-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_4/scaffold_4_5420816-5670803

-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.1217-T1
Valid prediction for Augustus_model.g6066.t1
Valid prediction for GlimmerHMM_glimmerT_9391-T1
Valid prediction for Augustus_model.g6059.t1
Valid prediction for snap_scaffold_4-snap.1221-T1
Valid prediction for snap_scaffold_4-snap.1218-T1
Couldn't classify 1344, 1405
Couldn't classify 2130, 2160
Sorry, prediction pasa_asmbl_42212.p2 fails validation.
(TGG)	 TG	1344-1405	GT	AGG
(AGA)	 AG	1582-1706	GT	GGG
(GAG)	 AG	1843-1960	GT	CAG
(AGT)	 AG	2130-2160	AA	AGA
-recovered pasa_asmbl_42212.p2, internal, 1582, 1706
-recovered pasa_asmbl_42212.p2, internal, 1843, 1960
Valid prediction for GlimmerHMM_glimmerT_9392-T1
Valid prediction for CodingQuarry_transcript_48997-T1
Couldn't classify 6308, 6368
Sorry, prediction pasa_asmbl_41346.p1 fails validation.
(AGC)	 GC	6308-6368	GT	CGG
(ACG)	 AG	6463-6557	GT	AGG
(GGT)	 AG	6780-6896	GT	AGG
(GAT)	 AG	7021-7182	GT	AGG
(GAG)	 AG	7616-7764	GT	AGG
(TCT)	 AG	7899-8034	GT	AGG
(GTA)	 AG	8192-8299	GA	GAG
-recovered pasa_asmbl_41346.p1, terminal, 8192, 8299
-recovered pasa_asmbl_41346.p1, internal, 6463, 6557
-recovered pasa_asmbl_41346.p1, internal, 6780, 6896
-recovered pasa_asmbl_41346.p1, internal, 7021, 7182
-recovered pasa_asmbl_41346.p1, internal, 7616, 7764
-recovered pasa_asmbl_41346.p1, internal, 7899, 8034
Valid prediction for Augustus_model.g6072.t1
Valid prediction for snap_scaffold_4-snap.1228-T1
Valid prediction for CodingQuarry_transcript_48998-T1
Valid prediction for GlimmerHMM_glimmerT_9409-T1
Valid prediction for snap_scaffold_4-snap.1209-T1
Couldn't classify 45634, 46050
Sorry, prediction pasa_asmbl_41348.p1 fails validation.
(CAA)	 AC	45634-46050	GA	AAG
Couldn't classify 48616, 48629
Sorry, prediction pasa_asmbl_41350.p1 fails validation.
(GCA)	 CA	48616-48629	GT	AGG
(GAT)	 AG	49164-49246	GT	GGG
(CGC)	 AG	49344-49396	GT	CAG
(ATC)	 AG	49480-49555	GT	AGG
(TCC)	 AG	49706-49812	GT	CGG
(AGG)	 AG	49970-50038	GT	GAG
-recovered pasa_asmbl_41350.p1, terminal, 49970, 50038
-recovered pasa_asmbl_41350.p1, internal, 49164, 49246
-recovered pasa_asmbl_41350.p1, internal, 49344, 49396
-recovered pasa_asmbl_41350.p1, internal, 49480, 49555
-recovered pasa_asmbl_41350.p1, internal, 49706, 49812
-recovered pasa_asmbl_41350.p1, internal, 49970, 50038
Valid prediction for GlimmerHMM_glimmerT_9401-T1
Valid prediction for GlimmerHMM_glimmerT_9413-T1
Couldn't classify 19151, 19212
Sorry, prediction pasa_asmbl_41347.p1 fails validation.
(GCC)	 TG	19151-19212	GT	TGG
(CTG)	 AG	19477-19628	GT	AGG
(GAA)	 AG	20039-20352	GA	AAG
-recovered pasa_asmbl_41347.p1, terminal, 20039, 20352
-recovered pasa_asmbl_41347.p1, internal, 19477, 19628
Valid prediction for GlimmerHMM_glimmerT_9416-T1
Valid prediction for snap_scaffold_4-snap.1225-T1
Valid prediction for GlimmerHMM_glimmerT_9410-T1
Valid prediction for snap_scaffold_4-snap.1238-T1
Couldn't classify 54961, 54973
Sorry, prediction pasa_asmbl_41355.p1 fails validation.
(TCG)	 CC	54961-54973	GT	AGG
(GCC)	 AG	55154-55363	GT	AGG
(GAC)	 AG	55466-55612	GT	AGG
(CTG)	 AG	55996-56144	TA	AGT
-recovered pasa_asmbl_41355.p1, terminal, 55996, 56144
-recovered pasa_asmbl_41355.p1, internal, 55154, 55363
-recovered pasa_asmbl_41355.p1, internal, 55466, 55612
Valid prediction for pasa_asmbl_41359.p1
Valid prediction for pasa_asmbl_41356.p1
Valid prediction for GlimmerHMM_glimmerT_9411-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_9397-T1
Valid prediction for Augustus_model.g6073.t1
Valid prediction for snap_scaffold_4-snap.1240-T1
Valid prediction for Augustus_model.g6056.t1
Valid prediction for GlimmerHMM_glimmerT_9405-T1
Valid prediction for GlimmerHMM_glimmerT_9403-T1
Valid prediction for snap_scaffold_4-snap.1212-T1
Valid prediction for GlimmerHMM_glimmerT_9394-T1
Couldn't classify 46213, 47334
Sorry, prediction pasa_asmbl_41349.p1 fails validation.
(GAG)	 AT	46213-47334	AC	AAA
Valid prediction for Augustus_model.g6081.t1
Valid prediction for HiQ_model.g6058.t1
Valid prediction for Augustus_model.g6077.t1
Valid prediction for snap_scaffold_4-snap.1203-T1
Valid prediction for snap_scaffold_4-snap.1204-T1
Valid prediction for Augustus_model.g6064.t1
Valid prediction for snap_scaffold_4-snap.1233-T1
Valid prediction for snap_scaffold_4-snap.1213-T1
Valid prediction for Augustus_model.g6065.t1
Valid prediction for CodingQuarry_transcript_48996-T1
Valid prediction for GlimmerHMM_glimmerT_9398-T1
Valid prediction for snap_scaffold_4-snap.1222-T1
Valid prediction for HiQ_model.g6062.t1
Valid prediction for GlimmerHMM_glimmerT_9399-T1
Valid prediction for pasa_asmbl_41357.p1
Valid prediction for snap_scaffold_4-snap.1234-T1
Valid prediction for GlimmerHMM_glimmerT_9389-T1
Valid prediction for GlimmerHMM_glimmerT_9407-T1
Valid prediction for snap_scaffold_4-snap.1215-T1
Valid prediction for snap_scaffold_4-snap.1210-T1
Valid prediction for HiQ_model.g6060.t1
Valid prediction for snap_scaffold_4-snap.1231-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 snap_scaffold_4-snap.1214-T1
Valid prediction for HiQ_model.g6079.t1
Valid prediction for GlimmerHMM_glimmerT_9402-T1
Valid prediction for GlimmerHMM_glimmerT_9406-T1
Valid prediction for snap_scaffold_4-snap.1223-T1
Valid prediction for snap_scaffold_4-snap.1226-T1
Valid prediction for GlimmerHMM_glimmerT_9393-T1
Valid prediction for snap_scaffold_4-snap.1232-T1
Valid prediction for Augustus_model.g6067.t1
Valid prediction for Augustus_model.g6078.t1
Valid prediction for Augustus_model.g6080.t1
Valid prediction for snap_scaffold_4-snap.1206-T1
Valid prediction for snap_scaffold_4-snap.1220-T1
Valid prediction for Augustus_model.g6076.t1
Valid prediction for Augustus_model.g6061.t1
Valid prediction for snap_scaffold_4-snap.1219-T1
Valid prediction for snap_scaffold_4-snap.1227-T1
Valid prediction for GlimmerHMM_glimmerT_9390-T1
Valid prediction for snap_scaffold_4-snap.1230-T1
Valid prediction for snap_scaffold_4-snap.1241-T1
Valid prediction for Augustus_model.g6063.t1
Valid prediction for GlimmerHMM_glimmerT_9395-T1
Valid prediction for snap_scaffold_4-snap.1208-T1
Valid prediction for Augustus_model.g6075.t1
Valid prediction for Augustus_model.g6074.t1
Valid prediction for GlimmerHMM_glimmerT_9414-T1
Valid prediction for snap_scaffold_4-snap.1224-T1
Valid prediction for snap_scaffold_4-snap.1229-T1
Valid prediction for snap_scaffold_4-snap.1237-T1
Valid prediction for snap_scaffold_4-snap.1205-T1
Valid prediction for Augustus_model.g6068.t1
Valid prediction for GlimmerHMM_glimmerT_9408-T1
Valid prediction for GlimmerHMM_glimmerT_9404-T1
Valid prediction for Augustus_model.g6069.t1
Valid prediction for CodingQuarry_transcript_48995-T1
Couldn't classify 218823, 219023
Sorry, prediction pasa_asmbl_42606.p1 fails validation.
(CCA)	 GC	218823-219023	GT	AGG
(GTG)	 AG	219051-219290	GT	AGG
(GAG)	 AG	219415-219463	GT	TGG
(ATC)	 AG	219540-219879	GT	CGG
(ATT)	 AG	220924-221650	GT	AGG
(TGC)	 AG	221820-221954	GT	AGG
(GAG)	 AG	222345-222481	GT	AGG
(GCA)	 AG	223045-223156	GT	AGG
(TTC)	 AG	224567-224641	GT	AGG
(ATG)	 AG	224765-224866	GT	AGG
(CTA)	 AG	225562-225723	TC	AGT
-recovered pasa_asmbl_42606.p1, initial, 224765, 224866
-recovered pasa_asmbl_42606.p1, terminal, 225562, 225723
-recovered pasa_asmbl_42606.p1, internal, 219051, 219290
-recovered pasa_asmbl_42606.p1, internal, 219415, 219463
-recovered pasa_asmbl_42606.p1, internal, 219540, 219879
-recovered pasa_asmbl_42606.p1, internal, 220924, 221650
-recovered pasa_asmbl_42606.p1, internal, 221820, 221954
-recovered pasa_asmbl_42606.p1, internal, 222345, 222481
-recovered pasa_asmbl_42606.p1, internal, 223045, 223156
-recovered pasa_asmbl_42606.p1, internal, 224567, 224641
-recovered pasa_asmbl_42606.p1, internal, 224765, 224866
Valid prediction for CodingQuarry_transcript_49002-T1
Couldn't classify 215362, 215489
Couldn't classify 217653, 218690
Sorry, prediction pasa_asmbl_42607.p1 fails validation.
(TCA)	 GC	215362-215489	GT	CCG
(GAA)	 AG	215647-215770	GT	AGG
(ATC)	 AG	215899-215976	GT	AGG
(TGG)	 AG	216147-216244	GT	GGG
(CAA)	 AG	216377-216521	GT	CGG
(GTG)	 AG	217059-217193	GT	AAG
(GAT)	 AG	217357-217485	GT	AGG
(ATC)	 AG	217653-218690	CT	ACC
-recovered pasa_asmbl_42607.p1, internal, 215647, 215770
-recovered pasa_asmbl_42607.p1, internal, 215899, 215976
-recovered pasa_asmbl_42607.p1, internal, 216147, 216244
-recovered pasa_asmbl_42607.p1, internal, 216377, 216521
-recovered pasa_asmbl_42607.p1, internal, 217059, 217193
-recovered pasa_asmbl_42607.p1, internal, 217357, 217485
Valid prediction for Augustus_model.g6082.t1
Valid prediction for CodingQuarry_transcript_49003-T1
Valid prediction for GlimmerHMM_glimmerT_9400-T1
Valid prediction for GlimmerHMM_glimmerT_9415-T1
Valid prediction for snap_scaffold_4-snap.1211-T1
Valid prediction for snap_scaffold_4-snap.1239-T1
Couldn't classify 184653, 184801
Couldn't classify 185530, 185607
Sorry, prediction pasa_asmbl_43562.p1 fails validation.
(GAC)	 CA	184653-184801	GT	GGG
(ACA)	 AG	185158-185221	GT	GAG
(ATC)	 AG	185337-185420	GT	AGG
(GGT)	 AG	185530-185607	AA	GTA
-recovered pasa_asmbl_43562.p1, internal, 185158, 185221
-recovered pasa_asmbl_43562.p1, internal, 185337, 185420
Valid prediction for HiQ_model.g6070.t1
Valid prediction for snap_scaffold_4-snap.1235-T1
Valid prediction for CodingQuarry_transcript_49004-T1
Valid prediction for snap_scaffold_4-snap.1207-T1
Valid prediction for pasa_asmbl_42610.p1
Valid prediction for Augustus_model.g6071.t1
Valid prediction for pasa_asmbl_42627.p1
Valid prediction for pasa_asmbl_42631.p1
Valid prediction for GlimmerHMM_glimmerT_9412-T1
Valid prediction for Augustus_model.g6057.t1
Couldn't classify 90283, 90345
Sorry, prediction pasa_asmbl_42612.p1 fails validation.
(AAT)	 AG	90283-90345	GT	AGG
(GCC)	 AG	90526-90586	GT	AGG
(ACG)	 AG	90796-90993	GT	CAG
(CTG)	 AG	91248-91303	GT	AAG
-recovered pasa_asmbl_42612.p1, terminal, 91248, 91303
-recovered pasa_asmbl_42612.p1, internal, 90283, 90345
-recovered pasa_asmbl_42612.p1, internal, 90526, 90586
-recovered pasa_asmbl_42612.p1, internal, 90796, 90993
-recovered pasa_asmbl_42612.p1, internal, 91248, 91303
Valid prediction for GlimmerHMM_glimmerT_9396-T1
Couldn't classify 211192, 211509
Sorry, prediction pasa_asmbl_43560.p1 fails validation.
(CTA)	 CA	211192-211509	AA	AGA
Valid prediction for snap_scaffold_4-snap.1236-T1
Valid prediction for GlimmerHMM_glimmerT_9417-T1
Valid prediction for CodingQuarry_transcript_49000-T1
Valid prediction for snap_scaffold_4-snap.1216-T1
Valid prediction for CodingQuarry_transcript_49001-T1
Couldn't classify 63747, 64742
Sorry, prediction pasa_asmbl_42615.p1 fails validation.
(GGG)	 TG	63747-64742	TG	AGT

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 224566, rend_intergenic: 224563  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98683, rend_intergenic: 94584  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131288, rend_intergenic: 109662  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138541, rend_intergenic: 131882  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147981, rend_intergenic: 141892  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166382, rend_intergenic: 161509  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175044, rend_intergenic: 168776  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188108, rend_intergenic: 184218  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198459, rend_intergenic: 191067  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 208861, rend_intergenic: 199704  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 233664, rend_intergenic: 229349  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 249988
-exon list size: 443


building trellis

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-found 33 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 224566, rend_intergenic: 224563  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98683, rend_intergenic: 94584  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131288, rend_intergenic: 109662  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138541, rend_intergenic: 131882  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147981, rend_intergenic: 141892  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166382, rend_intergenic: 161509  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175044, rend_intergenic: 168776  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188108, rend_intergenic: 184218  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198459, rend_intergenic: 191067  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 208861, rend_intergenic: 199704  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 233664, rend_intergenic: 229349  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 31 predictions persist after filtering for low support