-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_3/scaffold_3_4813974-5011739

-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: +)Couldn't classify 170038, 170060
Sorry, prediction pasa_asmbl_40050.p1 fails validation.
(CGT)	 TG	170038-170060	GT	AAG
(GGT)	 AG	170188-170263	GT	AGG
(GTT)	 AG	170564-170674	GT	CTG
(GAA)	 AG	171250-171386	GT	AGG
(AGC)	 AG	171844-171907	GT	AGG
(GCT)	 AG	172158-172238	AA	AAA
-recovered pasa_asmbl_40050.p1, terminal, 172158, 172238
-recovered pasa_asmbl_40050.p1, internal, 170188, 170263
-recovered pasa_asmbl_40050.p1, internal, 170564, 170674
-recovered pasa_asmbl_40050.p1, internal, 171250, 171386
-recovered pasa_asmbl_40050.p1, internal, 171844, 171907
Valid prediction for GlimmerHMM_glimmerT_6485-T1
Valid prediction for snap_scaffold_3-snap.1041-T1
Valid prediction for GlimmerHMM_glimmerT_6481-T1
Valid prediction for GlimmerHMM_glimmerT_6482-T1
Valid prediction for Augustus_model.g4214.t1
Valid prediction for GlimmerHMM_glimmerT_6474-T1
Valid prediction for GlimmerHMM_glimmerT_6475-T1
Couldn't classify 56430, 56643
Couldn't classify 57386, 57780
Sorry, prediction pasa_asmbl_40033.p1 fails validation.
(GTT)	 AC	56430-56643	GT	AGG
(GGG)	 AG	56848-57008	GT	GGG
(GCA)	 AG	57154-57271	GT	GGG
(GTG)	 AG	57386-57780	TG	ACT
-recovered pasa_asmbl_40033.p1, internal, 56848, 57008
-recovered pasa_asmbl_40033.p1, internal, 57154, 57271
Valid prediction for GlimmerHMM_glimmerT_6473-T1
Valid prediction for Augustus_model.g4198.t1
Valid prediction for snap_scaffold_3-snap.1039-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_3-snap.1066-T1
Valid prediction for Augustus_model.g4212.t1
Valid prediction for HiQ_model.g4202.t1
Valid prediction for Augustus_model.g4210.t1
Valid prediction for snap_scaffold_3-snap.1065-T1
Valid prediction for snap_scaffold_3-snap.1067-T1
Valid prediction for snap_scaffold_3-snap.1042-T1
Valid prediction for Augustus_model.g4196.t1
Valid prediction for GlimmerHMM_glimmerT_6499-T1
Valid prediction for snap_scaffold_3-snap.1056-T1
Couldn't classify 98765, 98984
Couldn't classify 99581, 99724
Sorry, prediction pasa_asmbl_40044.p1 fails validation.
(TTA)	 CC	98765-98984	GT	AAG
(TAC)	 AG	99113-99252	GT	AGG
(GGC)	 AG	99581-99724	AC	AGA
-recovered pasa_asmbl_40044.p1, internal, 99113, 99252
Valid prediction for snap_scaffold_3-snap.1072-T1
Valid prediction for snap_scaffold_3-snap.1080-T1
Valid prediction for CodingQuarry_transcript_46150-T1
Valid prediction for snap_scaffold_3-snap.1050-T1
Valid prediction for Augustus_model.g4215.t1
Valid prediction for Augustus_model.g4206.t1
Valid prediction for CodingQuarry_transcript_46152-T1
Couldn't classify 152490, 152623
Sorry, prediction pasa_asmbl_40049.p1 fails validation.
(GGC)	 AG	152490-152623	GT	AAG
(GTA)	 AG	152714-152863	GT	CGG
(AGG)	 AG	152961-153036	GT	AGG
(GCC)	 AG	153203-153364	GT	AGG
(GCA)	 AG	153461-153564	GT	AAG
(GTA)	 AG	153658-153767	GT	AGG
(GCA)	 AG	154090-154187	GT	AGG
(GCA)	 AG	154685-154798	GT	AGG
(GGC)	 AG	155193-155298	GT	AGG
(GAG)	 AG	155481-155623	GT	AGG
(GGC)	 AG	155826-155999	GT	AGG
(GCG)	 AG	156324-156422	GT	AGG
(ATT)	 AG	156583-156744	GC	GAG
add_exon() Sorry, pasa_asmbl_40049.p1 155193-155298-terminal-3 is invalid.
-recovered pasa_asmbl_40049.p1, terminal, 155193, 155298
-recovered pasa_asmbl_40049.p1, terminal, 156583, 156744
-recovered pasa_asmbl_40049.p1, internal, 152490, 152623
-recovered pasa_asmbl_40049.p1, internal, 152714, 152863
-recovered pasa_asmbl_40049.p1, internal, 152961, 153036
-recovered pasa_asmbl_40049.p1, internal, 153203, 153364
-recovered pasa_asmbl_40049.p1, internal, 153461, 153564
-recovered pasa_asmbl_40049.p1, internal, 153658, 153767
-recovered pasa_asmbl_40049.p1, internal, 154090, 154187
-recovered pasa_asmbl_40049.p1, internal, 154685, 154798
-recovered pasa_asmbl_40049.p1, internal, 155193, 155298
-recovered pasa_asmbl_40049.p1, internal, 155481, 155623
-recovered pasa_asmbl_40049.p1, internal, 155826, 155999
-recovered pasa_asmbl_40049.p1, internal, 156324, 156422
-recovered pasa_asmbl_40049.p1, internal, 156583, 156744
Valid prediction for HiQ_model.g4208.t1
Valid prediction for GlimmerHMM_glimmerT_6467-T1
Valid prediction for Augustus_model.g4201.t1
Valid prediction for GlimmerHMM_glimmerT_6480-T1
Valid prediction for snap_scaffold_3-snap.1059-T1
Valid prediction for GlimmerHMM_glimmerT_6488-T1
Valid prediction for Augustus_model.g4221.t1
Valid prediction for Augustus_model.g4197.t1
Valid prediction for GlimmerHMM_glimmerT_6471-T1
Valid prediction for Augustus_model.g4205.t1
Valid prediction for snap_scaffold_3-snap.1069-T1
Valid prediction for GlimmerHMM_glimmerT_6487-T1
Valid prediction for HiQ_model.g4219.t1
Valid prediction for snap_scaffold_3-snap.1062-T1
Valid prediction for GlimmerHMM_glimmerT_6465-T1
Valid prediction for CodingQuarry_transcript_46149-T1
Valid prediction for pasa_asmbl_40058.p1
Valid prediction for GlimmerHMM_glimmerT_6496-T1
Valid prediction for GlimmerHMM_glimmerT_6492-T1
Valid prediction for pasa_asmbl_40041.p1
Valid prediction for GlimmerHMM_glimmerT_6486-T1
Valid prediction for GlimmerHMM_glimmerT_6493-T1
Valid prediction for CodingQuarry_transcript_46154-T1
Valid prediction for CodingQuarry_transcript_46158-T1
Valid prediction for HiQ_model.g4209.t1
Valid prediction for GlimmerHMM_glimmerT_6501-T1
Valid prediction for CodingQuarry_transcript_46153-T1
Valid prediction for snap_scaffold_3-snap.1045-T1
Valid prediction for pasa_asmbl_40046.p1
Valid prediction for pasa_asmbl_40056.p1
Valid prediction for GlimmerHMM_glimmerT_6468-T1
Valid prediction for snap_scaffold_3-snap.1054-T1
Valid prediction for GlimmerHMM_glimmerT_6494-T1
Valid prediction for GlimmerHMM_glimmerT_6489-T1
Valid prediction for snap_scaffold_3-snap.1064-T1
Valid prediction for GlimmerHMM_glimmerT_6491-T1
Valid prediction for pasa_asmbl_40043.p1
Valid prediction for Augustus_model.g4193.t1
Valid prediction for snap_scaffold_3-snap.1048-T1
Valid prediction for GlimmerHMM_glimmerT_6477-T1
Valid prediction for snap_scaffold_3-snap.1043-T1
Valid prediction for CodingQuarry_transcript_46157-T1
Valid prediction for snap_scaffold_3-snap.1077-T1
Valid prediction for CodingQuarry_transcript_46155-T1
Couldn't classify 138485, 138660
Couldn't classify 138888, 139137
Sorry, prediction pasa_asmbl_40045.p1 fails validation.
(TTG)	 CT	138485-138660	GT	AGG
(GTG)	 AG	138888-139137	CC	CCC
Valid prediction for snap_scaffold_3-snap.1060-T1
Valid prediction for pasa_asmbl_40036.p1
Valid prediction for Augustus_model.g4211.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 pasa_asmbl_38820.p1
Valid prediction for snap_scaffold_3-snap.1071-T1
Valid prediction for snap_scaffold_3-snap.1049-T1
Valid prediction for snap_scaffold_3-snap.1063-T1
Valid prediction for Augustus_model.g4203.t1
Valid prediction for Augustus_model.g4213.t1
Valid prediction for CodingQuarry_transcript_46151-T1
Valid prediction for HiQ_model.g4207.t1
Valid prediction for snap_scaffold_3-snap.1079-T1
Valid prediction for snap_scaffold_3-snap.1058-T1
Valid prediction for snap_scaffold_3-snap.1052-T1
Valid prediction for pasa_asmbl_38830.p1
Couldn't classify 36927, 37229
Sorry, prediction pasa_asmbl_38826.p1 fails validation.
(TGC)	 GC	36927-37229	GT	GGG
Valid prediction for snap_scaffold_3-snap.1051-T1
Valid prediction for Augustus_model.g4195.t1
Valid prediction for Augustus_model.g4192.t1
Valid prediction for GlimmerHMM_glimmerT_6472-T1
Couldn't classify 29620, 29673
Sorry, prediction pasa_asmbl_38829.p1 fails validation.
(ATG)	 AG	28345-28381	GT	CGG
(GTC)	 AG	28977-29119	GT	AGG
(CTA)	 AG	29324-29482	GT	AGG
(GTC)	 AG	29620-29673	AA	ACA
-recovered pasa_asmbl_38829.p1, initial, 28345, 28381
-recovered pasa_asmbl_38829.p1, internal, 28345, 28381
-recovered pasa_asmbl_38829.p1, internal, 28977, 29119
-recovered pasa_asmbl_38829.p1, internal, 29324, 29482
Valid prediction for GlimmerHMM_glimmerT_6476-T1
Valid prediction for snap_scaffold_3-snap.1073-T1
Valid prediction for Augustus_model.g4217.t1
Valid prediction for Augustus_model.g4199.t1
Valid prediction for snap_scaffold_3-snap.1075-T1
Valid prediction for pasa_asmbl_38822.p1
Valid prediction for snap_scaffold_3-snap.1046-T1
Valid prediction for GlimmerHMM_glimmerT_6466-T1
Valid prediction for GlimmerHMM_glimmerT_6483-T1
Valid prediction for GlimmerHMM_glimmerT_6469-T1
Valid prediction for Augustus_model.g4200.t1
Valid prediction for GlimmerHMM_glimmerT_6497-T1
Valid prediction for Augustus_model.g4218.t1
Valid prediction for Augustus_model.g4194.t1
Valid prediction for snap_scaffold_3-snap.1053-T1
Valid prediction for snap_scaffold_3-snap.1070-T1
Valid prediction for CodingQuarry_transcript_46156-T1
Valid prediction for GlimmerHMM_glimmerT_6484-T1
Couldn't classify 32485, 32928
Sorry, prediction pasa_asmbl_38827.p1 fails validation.
(TCC)	 CC	32485-32928	AT	GAA
Valid prediction for CodingQuarry_transcript_46147-T1
Valid prediction for HiQ_model.g4220.t1
Valid prediction for GlimmerHMM_glimmerT_6498-T1
Valid prediction for GlimmerHMM_glimmerT_6495-T1
Valid prediction for snap_scaffold_3-snap.1047-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_6490-T1
Valid prediction for CodingQuarry_transcript_46148-T1
Valid prediction for snap_scaffold_3-snap.1044-T1
Valid prediction for snap_scaffold_3-snap.1081-T1
Valid prediction for GlimmerHMM_glimmerT_6479-T1
Valid prediction for snap_scaffold_3-snap.1074-T1
Valid prediction for snap_scaffold_3-snap.1040-T1
Valid prediction for GlimmerHMM_glimmerT_6464-T1
Valid prediction for snap_scaffold_3-snap.1061-T1
Valid prediction for snap_scaffold_3-snap.1068-T1
Valid prediction for GlimmerHMM_glimmerT_6500-T1
Valid prediction for GlimmerHMM_glimmerT_6470-T1
Valid prediction for snap_scaffold_3-snap.1057-T1
Valid prediction for HiQ_model.g4204.t1
Valid prediction for snap_scaffold_3-snap.1076-T1
Valid prediction for GlimmerHMM_glimmerT_6478-T1
Valid prediction for Augustus_model.g4216.t1
Valid prediction for snap_scaffold_3-snap.1078-T1
Couldn't classify 30007, 30045
Couldn't classify 30938, 30968
Sorry, prediction pasa_asmbl_38828.p1 fails validation.
(CTC)	 TC	30007-30045	GT	AGG
(GTC)	 AG	30156-30322	GT	GGG
(TTT)	 AG	30565-30729	GT	AAG
(GCT)	 AG	30938-30968	CA	CCC
-recovered pasa_asmbl_38828.p1, internal, 30156, 30322
-recovered pasa_asmbl_38828.p1, internal, 30565, 30729
Valid prediction for snap_scaffold_3-snap.1055-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13011, rend_intergenic: 4116  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22491, rend_intergenic: 13303  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29452, rend_intergenic: 27734  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38834, rend_intergenic: 30438  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49135, rend_intergenic: 38885  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52878, rend_intergenic: 50071  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58213, rend_intergenic: 52943  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76197, rend_intergenic: 73908  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81672, rend_intergenic: 79160  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86235, rend_intergenic: 84643  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117692, rend_intergenic: 109276  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139650, rend_intergenic: 130161  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146953, rend_intergenic: 142933  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153207, rend_intergenic: 149146  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156744, rend_intergenic: 153239  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188804, rend_intergenic: 181949  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195154, rend_intergenic: 190780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 197766
-exon list size: 506


building trellis

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89.4    
89.6    
89.8    
90.0    
90.2    
90.4    
90.6    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
91.9    
92.1    
92.3    
92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.7    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.0    
97.2    
97.4    
97.6    
97.8    
98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 40 predictions from path traversal
Error with prediction: snap lend_intergenic: 13011, rend_intergenic: 4116  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22491, rend_intergenic: 13303  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29452, rend_intergenic: 27734  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38834, rend_intergenic: 30438  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49135, rend_intergenic: 38885  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52878, rend_intergenic: 50071  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58213, rend_intergenic: 52943  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76197, rend_intergenic: 73908  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81672, rend_intergenic: 79160  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86235, rend_intergenic: 84643  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117692, rend_intergenic: 109276  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139650, rend_intergenic: 130161  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146953, rend_intergenic: 142933  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153207, rend_intergenic: 149146  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156744, rend_intergenic: 153239  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188804, rend_intergenic: 181949  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195154, rend_intergenic: 190780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 33 predictions persist after filtering for low support