-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_8/scaffold_8_6198894-6448467

-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 GeneMark_model.34779_t
Valid prediction for GeneMark_model.34755_t
Valid prediction for Augustus_model.g13581.t1
Couldn't classify 52904, 53994
Couldn't classify 56994, 57153
Sorry, prediction pasa_asmbl_51935.p1 fails validation.
(ATC)	 AC	52904-53994	GT	AGG
(GAC)	 AG	56994-57153	AA	TCA
Valid prediction for GeneMark_model.34774_t
Valid prediction for Augustus_model.g13596.t1
Valid prediction for GlimmerHMM_glimmerT_20306-T1
Valid prediction for snap_scaffold_8-snap.1283-T1
Valid prediction for snap_scaffold_8-snap.1259-T1
Valid prediction for GeneMark_model.34772_t
Valid prediction for GeneMark_model.34739_t
Valid prediction for snap_scaffold_8-snap.1255-T1
Valid prediction for snap_scaffold_8-snap.1263-T1
Valid prediction for GeneMark_model.34750_t
Valid prediction for GeneMark_model.34751_t
Valid prediction for snap_scaffold_8-snap.1248-T1
Couldn't classify 66923, 67134
Sorry, prediction pasa_asmbl_51938.p1 fails validation.
(GTA)	 CT	66923-67134	GT	AGG
(CAT)	 AG	67633-67805	GT	CTG
(CTC)	 AG	67910-68079	GT	AAG
-recovered pasa_asmbl_51938.p1, terminal, 67910, 68079
-recovered pasa_asmbl_51938.p1, internal, 67633, 67805
-recovered pasa_asmbl_51938.p1, internal, 67910, 68079
Valid prediction for snap_scaffold_8-snap.1267-T1
Valid prediction for GeneMark_model.34748_t
Valid prediction for Augustus_model.g13579.t1
Valid prediction for GeneMark_model.34771_t
Valid prediction for snap_scaffold_8-snap.1282-T1
Valid prediction for HiQ_model.g13587.t1
Valid prediction for CodingQuarry_transcript_59532-T1
Valid prediction for GeneMark_model.34762_t
Valid prediction for Augustus_model.g13588.t1
Couldn't classify 110188, 110458
Sorry, prediction pasa_asmbl_51946.p1 fails validation.
(GGA)	 GT	110188-110458	GT	TGG
(GAT)	 AG	110560-110663	GT	TGG
(GCC)	 AG	110836-110970	GT	AGG
(CCT)	 AG	111095-111285	GT	AGG
(GAG)	 AG	111401-111551	GA	GAG
-recovered pasa_asmbl_51946.p1, terminal, 111401, 111551
-recovered pasa_asmbl_51946.p1, internal, 110560, 110663
-recovered pasa_asmbl_51946.p1, internal, 110836, 110970
-recovered pasa_asmbl_51946.p1, internal, 111095, 111285
Valid prediction for snap_scaffold_8-snap.1257-T1
Valid prediction for GlimmerHMM_glimmerT_20318-T1
Valid prediction for Augustus_model.g13580.t1
Valid prediction for GeneMark_model.34735_t
Valid prediction for GeneMark_model.34763_t
Valid prediction for Augustus_model.g13583.t1
Valid prediction for GlimmerHMM_glimmerT_20301-T1
Valid prediction for snap_scaffold_8-snap.1288-T1
Valid prediction for GeneMark_model.34746_t
Valid prediction for GeneMark_model.34758_t
Valid prediction for GlimmerHMM_glimmerT_20311-T1
Valid prediction for snap_scaffold_8-snap.1252-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_20299-T1
Valid prediction for GlimmerHMM_glimmerT_20317-T1
Valid prediction for GeneMark_model.34759_t
Valid prediction for GeneMark_model.34741_t
Valid prediction for GeneMark_model.34769_t
Valid prediction for snap_scaffold_8-snap.1285-T1
Valid prediction for snap_scaffold_8-snap.1271-T1
Valid prediction for snap_scaffold_8-snap.1261-T1
Valid prediction for Augustus_model.g13595.t1
Valid prediction for GeneMark_model.34742_t
Valid prediction for snap_scaffold_8-snap.1268-T1
Valid prediction for snap_scaffold_8-snap.1260-T1
Valid prediction for GlimmerHMM_glimmerT_20307-T1
Valid prediction for snap_scaffold_8-snap.1249-T1
Couldn't classify 72182, 72238
Sorry, prediction pasa_asmbl_51941.p1 fails validation.
(GAT)	 TA	72182-72238	GT	GAG
(TCA)	 AG	72375-72501	GT	AGG
(TCC)	 AG	74224-75344	AT	AAA
-recovered pasa_asmbl_51941.p1, terminal, 74224, 75344
-recovered pasa_asmbl_51941.p1, internal, 72375, 72501
Valid prediction for GlimmerHMM_glimmerT_20304-T1
Valid prediction for GlimmerHMM_glimmerT_20302-T1
Valid prediction for pasa_asmbl_51945.p1
Valid prediction for snap_scaffold_8-snap.1272-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_8-snap.1280-T1
Valid prediction for snap_scaffold_8-snap.1281-T1
Valid prediction for snap_scaffold_8-snap.1274-T1
Valid prediction for GlimmerHMM_glimmerT_20310-T1
Valid prediction for pasa_asmbl_52870.p1
Valid prediction for GeneMark_model.34780_t
Valid prediction for GeneMark_model.34744_t
Valid prediction for snap_scaffold_8-snap.1250-T1
Valid prediction for Augustus_model.g13582.t1
Valid prediction for snap_scaffold_8-snap.1265-T1
Valid prediction for Augustus_model.g13598.t1
Valid prediction for GlimmerHMM_glimmerT_20321-T1
Valid prediction for GeneMark_model.34770_t
Valid prediction for snap_scaffold_8-snap.1253-T1
Valid prediction for Augustus_model.g13599.t1
Valid prediction for snap_scaffold_8-snap.1287-T1
Valid prediction for GeneMark_model.34775_t
Valid prediction for GeneMark_model.34733_t
Valid prediction for CodingQuarry_transcript_59534-T1
Valid prediction for GeneMark_model.34760_t
Valid prediction for pasa_asmbl_52874.p1
Valid prediction for Augustus_model.g13597.t1
Valid prediction for GeneMark_model.34743_t
Valid prediction for GlimmerHMM_glimmerT_20303-T1
Valid prediction for snap_scaffold_8-snap.1251-T1
Valid prediction for Augustus_model.g13584.t1
Valid prediction for snap_scaffold_8-snap.1277-T1
Valid prediction for GlimmerHMM_glimmerT_20315-T1
Valid prediction for GeneMark_model.34752_t
Valid prediction for GeneMark_model.34747_t
Valid prediction for snap_scaffold_8-snap.1247-T1
Valid prediction for GeneMark_model.34768_t
Valid prediction for snap_scaffold_8-snap.1262-T1
Valid prediction for GeneMark_model.34757_t
Valid prediction for snap_scaffold_8-snap.1270-T1
Valid prediction for snap_scaffold_8-snap.1273-T1
Valid prediction for GeneMark_model.34778_t
Valid prediction for Augustus_model.g13586.t1
Valid prediction for GeneMark_model.34754_t
Couldn't classify 61229, 61618
Sorry, prediction pasa_asmbl_52876.p1 fails validation.
(AAG)	 CA	61229-61618	GT	TGG
(CAC)	 AG	61934-62160	GT	AGG
(GAT)	 AG	62864-63012	GT	TGG
(AGC)	 AG	63677-63805	GT	AGG
(TGG)	 AG	63995-64168	GT	GTG
(TGC)	 AG	64645-64818	GT	TGG
(CCA)	 AG	65939-66112	GT	AGG
(GAT)	 AG	66240-66395	GT	TGG
(GTG)	 AG	66497-66623	GT	AGG
(GTT)	 AG	69151-69287	GT	AGG
(GCA)	 AG	69916-70075	GT	AGG
(GTA)	 AG	70286-70395	GT	AGG
(ATT)	 AG	71118-71221	GC	AAG
add_exon() Sorry, pasa_asmbl_52876.p1 70286-70395-terminal-2 is invalid.
-recovered pasa_asmbl_52876.p1, terminal, 70286, 70395
-recovered pasa_asmbl_52876.p1, terminal, 71118, 71221
-recovered pasa_asmbl_52876.p1, internal, 61934, 62160
-recovered pasa_asmbl_52876.p1, internal, 62864, 63012
-recovered pasa_asmbl_52876.p1, internal, 63677, 63805
-recovered pasa_asmbl_52876.p1, internal, 63995, 64168
-recovered pasa_asmbl_52876.p1, internal, 64645, 64818
-recovered pasa_asmbl_52876.p1, internal, 65939, 66112
-recovered pasa_asmbl_52876.p1, internal, 66240, 66395
-recovered pasa_asmbl_52876.p1, internal, 66497, 66623
-recovered pasa_asmbl_52876.p1, internal, 69151, 69287
-recovered pasa_asmbl_52876.p1, internal, 69916, 70075
-recovered pasa_asmbl_52876.p1, internal, 70286, 70395
-recovered pasa_asmbl_52876.p1, internal, 71118, 71221
Valid prediction for snap_scaffold_8-snap.1266-T1
Valid prediction for GeneMark_model.34766_t
Valid prediction for GlimmerHMM_glimmerT_20320-T1
Valid prediction for GeneMark_model.34740_t
Valid prediction for Augustus_model.g13591.t1
Valid prediction for HiQ_model.g13589.t1
Valid prediction for GeneMark_model.34753_t
Couldn't classify 145123, 145650
Sorry, prediction pasa_asmbl_52864.p1 fails validation.
(TCT)	 CA	145123-145650	AC	AGA
Valid prediction for GeneMark_model.34738_t
Valid prediction for snap_scaffold_8-snap.1269-T1
Valid prediction for HiQ_model.g13592.t1
Valid prediction for Augustus_model.g13594.t1
Valid prediction for GlimmerHMM_glimmerT_20300-T1
Valid prediction for snap_scaffold_8-snap.1254-T1
Valid prediction for GlimmerHMM_glimmerT_20319-T1
Valid prediction for snap_scaffold_8-snap.1256-T1
Valid prediction for snap_scaffold_8-snap.1286-T1
Valid prediction for GeneMark_model.34749_t
Valid prediction for GeneMark_model.34765_t
Couldn't classify 98150, 98227
Sorry, prediction pasa_asmbl_52873.p2 fails validation.
(ATT)	 AT	98150-98227	GT	TGG
(TTT)	 AG	99314-99481	GT	AGG
(AGG)	 AG	100139-100210	GT	CGG
(CTC)	 AG	100366-100389	CA	GAC
-recovered pasa_asmbl_52873.p2, terminal, 100366, 100389
-recovered pasa_asmbl_52873.p2, internal, 99314, 99481
-recovered pasa_asmbl_52873.p2, internal, 100139, 100210
Valid prediction for GlimmerHMM_glimmerT_20308-T1
Valid prediction for GeneMark_model.34773_t
Valid prediction for snap_scaffold_8-snap.1275-T1
Valid prediction for GeneMark_model.34767_t
Valid prediction for GeneMark_model.34764_t
Valid prediction for snap_scaffold_8-snap.1264-T1
Valid prediction for HiQ_model.g13593.t1
Valid prediction for Augustus_model.g13578.t1
Valid prediction for snap_scaffold_8-snap.1289-T1
Valid prediction for GeneMark_model.34745_t
Valid prediction for GlimmerHMM_glimmerT_20305-T1
Valid prediction for Augustus_model.g13590.t1
Valid prediction for CodingQuarry_transcript_59533-T1
Valid prediction for snap_scaffold_8-snap.1258-T1
Valid prediction for GeneMark_model.34734_t
Valid prediction for GeneMark_model.34776_t
Valid prediction for GeneMark_model.34756_t
Valid prediction for GeneMark_model.34736_t
Valid prediction for GeneMark_model.34781_t
Valid prediction for GlimmerHMM_glimmerT_20312-T1
Valid prediction for snap_scaffold_8-snap.1284-T1
Valid prediction for snap_scaffold_8-snap.1276-T1
Valid prediction for GlimmerHMM_glimmerT_20309-T1
Valid prediction for GlimmerHMM_glimmerT_20316-T1
Valid prediction for snap_scaffold_8-snap.1279-T1
Valid prediction for GlimmerHMM_glimmerT_20314-T1
Valid prediction for snap_scaffold_8-snap.1278-T1
Valid prediction for GlimmerHMM_glimmerT_20313-T1
Valid prediction for Augustus_model.g13585.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 51553, rend_intergenic: 44292  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52362, rend_intergenic: 52047  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58087, rend_intergenic: 53650  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59281, rend_intergenic: 59040  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66292, rend_intergenic: 59284  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79524, rend_intergenic: 77599  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 217094, rend_intergenic: 215987  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 249574
-exon list size: 602


building trellis

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99.8    
-found 37 predictions from path traversal
Error with prediction: snap lend_intergenic: 51553, rend_intergenic: 44292  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52362, rend_intergenic: 52047  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58087, rend_intergenic: 53650  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59281, rend_intergenic: 59040  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66292, rend_intergenic: 59284  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79524, rend_intergenic: 77599  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 217094, rend_intergenic: 215987  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