-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_23/scaffold_23_2579669-2791750

-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_50694-T1
Valid prediction for Augustus_model.g33855.t1
Valid prediction for HiQ_model.g33854.t1
Valid prediction for GlimmerHMM_glimmerT_50681-T1
Valid prediction for snap_scaffold_23-snap.521-T1
Valid prediction for GlimmerHMM_glimmerT_50673-T1
Valid prediction for HiQ_model.g33866.t1
Valid prediction for snap_scaffold_23-snap.494-T1
Valid prediction for Augustus_model.g33858.t1
Valid prediction for GlimmerHMM_glimmerT_50689-T1
Valid prediction for snap_scaffold_23-snap.526-T1
Valid prediction for snap_scaffold_23-snap.514-T1
Valid prediction for Augustus_model.g33863.t1
Valid prediction for GlimmerHMM_glimmerT_50691-T1
Valid prediction for snap_scaffold_23-snap.516-T1
Valid prediction for snap_scaffold_23-snap.511-T1
Valid prediction for snap_scaffold_23-snap.496-T1
Valid prediction for GlimmerHMM_glimmerT_50675-T1
Valid prediction for snap_scaffold_23-snap.499-T1
Valid prediction for pasa_asmbl_31410.p1
Valid prediction for snap_scaffold_23-snap.491-T1
Couldn't classify 44002, 44064
Sorry, prediction pasa_asmbl_31409.p1 fails validation.
(ATG)	 GA	42586-42705	GT	GGG
(ATG)	 AG	42894-43032	GT	GGG
(GTC)	 AG	43177-43225	GT	AGG
(GAG)	 AG	43343-43441	GT	AGG
(AGC)	 AG	43560-43620	GT	TGG
(CTC)	 AG	43832-43891	GT	TGG
(CTG)	 AG	44002-44064	TA	AGT
-recovered pasa_asmbl_31409.p1, initial, 42586, 42705
-recovered pasa_asmbl_31409.p1, initial, 42894, 43032
-recovered pasa_asmbl_31409.p1, internal, 42894, 43032
-recovered pasa_asmbl_31409.p1, internal, 43177, 43225
-recovered pasa_asmbl_31409.p1, internal, 43343, 43441
-recovered pasa_asmbl_31409.p1, internal, 43560, 43620
-recovered pasa_asmbl_31409.p1, internal, 43832, 43891
Couldn't classify 63947, 64253
Sorry, prediction pasa_asmbl_31416.p1 fails validation.
(CCT)	 CA	63947-64253	GT	AGG
(CCG)	 AG	64788-64898	GT	CGG
(GGT)	 AG	65075-65227	GT	AAG
(AAT)	 AG	65365-65496	GT	TGG
(TTT)	 AG	65652-65789	GT	AGG
(CTT)	 AG	65890-66015	GT	GGG
(ACG)	 AG	66107-66252	GT	ATG
(CCG)	 AG	66338-66482	GT	AGG
(TGC)	 AG	66650-66808	GT	AGG
(TTA)	 AG	67251-67385	GT	CGG
(ATC)	 AG	67619-67906	GT	TGG
(AGT)	 AG	68045-68142	GT	AGG
(GTG)	 AG	68255-68513	GT	TCG
(GAC)	 AG	68782-68942	GT	TAG
(AGA)	 AG	69023-69233	GT	AGG
(AGT)	 AG	69445-69555	GT	AGG
(GCT)	 AG	69701-69891	GT	AGG
(TTC)	 AG	69995-70108	GT	TGG
(GGC)	 AG	70270-70340	GT	GTG
(GTG)	 AG	70466-70506	GT	AGG
(GAG)	 AG	70620-70716	GT	GTG
(GTA)	 AG	71232-71331	GC	AGG
(ATG)	 AG	71424-71498	TC	GAT
-recovered pasa_asmbl_31416.p1, terminal, 70466, 70506
-recovered pasa_asmbl_31416.p1, terminal, 71424, 71498
-recovered pasa_asmbl_31416.p1, internal, 64788, 64898
-recovered pasa_asmbl_31416.p1, internal, 65075, 65227
-recovered pasa_asmbl_31416.p1, internal, 65365, 65496
-recovered pasa_asmbl_31416.p1, internal, 65652, 65789
-recovered pasa_asmbl_31416.p1, internal, 65890, 66015
-recovered pasa_asmbl_31416.p1, internal, 66107, 66252
-recovered pasa_asmbl_31416.p1, internal, 66338, 66482
-recovered pasa_asmbl_31416.p1, internal, 66650, 66808
-recovered pasa_asmbl_31416.p1, internal, 67251, 67385
-recovered pasa_asmbl_31416.p1, internal, 67619, 67906
-recovered pasa_asmbl_31416.p1, internal, 68045, 68142
-recovered pasa_asmbl_31416.p1, internal, 68255, 68513
-recovered pasa_asmbl_31416.p1, internal, 68782, 68942
-recovered pasa_asmbl_31416.p1, internal, 69023, 69233
-recovered pasa_asmbl_31416.p1, internal, 69445, 69555
-recovered pasa_asmbl_31416.p1, internal, 69701, 69891
-recovered pasa_asmbl_31416.p1, internal, 69995, 70108
-recovered pasa_asmbl_31416.p1, internal, 70270, 70340
-recovered pasa_asmbl_31416.p1, internal, 70466, 70506
-recovered pasa_asmbl_31416.p1, internal, 70620, 70716
-recovered pasa_asmbl_31416.p1, internal, 71232, 71331
Valid prediction for GlimmerHMM_glimmerT_50679-T1
Valid prediction for Augustus_model.g33867.t1
Valid prediction for snap_scaffold_23-snap.503-T1
Valid prediction for snap_scaffold_23-snap.507-T1
Valid prediction for snap_scaffold_23-snap.504-T1
Valid prediction for CodingQuarry_transcript_35596-T1
Valid prediction for Augustus_model.g33875.t1
Valid prediction for Augustus_model.g33864.t1
Valid prediction for snap_scaffold_23-snap.490-T1
Valid prediction for snap_scaffold_23-snap.492-T1
Valid prediction for Augustus_model.g33872.t1
Valid prediction for snap_scaffold_23-snap.498-T1
Valid prediction for snap_scaffold_23-snap.520-T1
Valid prediction for HiQ_model.g33852.t1
Valid prediction for GlimmerHMM_glimmerT_50677-T1
Valid prediction for snap_scaffold_23-snap.500-T1
Valid prediction for snap_scaffold_23-snap.489-T1
Valid prediction for snap_scaffold_23-snap.512-T1
Valid prediction for GlimmerHMM_glimmerT_50688-T1
Valid prediction for snap_scaffold_23-snap.508-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_23-snap.519-T1
Valid prediction for GlimmerHMM_glimmerT_50695-T1
Valid prediction for CodingQuarry_transcript_35595-T1
Valid prediction for GlimmerHMM_glimmerT_50676-T1
Valid prediction for GlimmerHMM_glimmerT_50684-T1
Valid prediction for pasa_asmbl_31422.p1
Valid prediction for snap_scaffold_23-snap.515-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 CodingQuarry_transcript_35591-T1
Valid prediction for snap_scaffold_23-snap.517-T1
Valid prediction for Augustus_model.g33848.t1
Couldn't classify 190662, 190673
Couldn't classify 191588, 191840
Sorry, prediction pasa_asmbl_30749.p1 fails validation.
(CCG)	 AG	190662-190673	GT	CAG
(GAA)	 AG	190774-190905	GT	AGG
(GTA)	 AG	190991-191078	GT	AGG
(GCC)	 AG	191192-191411	GT	TCG
(GTA)	 AG	191588-191840	AA	GGA
-recovered pasa_asmbl_30749.p1, terminal, 190991, 191078
-recovered pasa_asmbl_30749.p1, internal, 190662, 190673
-recovered pasa_asmbl_30749.p1, internal, 190774, 190905
-recovered pasa_asmbl_30749.p1, internal, 190991, 191078
-recovered pasa_asmbl_30749.p1, internal, 191192, 191411
Valid prediction for Augustus_model.g33859.t1
Valid prediction for Augustus_model.g33861.t1
Valid prediction for GlimmerHMM_glimmerT_50683-T1
Valid prediction for snap_scaffold_23-snap.486-T1
Valid prediction for GlimmerHMM_glimmerT_50685-T1
Couldn't classify 185476, 185625
Sorry, prediction pasa_asmbl_30750.p1 fails validation.
(TTC)	 TG	185476-185625	GT	ACG
(CCT)	 AG	185728-186005	GT	AGG
(GCC)	 AG	186106-186238	GT	AGG
(ATG)	 AG	186357-186486	GT	AGG
(GCT)	 AG	186825-186958	GT	AGG
(GTT)	 AG	187151-187275	GT	AAG
(GTA)	 AG	187435-187648	GC	GAG
-recovered pasa_asmbl_30750.p1, initial, 186357, 186486
add_exon() Sorry, pasa_asmbl_30750.p1 186357-186486-terminal-3 is invalid.
-recovered pasa_asmbl_30750.p1, terminal, 186357, 186486
-recovered pasa_asmbl_30750.p1, terminal, 187435, 187648
-recovered pasa_asmbl_30750.p1, internal, 185728, 186005
-recovered pasa_asmbl_30750.p1, internal, 186106, 186238
-recovered pasa_asmbl_30750.p1, internal, 186357, 186486
-recovered pasa_asmbl_30750.p1, internal, 186825, 186958
-recovered pasa_asmbl_30750.p1, internal, 187151, 187275
-recovered pasa_asmbl_30750.p1, internal, 187435, 187648
Valid prediction for GlimmerHMM_glimmerT_50692-T1
Valid prediction for GlimmerHMM_glimmerT_50668-T1
Valid prediction for Augustus_model.g33856.t1
Valid prediction for pasa_asmbl_30744.p1
Valid prediction for GlimmerHMM_glimmerT_50672-T1
Valid prediction for snap_scaffold_23-snap.487-T1
Valid prediction for CodingQuarry_transcript_35592-T1
Valid prediction for CodingQuarry_transcript_35590-T1
Valid prediction for HiQ_model.g33860.t1
Valid prediction for GlimmerHMM_glimmerT_50682-T1
Valid prediction for CodingQuarry_transcript_35589-T1
Valid prediction for snap_scaffold_23-snap.522-T1
Valid prediction for pasa_asmbl_31232.p1
Valid prediction for CodingQuarry_transcript_35588-T1
Valid prediction for GlimmerHMM_glimmerT_50693-T1
Valid prediction for snap_scaffold_23-snap.485-T1
Valid prediction for snap_scaffold_23-snap.484-T1
Valid prediction for snap_scaffold_23-snap.502-T1
Valid prediction for snap_scaffold_23-snap.497-T1
Valid prediction for GlimmerHMM_glimmerT_50696-T1
Valid prediction for Augustus_model.g33871.t1
Valid prediction for snap_scaffold_23-snap.518-T1
Valid prediction for snap_scaffold_23-snap.480-T1
Valid prediction for snap_scaffold_23-snap.488-T1
Valid prediction for Augustus_model.g33874.t1
Valid prediction for HiQ_model.g33851.t1
Valid prediction for snap_scaffold_23-snap.501-T1
Valid prediction for snap_scaffold_23-snap.513-T1
Valid prediction for GlimmerHMM_glimmerT_50669-T1
Valid prediction for Augustus_model.g33870.t1
Valid prediction for Augustus_model.g33850.t1
Valid prediction for snap_scaffold_23-snap.481-T1
Valid prediction for snap_scaffold_23-snap.483-T1
Valid prediction for GlimmerHMM_glimmerT_50667-T1
Valid prediction for snap_scaffold_23-snap.493-T1
Valid prediction for snap_scaffold_23-snap.505-T1
Valid prediction for HiQ_model.g33853.t1
Valid prediction for snap_scaffold_23-snap.523-T1
Valid prediction for pasa_asmbl_30761.p1
Valid prediction for GlimmerHMM_glimmerT_50686-T1
Valid prediction for GlimmerHMM_glimmerT_50678-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for Augustus_model.g33857.t1
Valid prediction for snap_scaffold_23-snap.495-T1
Couldn't classify 173650, 173745
Sorry, prediction pasa_asmbl_30752.p1 fails validation.
(GAG)	 AG	173650-173745	GT	AGG
(GTA)	 AG	173849-173980	GT	AGG
(AAT)	 AG	174905-175006	GT	AGG
(GCT)	 AG	175825-175847	GT	AGG
(GGT)	 AG	176314-176435	GT	CGG
(TCC)	 AG	178483-178692	GT	AGG
(ATT)	 AG	178808-178906	GT	AGG
(CTT)	 AG	179202-179331	GT	AGG
(TGC)	 AG	179802-179834	GT	AGG
(AAG)	 AG	181363-181460	GT	AGG
(GTG)	 AG	181762-182013	GT	CGG
(GAC)	 AG	182362-182450	GT	TGG
(GTG)	 AG	182867-182989	CC	AGC
-recovered pasa_asmbl_30752.p1, terminal, 175825, 175847
add_exon() Sorry, pasa_asmbl_30752.p1 181363-181460-terminal-2 is invalid.
-recovered pasa_asmbl_30752.p1, terminal, 181363, 181460
-recovered pasa_asmbl_30752.p1, terminal, 182867, 182989
-recovered pasa_asmbl_30752.p1, internal, 173650, 173745
-recovered pasa_asmbl_30752.p1, internal, 173849, 173980
-recovered pasa_asmbl_30752.p1, internal, 174905, 175006
-recovered pasa_asmbl_30752.p1, internal, 175825, 175847
-recovered pasa_asmbl_30752.p1, internal, 176314, 176435
-recovered pasa_asmbl_30752.p1, internal, 178483, 178692
-recovered pasa_asmbl_30752.p1, internal, 178808, 178906
-recovered pasa_asmbl_30752.p1, internal, 179202, 179331
-recovered pasa_asmbl_30752.p1, internal, 179802, 179834
-recovered pasa_asmbl_30752.p1, internal, 181363, 181460
-recovered pasa_asmbl_30752.p1, internal, 181762, 182013
-recovered pasa_asmbl_30752.p1, internal, 182362, 182450
Valid prediction for Augustus_model.g33849.t1
Valid prediction for Augustus_model.g33868.t1
Valid prediction for snap_scaffold_23-snap.525-T1
Valid prediction for Augustus_model.g33869.t1
Couldn't classify 195374, 195563
Sorry, prediction pasa_asmbl_31209.p1 fails validation.
(ATG)	 CA	194335-194469	GT	CAG
(GAA)	 AG	194568-194699	GT	AGG
(GTG)	 AG	194786-194873	GT	GGG
(GAC)	 AG	194978-195197	GT	TCG
(GTA)	 AG	195374-195563	AT	TAA
-recovered pasa_asmbl_31209.p1, initial, 194335, 194469
-recovered pasa_asmbl_31209.p1, internal, 194568, 194699
-recovered pasa_asmbl_31209.p1, internal, 194786, 194873
-recovered pasa_asmbl_31209.p1, internal, 194978, 195197
Valid prediction for HiQ_model.g33865.t1
Valid prediction for snap_scaffold_23-snap.482-T1
Valid prediction for GlimmerHMM_glimmerT_50690-T1
Valid prediction for snap_scaffold_23-snap.524-T1
Valid prediction for GlimmerHMM_glimmerT_50687-T1
Valid prediction for CodingQuarry_transcript_35593-T1
Valid prediction for GlimmerHMM_glimmerT_50674-T1
Couldn't classify 166317, 166503
Sorry, prediction pasa_asmbl_30759.p1 fails validation.
(CCG)	 CT	166317-166503	GT	AAG
(GCA)	 AG	166681-166863	GT	AGG
(ACC)	 AG	167105-167478	TG	GAT
-recovered pasa_asmbl_30759.p1, terminal, 167105, 167478
-recovered pasa_asmbl_30759.p1, internal, 166681, 166863
Valid prediction for GlimmerHMM_glimmerT_50671-T1
Valid prediction for snap_scaffold_23-snap.510-T1
Valid prediction for Augustus_model.g33873.t1
Valid prediction for snap_scaffold_23-snap.506-T1
Valid prediction for pasa_asmbl_30763.p1
Valid prediction for GlimmerHMM_glimmerT_50697-T1
Valid prediction for Augustus_model.g33862.t1
Valid prediction for snap_scaffold_23-snap.509-T1
Valid prediction for GlimmerHMM_glimmerT_50698-T1
Valid prediction for GlimmerHMM_glimmerT_50670-T1
Valid prediction for GlimmerHMM_glimmerT_50680-T1
Couldn't classify 108282, 109031
Sorry, prediction pasa_asmbl_30762.p1 fails validation.
(GAG)	 TT	108282-109031	GC	GAG

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 39993, rend_intergenic: 33960  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66867, rend_intergenic: 62246  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117920, rend_intergenic: 115340  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154179, rend_intergenic: 151547  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 212082
-exon list size: 446


building trellis

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85.3    
85.5    
85.7    
85.9    
86.2    
86.4    
86.6    
86.8    
87.1    
87.3    
87.5    
87.7    
87.9    
88.2    
88.4    
88.6    
88.8    
89.1    
89.3    
89.5    
89.7    
90.0    
90.2    
90.4    
90.6    
90.8    
91.1    
91.3    
91.5    
91.7    
92.0    
92.2    
92.4    
92.6    
92.9    
93.1    
93.3    
93.5    
93.8    
94.0    
94.2    
94.4    
94.6    
94.9    
95.1    
95.3    
95.5    
95.8    
96.0    
96.2    
96.4    
96.7    
96.9    
97.1    
97.3    
97.5    
97.8    
98.0    
98.2    
98.4    
98.7    
98.9    
99.1    
99.3    
99.6    
99.8    
-found 41 predictions from path traversal
Error with prediction: snap lend_intergenic: 39993, rend_intergenic: 33960  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66867, rend_intergenic: 62246  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117920, rend_intergenic: 115340  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154179, rend_intergenic: 151547  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 36 predictions persist after filtering for low support