-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_11/scaffold_11_9524208-9709289

-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 snap_scaffold_11-snap.2165-T1
Valid prediction for GlimmerHMM_glimmerT_28299-T1
Valid prediction for GeneMark_model.48868_t
Valid prediction for snap_scaffold_11-snap.2183-T1
Valid prediction for snap_scaffold_11-snap.2170-T1
Valid prediction for GlimmerHMM_glimmerT_28301-T1
Valid prediction for Augustus_model.g18886.t1
Valid prediction for snap_scaffold_11-snap.2184-T1
Valid prediction for Augustus_model.g18895.t1
Valid prediction for GeneMark_model.48890_t
Valid prediction for Augustus_model.g18883.t1
Valid prediction for snap_scaffold_11-snap.2182-T1
Valid prediction for GeneMark_model.48892_t
Valid prediction for snap_scaffold_11-snap.2180-T1
Valid prediction for GlimmerHMM_glimmerT_28303-T1
Valid prediction for GeneMark_model.48869_t
Valid prediction for GeneMark_model.48896_t
Valid prediction for snap_scaffold_11-snap.2186-T1
Valid prediction for GeneMark_model.48876_t
Valid prediction for GeneMark_model.48871_t
Valid prediction for GlimmerHMM_glimmerT_28306-T1
Valid prediction for Augustus_model.g18884.t1
Valid prediction for GeneMark_model.48904_t
Valid prediction for GeneMark_model.48883_t
Valid prediction for GlimmerHMM_glimmerT_28313-T1
Valid prediction for GlimmerHMM_glimmerT_28314-T1
Valid prediction for snap_scaffold_11-snap.2206-T1
Valid prediction for snap_scaffold_11-snap.2202-T1
Valid prediction for snap_scaffold_11-snap.2207-T1
Valid prediction for snap_scaffold_11-snap.2173-T1
Valid prediction for snap_scaffold_11-snap.2213-T1
Valid prediction for GeneMark_model.48878_t
Valid prediction for snap_scaffold_11-snap.2174-T1
Valid prediction for GeneMark_model.48888_t
Valid prediction for snap_scaffold_11-snap.2167-T1
Valid prediction for snap_scaffold_11-snap.2203-T1
Valid prediction for GeneMark_model.48899_t
Valid prediction for GeneMark_model.48885_t
Valid prediction for snap_scaffold_11-snap.2198-T1
Valid prediction for GlimmerHMM_glimmerT_28319-T1
Valid prediction for GeneMark_model.48875_t
Valid prediction for GeneMark_model.48907_t
Valid prediction for GeneMark_model.48879_t
Valid prediction for snap_scaffold_11-snap.2194-T1
Valid prediction for GlimmerHMM_glimmerT_28295-T1
Valid prediction for snap_scaffold_11-snap.2177-T1
Valid prediction for GeneMark_model.48881_t
Valid prediction for GlimmerHMM_glimmerT_28312-T1
Valid prediction for GlimmerHMM_glimmerT_28304-T1
Valid prediction for Augustus_model.g18888.t1
Valid prediction for snap_scaffold_11-snap.2190-T1
Valid prediction for snap_scaffold_11-snap.2178-T1
Valid prediction for GeneMark_model.48897_t
Valid prediction for GlimmerHMM_glimmerT_28297-T1
Valid prediction for Augustus_model.g18880.t1
Valid prediction for snap_scaffold_11-snap.2196-T1
Valid prediction for GeneMark_model.48894_t
Valid prediction for GlimmerHMM_glimmerT_28315-T1
Valid prediction for GeneMark_model.48901_t
Valid prediction for snap_scaffold_11-snap.2181-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g18890.t1
Valid prediction for Augustus_model.g18889.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 snap_scaffold_11-snap.2192-T1
Valid prediction for snap_scaffold_11-snap.2197-T1
Valid prediction for GlimmerHMM_glimmerT_28309-T1
Valid prediction for snap_scaffold_11-snap.2195-T1
Valid prediction for snap_scaffold_11-snap.2166-T1
Valid prediction for snap_scaffold_11-snap.2205-T1
Valid prediction for pasa_asmbl_6922.p1
Valid prediction for snap_scaffold_11-snap.2168-T1
Valid prediction for GeneMark_model.48900_t
Valid prediction for Augustus_model.g18887.t1
Valid prediction for GlimmerHMM_glimmerT_28322-T1
Valid prediction for GlimmerHMM_glimmerT_28326-T1
Valid prediction for snap_scaffold_11-snap.2200-T1
Valid prediction for Augustus_model.g18898.t1
Valid prediction for snap_scaffold_11-snap.2171-T1
Valid prediction for CodingQuarry_transcript_8178-T1
Couldn't classify 50529, 50709
Sorry, prediction pasa_asmbl_6928.p1 fails validation.
(ATG)	 GC	47570-47648	GT	AGG
(GGA)	 AG	50352-50409	GT	AGG
(GGA)	 AG	50529-50709	AC	GGA
-recovered pasa_asmbl_6928.p1, initial, 47570, 47648
-recovered pasa_asmbl_6928.p1, internal, 50352, 50409
Valid prediction for snap_scaffold_11-snap.2193-T1
Valid prediction for GeneMark_model.48891_t
Valid prediction for snap_scaffold_11-snap.2191-T1
Valid prediction for GlimmerHMM_glimmerT_28323-T1
Valid prediction for snap_scaffold_11-snap.2176-T1
Couldn't classify 53748, 53864
Couldn't classify 57249, 57380
Sorry, prediction pasa_asmbl_6925.p2 fails validation.
(ACA)	 TC	53748-53864	GT	AGG
(TTG)	 AG	53955-54074	GT	AGG
(TGG)	 AG	54153-54284	GT	TGG
(GCC)	 AG	54390-54554	GT	GGG
(AAC)	 AG	54642-54761	GT	AGG
(GGA)	 AG	55196-55330	GT	AGG
(GAT)	 AG	55644-55837	GT	GGG
(ATT)	 AG	56349-56381	GT	AGG
(GGA)	 AG	56866-57004	GT	AGG
(GTG)	 AG	57249-57380	GC	AGG
-recovered pasa_asmbl_6925.p2, internal, 53955, 54074
-recovered pasa_asmbl_6925.p2, internal, 54153, 54284
-recovered pasa_asmbl_6925.p2, internal, 54390, 54554
-recovered pasa_asmbl_6925.p2, internal, 54642, 54761
-recovered pasa_asmbl_6925.p2, internal, 55196, 55330
-recovered pasa_asmbl_6925.p2, internal, 55644, 55837
-recovered pasa_asmbl_6925.p2, internal, 56349, 56381
-recovered pasa_asmbl_6925.p2, internal, 56866, 57004
-recovered pasa_asmbl_6925.p2, internal, 57249, 57380
Valid prediction for GeneMark_model.48886_t
Valid prediction for GeneMark_model.48880_t
Valid prediction for GlimmerHMM_glimmerT_28308-T1
Valid prediction for snap_scaffold_11-snap.2164-T1
Valid prediction for GeneMark_model.48884_t
Valid prediction for snap_scaffold_11-snap.2209-T1
Valid prediction for snap_scaffold_11-snap.2214-T1
Valid prediction for snap_scaffold_11-snap.2199-T1
Valid prediction for GeneMark_model.48889_t
Valid prediction for GeneMark_model.48903_t
Valid prediction for GeneMark_model.48867_t
Valid prediction for snap_scaffold_11-snap.2211-T1
Valid prediction for GlimmerHMM_glimmerT_28302-T1
Valid prediction for snap_scaffold_11-snap.2210-T1
Valid prediction for GlimmerHMM_glimmerT_28310-T1
Valid prediction for GeneMark_model.48898_t
Valid prediction for GeneMark_model.48877_t
Valid prediction for GlimmerHMM_glimmerT_28300-T1
Valid prediction for GlimmerHMM_glimmerT_28307-T1
Valid prediction for GlimmerHMM_glimmerT_28324-T1
Valid prediction for snap_scaffold_11-snap.2204-T1
Valid prediction for GlimmerHMM_glimmerT_28316-T1
Valid prediction for pasa_asmbl_6934.p1
Valid prediction for GeneMark_model.48874_t
Valid prediction for snap_scaffold_11-snap.2201-T1
Valid prediction for snap_scaffold_11-snap.2185-T1
Valid prediction for HiQ_model.g18882.t1
Valid prediction for snap_scaffold_11-snap.2179-T1
Valid prediction for snap_scaffold_11-snap.2172-T1
Valid prediction for GeneMark_model.48872_t
Valid prediction for snap_scaffold_11-snap.2187-T1
Valid prediction for GlimmerHMM_glimmerT_28311-T1
Valid prediction for HiQ_model.g18897.t1
Valid prediction for GlimmerHMM_glimmerT_28296-T1
Valid prediction for GeneMark_model.48882_t
Valid prediction for Augustus_model.g18892.t1
Valid prediction for GeneMark_model.48887_t
Valid prediction for Augustus_model.g18893.t1
Valid prediction for GlimmerHMM_glimmerT_28298-T1
Valid prediction for GlimmerHMM_glimmerT_28318-T1
Valid prediction for snap_scaffold_11-snap.2175-T1
Valid prediction for GlimmerHMM_glimmerT_28320-T1
Valid prediction for Augustus_model.g18894.t1
Valid prediction for GeneMark_model.48870_t
Valid prediction for CodingQuarry_transcript_8179-T1
Valid prediction for GeneMark_model.48908_t
Valid prediction for Augustus_model.g18891.t1
Valid prediction for Augustus_model.g18881.t1
Valid prediction for snap_scaffold_11-snap.2208-T1
Valid prediction for Augustus_model.g18896.t1
Valid prediction for GeneMark_model.48902_t
Couldn't classify 17334, 17691
Sorry, prediction pasa_asmbl_6933.p1 fails validation.
(GTG)	 AG	17334-17691	GT	AGG
(ACG)	 AG	18754-18909	GT	GGG
(AGA)	 AG	19011-19108	GC	GAG
-recovered pasa_asmbl_6933.p1, terminal, 19011, 19108
-recovered pasa_asmbl_6933.p1, internal, 17334, 17691
-recovered pasa_asmbl_6933.p1, internal, 18754, 18909
-recovered pasa_asmbl_6933.p1, internal, 19011, 19108
Valid prediction for GeneMark_model.48895_t
Valid prediction for GlimmerHMM_glimmerT_28325-T1
Valid prediction for snap_scaffold_11-snap.2169-T1
Valid prediction for pasa_asmbl_6930.p1
Valid prediction for GeneMark_model.48906_t
Valid prediction for GeneMark_model.48873_t
Valid prediction for snap_scaffold_11-snap.2212-T1
Valid prediction for GlimmerHMM_glimmerT_28321-T1
Valid prediction for snap_scaffold_11-snap.2189-T1
Valid prediction for GlimmerHMM_glimmerT_28305-T1
Valid prediction for snap_scaffold_11-snap.2188-T1
Valid prediction for HiQ_model.g18879.t1
Valid prediction for GeneMark_model.48905_t
Valid prediction for CodingQuarry_transcript_8177-T1
Valid prediction for GlimmerHMM_glimmerT_28294-T1
Valid prediction for Augustus_model.g18885.t1
Valid prediction for GlimmerHMM_glimmerT_28317-T1
Valid prediction for GeneMark_model.48893_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15853, rend_intergenic: 11468  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23596, rend_intergenic: 17962  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36821, rend_intergenic: 31319  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42107, rend_intergenic: 37192  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47855, rend_intergenic: 42113  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57205, rend_intergenic: 50672  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59710, rend_intergenic: 57379  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73690, rend_intergenic: 59787  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76287, rend_intergenic: 74266  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90969, rend_intergenic: 81853  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95156, rend_intergenic: 93156  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100340, rend_intergenic: 95466  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103553, rend_intergenic: 100592  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110011, rend_intergenic: 105632  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117385, rend_intergenic: 115542  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119530, rend_intergenic: 118973  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122490, rend_intergenic: 119805  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134948, rend_intergenic: 130800  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147306, rend_intergenic: 140433  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151131, rend_intergenic: 149407  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156973, rend_intergenic: 154242  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180858, rend_intergenic: 176823  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 185082
-exon list size: 845


building trellis

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65.2    
65.3    
65.4    
65.5    
65.6    
65.8    
65.9    
66.0    
66.1    
66.2    
66.4    
66.5    
66.6    
66.7    
66.8    
66.9    
67.1    
67.2    
67.3    
67.4    
67.5    
67.7    
67.8    
67.9    
68.0    
68.1    
68.2    
68.4    
68.5    
68.6    
68.7    
68.8    
68.9    
69.1    
69.2    
69.3    
69.4    
69.5    
69.7    
69.8    
69.9    
70.0    
70.1    
70.2    
70.4    
70.5    
70.6    
70.7    
70.8    
71.0    
71.1    
71.2    
71.3    
71.4    
71.5    
71.7    
71.8    
71.9    
72.0    
72.1    
72.3    
72.4    
72.5    
72.6    
72.7    
72.8    
73.0    
73.1    
73.2    
73.3    
73.4    
73.6    
73.7    
73.8    
73.9    
74.0    
74.1    
74.3    
74.4    
74.5    
74.6    
74.7    
74.9    
75.0    
75.1    
75.2    
75.3    
75.4    
75.6    
75.7    
75.8    
75.9    
76.0    
76.2    
76.3    
76.4    
76.5    
76.6    
76.7    
76.9    
77.0    
77.1    
77.2    
77.3    
77.4    
77.6    
77.7    
77.8    
77.9    
78.0    
78.2    
78.3    
78.4    
78.5    
78.6    
78.7    
78.9    
79.0    
79.1    
79.2    
79.3    
79.5    
79.6    
79.7    
79.8    
79.9    
80.0    
80.2    
80.3    
80.4    
80.5    
80.6    
80.8    
80.9    
81.0    
81.1    
81.2    
81.3    
81.5    
81.6    
81.7    
81.8    
81.9    
82.1    
82.2    
82.3    
82.4    
82.5    
82.6    
82.8    
82.9    
83.0    
83.1    
83.2    
83.4    
83.5    
83.6    
83.7    
83.8    
83.9    
84.1    
84.2    
84.3    
84.4    
84.5    
84.7    
84.8    
84.9    
85.0    
85.1    
85.2    
85.4    
85.5    
85.6    
85.7    
85.8    
86.0    
86.1    
86.2    
86.3    
86.4    
86.5    
86.7    
86.8    
86.9    
87.0    
87.1    
87.2    
87.4    
87.5    
87.6    
87.7    
87.8    
88.0    
88.1    
88.2    
88.3    
88.4    
88.5    
88.7    
88.8    
88.9    
89.0    
89.1    
89.3    
89.4    
89.5    
89.6    
89.7    
89.8    
90.0    
90.1    
90.2    
90.3    
90.4    
90.6    
90.7    
90.8    
90.9    
91.0    
91.1    
91.3    
91.4    
91.5    
91.6    
91.7    
91.9    
92.0    
92.1    
92.2    
92.3    
92.4    
92.6    
92.7    
92.8    
92.9    
93.0    
93.2    
93.3    
93.4    
93.5    
93.6    
93.7    
93.9    
94.0    
94.1    
94.2    
94.3    
94.5    
94.6    
94.7    
94.8    
94.9    
95.0    
95.2    
95.3    
95.4    
95.5    
95.6    
95.7    
95.9    
96.0    
96.1    
96.2    
96.3    
96.5    
96.6    
96.7    
96.8    
96.9    
97.0    
97.2    
97.3    
97.4    
97.5    
97.6    
97.8    
97.9    
98.0    
98.1    
98.2    
98.3    
98.5    
98.6    
98.7    
98.8    
98.9    
99.1    
99.2    
99.3    
99.4    
99.5    
99.6    
99.8    
99.9    
-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 15853, rend_intergenic: 11468  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23596, rend_intergenic: 17962  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36821, rend_intergenic: 31319  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42107, rend_intergenic: 37192  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47855, rend_intergenic: 42113  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57205, rend_intergenic: 50672  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59710, rend_intergenic: 57379  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73690, rend_intergenic: 59787  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76287, rend_intergenic: 74266  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90969, rend_intergenic: 81853  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95156, rend_intergenic: 93156  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100340, rend_intergenic: 95466  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103553, rend_intergenic: 100592  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110011, rend_intergenic: 105632  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117385, rend_intergenic: 115542  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119530, rend_intergenic: 118973  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122490, rend_intergenic: 119805  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134948, rend_intergenic: 130800  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147306, rend_intergenic: 140433  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151131, rend_intergenic: 149407  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156973, rend_intergenic: 154242  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180858, rend_intergenic: 176823  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support