-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_2/scaffold_2_15073958-15332290

-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 CodingQuarry_transcript_28702-T1
Valid prediction for snap_scaffold_2-snap.2923-T1
Valid prediction for GeneMark_model.8298_t
Valid prediction for GlimmerHMM_glimmerT_5139-T1
Valid prediction for snap_scaffold_2-snap.2953-T1
Valid prediction for GlimmerHMM_glimmerT_5138-T1
Valid prediction for CodingQuarry_transcript_28701-T1
Valid prediction for GlimmerHMM_glimmerT_5154-T1
Valid prediction for snap_scaffold_2-snap.2915-T1
Valid prediction for GlimmerHMM_glimmerT_5148-T1
Valid prediction for GeneMark_model.8290_t
Valid prediction for snap_scaffold_2-snap.2954-T1
Valid prediction for GlimmerHMM_glimmerT_5137-T1
Valid prediction for GlimmerHMM_glimmerT_5156-T1
Couldn't classify 5775, 5886
Couldn't classify 6587, 6667
Sorry, prediction pasa_asmbl_25010.p1 fails validation.
(GTG)	 AG	5775-5886	GT	TGG
(CCG)	 AG	6059-6156	GT	AGG
(ATG)	 AG	6255-6338	GT	AGG
(AAC)	 AG	6587-6667	TG	CGT
-recovered pasa_asmbl_25010.p1, initial, 6255, 6338
-recovered pasa_asmbl_25010.p1, internal, 5775, 5886
-recovered pasa_asmbl_25010.p1, internal, 6059, 6156
-recovered pasa_asmbl_25010.p1, internal, 6255, 6338
Valid prediction for Augustus_model.g3462.t1
Valid prediction for snap_scaffold_2-snap.2958-T1
Valid prediction for snap_scaffold_2-snap.2921-T1
Valid prediction for Augustus_model.g3474.t1
Valid prediction for GlimmerHMM_glimmerT_5128-T1
Valid prediction for snap_scaffold_2-snap.2944-T1
Valid prediction for Augustus_model.g3470.t1
Valid prediction for snap_scaffold_2-snap.2933-T1
Valid prediction for GlimmerHMM_glimmerT_5142-T1
Valid prediction for pasa_asmbl_25035.p1
Valid prediction for GeneMark_model.8272_t
Valid prediction for GeneMark_model.8285_t
Valid prediction for GlimmerHMM_glimmerT_5147-T1
Valid prediction for snap_scaffold_2-snap.2925-T1
Valid prediction for GeneMark_model.8261_t
Valid prediction for CodingQuarry_transcript_28699-T1
Valid prediction for GeneMark_model.8270_t
Valid prediction for GeneMark_model.8283_t
Valid prediction for snap_scaffold_2-snap.2936-T1
Valid prediction for HiQ_model.g3485.t1
Valid prediction for snap_scaffold_2-snap.2937-T1
Valid prediction for Augustus_model.g3473.t1
Valid prediction for GlimmerHMM_glimmerT_5150-T1
Valid prediction for GeneMark_model.8275_t
Valid prediction for snap_scaffold_2-snap.2940-T1
Valid prediction for snap_scaffold_2-snap.2930-T1
Valid prediction for pasa_asmbl_25052.p1
Valid prediction for GeneMark_model.8277_t
Valid prediction for GlimmerHMM_glimmerT_5166-T1
Valid prediction for GlimmerHMM_glimmerT_5151-T1
Valid prediction for snap_scaffold_2-snap.2938-T1
Valid prediction for GlimmerHMM_glimmerT_5140-T1
Valid prediction for GlimmerHMM_glimmerT_5158-T1
Valid prediction for Augustus_model.g3467.t1
Valid prediction for Augustus_model.g3455.t1
Valid prediction for GlimmerHMM_glimmerT_5132-T1
Valid prediction for GeneMark_model.8279_t
Valid prediction for snap_scaffold_2-snap.2929-T1
Valid prediction for GeneMark_model.8269_t
Valid prediction for GeneMark_model.8287_t
Valid prediction for snap_scaffold_2-snap.2916-T1
Valid prediction for GeneMark_model.8248_t
Valid prediction for Augustus_model.g3454.t1
Valid prediction for GeneMark_model.8259_t
Valid prediction for Augustus_model.g3465.t1
Valid prediction for GlimmerHMM_glimmerT_5129-T1
Valid prediction for pasa_asmbl_25017.p1
Couldn't classify 154372, 154402
Sorry, prediction pasa_asmbl_25015.p1 fails validation.
(GGG)	 TT	154372-154402	GT	AGG
(GGG)	 AG	154555-154853	GA	GAG
-recovered pasa_asmbl_25015.p1, terminal, 154555, 154853
Valid prediction for Augustus_model.g3486.t1
Valid prediction for GeneMark_model.8267_t
Couldn't classify 222203, 222235
Sorry, prediction pasa_asmbl_25053.p1 fails validation.
(TTT)	 CC	222203-222235	GC	AGG
(TTC)	 AG	222892-223068	GT	AGG
(GTA)	 AG	225149-225358	GT	CTG
(ATC)	 AG	226537-226750	GT	AGG
(GCT)	 AG	227206-227384	GA	GAG
-recovered pasa_asmbl_25053.p1, terminal, 227206, 227384
-recovered pasa_asmbl_25053.p1, internal, 222892, 223068
-recovered pasa_asmbl_25053.p1, internal, 225149, 225358
-recovered pasa_asmbl_25053.p1, internal, 226537, 226750
Valid prediction for HiQ_model.g3484.t1
Valid prediction for GlimmerHMM_glimmerT_5161-T1
Valid prediction for snap_scaffold_2-snap.2926-T1
Valid prediction for snap_scaffold_2-snap.2946-T1
Valid prediction for snap_scaffold_2-snap.2943-T1
Valid prediction for snap_scaffold_2-snap.2955-T1
Valid prediction for HiQ_model.g3481.t1
Valid prediction for HiQ_model.g3480.t1
Valid prediction for snap_scaffold_2-snap.2947-T1
Valid prediction for pasa_asmbl_25020.p1
Valid prediction for GeneMark_model.8254_t
Valid prediction for HiQ_model.g3479.t1
Valid prediction for GeneMark_model.8265_t
Valid prediction for GeneMark_model.8256_t
Valid prediction for snap_scaffold_2-snap.2917-T1
Valid prediction for GlimmerHMM_glimmerT_5162-T1
Valid prediction for Augustus_model.g3477.t1
Valid prediction for GlimmerHMM_glimmerT_5149-T1
Valid prediction for GlimmerHMM_glimmerT_5164-T1
Valid prediction for GeneMark_model.8281_t
Valid prediction for GeneMark_model.8302_t
Valid prediction for Augustus_model.g3459.t1
Valid prediction for GeneMark_model.8300_t
Valid prediction for GeneMark_model.8304_t
Valid prediction for snap_scaffold_2-snap.2948-T1
Valid prediction for snap_scaffold_2-snap.2951-T1
Valid prediction for GeneMark_model.8303_t
Valid prediction for GeneMark_model.8292_t
Valid prediction for CodingQuarry_transcript_28705-T1
Valid prediction for snap_scaffold_2-snap.2960-T1
Valid prediction for GeneMark_model.8262_t
Valid prediction for pasa_asmbl_25047.p1
Valid prediction for GeneMark_model.8288_t
Valid prediction for GeneMark_model.8296_t
Valid prediction for GeneMark_model.8294_t
Valid prediction for GeneMark_model.8274_t
Valid prediction for GeneMark_model.8252_t
Valid prediction for GlimmerHMM_glimmerT_5153-T1
Valid prediction for GeneMark_model.8250_t
Valid prediction for GlimmerHMM_glimmerT_5163-T1
Valid prediction for snap_scaffold_2-snap.2934-T1
Valid prediction for CodingQuarry_transcript_28704-T1
Valid prediction for CodingQuarry_transcript_28700-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 GeneMark_model.8289_t
Valid prediction for GlimmerHMM_glimmerT_5133-T1
Valid prediction for GeneMark_model.8263_t
Valid prediction for snap_scaffold_2-snap.2919-T1
Valid prediction for HiQ_model.g3478.t1
Valid prediction for snap_scaffold_2-snap.2928-T1
Valid prediction for snap_scaffold_2-snap.2931-T1
Valid prediction for snap_scaffold_2-snap.2924-T1
Valid prediction for HiQ_model.g3487.t1
Valid prediction for GeneMark_model.8307_t
Valid prediction for CodingQuarry_transcript_28698-T1
Valid prediction for GeneMark_model.8253_t
Valid prediction for GlimmerHMM_glimmerT_5155-T1
Valid prediction for CodingQuarry_transcript_28706-T1
Valid prediction for snap_scaffold_2-snap.2945-T1
Valid prediction for snap_scaffold_2-snap.2957-T1
Valid prediction for Augustus_model.g3466.t1
Valid prediction for GlimmerHMM_glimmerT_5134-T1
Valid prediction for snap_scaffold_2-snap.2956-T1
Valid prediction for Augustus_model.g3471.t1
Valid prediction for GeneMark_model.8286_t
Valid prediction for GeneMark_model.8278_t
Valid prediction for Augustus_model.g3483.t1
Valid prediction for HiQ_model.g3482.t1
Valid prediction for Augustus_model.g3488.t1
Valid prediction for GeneMark_model.8301_t
Valid prediction for snap_scaffold_2-snap.2952-T1
Valid prediction for GeneMark_model.8299_t
Valid prediction for Augustus_model.g3475.t1
Valid prediction for pasa_asmbl_23631.p1
Valid prediction for snap_scaffold_2-snap.2949-T1
Valid prediction for GlimmerHMM_glimmerT_5165-T1
Valid prediction for snap_scaffold_2-snap.2950-T1
Valid prediction for GlimmerHMM_glimmerT_5144-T1
Valid prediction for GlimmerHMM_glimmerT_5141-T1
Valid prediction for GlimmerHMM_glimmerT_5143-T1
Valid prediction for Augustus_model.g3458.t1
Valid prediction for GlimmerHMM_glimmerT_5130-T1
Valid prediction for GeneMark_model.8251_t
Valid prediction for GeneMark_model.8306_t
Valid prediction for GeneMark_model.8264_t
Valid prediction for GeneMark_model.8295_t
Valid prediction for GeneMark_model.8273_t
Valid prediction for GlimmerHMM_glimmerT_5136-T1
Valid prediction for Augustus_model.g3456.t1
Valid prediction for Augustus_model.g3464.t1
Valid prediction for GeneMark_model.8260_t
Valid prediction for Augustus_model.g3460.t1
Valid prediction for GlimmerHMM_glimmerT_5146-T1
Valid prediction for snap_scaffold_2-snap.2927-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for snap_scaffold_2-snap.2941-T1
Valid prediction for GlimmerHMM_glimmerT_5152-T1
Valid prediction for GeneMark_model.8305_t
Valid prediction for GlimmerHMM_glimmerT_5135-T1
Valid prediction for GlimmerHMM_glimmerT_5157-T1
Valid prediction for GeneMark_model.8297_t
Valid prediction for GeneMark_model.8257_t
Valid prediction for pasa_asmbl_23629.p1
Valid prediction for GeneMark_model.8280_t
Valid prediction for snap_scaffold_2-snap.2920-T1
Valid prediction for GeneMark_model.8266_t
Valid prediction for GeneMark_model.8293_t
Valid prediction for GeneMark_model.8276_t
Valid prediction for GeneMark_model.8249_t
Valid prediction for GlimmerHMM_glimmerT_5159-T1
Valid prediction for Augustus_model.g3476.t1
Valid prediction for GeneMark_model.8271_t
Valid prediction for GeneMark_model.8258_t
Valid prediction for GlimmerHMM_glimmerT_5131-T1
Valid prediction for GeneMark_model.8268_t
Valid prediction for GeneMark_model.8291_t
Valid prediction for GeneMark_model.8255_t
Valid prediction for CodingQuarry_transcript_28703-T1
Valid prediction for Augustus_model.g3463.t1
Valid prediction for pasa_asmbl_23634.p1
Valid prediction for snap_scaffold_2-snap.2939-T1
Valid prediction for Augustus_model.g3469.t1
Valid prediction for snap_scaffold_2-snap.2935-T1
Valid prediction for GlimmerHMM_glimmerT_5145-T1
Valid prediction for snap_scaffold_2-snap.2918-T1
Valid prediction for snap_scaffold_2-snap.2932-T1
Valid prediction for GlimmerHMM_glimmerT_5167-T1
Valid prediction for GeneMark_model.8247_t
Valid prediction for snap_scaffold_2-snap.2942-T1
Valid prediction for snap_scaffold_2-snap.2959-T1
Valid prediction for Augustus_model.g3472.t1
Valid prediction for GeneMark_model.8282_t
Valid prediction for snap_scaffold_2-snap.2922-T1
Valid prediction for Augustus_model.g3468.t1
Valid prediction for GeneMark_model.8284_t
Valid prediction for GlimmerHMM_glimmerT_5160-T1
Valid prediction for Augustus_model.g3457.t1
Valid prediction for Augustus_model.g3461.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 25274, rend_intergenic: 23922  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33898, rend_intergenic: 26662  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37610, rend_intergenic: 37506  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40232, rend_intergenic: 38016  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53461, rend_intergenic: 40372  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78012, rend_intergenic: 58552  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99250, rend_intergenic: 82559  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102907, rend_intergenic: 100115  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123581, rend_intergenic: 103910  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139714, rend_intergenic: 130993  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 226818, rend_intergenic: 224745  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 253399, rend_intergenic: 251702  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 258333
-exon list size: 924


building trellis

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59.7    
59.8    
59.9    
60.0    
60.2    
60.3    
60.4    
60.5    
60.6    
60.7    
60.8    
60.9    
61.0    
61.1    
61.2    
61.3    
61.4    
61.6    
61.7    
61.8    
61.9    
62.0    
62.1    
62.2    
62.3    
62.4    
62.5    
62.6    
62.7    
62.9    
63.0    
63.1    
63.2    
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    
65.2    
65.3    
65.4    
65.6    
65.7    
65.8    
65.9    
66.0    
66.1    
66.2    
66.3    
66.4    
66.5    
66.6    
66.7    
66.8    
67.0    
67.1    
67.2    
67.3    
67.4    
67.5    
67.6    
67.7    
67.8    
67.9    
68.0    
68.1    
68.3    
68.4    
68.5    
68.6    
68.7    
68.8    
68.9    
69.0    
69.1    
69.2    
69.3    
69.4    
69.5    
69.7    
69.8    
69.9    
70.0    
70.1    
70.2    
70.3    
70.4    
70.5    
70.6    
70.7    
70.8    
71.0    
71.1    
71.2    
71.3    
71.4    
71.5    
71.6    
71.7    
71.8    
71.9    
72.0    
72.1    
72.2    
72.4    
72.5    
72.6    
72.7    
72.8    
72.9    
73.0    
73.1    
73.2    
73.3    
73.4    
73.5    
73.7    
73.8    
73.9    
74.0    
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    
76.0    
76.1    
76.2    
76.3    
76.5    
76.6    
76.7    
76.8    
76.9    
77.0    
77.1    
77.2    
77.3    
77.4    
77.5    
77.6    
77.8    
77.9    
78.0    
78.1    
78.2    
78.3    
78.4    
78.5    
78.6    
78.7    
78.8    
78.9    
79.0    
79.2    
79.3    
79.4    
79.5    
79.6    
79.7    
79.8    
79.9    
80.0    
80.1    
80.2    
80.3    
80.5    
80.6    
80.7    
80.8    
80.9    
81.0    
81.1    
81.2    
81.3    
81.4    
81.5    
81.6    
81.7    
81.9    
82.0    
82.1    
82.2    
82.3    
82.4    
82.5    
82.6    
82.7    
82.8    
82.9    
83.0    
83.2    
83.3    
83.4    
83.5    
83.6    
83.7    
83.8    
83.9    
84.0    
84.1    
84.2    
84.3    
84.4    
84.6    
84.7    
84.8    
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    
86.8    
86.9    
87.0    
87.1    
87.3    
87.4    
87.5    
87.6    
87.7    
87.8    
87.9    
88.0    
88.1    
88.2    
88.3    
88.4    
88.6    
88.7    
88.8    
88.9    
89.0    
89.1    
89.2    
89.3    
89.4    
89.5    
89.6    
89.7    
89.8    
90.0    
90.1    
90.2    
90.3    
90.4    
90.5    
90.6    
90.7    
90.8    
90.9    
91.0    
91.1    
91.3    
91.4    
91.5    
91.6    
91.7    
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    
93.6    
93.7    
93.8    
94.0    
94.1    
94.2    
94.3    
94.4    
94.5    
94.6    
94.7    
94.8    
94.9    
95.0    
95.1    
95.2    
95.4    
95.5    
95.6    
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    
97.5    
97.6    
97.7    
97.8    
97.9    
98.1    
98.2    
98.3    
98.4    
98.5    
98.6    
98.7    
98.8    
98.9    
99.0    
99.1    
99.2    
99.4    
99.5    
99.6    
99.7    
99.8    
99.9    
-found 56 predictions from path traversal
Error with prediction: snap lend_intergenic: 25274, rend_intergenic: 23922  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33898, rend_intergenic: 26662  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37610, rend_intergenic: 37506  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40232, rend_intergenic: 38016  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53461, rend_intergenic: 40372  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78012, rend_intergenic: 58552  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99250, rend_intergenic: 82559  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102907, rend_intergenic: 100115  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123581, rend_intergenic: 103910  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139714, rend_intergenic: 130993  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 226818, rend_intergenic: 224745  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 253399, rend_intergenic: 251702  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 28 predictions persist after filtering for low support