-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_14193732-14466039

-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: +)Couldn't classify 189315, 189510
Sorry, prediction pasa_asmbl_24928.p1 fails validation.
(AAC)	 GC	189315-189510	GT	AGG
(GAT)	 AG	192069-192151	GT	GGG
(ATG)	 AG	193972-194020	GT	CGG
(CGG)	 AG	194608-194742	GT	AGG
(GCT)	 AG	195988-196067	GT	AGG
(GGC)	 AG	197287-197448	GT	CTG
(TTG)	 AG	197601-197664	GT	GGG
(CTG)	 AG	198734-198862	GT	CGG
(GTA)	 AG	199042-199218	GT	GGG
(GAC)	 AG	199358-199501	GT	CGG
(GGT)	 AG	199885-200012	TC	GAT
-recovered pasa_asmbl_24928.p1, initial, 193972, 194020
-recovered pasa_asmbl_24928.p1, terminal, 199885, 200012
-recovered pasa_asmbl_24928.p1, internal, 192069, 192151
-recovered pasa_asmbl_24928.p1, internal, 193972, 194020
-recovered pasa_asmbl_24928.p1, internal, 194608, 194742
-recovered pasa_asmbl_24928.p1, internal, 195988, 196067
-recovered pasa_asmbl_24928.p1, internal, 197287, 197448
-recovered pasa_asmbl_24928.p1, internal, 197601, 197664
-recovered pasa_asmbl_24928.p1, internal, 198734, 198862
-recovered pasa_asmbl_24928.p1, internal, 199042, 199218
-recovered pasa_asmbl_24928.p1, internal, 199358, 199501
Valid prediction for snap_scaffold_2-snap.2736-T1
Valid prediction for snap_scaffold_2-snap.2707-T1
Valid prediction for GlimmerHMM_glimmerT_4889-T1
Valid prediction for snap_scaffold_2-snap.2741-T1
Valid prediction for CodingQuarry_transcript_28736-T1
Valid prediction for snap_scaffold_2-snap.2751-T1
Couldn't classify 161622, 162230
Sorry, prediction pasa_asmbl_24919.p1 fails validation.
(GAG)	 GT	161622-162230	AA	GCA
Valid prediction for HiQ_model.g3297.t1
Valid prediction for GlimmerHMM_glimmerT_4908-T1
Valid prediction for snap_scaffold_2-snap.2722-T1
Valid prediction for CodingQuarry_transcript_28735-T1
Valid prediction for HiQ_model.g3304.t1
Valid prediction for GlimmerHMM_glimmerT_4895-T1
Valid prediction for HiQ_model.g3295.t1
Valid prediction for Augustus_model.g3294.t1
Valid prediction for snap_scaffold_2-snap.2717-T1
Valid prediction for GlimmerHMM_glimmerT_4910-T1
Valid prediction for CodingQuarry_transcript_28734-T1
Valid prediction for snap_scaffold_2-snap.2737-T1
Valid prediction for GlimmerHMM_glimmerT_4899-T1
Valid prediction for GlimmerHMM_glimmerT_4900-T1
Valid prediction for GlimmerHMM_glimmerT_4916-T1
Valid prediction for snap_scaffold_2-snap.2727-T1
Valid prediction for HiQ_model.g3290.t1
Valid prediction for HiQ_model.g3293.t1
Valid prediction for Augustus_model.g3315.t1
Valid prediction for CodingQuarry_transcript_28724-T1
Valid prediction for Augustus_model.g3292.t1
Valid prediction for GlimmerHMM_glimmerT_4898-T1
Valid prediction for CodingQuarry_transcript_28725-T1
Valid prediction for GlimmerHMM_glimmerT_4919-T1
Valid prediction for snap_scaffold_2-snap.2733-T1
Couldn't classify 144616, 144669
Sorry, prediction pasa_asmbl_24917.p1 fails validation.
(CTG)	 AT	144616-144669	GT	AGG
(TCT)	 AG	144774-144941	GT	AGG
(GCC)	 AG	145038-145100	GT	AGG
(GCA)	 AG	145191-145287	GT	AGG
(ATC)	 AG	145376-145452	GT	GGG
(TTG)	 AG	145554-145811	GT	CTG
(ATT)	 AG	145977-146147	GT	CGG
(AAG)	 AG	146344-146530	GT	AGG
(CCA)	 AG	146659-147002	GT	AGG
-recovered pasa_asmbl_24917.p1, terminal, 146659, 147002
-recovered pasa_asmbl_24917.p1, internal, 144774, 144941
-recovered pasa_asmbl_24917.p1, internal, 145038, 145100
-recovered pasa_asmbl_24917.p1, internal, 145191, 145287
-recovered pasa_asmbl_24917.p1, internal, 145376, 145452
-recovered pasa_asmbl_24917.p1, internal, 145554, 145811
-recovered pasa_asmbl_24917.p1, internal, 145977, 146147
-recovered pasa_asmbl_24917.p1, internal, 146344, 146530
-recovered pasa_asmbl_24917.p1, internal, 146659, 147002
Valid prediction for snap_scaffold_2-snap.2735-T1
Valid prediction for pasa_asmbl_24920.p1
Valid prediction for Augustus_model.g3314.t1
Valid prediction for snap_scaffold_2-snap.2739-T1
Valid prediction for CodingQuarry_transcript_28726-T1
Valid prediction for GlimmerHMM_glimmerT_4911-T1
Valid prediction for CodingQuarry_transcript_28727-T1
Valid prediction for Augustus_model.g3299.t1
Valid prediction for Augustus_model.g3308.t1
Valid prediction for GlimmerHMM_glimmerT_4912-T1
Valid prediction for GlimmerHMM_glimmerT_4903-T1
Valid prediction for GlimmerHMM_glimmerT_4892-T1
Valid prediction for snap_scaffold_2-snap.2719-T1
Valid prediction for snap_scaffold_2-snap.2716-T1
Valid prediction for GlimmerHMM_glimmerT_4904-T1
Valid prediction for CodingQuarry_transcript_28730-T1
Valid prediction for pasa_asmbl_24911.p1
Valid prediction for HiQ_model.g3307.t1
Valid prediction for pasa_asmbl_24902.p2
Valid prediction for GlimmerHMM_glimmerT_4902-T1
Valid prediction for GlimmerHMM_glimmerT_4896-T1
Valid prediction for snap_scaffold_2-snap.2726-T1
Valid prediction for snap_scaffold_2-snap.2715-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_4909-T1
Valid prediction for GlimmerHMM_glimmerT_4897-T1
Valid prediction for Augustus_model.g3301.t1
Couldn't classify 262107, 262152
Sorry, prediction pasa_asmbl_24935.p1 fails validation.
(CTC)	 GC	262107-262152	GT	GGG
(TGT)	 AG	262270-262404	GT	AGG
(TTC)	 AG	262729-262837	GT	AAG
(GCC)	 AG	262943-263012	GC	AGG
(GTT)	 AG	263155-263286	AA	AAA
-recovered pasa_asmbl_24935.p1, terminal, 263155, 263286
-recovered pasa_asmbl_24935.p1, internal, 262270, 262404
-recovered pasa_asmbl_24935.p1, internal, 262729, 262837
-recovered pasa_asmbl_24935.p1, internal, 262943, 263012
Valid prediction for snap_scaffold_2-snap.2723-T1
Valid prediction for GlimmerHMM_glimmerT_4888-T1
Valid prediction for GlimmerHMM_glimmerT_4918-T1
Valid prediction for HiQ_model.g3298.t1
Valid prediction for snap_scaffold_2-snap.2730-T1
Valid prediction for CodingQuarry_transcript_28737-T1
Couldn't classify 260986, 261097
Couldn't classify 261987, 262004
Sorry, prediction pasa_asmbl_25344.p1 fails validation.
(TCT)	 CA	260986-261097	GT	CGG
(ATA)	 AG	261192-261287	GT	AGG
(AGA)	 AG	261411-261469	GT	AGG
(GTC)	 AG	261571-261651	GT	CTG
(ATG)	 AG	261822-261887	GT	AGG
(GCT)	 AG	261987-262004	AT	CTA
-recovered pasa_asmbl_25344.p1, initial, 261822, 261887
-recovered pasa_asmbl_25344.p1, internal, 261192, 261287
-recovered pasa_asmbl_25344.p1, internal, 261411, 261469
-recovered pasa_asmbl_25344.p1, internal, 261571, 261651
-recovered pasa_asmbl_25344.p1, internal, 261822, 261887
Valid prediction for Augustus_model.g3305.t1
Valid prediction for snap_scaffold_2-snap.2729-T1
Valid prediction for snap_scaffold_2-snap.2742-T1
Valid prediction for Augustus_model.g3288.t1
Valid prediction for GlimmerHMM_glimmerT_4907-T1
Valid prediction for snap_scaffold_2-snap.2724-T1
Valid prediction for GlimmerHMM_glimmerT_4906-T1
Valid prediction for Augustus_model.g3313.t1
Valid prediction for GlimmerHMM_glimmerT_4894-T1
Valid prediction for CodingQuarry_transcript_28729-T1
Valid prediction for snap_scaffold_2-snap.2713-T1
Valid prediction for pasa_asmbl_24924.p1
Valid prediction for HiQ_model.g3306.t1
Valid prediction for pasa_asmbl_24896.p1
Valid prediction for snap_scaffold_2-snap.2714-T1
Valid prediction for HiQ_model.g3302.t1
Valid prediction for pasa_asmbl_24897.p1
Valid prediction for snap_scaffold_2-snap.2750-T1
Valid prediction for snap_scaffold_2-snap.2745-T1
Valid prediction for HiQ_model.g3311.t1
Valid prediction for snap_scaffold_2-snap.2725-T1
Valid prediction for pasa_asmbl_24930.p1
Valid prediction for pasa_asmbl_24908.p1
Valid prediction for snap_scaffold_2-snap.2749-T1
Couldn't classify 113691, 113828
Couldn't classify 114976, 115085
Sorry, prediction pasa_asmbl_24909.p1 fails validation.
(GTC)	 CA	113691-113828	GT	AGG
(GAA)	 AG	113954-114135	GT	GCG
(CTT)	 AG	114553-114725	GT	TGG
(CTG)	 AG	114976-115085	GG	AGG
-recovered pasa_asmbl_24909.p1, internal, 113954, 114135
-recovered pasa_asmbl_24909.p1, internal, 114553, 114725
Valid prediction for snap_scaffold_2-snap.2731-T1
Valid prediction for pasa_asmbl_24932.p1
Valid prediction for CodingQuarry_transcript_28731-T1
Valid prediction for snap_scaffold_2-snap.2740-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_4887-T1
Valid prediction for snap_scaffold_2-snap.2712-T1
Valid prediction for pasa_asmbl_23583.p1
Valid prediction for pasa_asmbl_24055.p1
Valid prediction for CodingQuarry_transcript_28728-T1
Valid prediction for GlimmerHMM_glimmerT_4891-T1
Valid prediction for pasa_asmbl_23598.p1
Valid prediction for snap_scaffold_2-snap.2752-T1
Valid prediction for CodingQuarry_transcript_28720-T1
Valid prediction for snap_scaffold_2-snap.2711-T1
Valid prediction for HiQ_model.g3303.t1
Valid prediction for snap_scaffold_2-snap.2706-T1
Valid prediction for snap_scaffold_2-snap.2728-T1
Valid prediction for snap_scaffold_2-snap.2743-T1
Valid prediction for CodingQuarry_transcript_28722-T1
Valid prediction for Augustus_model.g3283.t1
Valid prediction for snap_scaffold_2-snap.2718-T1
Valid prediction for pasa_asmbl_23588.p1
Valid prediction for GlimmerHMM_glimmerT_4915-T1
Valid prediction for CodingQuarry_transcript_28732-T1
Valid prediction for Augustus_model.g3289.t1
Valid prediction for snap_scaffold_2-snap.2721-T1
Valid prediction for HiQ_model.g3287.t1
Valid prediction for Augustus_model.g3310.t1
Valid prediction for snap_scaffold_2-snap.2747-T1
Valid prediction for CodingQuarry_transcript_28721-T1
Valid prediction for pasa_asmbl_23595.p1
Valid prediction for snap_scaffold_2-snap.2720-T1
Valid prediction for snap_scaffold_2-snap.2748-T1
Valid prediction for Augustus_model.g3285.t1
Valid prediction for GlimmerHMM_glimmerT_4890-T1
Couldn't classify 246946, 247025
Sorry, prediction pasa_asmbl_23579.p1 fails validation.
(AAA)	 AA	246946-247025	GT	GGG
(GTG)	 AG	247597-248216	GT	AGG
(GTA)	 AG	248742-248917	GT	GAG
-recovered pasa_asmbl_23579.p1, terminal, 248742, 248917
-recovered pasa_asmbl_23579.p1, internal, 247597, 248216
-recovered pasa_asmbl_23579.p1, internal, 248742, 248917
Valid prediction for Augustus_model.g3309.t1
Valid prediction for HiQ_model.g3286.t1
Valid prediction for HiQ_model.g3316.t1
Valid prediction for GlimmerHMM_glimmerT_4913-T1
Valid prediction for CodingQuarry_transcript_28738-T1
Valid prediction for GlimmerHMM_glimmerT_4914-T1
Valid prediction for snap_scaffold_2-snap.2734-T1
Valid prediction for HiQ_model.g3300.t1
Couldn't classify 14934, 15045
Sorry, prediction pasa_asmbl_23600.p1 fails validation.
(CCT)	 AT	14934-15045	GT	TGG
(GTA)	 AG	16740-16948	GT	AGG
(AAC)	 AG	17472-18260	GT	AGG
(ACT)	 AG	19189-19311	GT	AGG
(TTC)	 AG	20170-20271	TT	GAT
-recovered pasa_asmbl_23600.p1, terminal, 20170, 20271
-recovered pasa_asmbl_23600.p1, internal, 16740, 16948
-recovered pasa_asmbl_23600.p1, internal, 17472, 18260
-recovered pasa_asmbl_23600.p1, internal, 19189, 19311
Valid prediction for GlimmerHMM_glimmerT_4917-T1
Valid prediction for Augustus_model.g3312.t1
Valid prediction for GlimmerHMM_glimmerT_4886-T1
Valid prediction for Augustus_model.g3291.t1
Valid prediction for Augustus_model.g3284.t1
Valid prediction for snap_scaffold_2-snap.2732-T1
Valid prediction for GlimmerHMM_glimmerT_4901-T1
Valid prediction for HiQ_model.g3282.t1
Valid prediction for GlimmerHMM_glimmerT_4905-T1
Valid prediction for pasa_asmbl_23594.p1
Valid prediction for snap_scaffold_2-snap.2738-T1
Valid prediction for HiQ_model.g3296.t1
Valid prediction for snap_scaffold_2-snap.2708-T1
Valid prediction for snap_scaffold_2-snap.2710-T1
Valid prediction for snap_scaffold_2-snap.2744-T1
Valid prediction for snap_scaffold_2-snap.2746-T1
Valid prediction for pasa_asmbl_23586.p1
Valid prediction for CodingQuarry_transcript_28733-T1
Couldn't classify 260999, 261132
Sorry, prediction pasa_asmbl_23573.p1 fails validation.
(AGC)	 TG	260999-261132	GT	AGG
(TGT)	 AG	261253-261691	GT	AGG
(GTT)	 AG	262903-262944	GT	AGG
(CAG)	 AG	263139-263197	GT	AGG
(CCC)	 AG	263535-263784	GT	AGG
(GAG)	 AG	264020-264154	GT	AGG
(ATT)	 AG	264987-265030	GT	AGG
(CAG)	 AG	265185-265263	GT	AGG
(AGC)	 AG	265413-265544	GT	AGG
(GAT)	 AG	265785-265880	GT	GGG
(GAC)	 AG	267082-267153	GT	AGG
(TAG)	 AG	267249-267251	AC	AGA
-recovered pasa_asmbl_23573.p1, terminal, 267249, 267251
-recovered pasa_asmbl_23573.p1, internal, 261253, 261691
-recovered pasa_asmbl_23573.p1, internal, 262903, 262944
-recovered pasa_asmbl_23573.p1, internal, 263139, 263197
-recovered pasa_asmbl_23573.p1, internal, 263535, 263784
-recovered pasa_asmbl_23573.p1, internal, 264020, 264154
-recovered pasa_asmbl_23573.p1, internal, 264987, 265030
-recovered pasa_asmbl_23573.p1, internal, 265185, 265263
-recovered pasa_asmbl_23573.p1, internal, 265413, 265544
-recovered pasa_asmbl_23573.p1, internal, 265785, 265880
-recovered pasa_asmbl_23573.p1, internal, 267082, 267153
Valid prediction for GlimmerHMM_glimmerT_4893-T1
Valid prediction for snap_scaffold_2-snap.2709-T1
Valid prediction for CodingQuarry_transcript_28723-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15303, rend_intergenic: 6562  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192304, rend_intergenic: 191680  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195740, rend_intergenic: 192315  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 250026, rend_intergenic: 236193  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 272308
-exon list size: 531


building trellis

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71.3    
71.5    
71.7    
71.9    
72.0    
72.2    
72.4    
72.6    
72.8    
73.0    
73.2    
73.4    
73.5    
73.7    
73.9    
74.1    
74.3    
74.5    
74.7    
74.9    
75.0    
75.2    
75.4    
75.6    
75.8    
76.0    
76.2    
76.4    
76.5    
76.7    
76.9    
77.1    
77.3    
77.5    
77.7    
77.9    
78.0    
78.2    
78.4    
78.6    
78.8    
79.0    
79.2    
79.4    
79.5    
79.7    
79.9    
80.1    
80.3    
80.5    
80.7    
80.9    
81.1    
81.2    
81.4    
81.6    
81.8    
82.0    
82.2    
82.4    
82.6    
82.7    
82.9    
83.1    
83.3    
83.5    
83.7    
83.9    
84.1    
84.2    
84.4    
84.6    
84.8    
85.0    
85.2    
85.4    
85.6    
85.7    
85.9    
86.1    
86.3    
86.5    
86.7    
86.9    
87.1    
87.2    
87.4    
87.6    
87.8    
88.0    
88.2    
88.4    
88.6    
88.7    
88.9    
89.1    
89.3    
89.5    
89.7    
89.9    
90.1    
90.2    
90.4    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.7    
91.9    
92.1    
92.3    
92.5    
92.7    
92.9    
93.1    
93.2    
93.4    
93.6    
93.8    
94.0    
94.2    
94.4    
94.6    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.2    
99.4    
99.6    
99.8    
-found 40 predictions from path traversal
Error with prediction: snap lend_intergenic: 15303, rend_intergenic: 6562  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192304, rend_intergenic: 191680  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195740, rend_intergenic: 192315  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 250026, rend_intergenic: 236193  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

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