-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_18/scaffold_18_11880067-12104969

-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 GeneMark_model.76774_t
Valid prediction for Augustus_model.g29596.t1
Valid prediction for GlimmerHMM_glimmerT_44218-T1
Valid prediction for GeneMark_model.76750_t
Valid prediction for GeneMark_model.76754_t
Valid prediction for GlimmerHMM_glimmerT_44214-T1
Valid prediction for snap_scaffold_18-snap.2559-T1
Valid prediction for Augustus_model.g29603.t1
Valid prediction for GlimmerHMM_glimmerT_44223-T1
Valid prediction for snap_scaffold_18-snap.2551-T1
Valid prediction for GeneMark_model.76776_t
Valid prediction for snap_scaffold_18-snap.2581-T1
Valid prediction for snap_scaffold_18-snap.2583-T1
Valid prediction for snap_scaffold_18-snap.2570-T1
Valid prediction for GeneMark_model.76759_t
Valid prediction for GlimmerHMM_glimmerT_44216-T1
Valid prediction for GeneMark_model.76767_t
Valid prediction for Augustus_model.g29593.t1
Valid prediction for Augustus_model.g29599.t1
Valid prediction for GlimmerHMM_glimmerT_44212-T1
Valid prediction for snap_scaffold_18-snap.2549-T1
Valid prediction for snap_scaffold_18-snap.2550-T1
Valid prediction for GlimmerHMM_glimmerT_44228-T1
Valid prediction for GeneMark_model.76743_t
Valid prediction for GeneMark_model.76765_t
Valid prediction for GeneMark_model.76741_t
Valid prediction for GlimmerHMM_glimmerT_44226-T1
Valid prediction for Augustus_model.g29594.t1
Valid prediction for snap_scaffold_18-snap.2568-T1
Valid prediction for GeneMark_model.76757_t
Valid prediction for Augustus_model.g29600.t1
Valid prediction for snap_scaffold_18-snap.2574-T1
Valid prediction for snap_scaffold_18-snap.2557-T1
Valid prediction for GeneMark_model.76792_t
Valid prediction for snap_scaffold_18-snap.2579-T1
Couldn't classify 29844, 29948
Couldn't classify 38650, 38733
Sorry, prediction pasa_asmbl_20978.p1 fails validation.
(GTC)	 TT	29844-29948	GT	ACG
(TTC)	 AG	32080-32238	GT	CGG
(ATG)	 AG	33910-34011	GT	AGG
(GTG)	 AG	34183-34261	GT	AGG
(GGT)	 AG	34714-34763	GT	AGG
(GAG)	 AG	34920-35009	GT	TGG
(GAA)	 AG	36361-36441	GT	AGG
(AGG)	 AG	38650-38733	GT	CTG
-recovered pasa_asmbl_20978.p1, initial, 33910, 34011
-recovered pasa_asmbl_20978.p1, internal, 32080, 32238
-recovered pasa_asmbl_20978.p1, internal, 33910, 34011
-recovered pasa_asmbl_20978.p1, internal, 34183, 34261
-recovered pasa_asmbl_20978.p1, internal, 34714, 34763
-recovered pasa_asmbl_20978.p1, internal, 34920, 35009
-recovered pasa_asmbl_20978.p1, internal, 36361, 36441
-recovered pasa_asmbl_20978.p1, internal, 38650, 38733
Valid prediction for snap_scaffold_18-snap.2587-T1
Valid prediction for Augustus_model.g29601.t1
Valid prediction for GlimmerHMM_glimmerT_44215-T1
Valid prediction for GeneMark_model.76789_t
Valid prediction for snap_scaffold_18-snap.2572-T1
Valid prediction for GeneMark_model.76746_t
Valid prediction for snap_scaffold_18-snap.2595-T1
Valid prediction for GeneMark_model.76772_t
Valid prediction for Augustus_model.g29597.t1
Valid prediction for GeneMark_model.76763_t
Valid prediction for GeneMark_model.76755_t
Valid prediction for GeneMark_model.76786_t
Valid prediction for GeneMark_model.76793_t
Valid prediction for GeneMark_model.76769_t
Valid prediction for GeneMark_model.76783_t
Valid prediction for snap_scaffold_18-snap.2576-T1
Valid prediction for snap_scaffold_18-snap.2567-T1
Valid prediction for Augustus_model.g29595.t1
Valid prediction for snap_scaffold_18-snap.2584-T1
Valid prediction for GeneMark_model.76740_t
Valid prediction for GeneMark_model.76739_t
Valid prediction for GeneMark_model.76748_t
Couldn't classify 53694, 53779
Sorry, prediction pasa_asmbl_20979.p1 fails validation.
(AAC)	 GC	53694-53779	GT	CCG
(ACA)	 AG	54559-54621	GT	AGG
(TGC)	 AG	54865-54980	GT	CAG
(TGA)	 AG	55242-55313	GT	AGG
(TCA)	 AG	55864-55931	GT	ATG
(TGC)	 AG	56051-56089	GT	CGG
(CAT)	 AG	56213-56284	GT	AGG
(ATT)	 AG	58147-58299	GT	TGG
(CCC)	 AG	61264-61316	GT	TGG
(GTC)	 AG	62138-62193	GT	AGG
(CTG)	 AG	63162-63291	GT	AGG
(GAT)	 AG	64623-64735	GT	TTG
(CTA)	 AG	66296-66378	GT	ATG
(GAG)	 AG	68516-68638	CC	GAC
-recovered pasa_asmbl_20979.p1, terminal, 68516, 68638
-recovered pasa_asmbl_20979.p1, internal, 54559, 54621
-recovered pasa_asmbl_20979.p1, internal, 54865, 54980
-recovered pasa_asmbl_20979.p1, internal, 55242, 55313
-recovered pasa_asmbl_20979.p1, internal, 55864, 55931
-recovered pasa_asmbl_20979.p1, internal, 56051, 56089
-recovered pasa_asmbl_20979.p1, internal, 56213, 56284
-recovered pasa_asmbl_20979.p1, internal, 58147, 58299
-recovered pasa_asmbl_20979.p1, internal, 61264, 61316
-recovered pasa_asmbl_20979.p1, internal, 62138, 62193
-recovered pasa_asmbl_20979.p1, internal, 63162, 63291
-recovered pasa_asmbl_20979.p1, internal, 64623, 64735
-recovered pasa_asmbl_20979.p1, internal, 66296, 66378
Valid prediction for snap_scaffold_18-snap.2555-T1
Valid prediction for GeneMark_model.76761_t
Valid prediction for snap_scaffold_18-snap.2552-T1
Valid prediction for GlimmerHMM_glimmerT_44232-T1
Valid prediction for snap_scaffold_18-snap.2561-T1
Valid prediction for snap_scaffold_18-snap.2588-T1
Valid prediction for snap_scaffold_18-snap.2565-T1
Valid prediction for GlimmerHMM_glimmerT_44227-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_18-snap.2594-T1
Valid prediction for GeneMark_model.76790_t
Valid prediction for snap_scaffold_18-snap.2598-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for Augustus_model.g29598.t1
Valid prediction for snap_scaffold_18-snap.2563-T1
Valid prediction for snap_scaffold_18-snap.2593-T1
Valid prediction for snap_scaffold_18-snap.2566-T1
Valid prediction for GeneMark_model.76785_t
Valid prediction for GlimmerHMM_glimmerT_44229-T1
Valid prediction for snap_scaffold_18-snap.2591-T1
Valid prediction for snap_scaffold_18-snap.2590-T1
Valid prediction for GlimmerHMM_glimmerT_44225-T1
Valid prediction for GeneMark_model.76753_t
Valid prediction for GlimmerHMM_glimmerT_44213-T1
Valid prediction for GlimmerHMM_glimmerT_44221-T1
Valid prediction for GeneMark_model.76745_t
Valid prediction for snap_scaffold_18-snap.2558-T1
Valid prediction for snap_scaffold_18-snap.2586-T1
Valid prediction for GeneMark_model.76794_t
Valid prediction for GeneMark_model.76760_t
Valid prediction for snap_scaffold_18-snap.2596-T1
Valid prediction for GeneMark_model.76751_t
Valid prediction for snap_scaffold_18-snap.2564-T1
Valid prediction for GlimmerHMM_glimmerT_44231-T1
Valid prediction for GlimmerHMM_glimmerT_44220-T1
Valid prediction for GeneMark_model.76758_t
Valid prediction for snap_scaffold_18-snap.2562-T1
Valid prediction for GlimmerHMM_glimmerT_44211-T1
Valid prediction for snap_scaffold_18-snap.2585-T1
Valid prediction for snap_scaffold_18-snap.2560-T1
Valid prediction for snap_scaffold_18-snap.2580-T1
Valid prediction for GeneMark_model.76770_t
Valid prediction for GeneMark_model.76762_t
Valid prediction for GeneMark_model.76782_t
Valid prediction for GlimmerHMM_glimmerT_44217-T1
Valid prediction for snap_scaffold_18-snap.2577-T1
Valid prediction for Augustus_model.g29602.t1
Valid prediction for snap_scaffold_18-snap.2575-T1
Valid prediction for GeneMark_model.76775_t
Valid prediction for Augustus_model.g29604.t1
Valid prediction for GeneMark_model.76766_t
Valid prediction for GeneMark_model.76771_t
Valid prediction for GlimmerHMM_glimmerT_44224-T1
Valid prediction for GlimmerHMM_glimmerT_44230-T1
Valid prediction for GeneMark_model.76781_t
Valid prediction for GlimmerHMM_glimmerT_44222-T1
Valid prediction for snap_scaffold_18-snap.2548-T1
Valid prediction for snap_scaffold_18-snap.2573-T1
Valid prediction for Augustus_model.g29605.t1
Valid prediction for snap_scaffold_18-snap.2556-T1
Valid prediction for snap_scaffold_18-snap.2554-T1
Valid prediction for snap_scaffold_18-snap.2592-T1
Valid prediction for GeneMark_model.76778_t
Valid prediction for GeneMark_model.76791_t
Valid prediction for snap_scaffold_18-snap.2547-T1
Valid prediction for GeneMark_model.76788_t
Valid prediction for snap_scaffold_18-snap.2578-T1
Valid prediction for GlimmerHMM_glimmerT_44219-T1
Valid prediction for GeneMark_model.76742_t
Valid prediction for snap_scaffold_18-snap.2582-T1
Valid prediction for snap_scaffold_18-snap.2569-T1
Valid prediction for GeneMark_model.76747_t
Valid prediction for GeneMark_model.76756_t
Valid prediction for GeneMark_model.76744_t
Valid prediction for GeneMark_model.76779_t
Valid prediction for GeneMark_model.76768_t
Valid prediction for GeneMark_model.76777_t
Valid prediction for snap_scaffold_18-snap.2553-T1
Valid prediction for snap_scaffold_18-snap.2571-T1
Valid prediction for snap_scaffold_18-snap.2597-T1
Valid prediction for GeneMark_model.76773_t
Valid prediction for snap_scaffold_18-snap.2589-T1
Valid prediction for GeneMark_model.76749_t
Valid prediction for GeneMark_model.76780_t
Valid prediction for GeneMark_model.76787_t
Valid prediction for GeneMark_model.76764_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 34116, rend_intergenic: 20052  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42952, rend_intergenic: 36436  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51767, rend_intergenic: 50695  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56685, rend_intergenic: 52963  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69224, rend_intergenic: 57439  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92303, rend_intergenic: 84940  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100882, rend_intergenic: 95403  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109472, rend_intergenic: 102933  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125652, rend_intergenic: 122223  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135726, rend_intergenic: 129990  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138465, rend_intergenic: 135947  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146200, rend_intergenic: 140167  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152861, rend_intergenic: 146571  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164371, rend_intergenic: 158786  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165164, rend_intergenic: 164477  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168996, rend_intergenic: 165347  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175494, rend_intergenic: 169001  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178568, rend_intergenic: 175569  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190585, rend_intergenic: 186915  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 208575, rend_intergenic: 202836  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 217557, rend_intergenic: 208636  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 224903
-exon list size: 896


building trellis

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62.8    
62.9    
63.0    
63.1    
63.3    
63.4    
63.5    
63.6    
63.7    
63.8    
63.9    
64.0    
64.1    
64.3    
64.4    
64.5    
64.6    
64.7    
64.8    
64.9    
65.0    
65.1    
65.3    
65.4    
65.5    
65.6    
65.7    
65.8    
65.9    
66.0    
66.1    
66.3    
66.4    
66.5    
66.6    
66.7    
66.8    
66.9    
67.0    
67.1    
67.3    
67.4    
67.5    
67.6    
67.7    
67.8    
67.9    
68.0    
68.2    
68.3    
68.4    
68.5    
68.6    
68.7    
68.8    
68.9    
69.0    
69.2    
69.3    
69.4    
69.5    
69.6    
69.7    
69.8    
69.9    
70.0    
70.2    
70.3    
70.4    
70.5    
70.6    
70.7    
70.8    
70.9    
71.0    
71.2    
71.3    
71.4    
71.5    
71.6    
71.7    
71.8    
71.9    
72.0    
72.2    
72.3    
72.4    
72.5    
72.6    
72.7    
72.8    
72.9    
73.1    
73.2    
73.3    
73.4    
73.5    
73.6    
73.7    
73.8    
73.9    
74.1    
74.2    
74.3    
74.4    
74.5    
74.6    
74.7    
74.8    
74.9    
75.1    
75.2    
75.3    
75.4    
75.5    
75.6    
75.7    
75.8    
75.9    
76.1    
76.2    
76.3    
76.4    
76.5    
76.6    
76.7    
76.8    
76.9    
77.1    
77.2    
77.3    
77.4    
77.5    
77.6    
77.7    
77.8    
78.0    
78.1    
78.2    
78.3    
78.4    
78.5    
78.6    
78.7    
78.8    
79.0    
79.1    
79.2    
79.3    
79.4    
79.5    
79.6    
79.7    
79.8    
80.0    
80.1    
80.2    
80.3    
80.4    
80.5    
80.6    
80.7    
80.8    
81.0    
81.1    
81.2    
81.3    
81.4    
81.5    
81.6    
81.7    
81.8    
82.0    
82.1    
82.2    
82.3    
82.4    
82.5    
82.6    
82.7    
82.9    
83.0    
83.1    
83.2    
83.3    
83.4    
83.5    
83.6    
83.7    
83.9    
84.0    
84.1    
84.2    
84.3    
84.4    
84.5    
84.6    
84.7    
84.9    
85.0    
85.1    
85.2    
85.3    
85.4    
85.5    
85.6    
85.7    
85.9    
86.0    
86.1    
86.2    
86.3    
86.4    
86.5    
86.6    
86.7    
86.9    
87.0    
87.1    
87.2    
87.3    
87.4    
87.5    
87.6    
87.8    
87.9    
88.0    
88.1    
88.2    
88.3    
88.4    
88.5    
88.6    
88.8    
88.9    
89.0    
89.1    
89.2    
89.3    
89.4    
89.5    
89.6    
89.8    
89.9    
90.0    
90.1    
90.2    
90.3    
90.4    
90.5    
90.6    
90.8    
90.9    
91.0    
91.1    
91.2    
91.3    
91.4    
91.5    
91.6    
91.8    
91.9    
92.0    
92.1    
92.2    
92.3    
92.4    
92.5    
92.7    
92.8    
92.9    
93.0    
93.1    
93.2    
93.3    
93.4    
93.5    
93.7    
93.8    
93.9    
94.0    
94.1    
94.2    
94.3    
94.4    
94.5    
94.7    
94.8    
94.9    
95.0    
95.1    
95.2    
95.3    
95.4    
95.5    
95.7    
95.8    
95.9    
96.0    
96.1    
96.2    
96.3    
96.4    
96.5    
96.7    
96.8    
96.9    
97.0    
97.1    
97.2    
97.3    
97.4    
97.6    
97.7    
97.8    
97.9    
98.0    
98.1    
98.2    
98.3    
98.4    
98.6    
98.7    
98.8    
98.9    
99.0    
99.1    
99.2    
99.3    
99.4    
99.6    
99.7    
99.8    
99.9    
-found 45 predictions from path traversal
Error with prediction: snap lend_intergenic: 34116, rend_intergenic: 20052  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42952, rend_intergenic: 36436  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51767, rend_intergenic: 50695  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56685, rend_intergenic: 52963  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69224, rend_intergenic: 57439  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92303, rend_intergenic: 84940  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100882, rend_intergenic: 95403  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109472, rend_intergenic: 102933  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125652, rend_intergenic: 122223  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135726, rend_intergenic: 129990  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138465, rend_intergenic: 135947  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146200, rend_intergenic: 140167  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152861, rend_intergenic: 146571  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164371, rend_intergenic: 158786  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165164, rend_intergenic: 164477  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168996, rend_intergenic: 165347  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175494, rend_intergenic: 169001  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178568, rend_intergenic: 175569  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190585, rend_intergenic: 186915  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 208575, rend_intergenic: 202836  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 217557, rend_intergenic: 208636  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support