-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_2/scaffold_2_4960298-5193936

-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_3772-T1
Valid prediction for GlimmerHMM_glimmerT_3766-T1
Valid prediction for snap_scaffold_2-snap.1152-T1
Valid prediction for snap_scaffold_2-snap.1124-T1
Valid prediction for snap_scaffold_2-snap.1147-T1
Valid prediction for snap_scaffold_2-snap.1151-T1
Valid prediction for snap_scaffold_2-snap.1157-T1
Valid prediction for snap_scaffold_2-snap.1154-T1
Valid prediction for snap_scaffold_2-snap.1161-T1
Valid prediction for GlimmerHMM_glimmerT_3777-T1
Valid prediction for snap_scaffold_2-snap.1125-T1
Valid prediction for snap_scaffold_2-snap.1127-T1
Valid prediction for GlimmerHMM_glimmerT_3775-T1
Valid prediction for snap_scaffold_2-snap.1129-T1
Valid prediction for snap_scaffold_2-snap.1158-T1
Valid prediction for Augustus_model.g2523.t1
Valid prediction for snap_scaffold_2-snap.1159-T1
Valid prediction for snap_scaffold_2-snap.1149-T1
Valid prediction for snap_scaffold_2-snap.1169-T1
Valid prediction for GlimmerHMM_glimmerT_3780-T1
Valid prediction for snap_scaffold_2-snap.1162-T1
Valid prediction for GlimmerHMM_glimmerT_3770-T1
Valid prediction for snap_scaffold_2-snap.1165-T1
Valid prediction for GlimmerHMM_glimmerT_3753-T1
Valid prediction for snap_scaffold_2-snap.1145-T1
Valid prediction for snap_scaffold_2-snap.1167-T1
Valid prediction for GlimmerHMM_glimmerT_3751-T1
Valid prediction for Augustus_model.g2517.t1
Valid prediction for snap_scaffold_2-snap.1138-T1
Valid prediction for GlimmerHMM_glimmerT_3749-T1
Valid prediction for GlimmerHMM_glimmerT_3778-T1
Valid prediction for GlimmerHMM_glimmerT_3747-T1
Valid prediction for Augustus_model.g2508.t1
Valid prediction for snap_scaffold_2-snap.1140-T1
Valid prediction for GlimmerHMM_glimmerT_3758-T1
Valid prediction for Augustus_model.g2521.t1
Valid prediction for snap_scaffold_2-snap.1132-T1
Valid prediction for GlimmerHMM_glimmerT_3769-T1
Valid prediction for snap_scaffold_2-snap.1164-T1
Couldn't classify 114937, 115010
Sorry, prediction pasa_asmbl_24388.p1 fails validation.
(ATG)	 TC	113934-114075	GT	AGG
(AGA)	 AG	114610-114780	GT	CAG
(GTG)	 AG	114937-115010	GG	TGG
-recovered pasa_asmbl_24388.p1, initial, 113934, 114075
-recovered pasa_asmbl_24388.p1, internal, 114610, 114780
Valid prediction for snap_scaffold_2-snap.1122-T1
Valid prediction for pasa_asmbl_23126.p1
Valid prediction for snap_scaffold_2-snap.1155-T1
Valid prediction for snap_scaffold_2-snap.1121-T1
Valid prediction for Augustus_model.g2524.t1
Valid prediction for GlimmerHMM_glimmerT_3762-T1
Valid prediction for Augustus_model.g2525.t1
Valid prediction for snap_scaffold_2-snap.1137-T1
Valid prediction for HiQ_model.g2514.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: -)Couldn't classify 123094, 123223
Sorry, prediction pasa_asmbl_23125.p1 fails validation.
(ATG)	 AG	120538-120604	GT	AGG
(ACG)	 AG	120953-121085	GT	AGG
(GAA)	 AG	121808-122042	GT	AGG
(GCT)	 AG	122208-122338	GT	AGG
(GGT)	 AG	123094-123223	AG	CCA
-recovered pasa_asmbl_23125.p1, initial, 120538, 120604
-recovered pasa_asmbl_23125.p1, internal, 120538, 120604
-recovered pasa_asmbl_23125.p1, internal, 120953, 121085
-recovered pasa_asmbl_23125.p1, internal, 121808, 122042
-recovered pasa_asmbl_23125.p1, internal, 122208, 122338
Valid prediction for HiQ_model.g2511.t1
Valid prediction for snap_scaffold_2-snap.1168-T1
Valid prediction for snap_scaffold_2-snap.1128-T1
Valid prediction for GlimmerHMM_glimmerT_3765-T1
Valid prediction for snap_scaffold_2-snap.1141-T1
Couldn't classify 86784, 87004
Sorry, prediction pasa_asmbl_23129.p1 fails validation.
(ATG)	 CC	82372-82746	GT	AGG
(GTG)	 AG	82861-83055	GT	AGG
(GTG)	 AG	83243-83579	GT	AGG
(GCG)	 AG	83918-84088	GT	AGG
(GAA)	 AG	84338-84471	GT	AGG
(GTG)	 AG	84581-84701	GT	TGG
(GCG)	 AG	85044-85193	GT	GGG
(GCG)	 AG	85289-85449	GT	AGG
(GAG)	 AG	85549-85731	GT	GGG
(AAT)	 AG	85877-86021	GT	TGG
(ATG)	 AG	86399-86659	GT	CAG
(CCA)	 AG	86784-87004	TG	GGT
-recovered pasa_asmbl_23129.p1, initial, 82372, 82746
-recovered pasa_asmbl_23129.p1, initial, 86399, 86659
-recovered pasa_asmbl_23129.p1, internal, 82861, 83055
-recovered pasa_asmbl_23129.p1, internal, 83243, 83579
-recovered pasa_asmbl_23129.p1, internal, 83918, 84088
-recovered pasa_asmbl_23129.p1, internal, 84338, 84471
-recovered pasa_asmbl_23129.p1, internal, 84581, 84701
-recovered pasa_asmbl_23129.p1, internal, 85044, 85193
-recovered pasa_asmbl_23129.p1, internal, 85289, 85449
-recovered pasa_asmbl_23129.p1, internal, 85549, 85731
-recovered pasa_asmbl_23129.p1, internal, 85877, 86021
-recovered pasa_asmbl_23129.p1, internal, 86399, 86659
Valid prediction for pasa_asmbl_23132.p1
Valid prediction for snap_scaffold_2-snap.1134-T1
Couldn't classify 186690, 186767
Couldn't classify 186997, 187413
Sorry, prediction pasa_asmbl_23120.p1 fails validation.
(AAA)	 TG	186690-186767	GT	CGG
(GTG)	 AG	186997-187413	CT	GCC
Valid prediction for GlimmerHMM_glimmerT_3750-T1
Valid prediction for CodingQuarry_transcript_28549-T1
Valid prediction for GlimmerHMM_glimmerT_3756-T1
Valid prediction for GlimmerHMM_glimmerT_3763-T1
Valid prediction for GlimmerHMM_glimmerT_3773-T1
Valid prediction for Augustus_model.g2510.t1
Valid prediction for Augustus_model.g2507.t1
Valid prediction for snap_scaffold_2-snap.1148-T1
Valid prediction for snap_scaffold_2-snap.1131-T1
Valid prediction for CodingQuarry_transcript_28550-T1
Valid prediction for snap_scaffold_2-snap.1135-T1
Valid prediction for Augustus_model.g2520.t1
Valid prediction for GlimmerHMM_glimmerT_3781-T1
Valid prediction for GlimmerHMM_glimmerT_3757-T1
Couldn't classify 69250, 69273
Sorry, prediction pasa_asmbl_23131.p1 fails validation.
(ATG)	 CC	63602-63699	GT	TGG
(GAA)	 AG	64165-64314	GT	CAG
(GTC)	 AG	64484-64562	GT	TGG
(GGG)	 AG	64749-64772	GT	AGG
(CAA)	 AG	64943-64996	GT	AGG
(ATC)	 AG	67700-67852	GT	AGG
(AAC)	 AG	68254-68317	GT	GGG
(GCT)	 AG	68489-68532	GT	AGG
(ATC)	 AG	69004-69129	GT	AGG
(GTG)	 AG	69250-69273	AA	CCA
-recovered pasa_asmbl_23131.p1, initial, 63602, 63699
-recovered pasa_asmbl_23131.p1, internal, 64165, 64314
-recovered pasa_asmbl_23131.p1, internal, 64484, 64562
-recovered pasa_asmbl_23131.p1, internal, 64749, 64772
-recovered pasa_asmbl_23131.p1, internal, 64943, 64996
-recovered pasa_asmbl_23131.p1, internal, 67700, 67852
-recovered pasa_asmbl_23131.p1, internal, 68254, 68317
-recovered pasa_asmbl_23131.p1, internal, 68489, 68532
-recovered pasa_asmbl_23131.p1, internal, 69004, 69129
Valid prediction for Augustus_model.g2515.t1
Valid prediction for snap_scaffold_2-snap.1143-T1
Valid prediction for snap_scaffold_2-snap.1166-T1
Valid prediction for GlimmerHMM_glimmerT_3755-T1
Valid prediction for snap_scaffold_2-snap.1126-T1
Valid prediction for GlimmerHMM_glimmerT_3768-T1
Valid prediction for snap_scaffold_2-snap.1156-T1
Valid prediction for GlimmerHMM_glimmerT_3779-T1
Valid prediction for snap_scaffold_2-snap.1146-T1
Valid prediction for GlimmerHMM_glimmerT_3761-T1
Valid prediction for snap_scaffold_2-snap.1139-T1
Valid prediction for GlimmerHMM_glimmerT_3767-T1
Valid prediction for snap_scaffold_2-snap.1120-T1
Valid prediction for snap_scaffold_2-snap.1123-T1
Valid prediction for CodingQuarry_transcript_28548-T1
Valid prediction for snap_scaffold_2-snap.1150-T1
Valid prediction for snap_scaffold_2-snap.1153-T1
Couldn't classify 187537, 188214
Couldn't classify 189555, 189938
Sorry, prediction pasa_asmbl_23119.p1 fails validation.
(GCA)	 AG	187537-188214	GT	AGG
(GGT)	 AG	189295-189381	GT	AGG
(CTG)	 AG	189555-189938	GT	TGG
-recovered pasa_asmbl_23119.p1, internal, 187537, 188214
-recovered pasa_asmbl_23119.p1, internal, 189295, 189381
-recovered pasa_asmbl_23119.p1, internal, 189555, 189938
Valid prediction for Augustus_model.g2522.t1
Valid prediction for snap_scaffold_2-snap.1142-T1
Valid prediction for Augustus_model.g2519.t1
Valid prediction for GlimmerHMM_glimmerT_3764-T1
Valid prediction for GlimmerHMM_glimmerT_3748-T1
Valid prediction for GlimmerHMM_glimmerT_3776-T1
Valid prediction for Augustus_model.g2512.t1
Valid prediction for Augustus_model.g2526.t1
Valid prediction for GlimmerHMM_glimmerT_3771-T1
Valid prediction for GlimmerHMM_glimmerT_3759-T1
Valid prediction for snap_scaffold_2-snap.1133-T1
Valid prediction for snap_scaffold_2-snap.1163-T1
Valid prediction for HiQ_model.g2518.t1
Valid prediction for Augustus_model.g2509.t1
Valid prediction for snap_scaffold_2-snap.1160-T1
Valid prediction for GlimmerHMM_glimmerT_3754-T1
Valid prediction for Augustus_model.g2516.t1
Valid prediction for GlimmerHMM_glimmerT_3774-T1
Valid prediction for snap_scaffold_2-snap.1136-T1
Valid prediction for GlimmerHMM_glimmerT_3752-T1
Valid prediction for Augustus_model.g2513.t1
Valid prediction for GlimmerHMM_glimmerT_3760-T1
Valid prediction for GlimmerHMM_glimmerT_3782-T1
Valid prediction for snap_scaffold_2-snap.1144-T1
Valid prediction for snap_scaffold_2-snap.1130-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8482, rend_intergenic: 2414  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 8833, rend_intergenic: 8493  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21385, rend_intergenic: 10099  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32503, rend_intergenic: 27372  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39313, rend_intergenic: 33708  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48360, rend_intergenic: 43442  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76321, rend_intergenic: 48581  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83128, rend_intergenic: 76593  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84848, rend_intergenic: 83695  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88189, rend_intergenic: 84851  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98331, rend_intergenic: 89688  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104720, rend_intergenic: 99873  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110567, rend_intergenic: 105096  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122365, rend_intergenic: 117516  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128042, rend_intergenic: 122757  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131455, rend_intergenic: 128197  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144830, rend_intergenic: 134814  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145302, rend_intergenic: 145180  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151558, rend_intergenic: 145943  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184960, rend_intergenic: 154524  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194433, rend_intergenic: 185623  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 218139, rend_intergenic: 208693  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 222546, rend_intergenic: 221846  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 232156, rend_intergenic: 223734  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 233639
-exon list size: 575


building trellis

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83.2    
83.4    
83.5    
83.7    
83.9    
84.1    
84.2    
84.4    
84.6    
84.7    
84.9    
85.1    
85.3    
85.4    
85.6    
85.8    
86.0    
86.1    
86.3    
86.5    
86.7    
86.8    
87.0    
87.2    
87.3    
87.5    
87.7    
87.9    
88.0    
88.2    
88.4    
88.6    
88.7    
88.9    
89.1    
89.3    
89.4    
89.6    
89.8    
89.9    
90.1    
90.3    
90.5    
90.6    
90.8    
91.0    
91.2    
91.3    
91.5    
91.7    
91.9    
92.0    
92.2    
92.4    
92.5    
92.7    
92.9    
93.1    
93.2    
93.4    
93.6    
93.8    
93.9    
94.1    
94.3    
94.5    
94.6    
94.8    
95.0    
95.1    
95.3    
95.5    
95.7    
95.8    
96.0    
96.2    
96.4    
96.5    
96.7    
96.9    
97.1    
97.2    
97.4    
97.6    
97.7    
97.9    
98.1    
98.3    
98.4    
98.6    
98.8    
99.0    
99.1    
99.3    
99.5    
99.7    
99.8    
-found 37 predictions from path traversal
Error with prediction: snap lend_intergenic: 8482, rend_intergenic: 2414  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 8833, rend_intergenic: 8493  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21385, rend_intergenic: 10099  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32503, rend_intergenic: 27372  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39313, rend_intergenic: 33708  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48360, rend_intergenic: 43442  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76321, rend_intergenic: 48581  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83128, rend_intergenic: 76593  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84848, rend_intergenic: 83695  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88189, rend_intergenic: 84851  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98331, rend_intergenic: 89688  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104720, rend_intergenic: 99873  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110567, rend_intergenic: 105096  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122365, rend_intergenic: 117516  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128042, rend_intergenic: 122757  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131455, rend_intergenic: 128197  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144830, rend_intergenic: 134814  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145302, rend_intergenic: 145180  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151558, rend_intergenic: 145943  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184960, rend_intergenic: 154524  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194433, rend_intergenic: 185623  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 218139, rend_intergenic: 208693  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 222546, rend_intergenic: 221846  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 232156, rend_intergenic: 223734  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support