-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_2/scaffold_2_17650154-17904823

-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 Augustus_model.g3765.t1
Valid prediction for snap_scaffold_2-snap.3487-T1
Valid prediction for GeneMark_model.8963_t
Valid prediction for GlimmerHMM_glimmerT_5579-T1
Valid prediction for Augustus_model.g3773.t1
Valid prediction for GeneMark_model.8959_t
Valid prediction for GlimmerHMM_glimmerT_5563-T1
Valid prediction for GlimmerHMM_glimmerT_5565-T1
Valid prediction for snap_scaffold_2-snap.3512-T1
Valid prediction for snap_scaffold_2-snap.3506-T1
Valid prediction for snap_scaffold_2-snap.3502-T1
Valid prediction for GeneMark_model.8948_t
Valid prediction for Augustus_model.g3780.t1
Valid prediction for snap_scaffold_2-snap.3490-T1
Valid prediction for Augustus_model.g3777.t1
Valid prediction for GlimmerHMM_glimmerT_5541-T1
Valid prediction for GlimmerHMM_glimmerT_5568-T1
Valid prediction for Augustus_model.g3783.t1
Valid prediction for GlimmerHMM_glimmerT_5576-T1
Valid prediction for snap_scaffold_2-snap.3507-T1
Valid prediction for snap_scaffold_2-snap.3499-T1
Valid prediction for snap_scaffold_2-snap.3511-T1
Valid prediction for GeneMark_model.8972_t
Valid prediction for GeneMark_model.8971_t
Valid prediction for snap_scaffold_2-snap.3494-T1
Valid prediction for snap_scaffold_2-snap.3496-T1
Valid prediction for Augustus_model.g3784.t1
Valid prediction for GlimmerHMM_glimmerT_5547-T1
Valid prediction for Augustus_model.g3775.t1
Valid prediction for Augustus_model.g3758.t1
Valid prediction for CodingQuarry_transcript_28778-T1
Valid prediction for GeneMark_model.8974_t
Valid prediction for snap_scaffold_2-snap.3468-T1
Valid prediction for GeneMark_model.8941_t
Valid prediction for GlimmerHMM_glimmerT_5566-T1
Valid prediction for GeneMark_model.8967_t
Valid prediction for Augustus_model.g3785.t1
Valid prediction for snap_scaffold_2-snap.3498-T1
Valid prediction for GlimmerHMM_glimmerT_5562-T1
Valid prediction for GlimmerHMM_glimmerT_5581-T1
Couldn't classify 55281, 55373
Couldn't classify 56195, 56269
Sorry, prediction pasa_asmbl_25228.p1 fails validation.
(TTG)	 TC	55281-55373	GT	ATG
(AAA)	 AG	55474-55569	GT	AGG
(TTG)	 AG	55654-55800	GT	GAG
(CAA)	 AG	55899-56009	GT	AGG
(CTA)	 AG	56195-56269	CT	CCC
-recovered pasa_asmbl_25228.p1, internal, 55474, 55569
-recovered pasa_asmbl_25228.p1, internal, 55654, 55800
-recovered pasa_asmbl_25228.p1, internal, 55899, 56009
Valid prediction for GlimmerHMM_glimmerT_5580-T1
Valid prediction for GeneMark_model.8973_t
Valid prediction for snap_scaffold_2-snap.3477-T1
Couldn't classify 71727, 71747
Sorry, prediction pasa_asmbl_25232.p1 fails validation.
(TCT)	 CA	71727-71747	GT	AGG
(AAT)	 AG	71871-72063	GT	AGG
(GTA)	 AG	72187-72428	GT	ACG
(GTC)	 AG	72540-72794	CT	AAC
-recovered pasa_asmbl_25232.p1, terminal, 72540, 72794
-recovered pasa_asmbl_25232.p1, internal, 71871, 72063
-recovered pasa_asmbl_25232.p1, internal, 72187, 72428
Valid prediction for GeneMark_model.8944_t
Couldn't classify 51396, 51552
Sorry, prediction pasa_asmbl_25227.p1 fails validation.
(TAT)	 CA	51396-51552	GT	CAG
(ACA)	 AG	51697-52019	TT	GAT
-recovered pasa_asmbl_25227.p1, terminal, 51697, 52019
Valid prediction for GlimmerHMM_glimmerT_5564-T1
Valid prediction for GeneMark_model.8970_t
Valid prediction for snap_scaffold_2-snap.3474-T1
Valid prediction for snap_scaffold_2-snap.3505-T1
Valid prediction for snap_scaffold_2-snap.3492-T1
Valid prediction for GeneMark_model.8965_t
Valid prediction for GeneMark_model.8960_t
Valid prediction for GlimmerHMM_glimmerT_5578-T1
Valid prediction for snap_scaffold_2-snap.3504-T1
Valid prediction for Augustus_model.g3762.t1
Valid prediction for Augustus_model.g3774.t1
Valid prediction for snap_scaffold_2-snap.3497-T1
Valid prediction for snap_scaffold_2-snap.3470-T1
Valid prediction for snap_scaffold_2-snap.3513-T1
Valid prediction for Augustus_model.g3776.t1
Valid prediction for Augustus_model.g3757.t1
Valid prediction for snap_scaffold_2-snap.3510-T1
Valid prediction for GlimmerHMM_glimmerT_5569-T1
Valid prediction for GlimmerHMM_glimmerT_5574-T1
Valid prediction for GeneMark_model.8958_t
Valid prediction for snap_scaffold_2-snap.3473-T1
Valid prediction for GeneMark_model.8939_t
Valid prediction for GlimmerHMM_glimmerT_5567-T1
Valid prediction for Augustus_model.g3782.t1
Valid prediction for snap_scaffold_2-snap.3467-T1
Valid prediction for Augustus_model.g3761.t1
Valid prediction for GeneMark_model.8957_t
Valid prediction for GeneMark_model.8968_t
Couldn't classify 54024, 54083
Sorry, prediction pasa_asmbl_25377.p1 fails validation.
(ATG)	 AC	53020-53030	GT	AGG
(TGA)	 AG	53559-53691	GT	AAG
(GAC)	 AG	53806-53928	GT	AGG
(GAA)	 AG	54024-54083	AT	TGA
-recovered pasa_asmbl_25377.p1, initial, 53020, 53030
-recovered pasa_asmbl_25377.p1, internal, 53559, 53691
-recovered pasa_asmbl_25377.p1, internal, 53806, 53928
Valid prediction for snap_scaffold_2-snap.3491-T1
Valid prediction for GeneMark_model.8961_t
Valid prediction for GlimmerHMM_glimmerT_5544-T1
Valid prediction for snap_scaffold_2-snap.3469-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 HiQ_model.g3778.t1
Valid prediction for snap_scaffold_2-snap.3475-T1
Valid prediction for snap_scaffold_2-snap.3482-T1
Valid prediction for GlimmerHMM_glimmerT_5545-T1
Valid prediction for snap_scaffold_2-snap.3486-T1
Valid prediction for snap_scaffold_2-snap.3472-T1
Valid prediction for snap_scaffold_2-snap.3489-T1
Valid prediction for snap_scaffold_2-snap.3483-T1
Valid prediction for pasa_asmbl_23763.p2
Valid prediction for GeneMark_model.8943_t
Valid prediction for snap_scaffold_2-snap.3508-T1
Valid prediction for GlimmerHMM_glimmerT_5573-T1
Valid prediction for GeneMark_model.8952_t
Valid prediction for GeneMark_model.8946_t
Valid prediction for Augustus_model.g3781.t1
Valid prediction for GlimmerHMM_glimmerT_5552-T1
Valid prediction for GlimmerHMM_glimmerT_5570-T1
Valid prediction for GlimmerHMM_glimmerT_5553-T1
Valid prediction for snap_scaffold_2-snap.3488-T1
Valid prediction for GeneMark_model.8947_t
Valid prediction for GeneMark_model.8964_t
Valid prediction for GeneMark_model.8950_t
Valid prediction for CodingQuarry_transcript_28780-T1
Valid prediction for GlimmerHMM_glimmerT_5560-T1
Valid prediction for GlimmerHMM_glimmerT_5543-T1
Valid prediction for Augustus_model.g3759.t1
Valid prediction for snap_scaffold_2-snap.3500-T1
Valid prediction for CodingQuarry_transcript_28771-T1
Valid prediction for GlimmerHMM_glimmerT_5551-T1
Valid prediction for GlimmerHMM_glimmerT_5554-T1
Couldn't classify 178501, 178551
Sorry, prediction pasa_asmbl_23760.p1 fails validation.
(CTC)	 AG	178501-178551	GT	TGG
(ATG)	 AG	178650-179165	GT	AGG
(GTC)	 AG	179245-179435	GT	AGG
(GCC)	 AG	179620-179780	GT	AGG
(GGT)	 AG	179919-180079	AT	GAA
-recovered pasa_asmbl_23760.p1, initial, 178650, 179165
add_exon() Sorry, pasa_asmbl_23760.p1 179620-179780-terminal-2 is invalid.
-recovered pasa_asmbl_23760.p1, terminal, 179620, 179780
-recovered pasa_asmbl_23760.p1, terminal, 179919, 180079
-recovered pasa_asmbl_23760.p1, internal, 178501, 178551
-recovered pasa_asmbl_23760.p1, internal, 178650, 179165
-recovered pasa_asmbl_23760.p1, internal, 179245, 179435
-recovered pasa_asmbl_23760.p1, internal, 179620, 179780
Valid prediction for GlimmerHMM_glimmerT_5572-T1
Valid prediction for GlimmerHMM_glimmerT_5548-T1
Valid prediction for GlimmerHMM_glimmerT_5577-T1
Valid prediction for CodingQuarry_transcript_28774-T1
Valid prediction for snap_scaffold_2-snap.3501-T1
Valid prediction for pasa_asmbl_23766.p1
Valid prediction for Augustus_model.g3763.t1
Valid prediction for GlimmerHMM_glimmerT_5540-T1
Valid prediction for GlimmerHMM_glimmerT_5557-T1
Valid prediction for GlimmerHMM_glimmerT_5542-T1
Valid prediction for GlimmerHMM_glimmerT_5549-T1
Valid prediction for GeneMark_model.8954_t
Valid prediction for pasa_asmbl_23759.p1
Valid prediction for GlimmerHMM_glimmerT_5575-T1
Valid prediction for Augustus_model.g3779.t1
Valid prediction for snap_scaffold_2-snap.3471-T1
Valid prediction for CodingQuarry_transcript_28777-T1
Valid prediction for pasa_asmbl_23753.p1
Valid prediction for GlimmerHMM_glimmerT_5556-T1
Valid prediction for GlimmerHMM_glimmerT_5559-T1
Valid prediction for snap_scaffold_2-snap.3478-T1
Couldn't classify 64739, 64746
Sorry, prediction pasa_asmbl_23768.p1 fails validation.
(CTC)	 TT	64739-64746	GT	AAG
(GGC)	 AG	64857-65090	GT	AGG
(GTA)	 AG	65286-65417	GT	AGG
(TCA)	 AG	65520-65628	GT	AGG
(GAA)	 AG	65733-65852	GT	AGG
(GCC)	 AG	65957-66121	GT	ACG
(GTG)	 AG	66209-66362	GC	AGG
(GCA)	 AG	66472-66575	GT	AAG
(GCC)	 AG	66662-66856	GT	AGG
(AGT)	 AG	67115-67243	GT	AGG
(CTG)	 AG	67463-67600	GA	GAG
-recovered pasa_asmbl_23768.p1, terminal, 67463, 67600
-recovered pasa_asmbl_23768.p1, internal, 64857, 65090
-recovered pasa_asmbl_23768.p1, internal, 65286, 65417
-recovered pasa_asmbl_23768.p1, internal, 65520, 65628
-recovered pasa_asmbl_23768.p1, internal, 65733, 65852
-recovered pasa_asmbl_23768.p1, internal, 65957, 66121
-recovered pasa_asmbl_23768.p1, internal, 66209, 66362
-recovered pasa_asmbl_23768.p1, internal, 66472, 66575
-recovered pasa_asmbl_23768.p1, internal, 66662, 66856
-recovered pasa_asmbl_23768.p1, internal, 67115, 67243
Valid prediction for GlimmerHMM_glimmerT_5546-T1
Valid prediction for Augustus_model.g3760.t1
Valid prediction for Augustus_model.g3786.t1
Couldn't classify 174712, 174870
Couldn't classify 175507, 175529
Sorry, prediction pasa_asmbl_23761.p1 fails validation.
(GAA)	 GG	174712-174870	GT	AGG
(GAG)	 AG	175048-175214	GT	AGG
(CAC)	 AG	175333-175406	GT	TGG
(CAA)	 AG	175507-175529	GC	GGG
-recovered pasa_asmbl_23761.p1, internal, 175048, 175214
-recovered pasa_asmbl_23761.p1, internal, 175333, 175406
-recovered pasa_asmbl_23761.p1, internal, 175507, 175529
Valid prediction for Augustus_model.g3769.t1
Valid prediction for Augustus_model.g3766.t1
Valid prediction for CodingQuarry_transcript_28776-T1
Valid prediction for GeneMark_model.8956_t
Valid prediction for snap_scaffold_2-snap.3480-T1
Valid prediction for HiQ_model.g3756.t1
Valid prediction for snap_scaffold_2-snap.3503-T1
Valid prediction for snap_scaffold_2-snap.3484-T1
Valid prediction for GlimmerHMM_glimmerT_5555-T1
Valid prediction for GlimmerHMM_glimmerT_5561-T1
Valid prediction for HiQ_model.g3770.t1
Valid prediction for Augustus_model.g3768.t1
Valid prediction for snap_scaffold_2-snap.3495-T1
Valid prediction for Augustus_model.g3772.t1
Couldn't classify 153414, 153465
Couldn't classify 154540, 154638
Sorry, prediction pasa_asmbl_23762.p1 fails validation.
(AAA)	 GG	153414-153465	GT	AGG
(CCG)	 AG	153576-153710	GT	CGG
(ACC)	 AG	153938-154092	GT	AGG
(AGG)	 AG	154181-154270	GT	AGG
(GCG)	 AG	154540-154638	AT	AGA
-recovered pasa_asmbl_23762.p1, internal, 153576, 153710
-recovered pasa_asmbl_23762.p1, internal, 153938, 154092
-recovered pasa_asmbl_23762.p1, internal, 154181, 154270
Valid prediction for GeneMark_model.8940_t
Valid prediction for snap_scaffold_2-snap.3476-T1
Valid prediction for GlimmerHMM_glimmerT_5558-T1
Valid prediction for HiQ_model.g3764.t1
Valid prediction for Augustus_model.g3767.t1
Valid prediction for GeneMark_model.8942_t
Valid prediction for GeneMark_model.8962_t
Valid prediction for snap_scaffold_2-snap.3485-T1
Valid prediction for GeneMark_model.8949_t
Valid prediction for GeneMark_model.8955_t
Valid prediction for GeneMark_model.8969_t
Valid prediction for GeneMark_model.8951_t
Couldn't classify 64314, 64411
Sorry, prediction pasa_asmbl_23772.p1 fails validation.
(ATG)	 AT	63443-64184	GT	AGG
(TGC)	 AG	64314-64411	CC	GCC
-recovered pasa_asmbl_23772.p1, initial, 63443, 64184
Valid prediction for snap_scaffold_2-snap.3493-T1
Valid prediction for snap_scaffold_2-snap.3481-T1
Valid prediction for snap_scaffold_2-snap.3514-T1
Valid prediction for Augustus_model.g3771.t1
Valid prediction for CodingQuarry_transcript_28775-T1
Valid prediction for GlimmerHMM_glimmerT_5550-T1
Valid prediction for snap_scaffold_2-snap.3479-T1
Valid prediction for snap_scaffold_2-snap.3515-T1
Valid prediction for pasa_asmbl_23767.p1
Valid prediction for snap_scaffold_2-snap.3509-T1
Valid prediction for GeneMark_model.8953_t
Valid prediction for GeneMark_model.8945_t
Valid prediction for CodingQuarry_transcript_28779-T1
Valid prediction for GlimmerHMM_glimmerT_5571-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 155927, rend_intergenic: 153639  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166885, rend_intergenic: 163022  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 216870, rend_intergenic: 214602  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 225626, rend_intergenic: 223308  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 254670
-exon list size: 799


building trellis

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55.6    
55.7    
55.8    
55.9    
56.1    
56.2    
56.3    
56.4    
56.6    
56.7    
56.8    
56.9    
57.1    
57.2    
57.3    
57.4    
57.6    
57.7    
57.8    
57.9    
58.1    
58.2    
58.3    
58.4    
58.6    
58.7    
58.8    
58.9    
59.1    
59.2    
59.3    
59.4    
59.6    
59.7    
59.8    
59.9    
60.0    
60.2    
60.3    
60.4    
60.5    
60.7    
60.8    
60.9    
61.0    
61.2    
61.3    
61.4    
61.5    
61.7    
61.8    
61.9    
62.0    
62.2    
62.3    
62.4    
62.5    
62.7    
62.8    
62.9    
63.0    
63.2    
63.3    
63.4    
63.5    
63.7    
63.8    
63.9    
64.0    
64.2    
64.3    
64.4    
64.5    
64.7    
64.8    
64.9    
65.0    
65.2    
65.3    
65.4    
65.5    
65.7    
65.8    
65.9    
66.0    
66.2    
66.3    
66.4    
66.5    
66.7    
66.8    
66.9    
67.0    
67.2    
67.3    
67.4    
67.5    
67.7    
67.8    
67.9    
68.0    
68.2    
68.3    
68.4    
68.5    
68.7    
68.8    
68.9    
69.0    
69.2    
69.3    
69.4    
69.5    
69.7    
69.8    
69.9    
70.0    
70.2    
70.3    
70.4    
70.5    
70.7    
70.8    
70.9    
71.0    
71.2    
71.3    
71.4    
71.5    
71.7    
71.8    
71.9    
72.0    
72.2    
72.3    
72.4    
72.5    
72.7    
72.8    
72.9    
73.0    
73.2    
73.3    
73.4    
73.5    
73.7    
73.8    
73.9    
74.0    
74.2    
74.3    
74.4    
74.5    
74.7    
74.8    
74.9    
75.0    
75.2    
75.3    
75.4    
75.5    
75.7    
75.8    
75.9    
76.0    
76.2    
76.3    
76.4    
76.5    
76.7    
76.8    
76.9    
77.0    
77.2    
77.3    
77.4    
77.5    
77.7    
77.8    
77.9    
78.0    
78.2    
78.3    
78.4    
78.5    
78.7    
78.8    
78.9    
79.0    
79.2    
79.3    
79.4    
79.5    
79.7    
79.8    
79.9    
80.0    
80.1    
80.3    
80.4    
80.5    
80.6    
80.8    
80.9    
81.0    
81.1    
81.3    
81.4    
81.5    
81.6    
81.8    
81.9    
82.0    
82.1    
82.3    
82.4    
82.5    
82.6    
82.8    
82.9    
83.0    
83.1    
83.3    
83.4    
83.5    
83.6    
83.8    
83.9    
84.0    
84.1    
84.3    
84.4    
84.5    
84.6    
84.8    
84.9    
85.0    
85.1    
85.3    
85.4    
85.5    
85.6    
85.8    
85.9    
86.0    
86.1    
86.3    
86.4    
86.5    
86.6    
86.8    
86.9    
87.0    
87.1    
87.3    
87.4    
87.5    
87.6    
87.8    
87.9    
88.0    
88.1    
88.3    
88.4    
88.5    
88.6    
88.8    
88.9    
89.0    
89.1    
89.3    
89.4    
89.5    
89.6    
89.8    
89.9    
90.0    
90.1    
90.3    
90.4    
90.5    
90.6    
90.8    
90.9    
91.0    
91.1    
91.3    
91.4    
91.5    
91.6    
91.8    
91.9    
92.0    
92.1    
92.3    
92.4    
92.5    
92.6    
92.8    
92.9    
93.0    
93.1    
93.3    
93.4    
93.5    
93.6    
93.8    
93.9    
94.0    
94.1    
94.3    
94.4    
94.5    
94.6    
94.8    
94.9    
95.0    
95.1    
95.3    
95.4    
95.5    
95.6    
95.8    
95.9    
96.0    
96.1    
96.3    
96.4    
96.5    
96.6    
96.8    
96.9    
97.0    
97.1    
97.3    
97.4    
97.5    
97.6    
97.8    
97.9    
98.0    
98.1    
98.3    
98.4    
98.5    
98.6    
98.8    
98.9    
99.0    
99.1    
99.3    
99.4    
99.5    
99.6    
99.8    
99.9    
-found 45 predictions from path traversal
Error with prediction: snap lend_intergenic: 155927, rend_intergenic: 153639  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166885, rend_intergenic: 163022  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 216870, rend_intergenic: 214602  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 225626, rend_intergenic: 223308  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 44 predictions persist after filtering for low support