-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_4/scaffold_4_3078439-3236668

-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_4-snap.711-T1
Valid prediction for GeneMark_model.15192_t
Valid prediction for snap_scaffold_4-snap.704-T1
Valid prediction for GlimmerHMM_glimmerT_9198-T1
Valid prediction for snap_scaffold_4-snap.694-T1
Valid prediction for Augustus_model.g5962.t1
Valid prediction for GeneMark_model.15165_t
Valid prediction for GlimmerHMM_glimmerT_9194-T1
Valid prediction for Augustus_model.g5960.t1
Couldn't classify 64531, 64838
Couldn't classify 65140, 65173
Sorry, prediction pasa_asmbl_42485.p1 fails validation.
(ACC)	 GC	64531-64838	GT	AGG
(GTA)	 AG	65140-65173	GA	GAG
Valid prediction for GlimmerHMM_glimmerT_9190-T1
Valid prediction for GeneMark_model.15179_t
Valid prediction for GeneMark_model.15177_t
Valid prediction for GeneMark_model.15188_t
Valid prediction for GeneMark_model.15194_t
Valid prediction for GlimmerHMM_glimmerT_9179-T1
Valid prediction for snap_scaffold_4-snap.707-T1
Valid prediction for GeneMark_model.15184_t
Valid prediction for snap_scaffold_4-snap.684-T1
Valid prediction for GeneMark_model.15163_t
Valid prediction for snap_scaffold_4-snap.700-T1
Valid prediction for GlimmerHMM_glimmerT_9193-T1
Valid prediction for snap_scaffold_4-snap.702-T1
Valid prediction for GeneMark_model.15191_t
Valid prediction for GeneMark_model.15169_t
Valid prediction for GeneMark_model.15176_t
Valid prediction for GeneMark_model.15207_t
Valid prediction for GeneMark_model.15186_t
Valid prediction for GeneMark_model.15181_t
Valid prediction for GeneMark_model.15199_t
Valid prediction for GeneMark_model.15203_t
Valid prediction for GlimmerHMM_glimmerT_9183-T1
Valid prediction for snap_scaffold_4-snap.693-T1
Valid prediction for GlimmerHMM_glimmerT_9191-T1
Valid prediction for GeneMark_model.15161_t
Valid prediction for snap_scaffold_4-snap.696-T1
Valid prediction for GlimmerHMM_glimmerT_9189-T1
Valid prediction for snap_scaffold_4-snap.712-T1
Valid prediction for GeneMark_model.15170_t
Valid prediction for Augustus_model.g5965.t1
Valid prediction for pasa_asmbl_41150.p1
Valid prediction for snap_scaffold_4-snap.699-T1
Valid prediction for snap_scaffold_4-snap.687-T1
Valid prediction for GlimmerHMM_glimmerT_9188-T1
Valid prediction for GeneMark_model.15193_t
Valid prediction for snap_scaffold_4-snap.686-T1
Valid prediction for GeneMark_model.15173_t
Valid prediction for GeneMark_model.15198_t
Valid prediction for snap_scaffold_4-snap.690-T1
Valid prediction for GeneMark_model.15201_t
Valid prediction for GlimmerHMM_glimmerT_9187-T1
Valid prediction for Augustus_model.g5958.t1
Valid prediction for snap_scaffold_4-snap.710-T1
Valid prediction for snap_scaffold_4-snap.708-T1
Valid prediction for GeneMark_model.15189_t
Valid prediction for snap_scaffold_4-snap.705-T1
Couldn't classify 68718, 68966
Couldn't classify 69828, 70017
Sorry, prediction pasa_asmbl_42486.p1 fails validation.
(AGG)	 AG	68718-68966	GT	AGG
(GAC)	 AG	69055-69191	GT	CGG
(GCT)	 AG	69828-70017	CC	CGC
-recovered pasa_asmbl_42486.p1, internal, 68718, 68966
-recovered pasa_asmbl_42486.p1, internal, 69055, 69191
Valid prediction for snap_scaffold_4-snap.715-T1
Valid prediction for snap_scaffold_4-snap.713-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.15202_t
Valid prediction for GeneMark_model.15187_t
Valid prediction for snap_scaffold_4-snap.691-T1
Valid prediction for snap_scaffold_4-snap.706-T1
Valid prediction for GeneMark_model.15182_t
Valid prediction for GeneMark_model.15209_t
Valid prediction for GeneMark_model.15167_t
Valid prediction for GeneMark_model.15208_t
Valid prediction for GeneMark_model.15168_t
Valid prediction for snap_scaffold_4-snap.689-T1
Valid prediction for GeneMark_model.15172_t
Valid prediction for snap_scaffold_4-snap.709-T1
Valid prediction for snap_scaffold_4-snap.685-T1
Valid prediction for GlimmerHMM_glimmerT_9195-T1
Valid prediction for snap_scaffold_4-snap.703-T1
Valid prediction for GeneMark_model.15174_t
Valid prediction for Augustus_model.g5961.t1
Valid prediction for GlimmerHMM_glimmerT_9201-T1
Valid prediction for GeneMark_model.15175_t
Valid prediction for GeneMark_model.15164_t
Valid prediction for GeneMark_model.15178_t
Valid prediction for GlimmerHMM_glimmerT_9192-T1
Valid prediction for GeneMark_model.15185_t
Valid prediction for GlimmerHMM_glimmerT_9199-T1
Valid prediction for GeneMark_model.15204_t
Valid prediction for GeneMark_model.15195_t
Valid prediction for snap_scaffold_4-snap.697-T1
Valid prediction for Augustus_model.g5963.t1
Valid prediction for GlimmerHMM_glimmerT_9196-T1
Valid prediction for Augustus_model.g5957.t1
Valid prediction for GlimmerHMM_glimmerT_9197-T1
Valid prediction for Augustus_model.g5966.t1
Valid prediction for GeneMark_model.15162_t
Valid prediction for GeneMark_model.15166_t
Valid prediction for GlimmerHMM_glimmerT_9185-T1
Valid prediction for Augustus_model.g5967.t1
Valid prediction for Augustus_model.g5959.t1
Valid prediction for GeneMark_model.15183_t
Valid prediction for GeneMark_model.15180_t
Valid prediction for GlimmerHMM_glimmerT_9182-T1
Valid prediction for GeneMark_model.15206_t
Valid prediction for GlimmerHMM_glimmerT_9181-T1
Valid prediction for GlimmerHMM_glimmerT_9180-T1
Valid prediction for GlimmerHMM_glimmerT_9184-T1
Valid prediction for snap_scaffold_4-snap.716-T1
Valid prediction for GeneMark_model.15190_t
Valid prediction for snap_scaffold_4-snap.695-T1
Sorry, intron length (3) is less than minimum required (10)
Couldn't classify 21568, 21577
Couldn't classify 23406, 23447
Sorry, prediction pasa_asmbl_41152.p1 fails validation.
(CAT)	 AG	21568-21577	GT	GGG
(GCA)	 AG	21722-21918	GT	AGG
(GCA)	 AG	22217-22348	GT	TGG
(GAG)	 AG	23038-23136	GT	AGG
(TGG)	 AG	23406-23447	GT	GGG
-recovered pasa_asmbl_41152.p1, internal, 21568, 21577
-recovered pasa_asmbl_41152.p1, internal, 21722, 21918
-recovered pasa_asmbl_41152.p1, internal, 22217, 22348
-recovered pasa_asmbl_41152.p1, internal, 23038, 23136
-recovered pasa_asmbl_41152.p1, internal, 23406, 23447
Valid prediction for snap_scaffold_4-snap.688-T1
Valid prediction for Augustus_model.g5964.t1
Valid prediction for snap_scaffold_4-snap.718-T1
Couldn't classify 15009, 15115
Couldn't classify 17003, 17059
Sorry, prediction pasa_asmbl_41155.p1 fails validation.
(CTC)	 AG	15009-15115	GT	AGG
(TCT)	 AG	15781-15931	GT	AGG
(TTT)	 AG	17003-17059	CG	TCC
-recovered pasa_asmbl_41155.p1, internal, 15009, 15115
-recovered pasa_asmbl_41155.p1, internal, 15781, 15931
Valid prediction for GeneMark_model.15205_t
Valid prediction for GeneMark_model.15196_t
Valid prediction for snap_scaffold_4-snap.692-T1
Valid prediction for snap_scaffold_4-snap.701-T1
Valid prediction for snap_scaffold_4-snap.717-T1
Valid prediction for GlimmerHMM_glimmerT_9186-T1
Valid prediction for snap_scaffold_4-snap.698-T1
Valid prediction for GeneMark_model.15171_t
Valid prediction for snap_scaffold_4-snap.714-T1
Couldn't classify 2137, 2238
Sorry, prediction pasa_asmbl_41158.p1 fails validation.
(GCA)	 GG	2137-2238	GT	CAG
(ATC)	 AG	4169-4356	GT	AAG
(AAT)	 AG	4552-4660	GT	AAG
(GTG)	 AG	4886-5053	GT	AGG
(GCG)	 AG	5638-5779	GT	CCG
(AGA)	 AG	7021-7151	CA	AGC
-recovered pasa_asmbl_41158.p1, terminal, 7021, 7151
-recovered pasa_asmbl_41158.p1, internal, 4169, 4356
-recovered pasa_asmbl_41158.p1, internal, 4552, 4660
-recovered pasa_asmbl_41158.p1, internal, 4886, 5053
-recovered pasa_asmbl_41158.p1, internal, 5638, 5779
Valid prediction for GlimmerHMM_glimmerT_9200-T1
Valid prediction for GeneMark_model.15200_t
Valid prediction for GlimmerHMM_glimmerT_9202-T1
Valid prediction for GeneMark_model.15197_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7006, rend_intergenic: 5802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14564, rend_intergenic: 7866  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19966, rend_intergenic: 14626  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37763, rend_intergenic: 26155  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57511, rend_intergenic: 48557  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70483, rend_intergenic: 61283  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73785, rend_intergenic: 70832  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79819, rend_intergenic: 74901  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89075, rend_intergenic: 87697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100672, rend_intergenic: 89808  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102467, rend_intergenic: 101265  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121868, rend_intergenic: 104392  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141433, rend_intergenic: 126746  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145201, rend_intergenic: 141739  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147394, rend_intergenic: 145508  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 158230
-exon list size: 829


building trellis

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84.5    
84.6    
84.7    
84.8    
85.0    
85.1    
85.2    
85.3    
85.4    
85.6    
85.7    
85.8    
85.9    
86.0    
86.2    
86.3    
86.4    
86.5    
86.6    
86.8    
86.9    
87.0    
87.1    
87.2    
87.4    
87.5    
87.6    
87.7    
87.8    
88.0    
88.1    
88.2    
88.3    
88.4    
88.6    
88.7    
88.8    
88.9    
89.0    
89.2    
89.3    
89.4    
89.5    
89.7    
89.8    
89.9    
90.0    
90.1    
90.3    
90.4    
90.5    
90.6    
90.7    
90.9    
91.0    
91.1    
91.2    
91.3    
91.5    
91.6    
91.7    
91.8    
91.9    
92.1    
92.2    
92.3    
92.4    
92.5    
92.7    
92.8    
92.9    
93.0    
93.1    
93.3    
93.4    
93.5    
93.6    
93.7    
93.9    
94.0    
94.1    
94.2    
94.3    
94.5    
94.6    
94.7    
94.8    
94.9    
95.1    
95.2    
95.3    
95.4    
95.5    
95.7    
95.8    
95.9    
96.0    
96.1    
96.3    
96.4    
96.5    
96.6    
96.8    
96.9    
97.0    
97.1    
97.2    
97.4    
97.5    
97.6    
97.7    
97.8    
98.0    
98.1    
98.2    
98.3    
98.4    
98.6    
98.7    
98.8    
98.9    
99.0    
99.2    
99.3    
99.4    
99.5    
99.6    
99.8    
99.9    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 7006, rend_intergenic: 5802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14564, rend_intergenic: 7866  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19966, rend_intergenic: 14626  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37763, rend_intergenic: 26155  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57511, rend_intergenic: 48557  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70483, rend_intergenic: 61283  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73785, rend_intergenic: 70832  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79819, rend_intergenic: 74901  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89075, rend_intergenic: 87697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100672, rend_intergenic: 89808  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102467, rend_intergenic: 101265  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121868, rend_intergenic: 104392  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141433, rend_intergenic: 126746  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145201, rend_intergenic: 141739  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147394, rend_intergenic: 145508  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 11 predictions persist after filtering for low support