-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_2/scaffold_2_15328927-15529106

-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 snap_scaffold_2-snap.2968-T1
Valid prediction for CodingQuarry_transcript_28714-T1
Valid prediction for CodingQuarry_transcript_28712-T1
Valid prediction for pasa_asmbl_25061.p1
Valid prediction for GlimmerHMM_glimmerT_5189-T1
Valid prediction for GlimmerHMM_glimmerT_5174-T1
Valid prediction for HiQ_model.g3515.t1
Valid prediction for GeneMark_model.8324_t
Couldn't classify 166950, 166983
Couldn't classify 168354, 168483
Sorry, prediction pasa_asmbl_25081.p1 fails validation.
(TCC)	 AC	166950-166983	GT	CAG
(GCA)	 AG	167195-167290	GT	AGG
(GTG)	 AG	167469-167554	GT	AGG
(GAC)	 AG	167683-167853	GT	AAG
(CTC)	 AG	167949-168094	GT	AAG
(GGA)	 AG	168354-168483	CG	ACC
add_exon() Sorry, pasa_asmbl_25081.p1 167195-167290-terminal-1 is invalid.
-recovered pasa_asmbl_25081.p1, terminal, 167195, 167290
-recovered pasa_asmbl_25081.p1, internal, 167195, 167290
-recovered pasa_asmbl_25081.p1, internal, 167469, 167554
-recovered pasa_asmbl_25081.p1, internal, 167683, 167853
-recovered pasa_asmbl_25081.p1, internal, 167949, 168094
Valid prediction for CodingQuarry_transcript_28720-T1
Valid prediction for Augustus_model.g3505.t1
Valid prediction for snap_scaffold_2-snap.2992-T1
Valid prediction for GlimmerHMM_glimmerT_5175-T1
Valid prediction for snap_scaffold_2-snap.2990-T1
Valid prediction for GeneMark_model.8342_t
Valid prediction for GeneMark_model.8322_t
Valid prediction for GeneMark_model.8317_t
Valid prediction for snap_scaffold_2-snap.2965-T1
Valid prediction for HiQ_model.g3489.t1
Valid prediction for GlimmerHMM_glimmerT_5170-T1
Valid prediction for GeneMark_model.8340_t
Couldn't classify 22752, 22942
Sorry, prediction pasa_asmbl_25060.p1 fails validation.
(AGG)	 CC	22752-22942	GT	AGG
(CCC)	 AG	23083-23188	GT	AAG
(GTA)	 AG	23302-23538	GT	GAG
(GTC)	 AG	23728-24027	GT	AGG
(GCT)	 AG	24148-24423	CG	AAC
-recovered pasa_asmbl_25060.p1, terminal, 24148, 24423
-recovered pasa_asmbl_25060.p1, internal, 23083, 23188
-recovered pasa_asmbl_25060.p1, internal, 23302, 23538
-recovered pasa_asmbl_25060.p1, internal, 23728, 24027
Valid prediction for CodingQuarry_transcript_28718-T1
Valid prediction for HiQ_model.g3509.t1
Valid prediction for snap_scaffold_2-snap.2970-T1
Valid prediction for HiQ_model.g3514.t1
Valid prediction for pasa_asmbl_25055.p1
Valid prediction for HiQ_model.g3517.t1
Valid prediction for Augustus_model.g3491.t1
Valid prediction for GeneMark_model.8308_t
Valid prediction for snap_scaffold_2-snap.2961-T1
Valid prediction for CodingQuarry_transcript_28721-T1
Valid prediction for Augustus_model.g3493.t1
Valid prediction for GlimmerHMM_glimmerT_5179-T1
Valid prediction for GlimmerHMM_glimmerT_5182-T1
Valid prediction for GlimmerHMM_glimmerT_5194-T1
Valid prediction for GeneMark_model.8333_t
Valid prediction for GlimmerHMM_glimmerT_5197-T1
Valid prediction for snap_scaffold_2-snap.2981-T1
Valid prediction for GeneMark_model.8314_t
Valid prediction for HiQ_model.g3497.t1
Valid prediction for snap_scaffold_2-snap.2991-T1
Valid prediction for GeneMark_model.8312_t
Valid prediction for pasa_asmbl_25083.p1
Valid prediction for CodingQuarry_transcript_28707-T1
Valid prediction for GlimmerHMM_glimmerT_5186-T1
Valid prediction for CodingQuarry_transcript_28719-T1
Valid prediction for Augustus_model.g3513.t1
Valid prediction for snap_scaffold_2-snap.2972-T1
Valid prediction for HiQ_model.g3508.t1
Valid prediction for Augustus_model.g3516.t1
Valid prediction for GeneMark_model.8318_t
Valid prediction for GlimmerHMM_glimmerT_5172-T1
Valid prediction for snap_scaffold_2-snap.2971-T1
Valid prediction for snap_scaffold_2-snap.2969-T1
Couldn't classify 121722, 121766
Sorry, prediction pasa_asmbl_25063.p2 fails validation.
(CTA)	 TA	121722-121766	GT	TGG
(CGG)	 AG	122110-122181	GT	TAG
(TCA)	 AG	122267-122332	GT	ATG
(TAT)	 AG	122414-122453	GT	TGG
(AAA)	 AG	122532-122651	GT	AGG
(AGC)	 AG	122741-122821	GT	ACG
(TTG)	 AG	122899-123075	GT	AGG
(AGT)	 AG	123185-123225	AG	GAA
-recovered pasa_asmbl_25063.p2, terminal, 123185, 123225
-recovered pasa_asmbl_25063.p2, internal, 122110, 122181
-recovered pasa_asmbl_25063.p2, internal, 122267, 122332
-recovered pasa_asmbl_25063.p2, internal, 122414, 122453
-recovered pasa_asmbl_25063.p2, internal, 122532, 122651
-recovered pasa_asmbl_25063.p2, internal, 122741, 122821
-recovered pasa_asmbl_25063.p2, internal, 122899, 123075
Valid prediction for snap_scaffold_2-snap.2997-T1
Valid prediction for snap_scaffold_2-snap.2995-T1
Valid prediction for snap_scaffold_2-snap.2963-T1
Valid prediction for Augustus_model.g3498.t1
Valid prediction for GeneMark_model.8336_t
Valid prediction for snap_scaffold_2-snap.2966-T1
Valid prediction for Augustus_model.g3495.t1
Valid prediction for snap_scaffold_2-snap.2985-T1
Valid prediction for GlimmerHMM_glimmerT_5195-T1
Valid prediction for GeneMark_model.8338_t
Valid prediction for GeneMark_model.8330_t
Valid prediction for GlimmerHMM_glimmerT_5196-T1
Valid prediction for Augustus_model.g3496.t1
Valid prediction for pasa_asmbl_25079.p1
Valid prediction for CodingQuarry_transcript_28708-T1
Valid prediction for GlimmerHMM_glimmerT_5168-T1
Couldn't classify 153473, 153536
Sorry, prediction pasa_asmbl_25071.p2 fails validation.
(CCA)	 AG	153473-153536	GT	TGG
(GCA)	 AG	153614-153689	GT	TAG
(CCA)	 AG	154020-154194	GT	CTG
(GGC)	 AG	154966-155094	GC	AAG
-recovered pasa_asmbl_25071.p2, terminal, 154966, 155094
-recovered pasa_asmbl_25071.p2, internal, 153473, 153536
-recovered pasa_asmbl_25071.p2, internal, 153614, 153689
-recovered pasa_asmbl_25071.p2, internal, 154020, 154194
-recovered pasa_asmbl_25071.p2, internal, 154966, 155094
Couldn't classify 184324, 184486
Couldn't classify 185941, 186161
Sorry, prediction pasa_asmbl_25409.p1 fails validation.
(CCT)	 AT	184324-184486	GT	AGG
(GTC)	 AG	185941-186161	GC	TGG
-recovered pasa_asmbl_25409.p1, internal, 185941, 186161
Valid prediction for CodingQuarry_transcript_28711-T1
Valid prediction for GlimmerHMM_glimmerT_5177-T1
Valid prediction for snap_scaffold_2-snap.2989-T1
Valid prediction for GeneMark_model.8323_t
Valid prediction for GeneMark_model.8316_t
Valid prediction for GeneMark_model.8337_t
Valid prediction for snap_scaffold_2-snap.2984-T1
Valid prediction for GlimmerHMM_glimmerT_5199-T1
Valid prediction for Augustus_model.g3519.t1
Valid prediction for CodingQuarry_transcript_28715-T1
Valid prediction for GlimmerHMM_glimmerT_5178-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.2974-T1
Valid prediction for snap_scaffold_2-snap.2983-T1
Valid prediction for GlimmerHMM_glimmerT_5171-T1
Valid prediction for snap_scaffold_2-snap.2975-T1
Valid prediction for Augustus_model.g3490.t1
Valid prediction for GlimmerHMM_glimmerT_5181-T1
Valid prediction for snap_scaffold_2-snap.2962-T1
Valid prediction for GlimmerHMM_glimmerT_5188-T1
Valid prediction for GlimmerHMM_glimmerT_5191-T1
Valid prediction for Augustus_model.g3512.t1
Valid prediction for pasa_asmbl_23654.p1
Valid prediction for snap_scaffold_2-snap.2988-T1
Valid prediction for GeneMark_model.8332_t
Couldn't classify 147944, 148061
Couldn't classify 148592, 148681
Sorry, prediction pasa_asmbl_23637.p1 fails validation.
(AAG)	 TG	147944-148061	GT	AGG
(CAG)	 AG	148162-148289	GT	AGG
(GAT)	 AG	148403-148486	GT	AGG
(CTT)	 AG	148592-148681	AC	CCA
-recovered pasa_asmbl_23637.p1, internal, 148162, 148289
-recovered pasa_asmbl_23637.p1, internal, 148403, 148486
Valid prediction for snap_scaffold_2-snap.2973-T1
Valid prediction for Augustus_model.g3504.t1
Valid prediction for snap_scaffold_2-snap.2979-T1
Valid prediction for snap_scaffold_2-snap.2987-T1
Valid prediction for CodingQuarry_transcript_28716-T1
Valid prediction for snap_scaffold_2-snap.2994-T1
Valid prediction for snap_scaffold_2-snap.2982-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for Augustus_model.g3503.t1
Valid prediction for GeneMark_model.8335_t
Couldn't classify 71395, 71466
Sorry, prediction pasa_asmbl_23640.p1 fails validation.
(AGT)	 TC	71395-71466	GT	AGG
(GTA)	 AG	71598-71741	GT	AGG
(GTT)	 AG	71866-71975	GT	CTG
(GCT)	 AG	72085-72164	GT	TGG
(GTT)	 AG	72246-72388	GT	AGG
(GCT)	 AG	72468-72571	GT	TAG
(CTG)	 AG	72718-72829	AT	AAA
-recovered pasa_asmbl_23640.p1, terminal, 72718, 72829
-recovered pasa_asmbl_23640.p1, internal, 71598, 71741
-recovered pasa_asmbl_23640.p1, internal, 71866, 71975
-recovered pasa_asmbl_23640.p1, internal, 72085, 72164
-recovered pasa_asmbl_23640.p1, internal, 72246, 72388
-recovered pasa_asmbl_23640.p1, internal, 72468, 72571
Valid prediction for GeneMark_model.8325_t
Valid prediction for GeneMark_model.8315_t
Valid prediction for GlimmerHMM_glimmerT_5176-T1
Valid prediction for GlimmerHMM_glimmerT_5187-T1
Valid prediction for Augustus_model.g3506.t1
Valid prediction for Augustus_model.g3502.t1
Valid prediction for snap_scaffold_2-snap.2993-T1
Valid prediction for snap_scaffold_2-snap.2978-T1
Valid prediction for Augustus_model.g3510.t1
Valid prediction for GeneMark_model.8341_t
Valid prediction for GeneMark_model.8311_t
Couldn't classify 89046, 90926
Sorry, prediction pasa_asmbl_23638.p1 fails validation.
(ACC)	 TC	89046-90926	GT	GAG
Valid prediction for snap_scaffold_2-snap.2986-T1
Valid prediction for GlimmerHMM_glimmerT_5185-T1
Valid prediction for Augustus_model.g3520.t1
Valid prediction for Augustus_model.g3499.t1
Valid prediction for GeneMark_model.8339_t
Valid prediction for GeneMark_model.8329_t
Valid prediction for GlimmerHMM_glimmerT_5200-T1
Valid prediction for CodingQuarry_transcript_28717-T1
Valid prediction for GlimmerHMM_glimmerT_5184-T1
Valid prediction for GlimmerHMM_glimmerT_5193-T1
Valid prediction for CodingQuarry_transcript_28710-T1
Valid prediction for GeneMark_model.8309_t
Valid prediction for snap_scaffold_2-snap.2964-T1
Valid prediction for CodingQuarry_transcript_28713-T1
Valid prediction for GlimmerHMM_glimmerT_5180-T1
Valid prediction for Augustus_model.g3492.t1
Couldn't classify 70317, 70344
Couldn't classify 71310, 71337
Sorry, prediction pasa_asmbl_23642.p1 fails validation.
(GTA)	 TG	70317-70344	GT	AGG
(ATA)	 AG	70434-70589	GT	AGG
(CCC)	 AG	70736-70818	GT	AGG
(GAC)	 AG	70909-71003	GT	AGG
(AGA)	 AG	71097-71201	GT	AGG
(GAA)	 AG	71310-71337	AT	CTA
add_exon() Sorry, pasa_asmbl_23642.p1 70434-70589-terminal-1 is invalid.
-recovered pasa_asmbl_23642.p1, terminal, 70434, 70589
-recovered pasa_asmbl_23642.p1, internal, 70434, 70589
-recovered pasa_asmbl_23642.p1, internal, 70736, 70818
-recovered pasa_asmbl_23642.p1, internal, 70909, 71003
-recovered pasa_asmbl_23642.p1, internal, 71097, 71201
Valid prediction for pasa_asmbl_23639.p1
Valid prediction for pasa_asmbl_23646.p1
Valid prediction for GlimmerHMM_glimmerT_5198-T1
Valid prediction for GeneMark_model.8319_t
Valid prediction for GlimmerHMM_glimmerT_5169-T1
Valid prediction for GlimmerHMM_glimmerT_5190-T1
Valid prediction for GeneMark_model.8320_t
Valid prediction for GlimmerHMM_glimmerT_5192-T1
Valid prediction for GlimmerHMM_glimmerT_5173-T1
Valid prediction for GeneMark_model.8321_t
Valid prediction for snap_scaffold_2-snap.2980-T1
Valid prediction for GeneMark_model.8328_t
Valid prediction for GeneMark_model.8326_t
Valid prediction for GeneMark_model.8327_t
Valid prediction for Augustus_model.g3494.t1
Valid prediction for GeneMark_model.8313_t
Valid prediction for snap_scaffold_2-snap.2976-T1
Valid prediction for GlimmerHMM_glimmerT_5202-T1
Valid prediction for snap_scaffold_2-snap.2996-T1
Valid prediction for GeneMark_model.8331_t
Valid prediction for snap_scaffold_2-snap.2967-T1
Valid prediction for Augustus_model.g3511.t1
Couldn't classify 69013, 69030
Couldn't classify 70046, 70129
Sorry, prediction pasa_asmbl_23644.p1 fails validation.
(CTT)	 AC	69013-69030	GT	CTG
(CAC)	 AG	69181-69276	GT	ATG
(CTG)	 AG	69418-69563	GT	AAG
(GGT)	 AG	69807-69930	GT	AGG
(ATC)	 AG	70046-70129	TT	CGT
-recovered pasa_asmbl_23644.p1, internal, 69181, 69276
-recovered pasa_asmbl_23644.p1, internal, 69418, 69563
-recovered pasa_asmbl_23644.p1, internal, 69807, 69930
Valid prediction for HiQ_model.g3507.t1
Valid prediction for Augustus_model.g3501.t1
Valid prediction for Augustus_model.g3500.t1
Couldn't classify 184854, 184914
Sorry, prediction pasa_asmbl_23636.p1 fails validation.
(CTC)	 AT	184854-184914	GT	TGG
(ACA)	 AG	186561-186640	GT	CTG
(AGG)	 AG	187089-187247	GT	CAG
(AGA)	 AG	187333-187365	GA	GAG
-recovered pasa_asmbl_23636.p1, terminal, 187333, 187365
-recovered pasa_asmbl_23636.p1, internal, 186561, 186640
-recovered pasa_asmbl_23636.p1, internal, 187089, 187247
Valid prediction for GlimmerHMM_glimmerT_5183-T1
Valid prediction for GeneMark_model.8334_t
Valid prediction for snap_scaffold_2-snap.2977-T1
Valid prediction for Augustus_model.g3518.t1
Valid prediction for CodingQuarry_transcript_28722-T1
Valid prediction for GlimmerHMM_glimmerT_5201-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 20749, rend_intergenic: 14369  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30098, rend_intergenic: 26521  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186160, rend_intergenic: 183829  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198002, rend_intergenic: 193747  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 200180
-exon list size: 655


building trellis

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60.6    
60.7    
60.9    
61.0    
61.2    
61.3    
61.5    
61.6    
61.8    
61.9    
62.1    
62.3    
62.4    
62.6    
62.7    
62.9    
63.0    
63.2    
63.3    
63.5    
63.6    
63.8    
63.9    
64.1    
64.2    
64.4    
64.5    
64.7    
64.8    
65.0    
65.1    
65.3    
65.4    
65.6    
65.8    
65.9    
66.1    
66.2    
66.4    
66.5    
66.7    
66.8    
67.0    
67.1    
67.3    
67.4    
67.6    
67.7    
67.9    
68.0    
68.2    
68.3    
68.5    
68.6    
68.8    
68.9    
69.1    
69.3    
69.4    
69.6    
69.7    
69.9    
70.0    
70.2    
70.3    
70.5    
70.6    
70.8    
70.9    
71.1    
71.2    
71.4    
71.5    
71.7    
71.8    
72.0    
72.1    
72.3    
72.5    
72.6    
72.8    
72.9    
73.1    
73.2    
73.4    
73.5    
73.7    
73.8    
74.0    
74.1    
74.3    
74.4    
74.6    
74.7    
74.9    
75.0    
75.2    
75.3    
75.5    
75.6    
75.8    
76.0    
76.1    
76.3    
76.4    
76.6    
76.7    
76.9    
77.0    
77.2    
77.3    
77.5    
77.6    
77.8    
77.9    
78.1    
78.2    
78.4    
78.5    
78.7    
78.8    
79.0    
79.1    
79.3    
79.5    
79.6    
79.8    
79.9    
80.1    
80.2    
80.4    
80.5    
80.7    
80.8    
81.0    
81.1    
81.3    
81.4    
81.6    
81.7    
81.9    
82.0    
82.2    
82.3    
82.5    
82.6    
82.8    
83.0    
83.1    
83.3    
83.4    
83.6    
83.7    
83.9    
84.0    
84.2    
84.3    
84.5    
84.6    
84.8    
84.9    
85.1    
85.2    
85.4    
85.5    
85.7    
85.8    
86.0    
86.1    
86.3    
86.5    
86.6    
86.8    
86.9    
87.1    
87.2    
87.4    
87.5    
87.7    
87.8    
88.0    
88.1    
88.3    
88.4    
88.6    
88.7    
88.9    
89.0    
89.2    
89.3    
89.5    
89.6    
89.8    
90.0    
90.1    
90.3    
90.4    
90.6    
90.7    
90.9    
91.0    
91.2    
91.3    
91.5    
91.6    
91.8    
91.9    
92.1    
92.2    
92.4    
92.5    
92.7    
92.8    
93.0    
93.2    
93.3    
93.5    
93.6    
93.8    
93.9    
94.1    
94.2    
94.4    
94.5    
94.7    
94.8    
95.0    
95.1    
95.3    
95.4    
95.6    
95.7    
95.9    
96.0    
96.2    
96.3    
96.5    
96.7    
96.8    
97.0    
97.1    
97.3    
97.4    
97.6    
97.7    
97.9    
98.0    
98.2    
98.3    
98.5    
98.6    
98.8    
98.9    
99.1    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 20749, rend_intergenic: 14369  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30098, rend_intergenic: 26521  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186160, rend_intergenic: 183829  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198002, rend_intergenic: 193747  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 35 predictions persist after filtering for low support