-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_10/scaffold_10_1942456-2119651

-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.42212_t
Valid prediction for GeneMark_model.42200_t
Valid prediction for GeneMark_model.42235_t
Valid prediction for GeneMark_model.42227_t
Valid prediction for GeneMark_model.42225_t
Valid prediction for snap_scaffold_10-snap.438-T1
Valid prediction for snap_scaffold_10-snap.424-T1
Valid prediction for snap_scaffold_10-snap.446-T1
Valid prediction for snap_scaffold_10-snap.419-T1
Valid prediction for GeneMark_model.42210_t
Valid prediction for GeneMark_model.42248_t
Valid prediction for GeneMark_model.42246_t
Valid prediction for GlimmerHMM_glimmerT_24739-T1
Valid prediction for GeneMark_model.42213_t
Valid prediction for GeneMark_model.42240_t
Valid prediction for snap_scaffold_10-snap.409-T1
Valid prediction for snap_scaffold_10-snap.414-T1
Valid prediction for Augustus_model.g16585.t1
Valid prediction for GeneMark_model.42253_t
Valid prediction for snap_scaffold_10-snap.444-T1
Valid prediction for snap_scaffold_10-snap.425-T1
Valid prediction for GlimmerHMM_glimmerT_24727-T1
Valid prediction for GlimmerHMM_glimmerT_24736-T1
Valid prediction for GeneMark_model.42232_t
Valid prediction for snap_scaffold_10-snap.422-T1
Valid prediction for GeneMark_model.42237_t
Valid prediction for GeneMark_model.42209_t
Valid prediction for GeneMark_model.42206_t
Valid prediction for GeneMark_model.42202_t
Valid prediction for Augustus_model.g16575.t1
Valid prediction for GeneMark_model.42223_t
Valid prediction for GlimmerHMM_glimmerT_24735-T1
Valid prediction for GlimmerHMM_glimmerT_24717-T1
Valid prediction for GeneMark_model.42244_t
Valid prediction for GeneMark_model.42198_t
Valid prediction for GlimmerHMM_glimmerT_24723-T1
Valid prediction for Augustus_model.g16572.t1
Valid prediction for snap_scaffold_10-snap.443-T1
Valid prediction for GeneMark_model.42250_t
Valid prediction for snap_scaffold_10-snap.435-T1
Valid prediction for GlimmerHMM_glimmerT_24737-T1
Valid prediction for GeneMark_model.42238_t
Valid prediction for snap_scaffold_10-snap.429-T1
Valid prediction for GeneMark_model.42208_t
Valid prediction for snap_scaffold_10-snap.413-T1
Valid prediction for GeneMark_model.42242_t
Valid prediction for snap_scaffold_10-snap.427-T1
Valid prediction for snap_scaffold_10-snap.416-T1
Valid prediction for GeneMark_model.42215_t
Valid prediction for snap_scaffold_10-snap.411-T1
Valid prediction for snap_scaffold_10-snap.432-T1
Valid prediction for GeneMark_model.42255_t
Valid prediction for snap_scaffold_10-snap.431-T1
Valid prediction for GeneMark_model.42203_t
Valid prediction for GeneMark_model.42220_t
Valid prediction for snap_scaffold_10-snap.436-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 GeneMark_model.42216_t
Valid prediction for GeneMark_model.42214_t
Valid prediction for Augustus_model.g16579.t1
Valid prediction for snap_scaffold_10-snap.442-T1
Valid prediction for snap_scaffold_10-snap.447-T1
Valid prediction for GlimmerHMM_glimmerT_24730-T1
Valid prediction for snap_scaffold_10-snap.440-T1
Valid prediction for snap_scaffold_10-snap.439-T1
Valid prediction for Augustus_model.g16588.t1
Valid prediction for snap_scaffold_10-snap.420-T1
Valid prediction for GeneMark_model.42249_t
Couldn't classify 134708, 134836
Sorry, prediction pasa_asmbl_3006.p1 fails validation.
(GCC)	 GC	134708-134836	GT	TGG
(GAG)	 AG	134996-135112	GT	AGG
(GAC)	 AG	135311-135380	GT	TGG
(GGT)	 AG	135529-135645	GT	AGG
(CTG)	 AG	135907-136055	GT	AGG
(GTG)	 AG	136230-136382	GT	CGG
(GAG)	 AG	136514-136630	GT	ACG
(GTG)	 AG	136730-136814	GT	TGG
(AAG)	 AG	137538-137653	GT	CGG
(GAT)	 AG	137821-137943	CC	GAC
-recovered pasa_asmbl_3006.p1, terminal, 137821, 137943
-recovered pasa_asmbl_3006.p1, internal, 134996, 135112
-recovered pasa_asmbl_3006.p1, internal, 135311, 135380
-recovered pasa_asmbl_3006.p1, internal, 135529, 135645
-recovered pasa_asmbl_3006.p1, internal, 135907, 136055
-recovered pasa_asmbl_3006.p1, internal, 136230, 136382
-recovered pasa_asmbl_3006.p1, internal, 136514, 136630
-recovered pasa_asmbl_3006.p1, internal, 136730, 136814
-recovered pasa_asmbl_3006.p1, internal, 137538, 137653
Valid prediction for GeneMark_model.42228_t
Valid prediction for GlimmerHMM_glimmerT_24719-T1
Valid prediction for Augustus_model.g16574.t1
Valid prediction for GeneMark_model.42245_t
Valid prediction for GeneMark_model.42239_t
Valid prediction for GlimmerHMM_glimmerT_24720-T1
Valid prediction for GeneMark_model.42231_t
Valid prediction for GeneMark_model.42229_t
Couldn't classify 124686, 124778
Couldn't classify 131564, 131663
Sorry, prediction pasa_asmbl_3007.p1 fails validation.
(GGG)	 GT	124686-124778	GT	AGG
(AAC)	 AG	125381-125458	GT	AGG
(GAA)	 AG	125601-125806	GT	GAG
(GAT)	 AG	126068-126199	GT	AGG
(ACA)	 AG	126289-126412	GT	TGG
(GTG)	 AG	127733-127846	GT	AGG
(GTG)	 AG	128303-128369	GT	AGG
(CCC)	 AG	128465-128614	GT	CGG
(GTC)	 AG	130941-131004	GT	AGG
(TGT)	 AG	131564-131663	CG	AGC
-recovered pasa_asmbl_3007.p1, internal, 125381, 125458
-recovered pasa_asmbl_3007.p1, internal, 125601, 125806
-recovered pasa_asmbl_3007.p1, internal, 126068, 126199
-recovered pasa_asmbl_3007.p1, internal, 126289, 126412
-recovered pasa_asmbl_3007.p1, internal, 127733, 127846
-recovered pasa_asmbl_3007.p1, internal, 128303, 128369
-recovered pasa_asmbl_3007.p1, internal, 128465, 128614
-recovered pasa_asmbl_3007.p1, internal, 130941, 131004
Valid prediction for GeneMark_model.42226_t
Valid prediction for GlimmerHMM_glimmerT_24738-T1
Valid prediction for GeneMark_model.42197_t
Valid prediction for GeneMark_model.42230_t
Valid prediction for Augustus_model.g16573.t1
Valid prediction for GeneMark_model.42201_t
Valid prediction for GlimmerHMM_glimmerT_24731-T1
Valid prediction for GlimmerHMM_glimmerT_24729-T1
Valid prediction for snap_scaffold_10-snap.418-T1
Valid prediction for GlimmerHMM_glimmerT_24721-T1
Valid prediction for GlimmerHMM_glimmerT_24724-T1
Valid prediction for GeneMark_model.42218_t
Valid prediction for GeneMark_model.42251_t
Valid prediction for snap_scaffold_10-snap.408-T1
Valid prediction for GeneMark_model.42222_t
Valid prediction for snap_scaffold_10-snap.428-T1
Valid prediction for GeneMark_model.42219_t
Valid prediction for snap_scaffold_10-snap.441-T1
Valid prediction for GeneMark_model.42236_t
Valid prediction for Augustus_model.g16586.t1
Valid prediction for Augustus_model.g16582.t1
Valid prediction for snap_scaffold_10-snap.434-T1
Valid prediction for snap_scaffold_10-snap.410-T1
Valid prediction for GeneMark_model.42241_t
Valid prediction for snap_scaffold_10-snap.407-T1
Valid prediction for GlimmerHMM_glimmerT_24741-T1
Valid prediction for GeneMark_model.42234_t
Valid prediction for Augustus_model.g16589.t1
Valid prediction for GlimmerHMM_glimmerT_24732-T1
Couldn't classify 62420, 62464
Couldn't classify 64776, 64903
Sorry, prediction pasa_asmbl_3018.p1 fails validation.
(AAC)	 CC	62420-62464	GT	AGG
(AGG)	 AG	62643-62786	GT	AGG
(CTG)	 AG	62947-63049	GT	TGG
(ACA)	 AG	63298-63500	GT	AGG
(GAG)	 AG	63688-63828	GT	AGG
(ACG)	 AG	64034-64133	GT	CGG
(ACG)	 AG	64776-64903	AG	CCA
-recovered pasa_asmbl_3018.p1, internal, 62643, 62786
-recovered pasa_asmbl_3018.p1, internal, 62947, 63049
-recovered pasa_asmbl_3018.p1, internal, 63298, 63500
-recovered pasa_asmbl_3018.p1, internal, 63688, 63828
-recovered pasa_asmbl_3018.p1, internal, 64034, 64133
Valid prediction for Augustus_model.g16576.t1
Valid prediction for GeneMark_model.42211_t
Valid prediction for snap_scaffold_10-snap.437-T1
Valid prediction for GeneMark_model.42217_t
Valid prediction for HiQ_model.g16583.t1
Couldn't classify 74523, 74572
Couldn't classify 75471, 75545
Sorry, prediction pasa_asmbl_3015.p1 fails validation.
(TAC)	 GG	74523-74572	GT	AGG
(CAG)	 AG	74664-74784	GT	GGG
(GAG)	 AG	75077-75250	GT	GGG
(GTG)	 AG	75471-75545	CA	GAC
-recovered pasa_asmbl_3015.p1, internal, 74664, 74784
-recovered pasa_asmbl_3015.p1, internal, 75077, 75250
Valid prediction for Augustus_model.g16580.t1
Valid prediction for snap_scaffold_10-snap.423-T1
Couldn't classify 97014, 97089
Sorry, prediction pasa_asmbl_3011.p1 fails validation.
(GTG)	 CA	97014-97089	GT	CAG
(TCA)	 AG	97485-97551	GT	AGG
(GTT)	 AG	97805-97889	GT	TTG
(GTG)	 AG	98079-98158	GT	AAG
(GCA)	 AG	98489-98588	GT	CGG
(ACA)	 AG	98727-98798	AA	GAA
-recovered pasa_asmbl_3011.p1, terminal, 98727, 98798
-recovered pasa_asmbl_3011.p1, internal, 97485, 97551
-recovered pasa_asmbl_3011.p1, internal, 97805, 97889
-recovered pasa_asmbl_3011.p1, internal, 98079, 98158
-recovered pasa_asmbl_3011.p1, internal, 98489, 98588
Valid prediction for snap_scaffold_10-snap.433-T1
Valid prediction for snap_scaffold_10-snap.426-T1
Valid prediction for Augustus_model.g16587.t1
Valid prediction for GlimmerHMM_glimmerT_24718-T1
Valid prediction for GeneMark_model.42224_t
Valid prediction for GeneMark_model.42233_t
Valid prediction for Augustus_model.g16571.t1
Valid prediction for GeneMark_model.42243_t
Valid prediction for GeneMark_model.42205_t
Valid prediction for GeneMark_model.42256_t
Valid prediction for snap_scaffold_10-snap.445-T1
Valid prediction for GlimmerHMM_glimmerT_24728-T1
Valid prediction for GeneMark_model.42252_t
Valid prediction for GlimmerHMM_glimmerT_24733-T1
Valid prediction for CodingQuarry_transcript_5285-T1
Valid prediction for GlimmerHMM_glimmerT_24725-T1
Valid prediction for GeneMark_model.42207_t
Valid prediction for Augustus_model.g16578.t1
Valid prediction for Augustus_model.g16584.t1
Valid prediction for Augustus_model.g16577.t1
Valid prediction for Augustus_model.g16581.t1
Valid prediction for snap_scaffold_10-snap.430-T1
Valid prediction for GeneMark_model.42221_t
Valid prediction for snap_scaffold_10-snap.421-T1
Valid prediction for CodingQuarry_transcript_5284-T1
Valid prediction for GlimmerHMM_glimmerT_24726-T1
Valid prediction for GlimmerHMM_glimmerT_24740-T1
Valid prediction for GlimmerHMM_glimmerT_24722-T1
Valid prediction for GeneMark_model.42247_t
Couldn't classify 75600, 75636
Couldn't classify 77628, 77737
Sorry, prediction pasa_asmbl_3013.p1 fails validation.
(CTG)	 GG	75600-75636	GT	CGG
(ACC)	 AG	76154-76345	GT	CGG
(CCA)	 AG	77628-77737	GA	GGG
-recovered pasa_asmbl_3013.p1, internal, 76154, 76345
Valid prediction for snap_scaffold_10-snap.417-T1
Valid prediction for GlimmerHMM_glimmerT_24734-T1
Valid prediction for GeneMark_model.42254_t
Valid prediction for snap_scaffold_10-snap.412-T1
Valid prediction for snap_scaffold_10-snap.415-T1
Valid prediction for GeneMark_model.42204_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 4990, rend_intergenic: 3052  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 6939, rend_intergenic: 6816  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11902, rend_intergenic: 8178  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19668, rend_intergenic: 14439  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30639, rend_intergenic: 26603  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57262, rend_intergenic: 50011  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86590, rend_intergenic: 78399  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100112, rend_intergenic: 99193  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106856, rend_intergenic: 100531  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119284, rend_intergenic: 113032  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127124, rend_intergenic: 120998  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130650, rend_intergenic: 129561  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144961, rend_intergenic: 132729  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169075, rend_intergenic: 167162  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175499, rend_intergenic: 170735  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 177196
-exon list size: 778


building trellis

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62.9    
63.1    
63.2    
63.3    
63.5    
63.6    
63.7    
63.8    
64.0    
64.1    
64.2    
64.4    
64.5    
64.6    
64.7    
64.9    
65.0    
65.1    
65.3    
65.4    
65.5    
65.6    
65.8    
65.9    
66.0    
66.2    
66.3    
66.4    
66.5    
66.7    
66.8    
66.9    
67.1    
67.2    
67.3    
67.4    
67.6    
67.7    
67.8    
67.9    
68.1    
68.2    
68.3    
68.5    
68.6    
68.7    
68.8    
69.0    
69.1    
69.2    
69.4    
69.5    
69.6    
69.7    
69.9    
70.0    
70.1    
70.3    
70.4    
70.5    
70.6    
70.8    
70.9    
71.0    
71.2    
71.3    
71.4    
71.5    
71.7    
71.8    
71.9    
72.1    
72.2    
72.3    
72.4    
72.6    
72.7    
72.8    
72.9    
73.1    
73.2    
73.3    
73.5    
73.6    
73.7    
73.8    
74.0    
74.1    
74.2    
74.4    
74.5    
74.6    
74.7    
74.9    
75.0    
75.1    
75.3    
75.4    
75.5    
75.6    
75.8    
75.9    
76.0    
76.2    
76.3    
76.4    
76.5    
76.7    
76.8    
76.9    
77.1    
77.2    
77.3    
77.4    
77.6    
77.7    
77.8    
77.9    
78.1    
78.2    
78.3    
78.5    
78.6    
78.7    
78.8    
79.0    
79.1    
79.2    
79.4    
79.5    
79.6    
79.7    
79.9    
80.0    
80.1    
80.3    
80.4    
80.5    
80.6    
80.8    
80.9    
81.0    
81.2    
81.3    
81.4    
81.5    
81.7    
81.8    
81.9    
82.1    
82.2    
82.3    
82.4    
82.6    
82.7    
82.8    
82.9    
83.1    
83.2    
83.3    
83.5    
83.6    
83.7    
83.8    
84.0    
84.1    
84.2    
84.4    
84.5    
84.6    
84.7    
84.9    
85.0    
85.1    
85.3    
85.4    
85.5    
85.6    
85.8    
85.9    
86.0    
86.2    
86.3    
86.4    
86.5    
86.7    
86.8    
86.9    
87.1    
87.2    
87.3    
87.4    
87.6    
87.7    
87.8    
87.9    
88.1    
88.2    
88.3    
88.5    
88.6    
88.7    
88.8    
89.0    
89.1    
89.2    
89.4    
89.5    
89.6    
89.7    
89.9    
90.0    
90.1    
90.3    
90.4    
90.5    
90.6    
90.8    
90.9    
91.0    
91.2    
91.3    
91.4    
91.5    
91.7    
91.8    
91.9    
92.1    
92.2    
92.3    
92.4    
92.6    
92.7    
92.8    
92.9    
93.1    
93.2    
93.3    
93.5    
93.6    
93.7    
93.8    
94.0    
94.1    
94.2    
94.4    
94.5    
94.6    
94.7    
94.9    
95.0    
95.1    
95.3    
95.4    
95.5    
95.6    
95.8    
95.9    
96.0    
96.2    
96.3    
96.4    
96.5    
96.7    
96.8    
96.9    
97.1    
97.2    
97.3    
97.4    
97.6    
97.7    
97.8    
97.9    
98.1    
98.2    
98.3    
98.5    
98.6    
98.7    
98.8    
99.0    
99.1    
99.2    
99.4    
99.5    
99.6    
99.7    
99.9    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 4990, rend_intergenic: 3052  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 6939, rend_intergenic: 6816  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11902, rend_intergenic: 8178  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19668, rend_intergenic: 14439  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30639, rend_intergenic: 26603  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57262, rend_intergenic: 50011  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86590, rend_intergenic: 78399  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100112, rend_intergenic: 99193  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106856, rend_intergenic: 100531  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119284, rend_intergenic: 113032  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127124, rend_intergenic: 120998  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130650, rend_intergenic: 129561  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144961, rend_intergenic: 132729  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169075, rend_intergenic: 167162  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175499, rend_intergenic: 170735  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support