-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_2/scaffold_2_11410603-11798013

-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_4561-T1
Couldn't classify 47679, 47809
Sorry, prediction pasa_asmbl_24753.p1 fails validation.
(ATG)	 GA	37804-37908	GT	TCG
(AGT)	 AG	39745-39879	GT	AGG
(GAA)	 AG	40046-40132	GT	ATG
(TCC)	 AG	40403-40499	GT	TGG
(AAA)	 AG	41755-41778	GT	TGG
(GCC)	 AG	44147-44408	GT	CAG
(ACA)	 AG	44930-44972	GT	ATG
(CTG)	 AG	46041-46194	GT	AGG
(CCC)	 AG	47679-47809	TC	CCT
-recovered pasa_asmbl_24753.p1, initial, 37804, 37908
-recovered pasa_asmbl_24753.p1, internal, 39745, 39879
-recovered pasa_asmbl_24753.p1, internal, 40046, 40132
-recovered pasa_asmbl_24753.p1, internal, 40403, 40499
-recovered pasa_asmbl_24753.p1, internal, 41755, 41778
-recovered pasa_asmbl_24753.p1, internal, 44147, 44408
-recovered pasa_asmbl_24753.p1, internal, 44930, 44972
-recovered pasa_asmbl_24753.p1, internal, 46041, 46194
Valid prediction for snap_scaffold_2-snap.2208-T1
Valid prediction for snap_scaffold_2-snap.2240-T1
Valid prediction for GlimmerHMM_glimmerT_4544-T1
Couldn't classify 379270, 379410
Couldn't classify 380794, 380867
Sorry, prediction pasa_asmbl_24772.p1 fails validation.
(AAC)	 GC	379270-379410	GT	AGG
(ATT)	 AG	379514-379578	GT	TTG
(TGC)	 AG	379743-379914	GT	CTG
(GTC)	 AG	380190-380353	GT	AGG
(GGG)	 AG	380599-380711	GT	AGG
(ATA)	 AG	380794-380867	AA	AGA
-recovered pasa_asmbl_24772.p1, internal, 379514, 379578
-recovered pasa_asmbl_24772.p1, internal, 379743, 379914
-recovered pasa_asmbl_24772.p1, internal, 380190, 380353
-recovered pasa_asmbl_24772.p1, internal, 380599, 380711
Valid prediction for snap_scaffold_2-snap.2202-T1
Valid prediction for snap_scaffold_2-snap.2228-T1
Couldn't classify 384562, 384726
Sorry, prediction pasa_asmbl_24774.p1 fails validation.
(CCA)	 GC	384562-384726	GT	ACG
(CGT)	 AG	385099-385266	GG	GAG
-recovered pasa_asmbl_24774.p1, terminal, 385099, 385266
Valid prediction for snap_scaffold_2-snap.2210-T1
Valid prediction for Augustus_model.g3070.t1
Valid prediction for GlimmerHMM_glimmerT_4550-T1
Valid prediction for pasa_asmbl_24758.p1
Valid prediction for Augustus_model.g3060.t1
Valid prediction for snap_scaffold_2-snap.2217-T1
Valid prediction for GlimmerHMM_glimmerT_4559-T1
Valid prediction for snap_scaffold_2-snap.2238-T1
Valid prediction for snap_scaffold_2-snap.2191-T1
Valid prediction for pasa_asmbl_24766.p1
Valid prediction for snap_scaffold_2-snap.2216-T1
Valid prediction for GlimmerHMM_glimmerT_4543-T1
Valid prediction for Augustus_model.g3057.t1
Valid prediction for snap_scaffold_2-snap.2200-T1
Valid prediction for HiQ_model.g3063.t1
Valid prediction for snap_scaffold_2-snap.2209-T1
Valid prediction for snap_scaffold_2-snap.2204-T1
Valid prediction for snap_scaffold_2-snap.2192-T1
Valid prediction for GlimmerHMM_glimmerT_4552-T1
Valid prediction for snap_scaffold_2-snap.2221-T1
Couldn't classify 367332, 367385
Couldn't classify 368306, 368532
Sorry, prediction pasa_asmbl_24769.p1 fails validation.
(GAG)	 TG	367332-367385	GT	AGG
(GAA)	 AG	367472-367522	GT	AGG
(GTT)	 AG	367689-367868	GT	AGG
(GCT)	 AG	368061-368178	GT	AAG
(CCC)	 AG	368306-368532	AC	CCA
-recovered pasa_asmbl_24769.p1, internal, 367472, 367522
-recovered pasa_asmbl_24769.p1, internal, 367689, 367868
-recovered pasa_asmbl_24769.p1, internal, 368061, 368178
Valid prediction for snap_scaffold_2-snap.2218-T1
Valid prediction for Augustus_model.g3062.t1
Couldn't classify 382162, 382273
Couldn't classify 384112, 384164
Sorry, prediction pasa_asmbl_24773.p1 fails validation.
(GTG)	 AG	382162-382273	GT	AGG
(GCG)	 AG	382357-382617	GT	AGG
(GGA)	 AG	382869-383101	GT	AGG
(GTG)	 AG	383243-383419	GT	AGG
(GTG)	 AG	383600-383671	GT	GCG
(GTC)	 AG	383821-383920	GT	GGG
(GGA)	 AG	384112-384164	CC	CCC
-recovered pasa_asmbl_24773.p1, internal, 382162, 382273
-recovered pasa_asmbl_24773.p1, internal, 382357, 382617
-recovered pasa_asmbl_24773.p1, internal, 382869, 383101
-recovered pasa_asmbl_24773.p1, internal, 383243, 383419
-recovered pasa_asmbl_24773.p1, internal, 383600, 383671
-recovered pasa_asmbl_24773.p1, internal, 383821, 383920
Valid prediction for snap_scaffold_2-snap.2189-T1
Valid prediction for snap_scaffold_2-snap.2211-T1
Valid prediction for snap_scaffold_2-snap.2205-T1
Valid prediction for CodingQuarry_transcript_28679-T1
Valid prediction for snap_scaffold_2-snap.2222-T1
Valid prediction for GlimmerHMM_glimmerT_4558-T1
Valid prediction for Augustus_model.g3055.t1
Valid prediction for snap_scaffold_2-snap.2207-T1
Valid prediction for GlimmerHMM_glimmerT_4545-T1
Valid prediction for GlimmerHMM_glimmerT_4549-T1
Valid prediction for snap_scaffold_2-snap.2244-T1
Valid prediction for HiQ_model.g3047.t1
Valid prediction for GlimmerHMM_glimmerT_4548-T1
Valid prediction for Augustus_model.g3069.t1
Valid prediction for snap_scaffold_2-snap.2203-T1
Valid prediction for snap_scaffold_2-snap.2223-T1
Valid prediction for GlimmerHMM_glimmerT_4554-T1
Valid prediction for snap_scaffold_2-snap.2201-T1
Valid prediction for Augustus_model.g3054.t1
Valid prediction for Augustus_model.g3058.t1
Valid prediction for CodingQuarry_transcript_28676-T1
Valid prediction for snap_scaffold_2-snap.2220-T1
Valid prediction for Augustus_model.g3056.t1
Valid prediction for Augustus_model.g3051.t1
Valid prediction for snap_scaffold_2-snap.2199-T1
Valid prediction for GlimmerHMM_glimmerT_4538-T1
Valid prediction for snap_scaffold_2-snap.2213-T1
Valid prediction for GlimmerHMM_glimmerT_4563-T1
Couldn't classify 48020, 48250
Sorry, prediction pasa_asmbl_24755.p1 fails validation.
(CCT)	 CC	48020-48250	GT	CTG
(GTC)	 AG	48405-48513	GT	AGG
(ATG)	 AG	48703-48764	CT	AGC
-recovered pasa_asmbl_24755.p1, terminal, 48703, 48764
-recovered pasa_asmbl_24755.p1, internal, 48405, 48513
Valid prediction for snap_scaffold_2-snap.2212-T1
Valid prediction for snap_scaffold_2-snap.2215-T1
Valid prediction for GlimmerHMM_glimmerT_4546-T1
Valid prediction for Augustus_model.g3052.t1
Valid prediction for Augustus_model.g3059.t1
Valid prediction for snap_scaffold_2-snap.2229-T1
Valid prediction for CodingQuarry_transcript_28678-T1
Valid prediction for CodingQuarry_transcript_28675-T1
Valid prediction for GlimmerHMM_glimmerT_4542-T1
Couldn't classify 370975, 371104
Sorry, prediction pasa_asmbl_24771.p1 fails validation.
(GAT)	 AC	370975-371104	GT	CGG
(ACG)	 AG	372120-372220	GT	AGG
(CCC)	 AG	373242-373428	GT	GAG
(CAA)	 AG	373611-373695	GT	AAG
(TAT)	 AG	373921-374057	GT	CAG
(TTG)	 AG	374329-374465	AT	AGA
-recovered pasa_asmbl_24771.p1, terminal, 374329, 374465
-recovered pasa_asmbl_24771.p1, internal, 372120, 372220
-recovered pasa_asmbl_24771.p1, internal, 373242, 373428
-recovered pasa_asmbl_24771.p1, internal, 373611, 373695
-recovered pasa_asmbl_24771.p1, internal, 373921, 374057
Valid prediction for snap_scaffold_2-snap.2243-T1
Valid prediction for Augustus_model.g3061.t1
Valid prediction for GlimmerHMM_glimmerT_4551-T1
Valid prediction for snap_scaffold_2-snap.2245-T1
Valid prediction for HiQ_model.g3065.t1
Valid prediction for GlimmerHMM_glimmerT_4562-T1
Valid prediction for snap_scaffold_2-snap.2232-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_2-snap.2197-T1
Valid prediction for snap_scaffold_2-snap.2186-T1
Valid prediction for snap_scaffold_2-snap.2234-T1
Valid prediction for GlimmerHMM_glimmerT_4556-T1
Valid prediction for snap_scaffold_2-snap.2227-T1
Valid prediction for Augustus_model.g3064.t1
Couldn't classify 121540, 121865
Couldn't classify 122764, 122769
Sorry, prediction pasa_asmbl_23456.p1 fails validation.
(AAG)	 AT	121540-121865	GT	ACG
(TGA)	 AG	121987-122171	GT	AGG
(GGG)	 AG	122270-122511	GT	AGG
(ACA)	 AG	122764-122769	GG	GCG
-recovered pasa_asmbl_23456.p1, internal, 121987, 122171
-recovered pasa_asmbl_23456.p1, internal, 122270, 122511
Valid prediction for snap_scaffold_2-snap.2242-T1
Valid prediction for GlimmerHMM_glimmerT_4536-T1
Valid prediction for GlimmerHMM_glimmerT_4539-T1
Valid prediction for Augustus_model.g3049.t1
Valid prediction for snap_scaffold_2-snap.2196-T1
Valid prediction for Augustus_model.g3068.t1
Valid prediction for snap_scaffold_2-snap.2190-T1
Couldn't classify 326390, 326490
Couldn't classify 327577, 327722
Sorry, prediction pasa_asmbl_23977.p1 fails validation.
(GAT)	 TG	326390-326490	GT	AGG
(CAA)	 AG	326593-326630	GT	AGG
(GTG)	 AG	327140-327271	GT	TGG
(CTT)	 AG	327577-327722	CC	CGC
-recovered pasa_asmbl_23977.p1, internal, 326593, 326630
-recovered pasa_asmbl_23977.p1, internal, 327140, 327271
Valid prediction for snap_scaffold_2-snap.2219-T1
Valid prediction for GlimmerHMM_glimmerT_4541-T1
Valid prediction for GlimmerHMM_glimmerT_4555-T1
Valid prediction for GlimmerHMM_glimmerT_4537-T1
Valid prediction for snap_scaffold_2-snap.2224-T1
Valid prediction for Augustus_model.g3043.t1
Valid prediction for Augustus_model.g3044.t1
Valid prediction for GlimmerHMM_glimmerT_4547-T1
Valid prediction for Augustus_model.g3046.t1
Couldn't classify 93232, 93241
Couldn't classify 93948, 93988
Sorry, prediction pasa_asmbl_23458.p1 fails validation.
(GAC)	 AG	93232-93241	GT	AGG
(AGT)	 AG	93439-93656	GC	AGG
(GTG)	 AG	93750-93846	GT	CTG
(CCT)	 AG	93948-93988	GA	GCG
-recovered pasa_asmbl_23458.p1, internal, 93232, 93241
-recovered pasa_asmbl_23458.p1, internal, 93439, 93656
-recovered pasa_asmbl_23458.p1, internal, 93750, 93846
Valid prediction for snap_scaffold_2-snap.2185-T1
Valid prediction for Augustus_model.g3067.t1
Valid prediction for snap_scaffold_2-snap.2198-T1
Valid prediction for snap_scaffold_2-snap.2195-T1
Valid prediction for snap_scaffold_2-snap.2246-T1
Valid prediction for GlimmerHMM_glimmerT_4557-T1
Valid prediction for pasa_asmbl_23455.p1
Valid prediction for snap_scaffold_2-snap.2193-T1
Valid prediction for Augustus_model.g3048.t1
Valid prediction for snap_scaffold_2-snap.2233-T1
Valid prediction for snap_scaffold_2-snap.2226-T1
Valid prediction for Augustus_model.g3066.t1
Valid prediction for snap_scaffold_2-snap.2239-T1
Valid prediction for Augustus_model.g3045.t1
Valid prediction for GlimmerHMM_glimmerT_4560-T1
Valid prediction for snap_scaffold_2-snap.2237-T1
Valid prediction for Augustus_model.g3053.t1
Valid prediction for snap_scaffold_2-snap.2187-T1
Couldn't classify 94088, 94311
Couldn't classify 94590, 94740
Sorry, prediction pasa_asmbl_24001.p2 fails validation.
(CCT)	 CC	94088-94311	GT	ATG
(GAA)	 AG	94590-94740	GA	AGG
Valid prediction for GlimmerHMM_glimmerT_4553-T1
Couldn't classify 94738, 94750
Sorry, prediction pasa_asmbl_23457.p1 fails validation.
(AAG)	 CA	94738-94750	GT	AGG
(AGG)	 AG	95030-95232	GT	AGG
(ATC)	 AG	95558-95761	GC	AGG
(CTC)	 AG	95999-96143	GT	AGG
(ATG)	 AG	96388-96595	GT	AAG
(GAA)	 AG	96795-96930	GT	AGG
(ATT)	 AG	97066-97236	GT	CGG
(GAA)	 AG	97378-97531	GT	AGG
(ATC)	 AG	97628-97764	GG	AAG
add_exon() Sorry, pasa_asmbl_23457.p1 96388-96595-initial-1 is invalid.
-recovered pasa_asmbl_23457.p1, initial, 96388, 96595
-recovered pasa_asmbl_23457.p1, terminal, 97628, 97764
-recovered pasa_asmbl_23457.p1, internal, 95030, 95232
-recovered pasa_asmbl_23457.p1, internal, 95558, 95761
-recovered pasa_asmbl_23457.p1, internal, 95999, 96143
-recovered pasa_asmbl_23457.p1, internal, 96388, 96595
-recovered pasa_asmbl_23457.p1, internal, 96795, 96930
-recovered pasa_asmbl_23457.p1, internal, 97066, 97236
-recovered pasa_asmbl_23457.p1, internal, 97378, 97531
Valid prediction for pasa_asmbl_23453.p1
Valid prediction for snap_scaffold_2-snap.2230-T1
Valid prediction for CodingQuarry_transcript_28677-T1
Valid prediction for snap_scaffold_2-snap.2188-T1
Valid prediction for snap_scaffold_2-snap.2231-T1
Valid prediction for snap_scaffold_2-snap.2214-T1
Valid prediction for snap_scaffold_2-snap.2225-T1
Valid prediction for snap_scaffold_2-snap.2241-T1
Valid prediction for Augustus_model.g3050.t1
Valid prediction for snap_scaffold_2-snap.2206-T1
Valid prediction for snap_scaffold_2-snap.2194-T1
Valid prediction for snap_scaffold_2-snap.2235-T1
Valid prediction for GlimmerHMM_glimmerT_4540-T1
Valid prediction for snap_scaffold_2-snap.2236-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 48764, rend_intergenic: 46133  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140732, rend_intergenic: 139439  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144408, rend_intergenic: 140956  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171624, rend_intergenic: 171226  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 280952, rend_intergenic: 275187  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 385266, rend_intergenic: 379761  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 387411
-exon list size: 595


building trellis

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66.7    
66.8    
67.0    
67.2    
67.3    
67.5    
67.7    
67.8    
68.0    
68.2    
68.3    
68.5    
68.7    
68.8    
69.0    
69.2    
69.3    
69.5    
69.7    
69.8    
70.0    
70.2    
70.4    
70.5    
70.7    
70.9    
71.0    
71.2    
71.4    
71.5    
71.7    
71.9    
72.0    
72.2    
72.4    
72.5    
72.7    
72.9    
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    
76.0    
76.2    
76.4    
76.5    
76.7    
76.9    
77.1    
77.2    
77.4    
77.6    
77.7    
77.9    
78.1    
78.2    
78.4    
78.6    
78.7    
78.9    
79.1    
79.2    
79.4    
79.6    
79.7    
79.9    
80.1    
80.2    
80.4    
80.6    
80.7    
80.9    
81.1    
81.2    
81.4    
81.6    
81.7    
81.9    
82.1    
82.2    
82.4    
82.6    
82.7    
82.9    
83.1    
83.2    
83.4    
83.6    
83.8    
83.9    
84.1    
84.3    
84.4    
84.6    
84.8    
84.9    
85.1    
85.3    
85.4    
85.6    
85.8    
85.9    
86.1    
86.3    
86.4    
86.6    
86.8    
86.9    
87.1    
87.3    
87.4    
87.6    
87.8    
87.9    
88.1    
88.3    
88.4    
88.6    
88.8    
88.9    
89.1    
89.3    
89.4    
89.6    
89.8    
89.9    
90.1    
90.3    
90.5    
90.6    
90.8    
91.0    
91.1    
91.3    
91.5    
91.6    
91.8    
92.0    
92.1    
92.3    
92.5    
92.6    
92.8    
93.0    
93.1    
93.3    
93.5    
93.6    
93.8    
94.0    
94.1    
94.3    
94.5    
94.6    
94.8    
95.0    
95.1    
95.3    
95.5    
95.6    
95.8    
96.0    
96.1    
96.3    
96.5    
96.6    
96.8    
97.0    
97.2    
97.3    
97.5    
97.7    
97.8    
98.0    
98.2    
98.3    
98.5    
98.7    
98.8    
99.0    
99.2    
99.3    
99.5    
99.7    
99.8    
-found 42 predictions from path traversal
Error with prediction: snap lend_intergenic: 48764, rend_intergenic: 46133  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140732, rend_intergenic: 139439  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144408, rend_intergenic: 140956  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171624, rend_intergenic: 171226  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 280952, rend_intergenic: 275187  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 385266, rend_intergenic: 379761  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 37 predictions persist after filtering for low support