmerT_14572-T1
Valid prediction for HiQ_model.g9713.t1
Valid prediction for GeneMark_model.24709_t
Valid prediction for snap_scaffold_6-snap.708-T1
Valid prediction for snap_scaffold_6-snap.691-T1
Valid prediction for GeneMark_model.24730_t
Valid prediction for pasa_asmbl_46738.p1
Valid prediction for GlimmerHMM_glimmerT_14586-T1
Valid prediction for CodingQuarry_transcript_54818-T1
Valid prediction for GlimmerHMM_glimmerT_14576-T1
Valid prediction for snap_scaffold_6-snap.683-T1
Valid prediction for snap_scaffold_6-snap.690-T1
Valid prediction for GeneMark_model.24720_t
Valid prediction for GeneMark_model.24743_t
Valid prediction for GeneMark_model.24713_t
Valid prediction for snap_scaffold_6-snap.698-T1
Valid prediction for GeneMark_model.24735_t
Valid prediction for pasa_asmbl_46737.p1
Valid prediction for GlimmerHMM_glimmerT_14588-T1
Valid prediction for HiQ_model.g9721.t1
Valid prediction for GeneMark_model.24727_t
Valid prediction for GeneMark_model.24719_t
Valid prediction for snap_scaffold_6-snap.677-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_14581-T1
Valid prediction for snap_scaffold_6-snap.707-T1
Valid prediction for GeneMark_model.24745_t
Valid prediction for snap_scaffold_6-snap.700-T1
Valid prediction for snap_scaffold_6-snap.693-T1
Valid prediction for GeneMark_model.24732_t
Valid prediction for GlimmerHMM_glimmerT_14595-T1
Valid prediction for CodingQuarry_transcript_54820-T1
Valid prediction for snap_scaffold_6-snap.685-T1
Valid prediction for GeneMark_model.24739_t
Valid prediction for GeneMark_model.24741_t
Valid prediction for snap_scaffold_6-snap.704-T1
Valid prediction for GlimmerHMM_glimmerT_14591-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: -)Couldn't classify 136913, 137058
Sorry, prediction pasa_asmbl_48136.p1 fails validation.
(ATG)	 AG	135831-135856	GT	GGG
(ACA)	 AG	135999-136113	GT	AGG
(CAA)	 AG	136325-136390	GT	TGG
(GAA)	 AG	136625-136814	GT	AGG
(GTG)	 AG	136913-137058	GT	TGG
-recovered pasa_asmbl_48136.p1, initial, 135831, 135856
-recovered pasa_asmbl_48136.p1, internal, 135831, 135856
-recovered pasa_asmbl_48136.p1, internal, 135999, 136113
-recovered pasa_asmbl_48136.p1, internal, 136325, 136390
-recovered pasa_asmbl_48136.p1, internal, 136625, 136814
-recovered pasa_asmbl_48136.p1, internal, 136913, 137058
Valid prediction for GeneMark_model.24729_t
Valid prediction for GlimmerHMM_glimmerT_14580-T1
Valid prediction for snap_scaffold_6-snap.699-T1
Valid prediction for GlimmerHMM_glimmerT_14579-T1
Valid prediction for CodingQuarry_transcript_54821-T1
Valid prediction for GeneMark_model.24734_t
Valid prediction for GlimmerHMM_glimmerT_14577-T1
Valid prediction for snap_scaffold_6-snap.694-T1
Valid prediction for GlimmerHMM_glimmerT_14573-T1
Valid prediction for snap_scaffold_6-snap.680-T1
Valid prediction for snap_scaffold_6-snap.679-T1
Valid prediction for HiQ_model.g9710.t1
Valid prediction for GeneMark_model.24712_t
Valid prediction for snap_scaffold_6-snap.687-T1
Valid prediction for CodingQuarry_transcript_54817-T1
Valid prediction for HiQ_model.g9722.t1
Valid prediction for GlimmerHMM_glimmerT_14584-T1
Valid prediction for GeneMark_model.24726_t
Valid prediction for GeneMark_model.24738_t
Valid prediction for Augustus_model.g9709.t1
Valid prediction for Augustus_model.g9723.t1
Valid prediction for snap_scaffold_6-snap.684-T1
Valid prediction for snap_scaffold_6-snap.688-T1
Valid prediction for GlimmerHMM_glimmerT_14592-T1
Couldn't classify 112435, 112548
Couldn't classify 114626, 114747
Sorry, prediction pasa_asmbl_48149.p1 fails validation.
(CTC)	 CC	112435-112548	GT	AGG
(CCC)	 AG	112688-112861	GT	AGG
(GTG)	 AG	112974-113061	GT	AGG
(GCG)	 AG	113180-113322	GT	AGG
(GAC)	 AG	114005-114032	GT	AGG
(ATG)	 AG	114158-114371	GT	AGG
(GGA)	 AG	114457-114530	GT	AGG
(GAG)	 AG	114626-114747	CC	CAC
-recovered pasa_asmbl_48149.p1, initial, 114158, 114371
-recovered pasa_asmbl_48149.p1, internal, 112688, 112861
-recovered pasa_asmbl_48149.p1, internal, 112974, 113061
-recovered pasa_asmbl_48149.p1, internal, 113180, 113322
-recovered pasa_asmbl_48149.p1, internal, 114005, 114032
-recovered pasa_asmbl_48149.p1, internal, 114158, 114371
-recovered pasa_asmbl_48149.p1, internal, 114457, 114530
Valid prediction for GlimmerHMM_glimmerT_14578-T1
Valid prediction for GeneMark_model.24740_t
Valid prediction for GlimmerHMM_glimmerT_14585-T1
Valid prediction for pasa_asmbl_48141.p1
Valid prediction for GlimmerHMM_glimmerT_14571-T1
Valid prediction for Augustus_model.g9711.t1
Valid prediction for HiQ_model.g9720.t1
Valid prediction for snap_scaffold_6-snap.705-T1
Valid prediction for Augustus_model.g9714.t1
Valid prediction for pasa_asmbl_48160.p1
Valid prediction for pasa_asmbl_48162.p1
Valid prediction for GlimmerHMM_glimmerT_14594-T1
Valid prediction for GeneMark_model.24708_t
Valid prediction for GlimmerHMM_glimmerT_14587-T1
Valid prediction for GeneMark_model.24725_t
Valid prediction for GeneMark_model.24742_t
Valid prediction for GlimmerHMM_glimmerT_14575-T1
Valid prediction for snap_scaffold_6-snap.681-T1
Valid prediction for GeneMark_model.24718_t
Valid prediction for GlimmerHMM_glimmerT_14582-T1
Couldn't classify 132509, 133039
Sorry, prediction pasa_asmbl_48137.p1 fails validation.
(GCC)	 CT	132509-133039	CC	CCC
Valid prediction for GlimmerHMM_glimmerT_14574-T1
Couldn't classify 115228, 115938
Couldn't classify 116158, 116506
Couldn't classify 116904, 117088
Sorry, prediction pasa_asmbl_48147.p2 fails validation.
(CCT)	 GC	115228-115938	GT	AGG
(GAG)	 AG	116158-116506	AT	TGA
(TTA)	 AC	116904-117088	GT	CTG
(GGC)	 AG	118098-118208	GT	AGG
(TTC)	 AG	118417-118536	GT	AGG
(ATG)	 AG	118667-118804	GT	CTG
(CCA)	 AG	118998-119171	AA	AAA
-recovered pasa_asmbl_48147.p2, initial, 118667, 118804
-recovered pasa_asmbl_48147.p2, terminal, 118998, 119171
-recovered pasa_asmbl_48147.p2, internal, 118098, 118208
-recovered pasa_asmbl_48147.p2, internal, 118417, 118536
-recovered pasa_asmbl_48147.p2, internal, 118667, 118804
Valid prediction for Augustus_model.g9716.t1
Valid prediction for Augustus_model.g9715.t1
Valid prediction for Augustus_model.g9717.t1
Valid prediction for GlimmerHMM_glimmerT_14593-T1
Valid prediction for GlimmerHMM_glimmerT_14590-T1
Couldn't classify 137767, 138165
Sorry, prediction pasa_asmbl_48134.p2 fails validation.
(GAG)	 CT	137767-138165	TT	AGT
Valid prediction for snap_scaffold_6-snap.701-T1
Couldn't classify 110668, 111318
Couldn't classify 111568, 111684
Sorry, prediction pasa_asmbl_48151.p1 fails validation.
(ACC)	 CA	110668-111318	GT	AGG
(ACG)	 AG	111568-111684	TC	CGT
Valid prediction for snap_scaffold_6-snap.682-T1
Valid prediction for GlimmerHMM_glimmerT_14589-T1
Valid prediction for GeneMark_model.24721_t
Valid prediction for CodingQuarry_transcript_54819-T1
Valid prediction for snap_scaffold_6-snap.703-T1
Valid prediction for GeneMark_model.24716_t
Valid prediction for GeneMark_model.24733_t
Couldn't classify 101617, 101734
Sorry, prediction pasa_asmbl_48152.p1 fails validation.
(TTT)	 TA	101617-101734	GT	AGG
(CCA)	 AG	102574-102863	GT	AGG
(GAC)	 AG	103023-103124	GT	CGG
(GTT)	 AG	103311-103485	GT	GGG
(GTG)	 AG	103601-103722	GT	AGG
(TTC)	 AG	103806-103871	GT	TGG
(CAA)	 AG	103972-104073	GT	TGG
(AGT)	 AG	104183-104293	GT	AGG
(ATG)	 AG	104506-104591	GT	GAG
(GGA)	 AG	104713-104771	GT	TGG
(TGC)	 AG	104886-104995	GT	AGG
(GGC)	 AG	105078-105245	GT	AGG
(GAA)	 AG	105389-105469	AG	GAA
-recovered pasa_asmbl_48152.p1, initial, 104506, 104591
-recovered pasa_asmbl_48152.p1, terminal, 105389, 105469
-recovered pasa_asmbl_48152.p1, internal, 102574, 102863
-recovered pasa_asmbl_48152.p1, internal, 103023, 103124
-recovered pasa_asmbl_48152.p1, internal, 103311, 103485
-recovered pasa_asmbl_48152.p1, internal, 103601, 103722
-recovered pasa_asmbl_48152.p1, internal, 103806, 103871
-recovered pasa_asmbl_48152.p1, internal, 103972, 104073
-recovered pasa_asmbl_48152.p1, internal, 104183, 104293
-recovered pasa_asmbl_48152.p1, internal, 104506, 104591
-recovered pasa_asmbl_48152.p1, internal, 104713, 104771
-recovered pasa_asmbl_48152.p1, internal, 104886, 104995
-recovered pasa_asmbl_48152.p1, internal, 105078, 105245
Valid prediction for GeneMark_model.24723_t
Valid prediction for HiQ_model.g9712.t1
Valid prediction for snap_scaffold_6-snap.697-T1
Valid prediction for GeneMark_model.24731_t
Valid prediction for Augustus_model.g9719.t1
Couldn't classify 52194, 52199
Sorry, prediction pasa_asmbl_48157.p1 fails validation.
(GCT)	 AC	52194-52199	GT	ATG
(GTA)	 AG	52599-52719	GT	CAG
(GTT)	 AG	53675-53808	GT	GTG
(GTT)	 AG	54248-54321	GT	AGG
(CCC)	 AG	54445-54512	GT	AGG
(ACC)	 AG	54762-54857	GT	AGG
(GCC)	 AG	55566-55727	GT	GTG
(CCC)	 AG	55831-55979	GT	AGG
(GAG)	 AG	57916-58047	GT	GGG
(GGC)	 AG	58201-58330	GT	AGG
(GTG)	 AG	58515-58692	GT	TGG
(GAG)	 AG	59636-59864	GG	GAG
-recovered pasa_asmbl_48157.p1, terminal, 59636, 59864
-recovered pasa_asmbl_48157.p1, internal, 52599, 52719
-recovered pasa_asmbl_48157.p1, internal, 53675, 53808
-recovered pasa_asmbl_48157.p1, internal, 54248, 54321
-recovered pasa_asmbl_48157.p1, internal, 54445, 54512
-recovered pasa_asmbl_48157.p1, internal, 54762, 54857
-recovered pasa_asmbl_48157.p1, internal, 55566, 55727
-recovered pasa_asmbl_48157.p1, internal, 55831, 55979
-recovered pasa_asmbl_48157.p1, internal, 57916, 58047
-recovered pasa_asmbl_48157.p1, internal, 58201, 58330
-recovered pasa_asmbl_48157.p1, internal, 58515, 58692
Valid prediction for snap_scaffold_6-snap.692-T1
Valid prediction for snap_scaffold_6-snap.696-T1
Couldn't classify 65949, 66400
Sorry, prediction pasa_asmbl_48155.p1 fails validation.
(GGT)	 AG	65949-66400	GT	AGG
(GCT)	 AG	67359-67419	GT	AGG
(GAT)	 AG	67512-67607	GT	AGG
(GAG)	 AG	67724-67885	GT	AGG
(TTT)	 AG	68477-68602	GT	CAG
(AAC)	 AG	68753-68973	GT	AGG
(GAT)	 AG	69117-69160	GT	AGG
(AGA)	 AG	69296-69378	GT	AGG
(ATC)	 AG	69600-69641	TC	GAT
-recovered pasa_asmbl_48155.p1, terminal, 69600, 69641
-recovered pasa_asmbl_48155.p1, internal, 65949, 66400
-recovered pasa_asmbl_48155.p1, internal, 67359, 67419
-recovered pasa_asmbl_48155.p1, internal, 67512, 67607
-recovered pasa_asmbl_48155.p1, internal, 67724, 67885
-recovered pasa_asmbl_48155.p1, internal, 68477, 68602
-recovered pasa_asmbl_48155.p1, internal, 68753, 68973
-recovered pasa_asmbl_48155.p1, internal, 69117, 69160
-recovered pasa_asmbl_48155.p1, internal, 69296, 69378
Valid prediction for GeneMark_model.24714_t
Valid prediction for Augustus_model.g9718.t1
Valid prediction for GlimmerHMM_glimmerT_14570-T1
Valid prediction for GeneMark_model.24710_t
Valid prediction for snap_scaffold_6-snap.678-T1
Valid prediction for GeneMark_model.24711_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11124, rend_intergenic: 6024  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56297, rend_intergenic: 52298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60192, rend_intergenic: 56747  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66415, rend_intergenic: 60820  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71990, rend_intergenic: 70735  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79666, rend_intergenic: 74704  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80979, rend_intergenic: 79934  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96796, rend_intergenic: 89315  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106289, rend_intergenic: 104288  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118036, rend_intergenic: 113681  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 144188
-exon list size: 591


building trellis

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71.3    
71.5    
71.7    
71.8    
72.0    
72.2    
72.3    
72.5    
72.7    
72.8    
73.0    
73.2    
73.4    
73.5    
73.7    
73.9    
74.0    
74.2    
74.4    
74.5    
74.7    
74.9    
75.0    
75.2    
75.4    
75.5    
75.7    
75.9    
76.1    
76.2    
76.4    
76.6    
76.7    
76.9    
77.1    
77.2    
77.4    
77.6    
77.7    
77.9    
78.1    
78.2    
78.4    
78.6    
78.8    
78.9    
79.1    
79.3    
79.4    
79.6    
79.8    
79.9    
80.1    
80.3    
80.4    
80.6    
80.8    
80.9    
81.1    
81.3    
81.5    
81.6    
81.8    
82.0    
82.1    
82.3    
82.5    
82.6    
82.8    
83.0    
83.1    
83.3    
83.5    
83.6    
83.8    
84.0    
84.1    
84.3    
84.5    
84.7    
84.8    
85.0    
85.2    
85.3    
85.5    
85.7    
85.8    
86.0    
86.2    
86.3    
86.5    
86.7    
86.8    
87.0    
87.2    
87.4    
87.5    
87.7    
87.9    
88.0    
88.2    
88.4    
88.5    
88.7    
88.9    
89.0    
89.2    
89.4    
89.5    
89.7    
89.9    
90.1    
90.2    
90.4    
90.6    
90.7    
90.9    
91.1    
91.2    
91.4    
91.6    
91.7    
91.9    
92.1    
92.2    
92.4    
92.6    
92.7    
92.9    
93.1    
93.3    
93.4    
93.6    
93.8    
93.9    
94.1    
94.3    
94.4    
94.6    
94.8    
94.9    
95.1    
95.3    
95.4    
95.6    
95.8    
96.0    
96.1    
96.3    
96.5    
96.6    
96.8    
97.0    
97.1    
97.3    
97.5    
97.6    
97.8    
98.0    
98.1    
98.3    
98.5    
98.7    
98.8    
99.0    
99.2    
99.3    
99.5    
99.7    
99.8    
-found 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 11124, rend_intergenic: 6024  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56297, rend_intergenic: 52298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60192, rend_intergenic: 56747  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66415, rend_intergenic: 60820  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71990, rend_intergenic: 70735  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79666, rend_intergenic: 74704  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80979, rend_intergenic: 79934  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96796, rend_intergenic: 89315  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106289, rend_intergenic: 104288  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118036, rend_intergenic: 113681  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support