-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_2/scaffold_2_2696239-2857596

-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 GlimmerHMM_glimmerT_3479-T1
Valid prediction for GeneMark_model.5660_t
Valid prediction for GeneMark_model.5651_t
Valid prediction for GlimmerHMM_glimmerT_3482-T1
Valid prediction for GlimmerHMM_glimmerT_3486-T1
Valid prediction for GeneMark_model.5658_t
Valid prediction for snap_scaffold_2-snap.623-T1
Valid prediction for Augustus_model.g2328.t1
Valid prediction for GeneMark_model.5684_t
Valid prediction for GeneMark_model.5648_t
Valid prediction for GeneMark_model.5674_t
Valid prediction for GlimmerHMM_glimmerT_3495-T1
Valid prediction for snap_scaffold_2-snap.625-T1
Valid prediction for GeneMark_model.5669_t
Valid prediction for snap_scaffold_2-snap.643-T1
Valid prediction for Augustus_model.g2317.t1
Valid prediction for GeneMark_model.5679_t
Valid prediction for GlimmerHMM_glimmerT_3488-T1
Valid prediction for Augustus_model.g2326.t1
Valid prediction for Augustus_model.g2339.t1
Valid prediction for GlimmerHMM_glimmerT_3485-T1
Valid prediction for snap_scaffold_2-snap.621-T1
Valid prediction for GlimmerHMM_glimmerT_3490-T1
Valid prediction for GlimmerHMM_glimmerT_3476-T1
Valid prediction for GeneMark_model.5688_t
Valid prediction for GlimmerHMM_glimmerT_3498-T1
Valid prediction for Augustus_model.g2313.t1
Valid prediction for GeneMark_model.5682_t
Valid prediction for Augustus_model.g2324.t1
Valid prediction for Augustus_model.g2323.t1
Valid prediction for HiQ_model.g2331.t1
Valid prediction for GeneMark_model.5686_t
Valid prediction for GeneMark_model.5644_t
Valid prediction for snap_scaffold_2-snap.638-T1
Valid prediction for GeneMark_model.5649_t
Valid prediction for GeneMark_model.5639_t
Valid prediction for snap_scaffold_2-snap.634-T1
Valid prediction for GeneMark_model.5646_t
Valid prediction for pasa_asmbl_25441.p1
Valid prediction for GeneMark_model.5656_t
Valid prediction for Augustus_model.g2319.t1
Valid prediction for snap_scaffold_2-snap.646-T1
Valid prediction for snap_scaffold_2-snap.647-T1
Valid prediction for GlimmerHMM_glimmerT_3502-T1
Valid prediction for snap_scaffold_2-snap.656-T1
Couldn't classify 102803, 103649
Sorry, prediction pasa_asmbl_24279.p1 fails validation.
(TCA)	 TT	102803-103649	GT	GGG
(TGA)	 AG	103738-103925	GT	CAG
(GAG)	 AG	104073-104170	GT	AGG
(GCT)	 AG	104512-104672	GT	TGG
(ACA)	 AG	104766-104958	GT	GGG
(GTG)	 AG	105101-105251	GT	AGG
(GTG)	 AG	105336-105408	GT	AAG
(GGA)	 AG	105556-105653	AC	AAA
add_exon() Sorry, pasa_asmbl_24279.p1 104073-104170-terminal-2 is invalid.
-recovered pasa_asmbl_24279.p1, terminal, 104073, 104170
-recovered pasa_asmbl_24279.p1, terminal, 105556, 105653
-recovered pasa_asmbl_24279.p1, internal, 103738, 103925
-recovered pasa_asmbl_24279.p1, internal, 104073, 104170
-recovered pasa_asmbl_24279.p1, internal, 104512, 104672
-recovered pasa_asmbl_24279.p1, internal, 104766, 104958
-recovered pasa_asmbl_24279.p1, internal, 105101, 105251
-recovered pasa_asmbl_24279.p1, internal, 105336, 105408
Valid prediction for snap_scaffold_2-snap.644-T1
Valid prediction for Augustus_model.g2314.t1
Valid prediction for GeneMark_model.5654_t
Valid prediction for GeneMark_model.5664_t
Valid prediction for HiQ_model.g2320.t1
Valid prediction for GeneMark_model.5667_t
Valid prediction for GlimmerHMM_glimmerT_3481-T1
Valid prediction for snap_scaffold_2-snap.641-T1
Valid prediction for snap_scaffold_2-snap.636-T1
Valid prediction for snap_scaffold_2-snap.633-T1
Valid prediction for snap_scaffold_2-snap.652-T1
Valid prediction for snap_scaffold_2-snap.629-T1
Valid prediction for GlimmerHMM_glimmerT_3497-T1
Valid prediction for snap_scaffold_2-snap.637-T1
Valid prediction for GeneMark_model.5677_t
Valid prediction for GeneMark_model.5672_t
Valid prediction for Augustus_model.g2333.t1
Valid prediction for snap_scaffold_2-snap.654-T1
Valid prediction for GlimmerHMM_glimmerT_3475-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 Augustus_model.g2318.t1
Valid prediction for GeneMark_model.5665_t
Valid prediction for CodingQuarry_transcript_28421-T1
Couldn't classify 68162, 68332
Sorry, prediction pasa_asmbl_23996.p1 fails validation.
(CCA)	 CC	68162-68332	GT	AGG
(AAC)	 AG	68557-68683	GT	AGG
(CCC)	 AG	68843-69036	GT	AGG
(TCG)	 AG	69189-69346	GT	ACG
(AGG)	 AG	69564-69657	TG	AAT
-recovered pasa_asmbl_23996.p1, terminal, 69564, 69657
-recovered pasa_asmbl_23996.p1, internal, 68557, 68683
-recovered pasa_asmbl_23996.p1, internal, 68843, 69036
-recovered pasa_asmbl_23996.p1, internal, 69189, 69346
Valid prediction for GeneMark_model.5657_t
Valid prediction for snap_scaffold_2-snap.640-T1
Couldn't classify 146861, 146989
Sorry, prediction pasa_asmbl_22937.p1 fails validation.
(CTC)	 AT	146861-146989	GT	AGG
(ATC)	 AG	147077-147406	AA	AGA
-recovered pasa_asmbl_22937.p1, terminal, 147077, 147406
Valid prediction for GeneMark_model.5680_t
Valid prediction for snap_scaffold_2-snap.620-T1
Valid prediction for snap_scaffold_2-snap.651-T1
Valid prediction for snap_scaffold_2-snap.627-T1
Valid prediction for GeneMark_model.5687_t
Couldn't classify 38838, 38985
Sorry, prediction pasa_asmbl_22947.p1 fails validation.
(CAG)	 CT	38838-38985	GT	CGG
(TGG)	 AG	39164-39308	GT	TTG
(CAT)	 AG	39401-39520	GT	AGG
(ACA)	 AG	41831-41939	AA	AGA
-recovered pasa_asmbl_22947.p1, terminal, 41831, 41939
-recovered pasa_asmbl_22947.p1, internal, 39164, 39308
-recovered pasa_asmbl_22947.p1, internal, 39401, 39520
Valid prediction for GeneMark_model.5676_t
Valid prediction for GeneMark_model.5640_t
Valid prediction for Augustus_model.g2327.t1
Valid prediction for GeneMark_model.5659_t
Valid prediction for Augustus_model.g2316.t1
Valid prediction for snap_scaffold_2-snap.631-T1
Valid prediction for GlimmerHMM_glimmerT_3483-T1
Valid prediction for Augustus_model.g2336.t1
Valid prediction for snap_scaffold_2-snap.649-T1
Couldn't classify 86673, 86705
Couldn't classify 87711, 87737
Sorry, prediction pasa_asmbl_23957.p1 fails validation.
(GTC)	 CC	86673-86705	GT	AGG
(AAG)	 AG	86915-87010	GT	CGG
(CAA)	 AG	87370-87603	GT	AGG
(AGT)	 AG	87711-87737	GA	CTG
-recovered pasa_asmbl_23957.p1, internal, 86915, 87010
-recovered pasa_asmbl_23957.p1, internal, 87370, 87603
Valid prediction for Augustus_model.g2330.t1
Valid prediction for snap_scaffold_2-snap.655-T1
Valid prediction for snap_scaffold_2-snap.645-T1
Valid prediction for GlimmerHMM_glimmerT_3491-T1
Valid prediction for snap_scaffold_2-snap.635-T1
Valid prediction for GeneMark_model.5641_t
Valid prediction for snap_scaffold_2-snap.653-T1
Couldn't classify 35519, 35659
Couldn't classify 37570, 37650
Sorry, prediction pasa_asmbl_22948.p1 fails validation.
(CTG)	 CC	35519-35659	GT	AGG
(GAC)	 AG	36008-36102	GT	AGG
(TCA)	 AG	37299-37449	GT	AGG
(GGT)	 AG	37570-37650	TA	GAT
-recovered pasa_asmbl_22948.p1, internal, 36008, 36102
-recovered pasa_asmbl_22948.p1, internal, 37299, 37449
Valid prediction for GlimmerHMM_glimmerT_3492-T1
Valid prediction for GeneMark_model.5652_t
Valid prediction for GeneMark_model.5685_t
Valid prediction for HiQ_model.g2315.t1
Valid prediction for snap_scaffold_2-snap.642-T1
Valid prediction for GlimmerHMM_glimmerT_3487-T1
Valid prediction for CodingQuarry_transcript_28422-T1
Valid prediction for GeneMark_model.5663_t
Valid prediction for snap_scaffold_2-snap.622-T1
Valid prediction for Augustus_model.g2325.t1
Valid prediction for GeneMark_model.5683_t
Valid prediction for GlimmerHMM_glimmerT_3501-T1
Couldn't classify 3541, 3670
Couldn't classify 4642, 4705
Sorry, prediction pasa_asmbl_23958.p1 fails validation.
(GCC)	 AC	3541-3670	GT	TGG
(GAG)	 AG	4280-4397	GT	GGG
(CTA)	 AG	4642-4705	TT	CCT
-recovered pasa_asmbl_23958.p1, internal, 4280, 4397
Valid prediction for GlimmerHMM_glimmerT_3493-T1
Valid prediction for snap_scaffold_2-snap.650-T1
Valid prediction for CodingQuarry_transcript_28419-T1
Valid prediction for GeneMark_model.5675_t
Valid prediction for GeneMark_model.5643_t
Valid prediction for HiQ_model.g2332.t1
Valid prediction for snap_scaffold_2-snap.639-T1
Valid prediction for GlimmerHMM_glimmerT_3499-T1
Couldn't classify 23121, 23148
Couldn't classify 25021, 25115
Sorry, prediction pasa_asmbl_24069.p1 fails validation.
(GAA)	 CG	23121-23148	GT	ATG
(TGT)	 AG	23265-23323	GT	AGG
(GCA)	 AG	23548-23692	GT	CTG
(TGT)	 AG	25021-25115	GT	AGG
-recovered pasa_asmbl_24069.p1, internal, 23265, 23323
-recovered pasa_asmbl_24069.p1, internal, 23548, 23692
-recovered pasa_asmbl_24069.p1, internal, 25021, 25115
Valid prediction for GeneMark_model.5638_t
Valid prediction for GeneMark_model.5681_t
Valid prediction for snap_scaffold_2-snap.628-T1
Couldn't classify 62201, 62333
Sorry, prediction pasa_asmbl_22942.p1 fails validation.
(GCA)	 CC	62201-62333	GT	CGG
(AGG)	 AG	63503-63586	GT	AGG
(AGG)	 AG	63735-63862	GT	CGG
(GAA)	 AG	64191-64371	GT	AGG
(TTG)	 AG	64486-64633	GT	AGG
(CAC)	 AG	64789-64894	GC	AGG
(GAG)	 AG	65087-65440	GT	GAG
(GCC)	 AG	65562-65754	GT	AAG
(CAC)	 AG	65919-66037	GT	AGG
(TTT)	 AG	66136-66240	GT	AGG
(ATG)	 AG	66542-66724	CG	GAC
-recovered pasa_asmbl_22942.p1, terminal, 66542, 66724
-recovered pasa_asmbl_22942.p1, internal, 63503, 63586
-recovered pasa_asmbl_22942.p1, internal, 63735, 63862
-recovered pasa_asmbl_22942.p1, internal, 64191, 64371
-recovered pasa_asmbl_22942.p1, internal, 64486, 64633
-recovered pasa_asmbl_22942.p1, internal, 64789, 64894
-recovered pasa_asmbl_22942.p1, internal, 65087, 65440
-recovered pasa_asmbl_22942.p1, internal, 65562, 65754
-recovered pasa_asmbl_22942.p1, internal, 65919, 66037
-recovered pasa_asmbl_22942.p1, internal, 66136, 66240
Couldn't classify 15155, 15317
Couldn't classify 19440, 19560
Sorry, prediction pasa_asmbl_24014.p1 fails validation.
(GTG)	 CT	15155-15317	GT	AGG
(AGA)	 AG	17459-17545	GT	GAG
(ATG)	 AG	17885-17945	GT	TGG
(GTT)	 AG	19440-19560	AA	GAA
-recovered pasa_asmbl_24014.p1, initial, 17885, 17945
-recovered pasa_asmbl_24014.p1, internal, 17459, 17545
-recovered pasa_asmbl_24014.p1, internal, 17885, 17945
Valid prediction for GeneMark_model.5661_t
Valid prediction for GlimmerHMM_glimmerT_3500-T1
Valid prediction for GeneMark_model.5666_t
Valid prediction for pasa_asmbl_22946.p1
Valid prediction for GeneMark_model.5662_t
Valid prediction for GlimmerHMM_glimmerT_3503-T1
Valid prediction for snap_scaffold_2-snap.648-T1
Valid prediction for GeneMark_model.5671_t
Valid prediction for GlimmerHMM_glimmerT_3494-T1
Valid prediction for GeneMark_model.5653_t
Valid prediction for GeneMark_model.5655_t
Valid prediction for snap_scaffold_2-snap.632-T1
Valid prediction for GlimmerHMM_glimmerT_3480-T1
Valid prediction for GeneMark_model.5645_t
Valid prediction for GeneMark_model.5678_t
Valid prediction for GlimmerHMM_glimmerT_3478-T1
Valid prediction for GeneMark_model.5647_t
Valid prediction for Augustus_model.g2338.t1
Couldn't classify 9333, 9499
Sorry, prediction pasa_asmbl_22952.p1 fails validation.
(GTG)	 AG	9333-9499	GT	GGG
(GGA)	 AG	10886-10999	GT	AGG
(ACA)	 AG	11764-11937	GT	TGG
(GTG)	 AG	12060-12189	GC	GAG
-recovered pasa_asmbl_22952.p1, terminal, 12060, 12189
-recovered pasa_asmbl_22952.p1, internal, 9333, 9499
-recovered pasa_asmbl_22952.p1, internal, 10886, 10999
-recovered pasa_asmbl_22952.p1, internal, 11764, 11937
-recovered pasa_asmbl_22952.p1, internal, 12060, 12189
Valid prediction for Augustus_model.g2334.t1
Valid prediction for snap_scaffold_2-snap.624-T1
Valid prediction for GeneMark_model.5673_t
Valid prediction for snap_scaffold_2-snap.626-T1
Valid prediction for Augustus_model.g2337.t1
Valid prediction for GlimmerHMM_glimmerT_3484-T1
Valid prediction for Augustus_model.g2335.t1
Valid prediction for GlimmerHMM_glimmerT_3489-T1
Valid prediction for Augustus_model.g2321.t1
Valid prediction for GlimmerHMM_glimmerT_3477-T1
Valid prediction for snap_scaffold_2-snap.630-T1
Couldn't classify 35018, 35251
Sorry, prediction pasa_asmbl_22949.p1 fails validation.
(ATG)	 AA	34135-34218	GT	AAG
(AAT)	 AG	34718-34765	GT	GCG
(GAG)	 AG	35018-35251	GA	AGG
-recovered pasa_asmbl_22949.p1, initial, 34135, 34218
-recovered pasa_asmbl_22949.p1, internal, 34718, 34765
Valid prediction for Augustus_model.g2322.t1
Valid prediction for Augustus_model.g2329.t1
Valid prediction for GeneMark_model.5668_t
Valid prediction for GlimmerHMM_glimmerT_3496-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 5079, rend_intergenic: 3775  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 8520, rend_intergenic: 7732  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31155, rend_intergenic: 20200  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44189, rend_intergenic: 34795  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56619, rend_intergenic: 45724  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60209, rend_intergenic: 58167  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89213, rend_intergenic: 79852  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97800, rend_intergenic: 91340  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135513, rend_intergenic: 132291  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153568, rend_intergenic: 149170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 161358
-exon list size: 715


building trellis

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54.3    
54.4    
54.5    
54.7    
54.8    
55.0    
55.1    
55.2    
55.4    
55.5    
55.6    
55.8    
55.9    
56.1    
56.2    
56.3    
56.5    
56.6    
56.8    
56.9    
57.0    
57.2    
57.3    
57.5    
57.6    
57.7    
57.9    
58.0    
58.2    
58.3    
58.4    
58.6    
58.7    
58.9    
59.0    
59.1    
59.3    
59.4    
59.6    
59.7    
59.8    
60.0    
60.1    
60.3    
60.4    
60.5    
60.7    
60.8    
60.9    
61.1    
61.2    
61.4    
61.5    
61.6    
61.8    
61.9    
62.1    
62.2    
62.3    
62.5    
62.6    
62.8    
62.9    
63.0    
63.2    
63.3    
63.5    
63.6    
63.7    
63.9    
64.0    
64.2    
64.3    
64.4    
64.6    
64.7    
64.9    
65.0    
65.1    
65.3    
65.4    
65.6    
65.7    
65.8    
66.0    
66.1    
66.2    
66.4    
66.5    
66.7    
66.8    
66.9    
67.1    
67.2    
67.4    
67.5    
67.6    
67.8    
67.9    
68.1    
68.2    
68.3    
68.5    
68.6    
68.8    
68.9    
69.0    
69.2    
69.3    
69.5    
69.6    
69.7    
69.9    
70.0    
70.2    
70.3    
70.4    
70.6    
70.7    
70.9    
71.0    
71.1    
71.3    
71.4    
71.5    
71.7    
71.8    
72.0    
72.1    
72.2    
72.4    
72.5    
72.7    
72.8    
72.9    
73.1    
73.2    
73.4    
73.5    
73.6    
73.8    
73.9    
74.1    
74.2    
74.3    
74.5    
74.6    
74.8    
74.9    
75.0    
75.2    
75.3    
75.5    
75.6    
75.7    
75.9    
76.0    
76.2    
76.3    
76.4    
76.6    
76.7    
76.8    
77.0    
77.1    
77.3    
77.4    
77.5    
77.7    
77.8    
78.0    
78.1    
78.2    
78.4    
78.5    
78.7    
78.8    
78.9    
79.1    
79.2    
79.4    
79.5    
79.6    
79.8    
79.9    
80.1    
80.2    
80.3    
80.5    
80.6    
80.8    
80.9    
81.0    
81.2    
81.3    
81.5    
81.6    
81.7    
81.9    
82.0    
82.1    
82.3    
82.4    
82.6    
82.7    
82.8    
83.0    
83.1    
83.3    
83.4    
83.5    
83.7    
83.8    
84.0    
84.1    
84.2    
84.4    
84.5    
84.7    
84.8    
84.9    
85.1    
85.2    
85.4    
85.5    
85.6    
85.8    
85.9    
86.1    
86.2    
86.3    
86.5    
86.6    
86.8    
86.9    
87.0    
87.2    
87.3    
87.4    
87.6    
87.7    
87.9    
88.0    
88.1    
88.3    
88.4    
88.6    
88.7    
88.8    
89.0    
89.1    
89.3    
89.4    
89.5    
89.7    
89.8    
90.0    
90.1    
90.2    
90.4    
90.5    
90.7    
90.8    
90.9    
91.1    
91.2    
91.4    
91.5    
91.6    
91.8    
91.9    
92.1    
92.2    
92.3    
92.5    
92.6    
92.7    
92.9    
93.0    
93.2    
93.3    
93.4    
93.6    
93.7    
93.9    
94.0    
94.1    
94.3    
94.4    
94.6    
94.7    
94.8    
95.0    
95.1    
95.3    
95.4    
95.5    
95.7    
95.8    
96.0    
96.1    
96.2    
96.4    
96.5    
96.7    
96.8    
96.9    
97.1    
97.2    
97.4    
97.5    
97.6    
97.8    
97.9    
98.0    
98.2    
98.3    
98.5    
98.6    
98.7    
98.9    
99.0    
99.2    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 5079, rend_intergenic: 3775  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 8520, rend_intergenic: 7732  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31155, rend_intergenic: 20200  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44189, rend_intergenic: 34795  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56619, rend_intergenic: 45724  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60209, rend_intergenic: 58167  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89213, rend_intergenic: 79852  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97800, rend_intergenic: 91340  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135513, rend_intergenic: 132291  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153568, rend_intergenic: 149170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 26 predictions persist after filtering for low support