-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_28/scaffold_28_9667849-9873027

-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_60893-T1
Valid prediction for GeneMark_model.106091_t
Valid prediction for snap_scaffold_28-snap.2179-T1
Valid prediction for GeneMark_model.106055_t
Valid prediction for GeneMark_model.106058_t
Valid prediction for GlimmerHMM_glimmerT_60874-T1
Valid prediction for GeneMark_model.106090_t
Valid prediction for snap_scaffold_28-snap.2212-T1
Valid prediction for GeneMark_model.106067_t
Valid prediction for snap_scaffold_28-snap.2210-T1
Couldn't classify 99895, 100058
Couldn't classify 100448, 100601
Sorry, prediction pasa_asmbl_38560.p1 fails validation.
(GGC)	 CG	99895-100058	GT	CGG
(GAT)	 AG	100448-100601	AT	GGA
Valid prediction for snap_scaffold_28-snap.2215-T1
Valid prediction for GlimmerHMM_glimmerT_60887-T1
Valid prediction for CodingQuarry_transcript_43667-T1
Valid prediction for GeneMark_model.106088_t
Valid prediction for snap_scaffold_28-snap.2216-T1
Valid prediction for GlimmerHMM_glimmerT_60888-T1
Valid prediction for GlimmerHMM_glimmerT_60886-T1
Valid prediction for HiQ_model.g40512.t1
Valid prediction for snap_scaffold_28-snap.2203-T1
Valid prediction for GeneMark_model.106074_t
Valid prediction for GlimmerHMM_glimmerT_60877-T1
Valid prediction for GlimmerHMM_glimmerT_60885-T1
Valid prediction for pasa_asmbl_38496.p1
Valid prediction for GlimmerHMM_glimmerT_60891-T1
Valid prediction for GeneMark_model.106070_t
Valid prediction for snap_scaffold_28-snap.2190-T1
Couldn't classify 101512, 101593
Sorry, prediction pasa_asmbl_38499.p1 fails validation.
(GCT)	 CA	101512-101593	GT	AGG
(GTC)	 AG	101807-101966	GT	AGG
(GAA)	 AG	102248-102364	GT	AAG
(GTT)	 AG	102793-102959	GT	GGG
(GTC)	 AG	103154-103359	GT	TGG
(GAT)	 AG	103484-103630	GT	AGG
(GTG)	 AG	103842-104480	TC	GAT
-recovered pasa_asmbl_38499.p1, terminal, 103842, 104480
-recovered pasa_asmbl_38499.p1, internal, 101807, 101966
-recovered pasa_asmbl_38499.p1, internal, 102248, 102364
-recovered pasa_asmbl_38499.p1, internal, 102793, 102959
-recovered pasa_asmbl_38499.p1, internal, 103154, 103359
-recovered pasa_asmbl_38499.p1, internal, 103484, 103630
Couldn't classify 125707, 125776
Couldn't classify 131384, 131389
Sorry, prediction pasa_asmbl_38503.p1 fails validation.
(CTG)	 AC	125707-125776	GT	AGG
(CGG)	 AG	125873-126015	GC	AGG
(GTG)	 AG	126329-126450	GT	AAG
(ATA)	 AG	127058-127139	GT	GGG
(GCG)	 AG	127814-127946	GT	CAG
(GAT)	 AG	128187-128290	GT	TTG
(AGC)	 AG	128473-128552	GT	AGG
(GAT)	 AG	130674-130813	GT	AGG
(CAC)	 AG	130981-131144	GT	AGG
(TAC)	 AG	131384-131389	CA	AGC
-recovered pasa_asmbl_38503.p1, internal, 125873, 126015
-recovered pasa_asmbl_38503.p1, internal, 126329, 126450
-recovered pasa_asmbl_38503.p1, internal, 127058, 127139
-recovered pasa_asmbl_38503.p1, internal, 127814, 127946
-recovered pasa_asmbl_38503.p1, internal, 128187, 128290
-recovered pasa_asmbl_38503.p1, internal, 128473, 128552
-recovered pasa_asmbl_38503.p1, internal, 130674, 130813
-recovered pasa_asmbl_38503.p1, internal, 130981, 131144
Valid prediction for snap_scaffold_28-snap.2197-T1
Valid prediction for snap_scaffold_28-snap.2204-T1
Valid prediction for GlimmerHMM_glimmerT_60871-T1
Valid prediction for GeneMark_model.106093_t
Valid prediction for snap_scaffold_28-snap.2217-T1
Valid prediction for snap_scaffold_28-snap.2185-T1
Valid prediction for snap_scaffold_28-snap.2181-T1
Valid prediction for snap_scaffold_28-snap.2205-T1
Valid prediction for GlimmerHMM_glimmerT_60878-T1
Valid prediction for Augustus_model.g40517.t1
Valid prediction for GlimmerHMM_glimmerT_60879-T1
Valid prediction for GlimmerHMM_glimmerT_60870-T1
Couldn't classify 141088, 141132
Couldn't classify 141157, 141357
Sorry, prediction CodingQuarry_transcript_43668-T1 fails validation.
(ATG)	 TT	141088-141132	AT	ACA
(ATC)	 AC	141157-141357	CT	GAC
Valid prediction for GlimmerHMM_glimmerT_60883-T1
Valid prediction for HiQ_model.g40515.t1
Valid prediction for Augustus_model.g40516.t1
Valid prediction for snap_scaffold_28-snap.2214-T1
Valid prediction for snap_scaffold_28-snap.2186-T1
Valid prediction for pasa_asmbl_38501.p1
Valid prediction for GlimmerHMM_glimmerT_60880-T1
Valid prediction for snap_scaffold_28-snap.2178-T1
Valid prediction for snap_scaffold_28-snap.2208-T1
Valid prediction for GlimmerHMM_glimmerT_60892-T1
Valid prediction for Augustus_model.g40513.t1
Valid prediction for GeneMark_model.106072_t
Couldn't classify 106366, 106386
Couldn't classify 108883, 108999
Sorry, prediction pasa_asmbl_38500.p1 fails validation.
(GGT)	 GA	106366-106386	GT	AGG
(TTT)	 AG	106603-106644	GT	GGG
(GAT)	 AG	106748-106798	GT	CTG
(ACT)	 AG	106938-107025	GT	GGG
(GCA)	 AG	108509-108603	GT	GAG
(ACG)	 AG	108883-108999	AG	TGA
-recovered pasa_asmbl_38500.p1, internal, 106603, 106644
-recovered pasa_asmbl_38500.p1, internal, 106748, 106798
-recovered pasa_asmbl_38500.p1, internal, 106938, 107025
-recovered pasa_asmbl_38500.p1, internal, 108509, 108603
Valid prediction for GeneMark_model.106061_t
Valid prediction for Augustus_model.g40514.t1
Valid prediction for GeneMark_model.106076_t
Valid prediction for GeneMark_model.106080_t
Valid prediction for CodingQuarry_transcript_43666-T1
Valid prediction for GeneMark_model.106064_t
Valid prediction for snap_scaffold_28-snap.2199-T1
Valid prediction for GlimmerHMM_glimmerT_60873-T1
Valid prediction for snap_scaffold_28-snap.2182-T1
Valid prediction for snap_scaffold_28-snap.2202-T1
Valid prediction for GlimmerHMM_glimmerT_60881-T1
Valid prediction for GeneMark_model.106084_t
Couldn't classify 138881, 140260
Sorry, prediction pasa_asmbl_38506.p1 fails validation.
(GCA)	 CA	138881-140260	AC	GAA
Valid prediction for snap_scaffold_28-snap.2188-T1
Valid prediction for GeneMark_model.106086_t

-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 snap_scaffold_28-snap.2180-T1
Valid prediction for GlimmerHMM_glimmerT_60890-T1
Valid prediction for GeneMark_model.106083_t
Valid prediction for GeneMark_model.106062_t
Valid prediction for GeneMark_model.106065_t
Valid prediction for GeneMark_model.106087_t
Valid prediction for GeneMark_model.106075_t
Couldn't classify 60945, 61136
Sorry, prediction pasa_asmbl_37857.p1 fails validation.
(TAC)	 AG	60945-61136	GT	AGG
(GTA)	 AG	61351-61441	GT	AGG
(GCC)	 AG	61792-61934	GA	AGG
-recovered pasa_asmbl_37857.p1, terminal, 61792, 61934
-recovered pasa_asmbl_37857.p1, internal, 60945, 61136
-recovered pasa_asmbl_37857.p1, internal, 61351, 61441
Couldn't classify 59308, 59463
Sorry, prediction pasa_asmbl_37858.p1 fails validation.
(ATG)	 AA	58003-58063	GT	AGG
(TGC)	 AG	58501-58723	GT	AGG
(CAT)	 AG	58992-59154	GT	AGG
(GTG)	 AG	59308-59463	GT	ACG
-recovered pasa_asmbl_37858.p1, initial, 58003, 58063
-recovered pasa_asmbl_37858.p1, internal, 58501, 58723
-recovered pasa_asmbl_37858.p1, internal, 58992, 59154
-recovered pasa_asmbl_37858.p1, internal, 59308, 59463
Valid prediction for snap_scaffold_28-snap.2191-T1
Valid prediction for GlimmerHMM_glimmerT_60882-T1
Valid prediction for GlimmerHMM_glimmerT_60872-T1
Valid prediction for snap_scaffold_28-snap.2189-T1
Valid prediction for GlimmerHMM_glimmerT_60884-T1
Valid prediction for Augustus_model.g40511.t1
Valid prediction for GeneMark_model.106060_t
Valid prediction for GlimmerHMM_glimmerT_60876-T1
Valid prediction for GeneMark_model.106059_t
Valid prediction for GeneMark_model.106069_t
Valid prediction for snap_scaffold_28-snap.2187-T1
Valid prediction for snap_scaffold_28-snap.2196-T1
Valid prediction for GlimmerHMM_glimmerT_60894-T1
Valid prediction for snap_scaffold_28-snap.2209-T1
Valid prediction for snap_scaffold_28-snap.2195-T1
Valid prediction for snap_scaffold_28-snap.2200-T1
Valid prediction for GeneMark_model.106057_t
Valid prediction for snap_scaffold_28-snap.2177-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_28-snap.2183-T1
Valid prediction for GeneMark_model.106068_t
Valid prediction for GeneMark_model.106085_t
Valid prediction for GeneMark_model.106056_t
Valid prediction for snap_scaffold_28-snap.2192-T1
Valid prediction for Augustus_model.g40518.t1
Valid prediction for GeneMark_model.106071_t
Valid prediction for GeneMark_model.106073_t
Valid prediction for Augustus_model.g40519.t1
Valid prediction for GeneMark_model.106063_t
Valid prediction for GeneMark_model.106077_t
Valid prediction for GeneMark_model.106066_t
Valid prediction for snap_scaffold_28-snap.2213-T1
Valid prediction for GlimmerHMM_glimmerT_60875-T1
Valid prediction for snap_scaffold_28-snap.2206-T1
Valid prediction for snap_scaffold_28-snap.2193-T1
Valid prediction for snap_scaffold_28-snap.2198-T1
Couldn't classify 200310, 200443
Sorry, prediction pasa_asmbl_37855.p1 fails validation.
(ATG)	 TC	196320-196380	GT	TGG
(GGC)	 AG	197368-197554	GT	AGG
(GGA)	 AG	197780-197865	GT	AGG
(GCA)	 AG	197967-198056	GT	AGG
(TGC)	 AG	198171-198239	GT	AGG
(CCG)	 AG	198702-198859	GT	AGG
(GAG)	 AG	199202-199356	GT	AAG
(GTT)	 AG	199524-199675	GT	AGG
(GTC)	 AG	199925-200140	GT	TGG
(GTG)	 AG	200310-200443	GG	ATG
-recovered pasa_asmbl_37855.p1, initial, 196320, 196380
-recovered pasa_asmbl_37855.p1, internal, 197368, 197554
-recovered pasa_asmbl_37855.p1, internal, 197780, 197865
-recovered pasa_asmbl_37855.p1, internal, 197967, 198056
-recovered pasa_asmbl_37855.p1, internal, 198171, 198239
-recovered pasa_asmbl_37855.p1, internal, 198702, 198859
-recovered pasa_asmbl_37855.p1, internal, 199202, 199356
-recovered pasa_asmbl_37855.p1, internal, 199524, 199675
-recovered pasa_asmbl_37855.p1, internal, 199925, 200140
Valid prediction for snap_scaffold_28-snap.2207-T1
Valid prediction for snap_scaffold_28-snap.2211-T1
Valid prediction for GeneMark_model.106079_t
Valid prediction for GeneMark_model.106089_t
Valid prediction for snap_scaffold_28-snap.2194-T1
Valid prediction for GeneMark_model.106092_t
Valid prediction for GlimmerHMM_glimmerT_60868-T1
Valid prediction for GeneMark_model.106054_t
Valid prediction for GeneMark_model.106082_t
Valid prediction for GlimmerHMM_glimmerT_60869-T1
Valid prediction for snap_scaffold_28-snap.2184-T1
Valid prediction for GlimmerHMM_glimmerT_60889-T1
Valid prediction for GlimmerHMM_glimmerT_60867-T1
Valid prediction for snap_scaffold_28-snap.2201-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 21758, rend_intergenic: 18755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28692, rend_intergenic: 26750  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45208, rend_intergenic: 44535  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59194, rend_intergenic: 45230  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104480, rend_intergenic: 59277  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111914, rend_intergenic: 109648  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127615, rend_intergenic: 125026  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160450, rend_intergenic: 151203  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164875, rend_intergenic: 160741  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175822, rend_intergenic: 170178  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 205179
-exon list size: 734


building trellis

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72.1    
72.3    
72.4    
72.6    
72.7    
72.8    
73.0    
73.1    
73.2    
73.4    
73.5    
73.6    
73.8    
73.9    
74.0    
74.2    
74.3    
74.5    
74.6    
74.7    
74.9    
75.0    
75.1    
75.3    
75.4    
75.5    
75.7    
75.8    
76.0    
76.1    
76.2    
76.4    
76.5    
76.6    
76.8    
76.9    
77.0    
77.2    
77.3    
77.4    
77.6    
77.7    
77.9    
78.0    
78.1    
78.3    
78.4    
78.5    
78.7    
78.8    
78.9    
79.1    
79.2    
79.3    
79.5    
79.6    
79.8    
79.9    
80.0    
80.2    
80.3    
80.4    
80.6    
80.7    
80.8    
81.0    
81.1    
81.2    
81.4    
81.5    
81.7    
81.8    
81.9    
82.1    
82.2    
82.3    
82.5    
82.6    
82.7    
82.9    
83.0    
83.2    
83.3    
83.4    
83.6    
83.7    
83.8    
84.0    
84.1    
84.2    
84.4    
84.5    
84.6    
84.8    
84.9    
85.1    
85.2    
85.3    
85.5    
85.6    
85.7    
85.9    
86.0    
86.1    
86.3    
86.4    
86.5    
86.7    
86.8    
87.0    
87.1    
87.2    
87.4    
87.5    
87.6    
87.8    
87.9    
88.0    
88.2    
88.3    
88.5    
88.6    
88.7    
88.9    
89.0    
89.1    
89.3    
89.4    
89.5    
89.7    
89.8    
89.9    
90.1    
90.2    
90.4    
90.5    
90.6    
90.8    
90.9    
91.0    
91.2    
91.3    
91.4    
91.6    
91.7    
91.8    
92.0    
92.1    
92.3    
92.4    
92.5    
92.7    
92.8    
92.9    
93.1    
93.2    
93.3    
93.5    
93.6    
93.8    
93.9    
94.0    
94.2    
94.3    
94.4    
94.6    
94.7    
94.8    
95.0    
95.1    
95.2    
95.4    
95.5    
95.7    
95.8    
95.9    
96.1    
96.2    
96.3    
96.5    
96.6    
96.7    
96.9    
97.0    
97.1    
97.3    
97.4    
97.6    
97.7    
97.8    
98.0    
98.1    
98.2    
98.4    
98.5    
98.6    
98.8    
98.9    
99.0    
99.2    
99.3    
99.5    
99.6    
99.7    
99.9    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 21758, rend_intergenic: 18755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28692, rend_intergenic: 26750  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45208, rend_intergenic: 44535  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59194, rend_intergenic: 45230  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104480, rend_intergenic: 59277  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111914, rend_intergenic: 109648  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127615, rend_intergenic: 125026  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160450, rend_intergenic: 151203  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164875, rend_intergenic: 160741  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175822, rend_intergenic: 170178  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

-building DP trellis

-building trellis in range 189447 - 205179
-exon list size: 44


building trellis

2.2    
4.3    
6.5    
8.7    
10.9    
13.0    
15.2    
17.4    
19.6    
21.7    
23.9    
26.1    
28.3    
30.4    
32.6    
34.8    
37.0    
39.1    
41.3    
43.5    
45.7    
47.8    
50.0    
52.2    
54.3    
56.5    
58.7    
60.9    
63.0    
65.2    
67.4    
69.6    
71.7    
73.9    
76.1    
78.3    
80.4    
82.6    
84.8    
87.0    
89.1    
91.3    
93.5    
95.7    
97.8    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support