-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_27/scaffold_27_4916078-5126704

-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 CodingQuarry_transcript_41892-T1
Valid prediction for snap_scaffold_27-snap.1186-T1
Valid prediction for snap_scaffold_27-snap.1183-T1
Valid prediction for CodingQuarry_transcript_41889-T1
Valid prediction for snap_scaffold_27-snap.1170-T1
Valid prediction for GlimmerHMM_glimmerT_57273-T1
Valid prediction for Augustus_model.g37961.t1
Valid prediction for pasa_asmbl_36325.p1
Couldn't classify 44432, 44740
Sorry, prediction pasa_asmbl_36331.p1 fails validation.
(ATG)	 AA	41603-41608	GT	AGG
(GAA)	 AG	41934-42081	GT	GAG
(TCG)	 AG	42924-42976	GT	GGG
(GTG)	 AG	43247-43344	GT	AGG
(GCT)	 AG	43869-44055	GT	CTG
(GAG)	 AG	44432-44740	GC	AGG
-recovered pasa_asmbl_36331.p1, initial, 41603, 41608
-recovered pasa_asmbl_36331.p1, internal, 41934, 42081
-recovered pasa_asmbl_36331.p1, internal, 42924, 42976
-recovered pasa_asmbl_36331.p1, internal, 43247, 43344
-recovered pasa_asmbl_36331.p1, internal, 43869, 44055
-recovered pasa_asmbl_36331.p1, internal, 44432, 44740
Valid prediction for snap_scaffold_27-snap.1152-T1
Valid prediction for GlimmerHMM_glimmerT_57269-T1
Valid prediction for snap_scaffold_27-snap.1173-T1
Valid prediction for snap_scaffold_27-snap.1162-T1
Valid prediction for CodingQuarry_transcript_41891-T1
Valid prediction for snap_scaffold_27-snap.1157-T1
Valid prediction for pasa_asmbl_36339.p1
Valid prediction for snap_scaffold_27-snap.1171-T1
Valid prediction for snap_scaffold_27-snap.1179-T1
Valid prediction for snap_scaffold_27-snap.1168-T1
Valid prediction for HiQ_model.g37970.t1
Valid prediction for HiQ_model.g37974.t1
Valid prediction for HiQ_model.g37960.t1
Valid prediction for Augustus_model.g37965.t1
Couldn't classify 101638, 101757
Sorry, prediction pasa_asmbl_36335.p2 fails validation.
(ATG)	 AG	99242-99283	GT	AGG
(CGC)	 AG	99451-99602	GT	AGG
(GAA)	 AG	99774-99831	GT	TAG
(GCG)	 AG	100965-101021	GT	AGG
(GAA)	 AG	101638-101757	GG	CTG
-recovered pasa_asmbl_36335.p2, initial, 99242, 99283
-recovered pasa_asmbl_36335.p2, internal, 99242, 99283
-recovered pasa_asmbl_36335.p2, internal, 99451, 99602
-recovered pasa_asmbl_36335.p2, internal, 99774, 99831
-recovered pasa_asmbl_36335.p2, internal, 100965, 101021
Valid prediction for Augustus_model.g37973.t1
Valid prediction for snap_scaffold_27-snap.1175-T1
Valid prediction for snap_scaffold_27-snap.1187-T1
Valid prediction for pasa_asmbl_36340.p1
Valid prediction for Augustus_model.g37972.t1
Valid prediction for snap_scaffold_27-snap.1160-T1
Valid prediction for snap_scaffold_27-snap.1147-T1
Valid prediction for snap_scaffold_27-snap.1192-T1
Valid prediction for snap_scaffold_27-snap.1165-T1
Valid prediction for GlimmerHMM_glimmerT_57281-T1
Valid prediction for GlimmerHMM_glimmerT_57274-T1
Valid prediction for GlimmerHMM_glimmerT_57271-T1
Valid prediction for snap_scaffold_27-snap.1158-T1
Valid prediction for snap_scaffold_27-snap.1151-T1
Valid prediction for snap_scaffold_27-snap.1181-T1
Valid prediction for snap_scaffold_27-snap.1191-T1
Valid prediction for GlimmerHMM_glimmerT_57268-T1
Valid prediction for CodingQuarry_transcript_41888-T1
Couldn't classify 108140, 108595
Sorry, prediction pasa_asmbl_36337.p1 fails validation.
(GGC)	 CA	108140-108595	GT	AGG
(GCC)	 AG	109025-109112	GT	AGG
(AGA)	 AG	109265-109317	AC	AGA
-recovered pasa_asmbl_36337.p1, terminal, 109265, 109317
-recovered pasa_asmbl_36337.p1, internal, 109025, 109112
Valid prediction for snap_scaffold_27-snap.1149-T1
Valid prediction for GlimmerHMM_glimmerT_57278-T1
Valid prediction for GlimmerHMM_glimmerT_57276-T1
Couldn't classify 44834, 45807
Sorry, prediction pasa_asmbl_36332.p1 fails validation.
(GAT)	 TG	44834-45807	GT	GAG
(GAG)	 AG	45839-45911	CA	GAC
-recovered pasa_asmbl_36332.p1, terminal, 45839, 45911
Valid prediction for snap_scaffold_27-snap.1155-T1
Couldn't classify 93545, 93581
Couldn't classify 97834, 97971
Sorry, prediction pasa_asmbl_36595.p1 fails validation.
(GGA)	 AG	93545-93581	GT	AGG
(ATG)	 AG	94689-94801	GT	GGG
(GTA)	 AG	95609-95683	GT	AGG
(GGA)	 AG	97834-97971	GA	GGG
add_exon() Sorry, pasa_asmbl_36595.p1 94689-94801-initial-1 is invalid.
-recovered pasa_asmbl_36595.p1, initial, 94689, 94801
-recovered pasa_asmbl_36595.p1, internal, 93545, 93581
-recovered pasa_asmbl_36595.p1, internal, 94689, 94801
-recovered pasa_asmbl_36595.p1, internal, 95609, 95683
Valid prediction for snap_scaffold_27-snap.1177-T1
Valid prediction for GlimmerHMM_glimmerT_57285-T1
Valid prediction for snap_scaffold_27-snap.1144-T1
Valid prediction for GlimmerHMM_glimmerT_57267-T1
Valid prediction for snap_scaffold_27-snap.1164-T1
Valid prediction for GlimmerHMM_glimmerT_57283-T1
Valid prediction for Augustus_model.g37963.t1
Valid prediction for CodingQuarry_transcript_41887-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_27-snap.1189-T1
Couldn't classify 65316, 65405
Sorry, prediction pasa_asmbl_36984.p1 fails validation.
(TGC)	 TC	65316-65405	GT	AGG
(GTG)	 AG	66161-66301	GT	TAG
(GTG)	 AG	66886-67076	GT	CGG
(GGA)	 AG	68615-68652	GT	CGG
(GCC)	 AG	70343-70432	GT	GGG
(CTC)	 AG	70745-70953	GT	TGG
(CTG)	 AG	71174-71311	GT	ATG
(CCT)	 AG	71889-72026	GT	AGG
(ATG)	 AG	72398-72532	GT	AGG
(GAC)	 AG	72975-73025	CG	GAC
-recovered pasa_asmbl_36984.p1, initial, 72398, 72532
-recovered pasa_asmbl_36984.p1, terminal, 72975, 73025
-recovered pasa_asmbl_36984.p1, internal, 66161, 66301
-recovered pasa_asmbl_36984.p1, internal, 66886, 67076
-recovered pasa_asmbl_36984.p1, internal, 68615, 68652
-recovered pasa_asmbl_36984.p1, internal, 70343, 70432
-recovered pasa_asmbl_36984.p1, internal, 70745, 70953
-recovered pasa_asmbl_36984.p1, internal, 71174, 71311
-recovered pasa_asmbl_36984.p1, internal, 71889, 72026
-recovered pasa_asmbl_36984.p1, internal, 72398, 72532
Valid prediction for snap_scaffold_27-snap.1153-T1
Valid prediction for snap_scaffold_27-snap.1148-T1
Valid prediction for GlimmerHMM_glimmerT_57284-T1
Valid prediction for snap_scaffold_27-snap.1185-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_27-snap.1166-T1
Valid prediction for snap_scaffold_27-snap.1145-T1
Valid prediction for snap_scaffold_27-snap.1146-T1
Valid prediction for snap_scaffold_27-snap.1163-T1
Valid prediction for snap_scaffold_27-snap.1174-T1
Valid prediction for Augustus_model.g37968.t1
Valid prediction for CodingQuarry_transcript_41890-T1
Valid prediction for GlimmerHMM_glimmerT_57270-T1
Valid prediction for snap_scaffold_27-snap.1154-T1
Valid prediction for GlimmerHMM_glimmerT_57275-T1
Valid prediction for snap_scaffold_27-snap.1176-T1
Couldn't classify 188964, 189000
Couldn't classify 191558, 191697
Sorry, prediction pasa_asmbl_36979.p1 fails validation.
(GGA)	 AT	188964-189000	GT	GGG
(TCA)	 AG	189528-189631	GT	AGG
(AGC)	 AG	190817-190912	GT	GCG
(GCC)	 AG	191154-191301	GT	AGG
(CAG)	 AG	191558-191697	AT	CCA
-recovered pasa_asmbl_36979.p1, internal, 189528, 189631
-recovered pasa_asmbl_36979.p1, internal, 190817, 190912
-recovered pasa_asmbl_36979.p1, internal, 191154, 191301
Valid prediction for Augustus_model.g37964.t1
Valid prediction for snap_scaffold_27-snap.1159-T1
Valid prediction for snap_scaffold_27-snap.1188-T1
Valid prediction for GlimmerHMM_glimmerT_57280-T1
Valid prediction for GlimmerHMM_glimmerT_57282-T1
Valid prediction for Augustus_model.g37969.t1
Couldn't classify 60642, 60758
Couldn't classify 65342, 65396
Sorry, prediction pasa_asmbl_36986.p1 fails validation.
(ACA)	 CC	60642-60758	GT	TGG
(GCG)	 AG	61933-62010	GT	AGG
(TCT)	 AG	62203-62300	GT	AAG
(GTT)	 AG	63698-63790	GT	AGG
(ACA)	 AG	65342-65396	TT	GTT
-recovered pasa_asmbl_36986.p1, internal, 61933, 62010
-recovered pasa_asmbl_36986.p1, internal, 62203, 62300
-recovered pasa_asmbl_36986.p1, internal, 63698, 63790
Valid prediction for GlimmerHMM_glimmerT_57263-T1
Valid prediction for GlimmerHMM_glimmerT_57265-T1
Valid prediction for snap_scaffold_27-snap.1190-T1
Valid prediction for snap_scaffold_27-snap.1182-T1
Valid prediction for GlimmerHMM_glimmerT_57266-T1
Valid prediction for GlimmerHMM_glimmerT_57277-T1
Valid prediction for snap_scaffold_27-snap.1172-T1
Valid prediction for Augustus_model.g37966.t1
Valid prediction for GlimmerHMM_glimmerT_57279-T1
Valid prediction for GlimmerHMM_glimmerT_57272-T1
Valid prediction for Augustus_model.g37962.t1
Valid prediction for snap_scaffold_27-snap.1184-T1
Valid prediction for Augustus_model.g37967.t1
Valid prediction for Augustus_model.g37971.t1
Valid prediction for snap_scaffold_27-snap.1193-T1
Valid prediction for snap_scaffold_27-snap.1167-T1
Valid prediction for GlimmerHMM_glimmerT_57264-T1
Valid prediction for snap_scaffold_27-snap.1178-T1
Valid prediction for snap_scaffold_27-snap.1156-T1
Valid prediction for Augustus_model.g37959.t1
Valid prediction for snap_scaffold_27-snap.1180-T1
Valid prediction for snap_scaffold_27-snap.1150-T1
Valid prediction for snap_scaffold_27-snap.1161-T1
Valid prediction for snap_scaffold_27-snap.1169-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14012, rend_intergenic: 2129  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20679, rend_intergenic: 17949  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30331, rend_intergenic: 23470  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40858, rend_intergenic: 36786  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46504, rend_intergenic: 42494  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51637, rend_intergenic: 48197  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66541, rend_intergenic: 54367  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73785, rend_intergenic: 67168  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79653, rend_intergenic: 76740  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92693, rend_intergenic: 79914  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109317, rend_intergenic: 93490  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120306, rend_intergenic: 113041  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125478, rend_intergenic: 124044  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133023, rend_intergenic: 126478  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139027, rend_intergenic: 137603  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140533, rend_intergenic: 139324  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144550, rend_intergenic: 141594  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154974, rend_intergenic: 145896  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161290, rend_intergenic: 155357  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180241, rend_intergenic: 174457  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196378, rend_intergenic: 180341  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200619, rend_intergenic: 198112  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 208770, rend_intergenic: 203056  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 210627
-exon list size: 431


building trellis

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-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 14012, rend_intergenic: 2129  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20679, rend_intergenic: 17949  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30331, rend_intergenic: 23470  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40858, rend_intergenic: 36786  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46504, rend_intergenic: 42494  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51637, rend_intergenic: 48197  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66541, rend_intergenic: 54367  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73785, rend_intergenic: 67168  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79653, rend_intergenic: 76740  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92693, rend_intergenic: 79914  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109317, rend_intergenic: 93490  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120306, rend_intergenic: 113041  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125478, rend_intergenic: 124044  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133023, rend_intergenic: 126478  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139027, rend_intergenic: 137603  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140533, rend_intergenic: 139324  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144550, rend_intergenic: 141594  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154974, rend_intergenic: 145896  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161290, rend_intergenic: 155357  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180241, rend_intergenic: 174457  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196378, rend_intergenic: 180341  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200619, rend_intergenic: 198112  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 208770, rend_intergenic: 203056  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support