-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_24/scaffold_24_2130215-2296463

-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.g35759.t1
Valid prediction for snap_scaffold_24-snap.518-T1
Valid prediction for GeneMark_model.92979_t
Valid prediction for snap_scaffold_24-snap.517-T1
Valid prediction for GeneMark_model.92952_t
Valid prediction for GeneMark_model.92971_t
Valid prediction for snap_scaffold_24-snap.506-T1
Valid prediction for snap_scaffold_24-snap.524-T1
Valid prediction for GeneMark_model.92960_t
Valid prediction for Augustus_model.g35767.t1
Couldn't classify 54634, 54774
Sorry, prediction pasa_asmbl_32092.p2 fails validation.
(GCG)	 AG	54634-54774	GT	AGG
(ATG)	 AG	54863-54999	GT	AGG
(CTC)	 AG	55159-55266	GT	AGG
(TGG)	 AG	55560-55752	GT	AGG
(ACG)	 AG	56216-56233	CA	GAC
-recovered pasa_asmbl_32092.p2, initial, 54863, 54999
-recovered pasa_asmbl_32092.p2, terminal, 56216, 56233
-recovered pasa_asmbl_32092.p2, internal, 54634, 54774
-recovered pasa_asmbl_32092.p2, internal, 54863, 54999
-recovered pasa_asmbl_32092.p2, internal, 55159, 55266
-recovered pasa_asmbl_32092.p2, internal, 55560, 55752
Valid prediction for GeneMark_model.92958_t
Valid prediction for GeneMark_model.92964_t
Valid prediction for Augustus_model.g35756.t1
Valid prediction for Augustus_model.g35766.t1
Valid prediction for GeneMark_model.92989_t
Valid prediction for snap_scaffold_24-snap.510-T1
Valid prediction for GlimmerHMM_glimmerT_53379-T1
Valid prediction for snap_scaffold_24-snap.500-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.92949_t
Valid prediction for GeneMark_model.92981_t
Valid prediction for GlimmerHMM_glimmerT_53387-T1
Valid prediction for GeneMark_model.92939_t
Valid prediction for GeneMark_model.92991_t
Valid prediction for GeneMark_model.92993_t
Valid prediction for GeneMark_model.92996_t
Valid prediction for GeneMark_model.92948_t
Valid prediction for GeneMark_model.92969_t
Valid prediction for Augustus_model.g35760.t1
Valid prediction for snap_scaffold_24-snap.495-T1
Valid prediction for GlimmerHMM_glimmerT_53373-T1
Valid prediction for Augustus_model.g35763.t1
Valid prediction for GeneMark_model.92980_t
Valid prediction for GlimmerHMM_glimmerT_53382-T1
Valid prediction for GeneMark_model.92983_t
Valid prediction for GeneMark_model.92977_t
Valid prediction for GeneMark_model.92956_t
Valid prediction for Augustus_model.g35761.t1
Valid prediction for GeneMark_model.92943_t
Valid prediction for GeneMark_model.92946_t
Valid prediction for GeneMark_model.92941_t
Couldn't classify 42051, 42333
Couldn't classify 42727, 42803
Sorry, prediction pasa_asmbl_32091.p2 fails validation.
(GGC)	 CG	42051-42333	GT	AGG
(GCT)	 AG	42727-42803	AG	GCA
Valid prediction for GlimmerHMM_glimmerT_53380-T1
Valid prediction for Augustus_model.g35762.t1
Valid prediction for GeneMark_model.92967_t
Valid prediction for GeneMark_model.92937_t
Valid prediction for snap_scaffold_24-snap.515-T1
Couldn't classify 46998, 47300
Sorry, prediction pasa_asmbl_32637.p1 fails validation.
(GCA)	 CG	46998-47300	CT	AGC
Valid prediction for GlimmerHMM_glimmerT_53386-T1
Valid prediction for snap_scaffold_24-snap.513-T1
Valid prediction for GeneMark_model.92985_t
Valid prediction for GeneMark_model.92944_t
Valid prediction for GeneMark_model.92974_t
Valid prediction for GeneMark_model.92976_t
Valid prediction for GeneMark_model.92962_t
Valid prediction for GeneMark_model.92988_t
Valid prediction for GlimmerHMM_glimmerT_53384-T1
Couldn't classify 64338, 64386
Couldn't classify 67296, 67810
Sorry, prediction pasa_asmbl_32094.p1 fails validation.
(ACT)	 GG	64338-64386	GT	CGG
(AGC)	 AG	66065-66225	GT	AGG
(TCC)	 AG	66662-66795	GT	AGG
(ATC)	 AG	67031-67098	GT	TGG
(ATG)	 AG	67296-67810	CA	AGC
-recovered pasa_asmbl_32094.p1, internal, 66065, 66225
-recovered pasa_asmbl_32094.p1, internal, 66662, 66795
-recovered pasa_asmbl_32094.p1, internal, 67031, 67098
Valid prediction for snap_scaffold_24-snap.521-T1
Couldn't classify 69811, 70329
Sorry, prediction pasa_asmbl_32600.p1 fails validation.
(ATG)	 GG	68102-69124	GT	CGG
(GAG)	 AG	69811-70329	AG	ACA
-recovered pasa_asmbl_32600.p1, initial, 68102, 69124
Couldn't classify 96218, 97156
Sorry, prediction pasa_asmbl_32096.p1 fails validation.
(GGA)	 CA	96218-97156	GA	GAG
Valid prediction for GlimmerHMM_glimmerT_53376-T1
Valid prediction for snap_scaffold_24-snap.492-T1
Valid prediction for GeneMark_model.92999_t
Couldn't classify 79873, 79920
Couldn't classify 82809, 82932
Sorry, prediction pasa_asmbl_32658.p1 fails validation.
(CAC)	 AG	79873-79920	GT	AGG
(GTG)	 AG	80166-80311	GT	GTG
(GCA)	 AG	82809-82932	GT	GGG
-recovered pasa_asmbl_32658.p1, internal, 79873, 79920
-recovered pasa_asmbl_32658.p1, internal, 80166, 80311
-recovered pasa_asmbl_32658.p1, internal, 82809, 82932

-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.92990_t
Valid prediction for Augustus_model.g35758.t1
Valid prediction for snap_scaffold_24-snap.493-T1
Valid prediction for GeneMark_model.92954_t
Valid prediction for GlimmerHMM_glimmerT_53381-T1
Valid prediction for snap_scaffold_24-snap.505-T1
Valid prediction for snap_scaffold_24-snap.511-T1
Valid prediction for snap_scaffold_24-snap.502-T1
Valid prediction for GeneMark_model.92959_t
Valid prediction for GlimmerHMM_glimmerT_53383-T1
Valid prediction for GeneMark_model.92965_t
Valid prediction for GeneMark_model.92955_t
Valid prediction for GeneMark_model.92940_t
Valid prediction for GeneMark_model.92966_t
Valid prediction for Augustus_model.g35764.t1
Valid prediction for GeneMark_model.92998_t
Valid prediction for GlimmerHMM_glimmerT_53374-T1
Valid prediction for GeneMark_model.92997_t
Valid prediction for GlimmerHMM_glimmerT_53375-T1
Valid prediction for snap_scaffold_24-snap.512-T1
Valid prediction for GeneMark_model.92995_t
Valid prediction for GeneMark_model.92970_t
Valid prediction for snap_scaffold_24-snap.504-T1
Valid prediction for snap_scaffold_24-snap.498-T1
Valid prediction for snap_scaffold_24-snap.516-T1
Valid prediction for snap_scaffold_24-snap.507-T1
Valid prediction for GlimmerHMM_glimmerT_53388-T1
Valid prediction for GeneMark_model.92984_t
Valid prediction for GeneMark_model.92968_t
Valid prediction for HiQ_model.g35769.t1
Valid prediction for GeneMark_model.92975_t
Valid prediction for GeneMark_model.92963_t
Valid prediction for snap_scaffold_24-snap.497-T1
Valid prediction for snap_scaffold_24-snap.523-T1
Valid prediction for GeneMark_model.92973_t
Valid prediction for snap_scaffold_24-snap.519-T1
Valid prediction for GeneMark_model.92986_t
Valid prediction for GeneMark_model.92961_t
Valid prediction for GeneMark_model.92957_t
Valid prediction for GeneMark_model.92951_t
Valid prediction for GeneMark_model.92942_t
Valid prediction for GeneMark_model.92994_t
Valid prediction for GeneMark_model.92982_t
Valid prediction for GeneMark_model.92950_t
Valid prediction for snap_scaffold_24-snap.503-T1
Valid prediction for GlimmerHMM_glimmerT_53385-T1
Valid prediction for snap_scaffold_24-snap.501-T1
Valid prediction for GlimmerHMM_glimmerT_53389-T1
Valid prediction for GeneMark_model.92987_t
Valid prediction for GlimmerHMM_glimmerT_53377-T1
Valid prediction for snap_scaffold_24-snap.520-T1
Valid prediction for snap_scaffold_24-snap.522-T1
Valid prediction for Augustus_model.g35768.t1
Valid prediction for GeneMark_model.92947_t
Valid prediction for GeneMark_model.92992_t
Valid prediction for GeneMark_model.92972_t
Valid prediction for snap_scaffold_24-snap.508-T1
Couldn't classify 4705, 4782
Sorry, prediction pasa_asmbl_32766.p1 fails validation.
(ATG)	 AA	1836-2111	GT	AGG
(GTA)	 AG	2546-2610	GT	TGG
(GCA)	 AG	3056-3152	GT	AGG
(GAC)	 AG	4705-4782	TA	GGT
-recovered pasa_asmbl_32766.p1, initial, 1836, 2111
-recovered pasa_asmbl_32766.p1, internal, 2546, 2610
-recovered pasa_asmbl_32766.p1, internal, 3056, 3152
Valid prediction for snap_scaffold_24-snap.509-T1
Valid prediction for snap_scaffold_24-snap.499-T1
Valid prediction for GeneMark_model.92945_t
Valid prediction for snap_scaffold_24-snap.514-T1
Valid prediction for Augustus_model.g35757.t1
Valid prediction for GlimmerHMM_glimmerT_53378-T1
Valid prediction for GeneMark_model.92978_t
Valid prediction for GeneMark_model.92938_t
Valid prediction for snap_scaffold_24-snap.494-T1
Valid prediction for snap_scaffold_24-snap.496-T1
Valid prediction for GeneMark_model.92953_t
Valid prediction for Augustus_model.g35765.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 4479, rend_intergenic: 1707  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14393, rend_intergenic: 7875  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25820, rend_intergenic: 15361  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72185, rend_intergenic: 39959  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97156, rend_intergenic: 78135  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117663, rend_intergenic: 112573  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122343, rend_intergenic: 122086  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123628, rend_intergenic: 122406  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125775, rend_intergenic: 123643  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127967, rend_intergenic: 126329  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150754, rend_intergenic: 134420  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160408, rend_intergenic: 152165  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164414, rend_intergenic: 160468  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 166249
-exon list size: 722


building trellis

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92.1    
92.3    
92.4    
92.5    
92.7    
92.8    
93.0    
93.1    
93.2    
93.4    
93.5    
93.6    
93.8    
93.9    
94.1    
94.2    
94.3    
94.5    
94.6    
94.8    
94.9    
95.0    
95.2    
95.3    
95.4    
95.6    
95.7    
95.9    
96.0    
96.1    
96.3    
96.4    
96.5    
96.7    
96.8    
97.0    
97.1    
97.2    
97.4    
97.5    
97.7    
97.8    
97.9    
98.1    
98.2    
98.3    
98.5    
98.6    
98.8    
98.9    
99.0    
99.2    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 4479, rend_intergenic: 1707  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14393, rend_intergenic: 7875  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25820, rend_intergenic: 15361  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72185, rend_intergenic: 39959  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97156, rend_intergenic: 78135  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117663, rend_intergenic: 112573  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122343, rend_intergenic: 122086  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123628, rend_intergenic: 122406  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125775, rend_intergenic: 123643  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127967, rend_intergenic: 126329  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150754, rend_intergenic: 134420  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160408, rend_intergenic: 152165  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164414, rend_intergenic: 160468  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 13 predictions persist after filtering for low support