-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_2/scaffold_2_18940145-19189483

-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_28807-T1
Valid prediction for snap_scaffold_2-snap.3757-T1
Valid prediction for GeneMark_model.9371_t
Valid prediction for snap_scaffold_2-snap.3758-T1
Valid prediction for GeneMark_model.9382_t
Valid prediction for snap_scaffold_2-snap.3754-T1
Valid prediction for GeneMark_model.9380_t
Valid prediction for GlimmerHMM_glimmerT_5744-T1
Valid prediction for GeneMark_model.9339_t
Valid prediction for GeneMark_model.9323_t
Valid prediction for GeneMark_model.9354_t
Valid prediction for snap_scaffold_2-snap.3773-T1
Valid prediction for GeneMark_model.9387_t
Valid prediction for GeneMark_model.9349_t
Couldn't classify 23829, 24380
Sorry, prediction pasa_asmbl_25293.p1 fails validation.
(GAT)	 TG	23829-24380	AT	GAA
Valid prediction for snap_scaffold_2-snap.3785-T1
Valid prediction for GeneMark_model.9368_t
Valid prediction for snap_scaffold_2-snap.3756-T1
Valid prediction for GlimmerHMM_glimmerT_5728-T1
Valid prediction for GlimmerHMM_glimmerT_5733-T1
Valid prediction for GeneMark_model.9333_t
Valid prediction for snap_scaffold_2-snap.3751-T1
Valid prediction for GeneMark_model.9376_t
Valid prediction for snap_scaffold_2-snap.3755-T1
Valid prediction for GeneMark_model.9324_t
Valid prediction for GlimmerHMM_glimmerT_5736-T1
Valid prediction for GeneMark_model.9329_t
Valid prediction for GlimmerHMM_glimmerT_5742-T1
Valid prediction for snap_scaffold_2-snap.3759-T1
Valid prediction for CodingQuarry_transcript_28806-T1
Valid prediction for snap_scaffold_2-snap.3778-T1
Valid prediction for snap_scaffold_2-snap.3752-T1
Valid prediction for GeneMark_model.9362_t
Valid prediction for snap_scaffold_2-snap.3765-T1
Valid prediction for snap_scaffold_2-snap.3771-T1
Valid prediction for GlimmerHMM_glimmerT_5735-T1
Valid prediction for GeneMark_model.9345_t
Valid prediction for Augustus_model.g3866.t1
Valid prediction for GlimmerHMM_glimmerT_5752-T1
Valid prediction for snap_scaffold_2-snap.3788-T1
Valid prediction for GeneMark_model.9364_t
Valid prediction for GlimmerHMM_glimmerT_5746-T1
Valid prediction for GeneMark_model.9319_t
Valid prediction for GeneMark_model.9328_t
Valid prediction for GeneMark_model.9340_t
Valid prediction for GeneMark_model.9320_t
Valid prediction for GeneMark_model.9359_t
Valid prediction for GeneMark_model.9335_t
Valid prediction for Augustus_model.g3870.t1
Valid prediction for Augustus_model.g3862.t1
Valid prediction for GlimmerHMM_glimmerT_5740-T1
Valid prediction for GlimmerHMM_glimmerT_5743-T1
Valid prediction for GeneMark_model.9356_t
Valid prediction for snap_scaffold_2-snap.3782-T1
Valid prediction for snap_scaffold_2-snap.3779-T1
Valid prediction for GlimmerHMM_glimmerT_5754-T1
Valid prediction for GeneMark_model.9384_t
Valid prediction for GeneMark_model.9377_t
Valid prediction for GeneMark_model.9360_t
Valid prediction for Augustus_model.g3868.t1
Valid prediction for GeneMark_model.9331_t
Valid prediction for GeneMark_model.9366_t
Valid prediction for CodingQuarry_transcript_28805-T1
Valid prediction for Augustus_model.g3865.t1
Valid prediction for snap_scaffold_2-snap.3768-T1
Valid prediction for GeneMark_model.9343_t
Valid prediction for pasa_asmbl_25287.p1
Valid prediction for snap_scaffold_2-snap.3747-T1
Valid prediction for GeneMark_model.9347_t
Valid prediction for Augustus_model.g3860.t1
Couldn't classify 183726, 183893
Sorry, prediction pasa_asmbl_25298.p1 fails validation.
(GGA)	 CA	183726-183893	GT	AGG
(GAC)	 AG	184192-184351	GT	TGG
(ACA)	 AG	184652-184775	GT	AGG
(ATT)	 AG	185138-186347	CA	GAC
-recovered pasa_asmbl_25298.p1, terminal, 185138, 186347
-recovered pasa_asmbl_25298.p1, internal, 184192, 184351
-recovered pasa_asmbl_25298.p1, internal, 184652, 184775
Valid prediction for GlimmerHMM_glimmerT_5749-T1
Valid prediction for GeneMark_model.9325_t
Valid prediction for GlimmerHMM_glimmerT_5748-T1
Valid prediction for snap_scaffold_2-snap.3781-T1
Valid prediction for HiQ_model.g3859.t1
Valid prediction for GeneMark_model.9373_t
Valid prediction for GeneMark_model.9317_t
Valid prediction for snap_scaffold_2-snap.3777-T1
Valid prediction for snap_scaffold_2-snap.3784-T1
Valid prediction for Augustus_model.g3864.t1
Valid prediction for GlimmerHMM_glimmerT_5727-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.9383_t
Valid prediction for snap_scaffold_2-snap.3750-T1
Valid prediction for GeneMark_model.9336_t
Valid prediction for snap_scaffold_2-snap.3769-T1
Valid prediction for GeneMark_model.9327_t
Valid prediction for GeneMark_model.9372_t
Valid prediction for snap_scaffold_2-snap.3749-T1
Valid prediction for GeneMark_model.9342_t
Valid prediction for GeneMark_model.9363_t
Valid prediction for GlimmerHMM_glimmerT_5739-T1
Valid prediction for GeneMark_model.9326_t
Valid prediction for GeneMark_model.9381_t
Valid prediction for Augustus_model.g3863.t1
Valid prediction for GlimmerHMM_glimmerT_5758-T1
Valid prediction for GlimmerHMM_glimmerT_5751-T1
Valid prediction for GeneMark_model.9358_t
Couldn't classify 69887, 70192
Sorry, prediction pasa_asmbl_25297.p1 fails validation.
(TCT)	 TC	69887-70192	CC	AAC
Valid prediction for GeneMark_model.9361_t
Valid prediction for snap_scaffold_2-snap.3763-T1
Valid prediction for Augustus_model.g3867.t1
Valid prediction for GeneMark_model.9348_t
Valid prediction for GeneMark_model.9370_t
Valid prediction for GeneMark_model.9375_t
Valid prediction for GlimmerHMM_glimmerT_5757-T1
Valid prediction for GlimmerHMM_glimmerT_5756-T1
Valid prediction for pasa_asmbl_23858.p1
Valid prediction for GeneMark_model.9344_t
Valid prediction for snap_scaffold_2-snap.3748-T1
Valid prediction for GeneMark_model.9351_t
Valid prediction for GeneMark_model.9337_t
Couldn't classify 159670, 159757
Couldn't classify 160893, 161173
Sorry, prediction pasa_asmbl_23863.p1 fails validation.
(TTA)	 GG	159670-159757	GT	GTG
(TTC)	 AG	159845-160114	GT	ACG
(GTC)	 AG	160337-160606	GT	AAG
(AAG)	 AG	160893-161173	AT	GCA
-recovered pasa_asmbl_23863.p1, internal, 159845, 160114
-recovered pasa_asmbl_23863.p1, internal, 160337, 160606
Valid prediction for GeneMark_model.9379_t
Valid prediction for GeneMark_model.9346_t
Valid prediction for GeneMark_model.9357_t
Valid prediction for GeneMark_model.9332_t
Valid prediction for snap_scaffold_2-snap.3764-T1
Valid prediction for CodingQuarry_transcript_28811-T1
Valid prediction for snap_scaffold_2-snap.3762-T1
Valid prediction for snap_scaffold_2-snap.3786-T1
Valid prediction for GeneMark_model.9341_t
Valid prediction for snap_scaffold_2-snap.3783-T1
Valid prediction for snap_scaffold_2-snap.3787-T1
Valid prediction for GlimmerHMM_glimmerT_5730-T1
Valid prediction for GlimmerHMM_glimmerT_5732-T1
Valid prediction for snap_scaffold_2-snap.3772-T1
Valid prediction for GeneMark_model.9374_t
Valid prediction for GlimmerHMM_glimmerT_5750-T1
Valid prediction for GeneMark_model.9355_t
Valid prediction for GeneMark_model.9365_t
Valid prediction for GeneMark_model.9353_t
Valid prediction for GeneMark_model.9322_t
Valid prediction for GlimmerHMM_glimmerT_5729-T1
Valid prediction for GlimmerHMM_glimmerT_5734-T1
Valid prediction for GeneMark_model.9352_t
Couldn't classify 158210, 158429
Couldn't classify 158976, 159082
Sorry, prediction pasa_asmbl_23864.p1 fails validation.
(AGG)	 AA	158210-158429	GT	CAG
(AGC)	 AG	158531-158794	GT	ACG
(AAC)	 AG	158976-159082	GC	TCG
-recovered pasa_asmbl_23864.p1, internal, 158531, 158794
-recovered pasa_asmbl_23864.p1, internal, 158976, 159082
Valid prediction for GeneMark_model.9334_t
Valid prediction for GeneMark_model.9318_t
Valid prediction for snap_scaffold_2-snap.3761-T1
Valid prediction for snap_scaffold_2-snap.3770-T1
Valid prediction for snap_scaffold_2-snap.3775-T1
Valid prediction for GlimmerHMM_glimmerT_5731-T1
Valid prediction for snap_scaffold_2-snap.3753-T1
Valid prediction for pasa_asmbl_23862.p2
Valid prediction for snap_scaffold_2-snap.3767-T1
Valid prediction for GlimmerHMM_glimmerT_5753-T1
Valid prediction for HiQ_model.g3861.t1
Valid prediction for CodingQuarry_transcript_28810-T1
Valid prediction for GlimmerHMM_glimmerT_5738-T1
Valid prediction for snap_scaffold_2-snap.3776-T1
Valid prediction for GeneMark_model.9367_t
Valid prediction for GlimmerHMM_glimmerT_5755-T1
Valid prediction for GeneMark_model.9330_t
Valid prediction for GeneMark_model.9338_t
Valid prediction for GlimmerHMM_glimmerT_5737-T1
Valid prediction for Augustus_model.g3869.t1
Valid prediction for GeneMark_model.9386_t
Valid prediction for GeneMark_model.9385_t
Valid prediction for GlimmerHMM_glimmerT_5741-T1
Valid prediction for snap_scaffold_2-snap.3766-T1
Valid prediction for GeneMark_model.9378_t
Valid prediction for snap_scaffold_2-snap.3774-T1
Valid prediction for snap_scaffold_2-snap.3760-T1
Valid prediction for GlimmerHMM_glimmerT_5745-T1
Valid prediction for CodingQuarry_transcript_28809-T1
Valid prediction for snap_scaffold_2-snap.3780-T1
Valid prediction for GlimmerHMM_glimmerT_5747-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12240, rend_intergenic: 7380  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22873, rend_intergenic: 17005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71549, rend_intergenic: 26521  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125669, rend_intergenic: 117952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133731, rend_intergenic: 127662  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148866, rend_intergenic: 141575  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157088, rend_intergenic: 148926  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168247, rend_intergenic: 157271  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186347, rend_intergenic: 168852  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197443, rend_intergenic: 190015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209095, rend_intergenic: 202819  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 216038, rend_intergenic: 209620  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 236223, rend_intergenic: 218380  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 246331, rend_intergenic: 241421  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 249339
-exon list size: 976


building trellis

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64.5    
64.6    
64.7    
64.8    
64.9    
65.0    
65.1    
65.2    
65.3    
65.4    
65.5    
65.6    
65.7    
65.8    
66.0    
66.1    
66.2    
66.3    
66.4    
66.5    
66.6    
66.7    
66.8    
66.9    
67.0    
67.1    
67.2    
67.3    
67.4    
67.5    
67.6    
67.7    
67.8    
67.9    
68.0    
68.1    
68.2    
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    
69.6    
69.7    
69.8    
69.9    
70.0    
70.1    
70.2    
70.3    
70.4    
70.6    
70.7    
70.8    
70.9    
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    
72.3    
72.4    
72.5    
72.6    
72.7    
72.8    
72.9    
73.0    
73.1    
73.2    
73.3    
73.4    
73.5    
73.6    
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    
76.4    
76.5    
76.6    
76.7    
76.8    
76.9    
77.0    
77.1    
77.2    
77.3    
77.4    
77.5    
77.6    
77.7    
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    
79.1    
79.2    
79.3    
79.4    
79.6    
79.7    
79.8    
79.9    
80.0    
80.1    
80.2    
80.3    
80.4    
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    
81.8    
81.9    
82.0    
82.1    
82.2    
82.3    
82.4    
82.5    
82.6    
82.7    
82.8    
82.9    
83.0    
83.1    
83.2    
83.3    
83.4    
83.5    
83.6    
83.7    
83.8    
83.9    
84.0    
84.2    
84.3    
84.4    
84.5    
84.6    
84.7    
84.8    
84.9    
85.0    
85.1    
85.2    
85.3    
85.4    
85.5    
85.6    
85.7    
85.8    
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    
87.2    
87.3    
87.4    
87.5    
87.6    
87.7    
87.8    
87.9    
88.0    
88.1    
88.2    
88.3    
88.4    
88.5    
88.7    
88.8    
88.9    
89.0    
89.1    
89.2    
89.3    
89.4    
89.5    
89.6    
89.7    
89.8    
89.9    
90.0    
90.1    
90.2    
90.3    
90.4    
90.5    
90.6    
90.7    
90.8    
90.9    
91.0    
91.1    
91.2    
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    
92.6    
92.7    
92.8    
92.9    
93.0    
93.1    
93.3    
93.4    
93.5    
93.6    
93.7    
93.8    
93.9    
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    
95.3    
95.4    
95.5    
95.6    
95.7    
95.8    
95.9    
96.0    
96.1    
96.2    
96.3    
96.4    
96.5    
96.6    
96.7    
96.8    
96.9    
97.0    
97.1    
97.2    
97.3    
97.4    
97.5    
97.6    
97.8    
97.9    
98.0    
98.1    
98.2    
98.3    
98.4    
98.5    
98.6    
98.7    
98.8    
98.9    
99.0    
99.1    
99.2    
99.3    
99.4    
99.5    
99.6    
99.7    
99.8    
99.9    
-found 46 predictions from path traversal
Error with prediction: snap lend_intergenic: 12240, rend_intergenic: 7380  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22873, rend_intergenic: 17005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71549, rend_intergenic: 26521  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125669, rend_intergenic: 117952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133731, rend_intergenic: 127662  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148866, rend_intergenic: 141575  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157088, rend_intergenic: 148926  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168247, rend_intergenic: 157271  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186347, rend_intergenic: 168852  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197443, rend_intergenic: 190015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209095, rend_intergenic: 202819  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 216038, rend_intergenic: 209620  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 236223, rend_intergenic: 218380  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 246331, rend_intergenic: 241421  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support