-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_24/scaffold_24_3384613-3655128

-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_24-snap.771-T1
Valid prediction for GlimmerHMM_glimmerT_52283-T1
Valid prediction for snap_scaffold_24-snap.773-T1
Valid prediction for snap_scaffold_24-snap.754-T1
Valid prediction for GlimmerHMM_glimmerT_52299-T1
Valid prediction for Augustus_model.g34824.t1
Valid prediction for snap_scaffold_24-snap.744-T1
Valid prediction for GlimmerHMM_glimmerT_52301-T1
Valid prediction for snap_scaffold_24-snap.790-T1
Valid prediction for GlimmerHMM_glimmerT_52275-T1
Valid prediction for Augustus_model.g34822.t1
Valid prediction for GlimmerHMM_glimmerT_52286-T1
Valid prediction for snap_scaffold_24-snap.762-T1
Valid prediction for Augustus_model.g34825.t1
Valid prediction for GlimmerHMM_glimmerT_52289-T1
Valid prediction for snap_scaffold_24-snap.785-T1
Valid prediction for snap_scaffold_24-snap.760-T1
Valid prediction for snap_scaffold_24-snap.777-T1
Valid prediction for GlimmerHMM_glimmerT_52306-T1
Valid prediction for GlimmerHMM_glimmerT_52277-T1
Valid prediction for GlimmerHMM_glimmerT_52305-T1
Valid prediction for pasa_asmbl_32144.p1
Valid prediction for GlimmerHMM_glimmerT_52281-T1
Valid prediction for GlimmerHMM_glimmerT_52291-T1
Valid prediction for snap_scaffold_24-snap.751-T1
Valid prediction for GlimmerHMM_glimmerT_52307-T1
Valid prediction for snap_scaffold_24-snap.764-T1
Valid prediction for snap_scaffold_24-snap.776-T1
Valid prediction for snap_scaffold_24-snap.768-T1
Valid prediction for snap_scaffold_24-snap.779-T1
Valid prediction for GlimmerHMM_glimmerT_52300-T1
Valid prediction for GlimmerHMM_glimmerT_52284-T1
Valid prediction for snap_scaffold_24-snap.746-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_52298-T1
Valid prediction for snap_scaffold_24-snap.748-T1
Valid prediction for GlimmerHMM_glimmerT_52288-T1
Valid prediction for GlimmerHMM_glimmerT_52282-T1
Valid prediction for snap_scaffold_24-snap.780-T1
Valid prediction for snap_scaffold_24-snap.794-T1
Valid prediction for snap_scaffold_24-snap.752-T1
Valid prediction for Augustus_model.g34836.t1
Valid prediction for snap_scaffold_24-snap.756-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_37278-T1
Valid prediction for snap_scaffold_24-snap.759-T1
Valid prediction for snap_scaffold_24-snap.792-T1
Valid prediction for snap_scaffold_24-snap.796-T1
Valid prediction for HiQ_model.g34817.t1
Valid prediction for GlimmerHMM_glimmerT_52279-T1
Valid prediction for Augustus_model.g34835.t1
Valid prediction for snap_scaffold_24-snap.774-T1
Valid prediction for snap_scaffold_24-snap.799-T1
Valid prediction for GlimmerHMM_glimmerT_52293-T1
Valid prediction for snap_scaffold_24-snap.747-T1
Valid prediction for GlimmerHMM_glimmerT_52270-T1
Valid prediction for Augustus_model.g34823.t1
Valid prediction for GlimmerHMM_glimmerT_52273-T1
Valid prediction for GlimmerHMM_glimmerT_52308-T1
Valid prediction for snap_scaffold_24-snap.766-T1
Valid prediction for GlimmerHMM_glimmerT_52304-T1
Valid prediction for snap_scaffold_24-snap.755-T1
Valid prediction for GlimmerHMM_glimmerT_52276-T1
Valid prediction for snap_scaffold_24-snap.787-T1
Valid prediction for snap_scaffold_24-snap.758-T1
Valid prediction for GlimmerHMM_glimmerT_52266-T1
Valid prediction for snap_scaffold_24-snap.791-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 GlimmerHMM_glimmerT_52290-T1
Valid prediction for snap_scaffold_24-snap.778-T1
Valid prediction for snap_scaffold_24-snap.749-T1
Valid prediction for GlimmerHMM_glimmerT_52274-T1
Valid prediction for snap_scaffold_24-snap.753-T1
Valid prediction for pasa_asmbl_32825.p1
Valid prediction for snap_scaffold_24-snap.795-T1
Valid prediction for Augustus_model.g34821.t1
Couldn't classify 252220, 252300
Sorry, prediction pasa_asmbl_33266.p1 fails validation.
(CCT)	 CT	252220-252300	GT	AGG
(CCT)	 AG	252476-252556	GT	TGG
(ATG)	 AG	252781-252945	GT	AGG
(GCG)	 AG	253510-253647	GT	CGG
(GTT)	 AG	253990-254180	GT	CAG
(GCA)	 AG	254467-254585	GT	GAG
(GGA)	 AG	254816-254902	GT	AGG
(TTG)	 AG	255021-255122	GT	AAG
(ACA)	 AG	255207-255370	GT	AGG
(TGT)	 AG	255746-255934	GT	AGG
(GGC)	 AG	256091-256228	GT	AGG
(CTC)	 AG	256371-256636	GT	AGG
(GAT)	 AG	256998-257229	GT	AGG
(AGC)	 AG	257504-257609	GT	CGG
(GCA)	 AG	258331-258851	AC	AAA
-recovered pasa_asmbl_33266.p1, initial, 252781, 252945
-recovered pasa_asmbl_33266.p1, terminal, 258331, 258851
-recovered pasa_asmbl_33266.p1, internal, 252476, 252556
-recovered pasa_asmbl_33266.p1, internal, 252781, 252945
-recovered pasa_asmbl_33266.p1, internal, 253510, 253647
-recovered pasa_asmbl_33266.p1, internal, 253990, 254180
-recovered pasa_asmbl_33266.p1, internal, 254467, 254585
-recovered pasa_asmbl_33266.p1, internal, 254816, 254902
-recovered pasa_asmbl_33266.p1, internal, 255021, 255122
-recovered pasa_asmbl_33266.p1, internal, 255207, 255370
-recovered pasa_asmbl_33266.p1, internal, 255746, 255934
-recovered pasa_asmbl_33266.p1, internal, 256091, 256228
-recovered pasa_asmbl_33266.p1, internal, 256371, 256636
-recovered pasa_asmbl_33266.p1, internal, 256998, 257229
-recovered pasa_asmbl_33266.p1, internal, 257504, 257609
Valid prediction for GlimmerHMM_glimmerT_52264-T1
Valid prediction for GlimmerHMM_glimmerT_52297-T1
Valid prediction for GlimmerHMM_glimmerT_52294-T1
Valid prediction for Augustus_model.g34832.t1
Valid prediction for snap_scaffold_24-snap.772-T1
Valid prediction for GlimmerHMM_glimmerT_52271-T1
Valid prediction for snap_scaffold_24-snap.745-T1
Valid prediction for snap_scaffold_24-snap.763-T1
Valid prediction for snap_scaffold_24-snap.782-T1
Valid prediction for snap_scaffold_24-snap.793-T1
Valid prediction for snap_scaffold_24-snap.765-T1
Valid prediction for snap_scaffold_24-snap.750-T1
Valid prediction for HiQ_model.g34818.t1
Valid prediction for GlimmerHMM_glimmerT_52309-T1
Valid prediction for Augustus_model.g34828.t1
Valid prediction for GlimmerHMM_glimmerT_52278-T1
Valid prediction for HiQ_model.g34816.t1
Valid prediction for snap_scaffold_24-snap.798-T1
Couldn't classify 245778, 245994
Couldn't classify 251280, 251308
Sorry, prediction pasa_asmbl_32826.p1 fails validation.
(CCC)	 GG	245778-245994	GT	GGG
(ACA)	 AG	248515-248658	GT	AGG
(GAT)	 AG	248868-248952	GT	AAG
(TGT)	 AG	250130-250202	GT	GGG
(TCT)	 AG	250722-250791	GT	GGG
(CCA)	 AG	250900-251034	GT	AGG
(AGA)	 AG	251280-251308	CT	GAC
add_exon() Sorry, pasa_asmbl_32826.p1 250900-251034-terminal-1 is invalid.
-recovered pasa_asmbl_32826.p1, terminal, 250900, 251034
-recovered pasa_asmbl_32826.p1, internal, 248515, 248658
-recovered pasa_asmbl_32826.p1, internal, 248868, 248952
-recovered pasa_asmbl_32826.p1, internal, 250130, 250202
-recovered pasa_asmbl_32826.p1, internal, 250722, 250791
-recovered pasa_asmbl_32826.p1, internal, 250900, 251034
Valid prediction for snap_scaffold_24-snap.788-T1
Valid prediction for GlimmerHMM_glimmerT_52267-T1
Valid prediction for Augustus_model.g34831.t1
Valid prediction for GlimmerHMM_glimmerT_52303-T1
Valid prediction for snap_scaffold_24-snap.783-T1
Valid prediction for GlimmerHMM_glimmerT_52272-T1
Valid prediction for Augustus_model.g34834.t1
Valid prediction for GlimmerHMM_glimmerT_52280-T1
Valid prediction for snap_scaffold_24-snap.797-T1
Valid prediction for snap_scaffold_24-snap.761-T1
Valid prediction for snap_scaffold_24-snap.770-T1
Valid prediction for Augustus_model.g34833.t1
Valid prediction for GlimmerHMM_glimmerT_52268-T1
Valid prediction for Augustus_model.g34829.t1
Valid prediction for GlimmerHMM_glimmerT_52292-T1
Valid prediction for snap_scaffold_24-snap.786-T1
Valid prediction for Augustus_model.g34819.t1
Valid prediction for Augustus_model.g34820.t1
Valid prediction for GlimmerHMM_glimmerT_52295-T1
Valid prediction for Augustus_model.g34826.t1
Valid prediction for Augustus_model.g34830.t1
Valid prediction for snap_scaffold_24-snap.784-T1
Valid prediction for pasa_asmbl_32832.p1
Valid prediction for GlimmerHMM_glimmerT_52302-T1
Valid prediction for GlimmerHMM_glimmerT_52265-T1
Valid prediction for snap_scaffold_24-snap.781-T1
Sorry, intron length (3) is less than minimum required (10)
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_24-snap.767-T1
Valid prediction for CodingQuarry_transcript_37277-T1
Valid prediction for GlimmerHMM_glimmerT_52296-T1
Valid prediction for snap_scaffold_24-snap.757-T1
Valid prediction for Augustus_model.g34827.t1
Valid prediction for snap_scaffold_24-snap.743-T1
Valid prediction for snap_scaffold_24-snap.769-T1
Valid prediction for GlimmerHMM_glimmerT_52269-T1
Couldn't classify 200355, 200382
Couldn't classify 201557, 201688
Sorry, prediction pasa_asmbl_32834.p1 fails validation.
(ACC)	 AC	200355-200382	GT	ATG
(CCA)	 AG	200793-200953	GT	AGG
(CAA)	 AG	201557-201688	TG	TGT
-recovered pasa_asmbl_32834.p1, internal, 200793, 200953
Valid prediction for snap_scaffold_24-snap.789-T1
Valid prediction for GlimmerHMM_glimmerT_52287-T1
Valid prediction for GlimmerHMM_glimmerT_52285-T1
Valid prediction for snap_scaffold_24-snap.775-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 26246, rend_intergenic: 12309  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44731, rend_intergenic: 32380  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70748, rend_intergenic: 51055  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90017, rend_intergenic: 71416  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93754, rend_intergenic: 90653  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97906, rend_intergenic: 95864  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100116, rend_intergenic: 98314  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121924, rend_intergenic: 113755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138618, rend_intergenic: 135393  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154750, rend_intergenic: 139669  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159985, rend_intergenic: 158717  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165491, rend_intergenic: 160071  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168877, rend_intergenic: 166126  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178659, rend_intergenic: 170272  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190363, rend_intergenic: 178664  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206797, rend_intergenic: 200444  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209246, rend_intergenic: 206917  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 210250, rend_intergenic: 209522  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 220880, rend_intergenic: 210780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 238918, rend_intergenic: 223462  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 241720, rend_intergenic: 239131  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 251327, rend_intergenic: 249697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 255357, rend_intergenic: 252632  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 260648, rend_intergenic: 255388  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 267678, rend_intergenic: 264131  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 270516
-exon list size: 691


building trellis

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70.3    
70.4    
70.6    
70.7    
70.9    
71.0    
71.1    
71.3    
71.4    
71.6    
71.7    
71.9    
72.0    
72.2    
72.3    
72.4    
72.6    
72.7    
72.9    
73.0    
73.2    
73.3    
73.4    
73.6    
73.7    
73.9    
74.0    
74.2    
74.3    
74.5    
74.6    
74.7    
74.9    
75.0    
75.2    
75.3    
75.5    
75.6    
75.8    
75.9    
76.0    
76.2    
76.3    
76.5    
76.6    
76.8    
76.9    
77.1    
77.2    
77.3    
77.5    
77.6    
77.8    
77.9    
78.1    
78.2    
78.4    
78.5    
78.6    
78.8    
78.9    
79.1    
79.2    
79.4    
79.5    
79.7    
79.8    
79.9    
80.1    
80.2    
80.4    
80.5    
80.7    
80.8    
81.0    
81.1    
81.2    
81.4    
81.5    
81.7    
81.8    
82.0    
82.1    
82.3    
82.4    
82.5    
82.7    
82.8    
83.0    
83.1    
83.3    
83.4    
83.5    
83.7    
83.8    
84.0    
84.1    
84.3    
84.4    
84.6    
84.7    
84.8    
85.0    
85.1    
85.3    
85.4    
85.6    
85.7    
85.9    
86.0    
86.1    
86.3    
86.4    
86.6    
86.7    
86.9    
87.0    
87.2    
87.3    
87.4    
87.6    
87.7    
87.9    
88.0    
88.2    
88.3    
88.5    
88.6    
88.7    
88.9    
89.0    
89.2    
89.3    
89.5    
89.6    
89.8    
89.9    
90.0    
90.2    
90.3    
90.5    
90.6    
90.8    
90.9    
91.1    
91.2    
91.3    
91.5    
91.6    
91.8    
91.9    
92.1    
92.2    
92.4    
92.5    
92.6    
92.8    
92.9    
93.1    
93.2    
93.4    
93.5    
93.7    
93.8    
93.9    
94.1    
94.2    
94.4    
94.5    
94.7    
94.8    
94.9    
95.1    
95.2    
95.4    
95.5    
95.7    
95.8    
96.0    
96.1    
96.2    
96.4    
96.5    
96.7    
96.8    
97.0    
97.1    
97.3    
97.4    
97.5    
97.7    
97.8    
98.0    
98.1    
98.3    
98.4    
98.6    
98.7    
98.8    
99.0    
99.1    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 41 predictions from path traversal
Error with prediction: snap lend_intergenic: 26246, rend_intergenic: 12309  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44731, rend_intergenic: 32380  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70748, rend_intergenic: 51055  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90017, rend_intergenic: 71416  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93754, rend_intergenic: 90653  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97906, rend_intergenic: 95864  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100116, rend_intergenic: 98314  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121924, rend_intergenic: 113755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138618, rend_intergenic: 135393  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154750, rend_intergenic: 139669  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159985, rend_intergenic: 158717  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165491, rend_intergenic: 160071  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168877, rend_intergenic: 166126  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178659, rend_intergenic: 170272  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190363, rend_intergenic: 178664  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206797, rend_intergenic: 200444  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209246, rend_intergenic: 206917  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 210250, rend_intergenic: 209522  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 220880, rend_intergenic: 210780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 238918, rend_intergenic: 223462  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 241720, rend_intergenic: 239131  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 251327, rend_intergenic: 249697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 255357, rend_intergenic: 252632  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 260648, rend_intergenic: 255388  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 267678, rend_intergenic: 264131  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 260301 - 270516
-exon list size: 13


building trellis

6.7    
13.3    
20.0    
26.7    
33.3    
40.0    
46.7    
53.3    
60.0    
66.7    
73.3    
80.0    
86.7    
93.3    
-found 1 predictions from path traversal

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