-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_23/scaffold_23_5741528-5929384

-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_23-snap.1048-T1
Valid prediction for GlimmerHMM_glimmerT_51083-T1
Valid prediction for GlimmerHMM_glimmerT_51097-T1
Couldn't classify 114453, 114555
Sorry, prediction pasa_asmbl_31603.p1 fails validation.
(GTA)	 AG	114453-114555	GT	AGG
(CTA)	 AG	114681-114715	GT	AAG
(GAA)	 AG	114793-114843	GT	AGG
(TTA)	 AG	114963-115074	GT	CGG
(GAG)	 AG	115229-115289	GT	CTG
(AGA)	 AG	115454-115564	GT	TCG
(TCA)	 AG	115749-115912	GT	TGG
(AGG)	 AG	116006-116088	GT	AGG
(AGC)	 AG	116183-116296	GC	AGG
(CTC)	 AG	116392-116511	AA	AGA
-recovered pasa_asmbl_31603.p1, terminal, 116392, 116511
-recovered pasa_asmbl_31603.p1, internal, 114453, 114555
-recovered pasa_asmbl_31603.p1, internal, 114681, 114715
-recovered pasa_asmbl_31603.p1, internal, 114793, 114843
-recovered pasa_asmbl_31603.p1, internal, 114963, 115074
-recovered pasa_asmbl_31603.p1, internal, 115229, 115289
-recovered pasa_asmbl_31603.p1, internal, 115454, 115564
-recovered pasa_asmbl_31603.p1, internal, 115749, 115912
-recovered pasa_asmbl_31603.p1, internal, 116006, 116088
-recovered pasa_asmbl_31603.p1, internal, 116183, 116296
Valid prediction for snap_scaffold_23-snap.1055-T1
Valid prediction for pasa_asmbl_31608.p1
Valid prediction for pasa_asmbl_31606.p1
Valid prediction for snap_scaffold_23-snap.1046-T1
Valid prediction for snap_scaffold_23-snap.1057-T1
Valid prediction for snap_scaffold_23-snap.1041-T1
Valid prediction for HiQ_model.g34181.t1
Valid prediction for GlimmerHMM_glimmerT_51069-T1
Valid prediction for snap_scaffold_23-snap.1059-T1
Valid prediction for GlimmerHMM_glimmerT_51076-T1
Valid prediction for GlimmerHMM_glimmerT_51084-T1
Valid prediction for HiQ_model.g34182.t1
Valid prediction for CodingQuarry_transcript_35674-T1
Valid prediction for GlimmerHMM_glimmerT_51075-T1
Valid prediction for CodingQuarry_transcript_35678-T1
Valid prediction for HiQ_model.g34179.t1
Valid prediction for snap_scaffold_23-snap.1045-T1
Valid prediction for GlimmerHMM_glimmerT_51079-T1
Valid prediction for snap_scaffold_23-snap.1031-T1
Valid prediction for pasa_asmbl_31605.p1
Valid prediction for snap_scaffold_23-snap.1061-T1
Valid prediction for GlimmerHMM_glimmerT_51085-T1
Valid prediction for pasa_asmbl_31600.p1
Valid prediction for GlimmerHMM_glimmerT_51087-T1
Valid prediction for HiQ_model.g34177.t1
Couldn't classify 113452, 113524
Couldn't classify 113980, 114237
Sorry, prediction pasa_asmbl_31602.p1 fails validation.
(CTT)	 AA	113452-113524	GC	TGG
(GTT)	 AG	113745-113851	GT	AGG
(GAG)	 AG	113980-114237	GT	GGG
-recovered pasa_asmbl_31602.p1, internal, 113745, 113851
-recovered pasa_asmbl_31602.p1, internal, 113980, 114237
Valid prediction for Augustus_model.g34167.t1
Couldn't classify 14527, 14611
Sorry, prediction pasa_asmbl_31597.p1 fails validation.
(TCC)	 CC	14527-14611	GT	AGG
(GCA)	 AG	14708-14842	GT	AGG
(ACA)	 AG	14931-14994	GT	AGG
(GTG)	 AG	15081-15147	GT	TGG
(CCC)	 AG	15314-15474	GT	ACG
(CGG)	 AG	15752-15918	GT	GGG
(ACG)	 AG	16163-16261	GT	CGG
(GGG)	 AG	16413-16549	AG	AGA
-recovered pasa_asmbl_31597.p1, terminal, 16413, 16549
-recovered pasa_asmbl_31597.p1, internal, 14708, 14842
-recovered pasa_asmbl_31597.p1, internal, 14931, 14994
-recovered pasa_asmbl_31597.p1, internal, 15081, 15147
-recovered pasa_asmbl_31597.p1, internal, 15314, 15474
-recovered pasa_asmbl_31597.p1, internal, 15752, 15918
-recovered pasa_asmbl_31597.p1, internal, 16163, 16261
Valid prediction for snap_scaffold_23-snap.1054-T1
Valid prediction for snap_scaffold_23-snap.1049-T1
Valid prediction for CodingQuarry_transcript_35677-T1
Valid prediction for Augustus_model.g34170.t1
Valid prediction for CodingQuarry_transcript_35675-T1
Valid prediction for Augustus_model.g34178.t1
Valid prediction for snap_scaffold_23-snap.1036-T1
Valid prediction for snap_scaffold_23-snap.1037-T1
Valid prediction for GlimmerHMM_glimmerT_51088-T1
Valid prediction for Augustus_model.g34171.t1
Valid prediction for snap_scaffold_23-snap.1033-T1
Valid prediction for GlimmerHMM_glimmerT_51071-T1
Valid prediction for CodingQuarry_transcript_35673-T1
Valid prediction for Augustus_model.g34174.t1
Valid prediction for GlimmerHMM_glimmerT_51093-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 GlimmerHMM_glimmerT_51073-T1
Valid prediction for HiQ_model.g34169.t1
Valid prediction for Augustus_model.g34188.t1
Valid prediction for snap_scaffold_23-snap.1040-T1
Valid prediction for Augustus_model.g34172.t1
Valid prediction for Augustus_model.g34173.t1
Valid prediction for CodingQuarry_transcript_35679-T1
Valid prediction for GlimmerHMM_glimmerT_51082-T1
Valid prediction for GlimmerHMM_glimmerT_51077-T1
Valid prediction for GlimmerHMM_glimmerT_51092-T1
Valid prediction for snap_scaffold_23-snap.1051-T1
Valid prediction for Augustus_model.g34168.t1
Couldn't classify 50299, 50374
Couldn't classify 52447, 52490
Sorry, prediction pasa_asmbl_30957.p1 fails validation.
(GGC)	 TT	50299-50374	GT	AGG
(CTC)	 AG	50628-50875	GT	GAG
(ACT)	 AG	50993-51183	GT	AGG
(GTC)	 AG	51309-51424	GT	AGG
(CGC)	 AG	52125-52250	GT	CGG
(GCT)	 AG	52447-52490	CA	GAC
add_exon() Sorry, pasa_asmbl_30957.p1 51309-51424-terminal-2 is invalid.
-recovered pasa_asmbl_30957.p1, terminal, 51309, 51424
-recovered pasa_asmbl_30957.p1, internal, 50628, 50875
-recovered pasa_asmbl_30957.p1, internal, 50993, 51183
-recovered pasa_asmbl_30957.p1, internal, 51309, 51424
-recovered pasa_asmbl_30957.p1, internal, 52125, 52250
Valid prediction for GlimmerHMM_glimmerT_51081-T1
Valid prediction for Augustus_model.g34190.t1
Valid prediction for snap_scaffold_23-snap.1058-T1
Valid prediction for snap_scaffold_23-snap.1032-T1
Valid prediction for GlimmerHMM_glimmerT_51090-T1
Valid prediction for GlimmerHMM_glimmerT_51080-T1
Valid prediction for CodingQuarry_transcript_35667-T1
Valid prediction for GlimmerHMM_glimmerT_51078-T1
Valid prediction for pasa_asmbl_30955.p1
Valid prediction for CodingQuarry_transcript_35668-T1
Valid prediction for pasa_asmbl_30951.p1
Couldn't classify 30811, 30850
Couldn't classify 33167, 33447
Sorry, prediction pasa_asmbl_30959.p1 fails validation.
(TAC)	 TC	30811-30850	GT	AGG
(GTC)	 AG	31563-31820	GT	TGG
(GCT)	 AG	33167-33447	AG	CCA
-recovered pasa_asmbl_30959.p1, internal, 31563, 31820
Valid prediction for GlimmerHMM_glimmerT_51070-T1
Valid prediction for CodingQuarry_transcript_35676-T1
Valid prediction for Augustus_model.g34189.t1
Valid prediction for snap_scaffold_23-snap.1044-T1
Valid prediction for Augustus_model.g34185.t1
Valid prediction for GlimmerHMM_glimmerT_51074-T1
Valid prediction for snap_scaffold_23-snap.1035-T1
Valid prediction for snap_scaffold_23-snap.1052-T1
Sorry, intron length (3) is less than minimum required (10)
Couldn't classify 104199, 104299
Couldn't classify 104665, 104839
Sorry, prediction pasa_asmbl_31257.p1 fails validation.
(ATC)	 GC	104199-104299	GT	AGG
(AAA)	 AG	104394-104510	GT	AAG
(GTT)	 AG	104665-104839	GT	AGG
-recovered pasa_asmbl_31257.p1, internal, 104394, 104510
-recovered pasa_asmbl_31257.p1, internal, 104665, 104839
Valid prediction for snap_scaffold_23-snap.1042-T1
Valid prediction for snap_scaffold_23-snap.1050-T1
Valid prediction for snap_scaffold_23-snap.1039-T1
Valid prediction for Augustus_model.g34187.t1
Valid prediction for pasa_asmbl_30943.p1
Valid prediction for snap_scaffold_23-snap.1056-T1
Valid prediction for HiQ_model.g34180.t1
Valid prediction for GlimmerHMM_glimmerT_51068-T1
Valid prediction for Augustus_model.g34186.t1
Valid prediction for Augustus_model.g34166.t1
Valid prediction for GlimmerHMM_glimmerT_51089-T1
Valid prediction for HiQ_model.g34183.t1
Valid prediction for snap_scaffold_23-snap.1038-T1
Couldn't classify 181192, 181249
Sorry, prediction pasa_asmbl_30940.p1 fails validation.
(ATG)	 AT	180601-180911	GT	AGG
(GTA)	 AG	181192-181249	CT	ACC
-recovered pasa_asmbl_30940.p1, initial, 180601, 180911
Valid prediction for CodingQuarry_transcript_35670-T1
Valid prediction for GlimmerHMM_glimmerT_51096-T1
Valid prediction for Augustus_model.g34184.t1
Couldn't classify 84440, 84514
Sorry, prediction pasa_asmbl_30946.p2 fails validation.
(CAT)	 GG	84440-84514	GT	AGG
(CGA)	 AG	84637-84752	GT	CGG
(CAT)	 AG	85087-85186	GT	AGG
(GTC)	 AG	85569-85595	AC	AGA
-recovered pasa_asmbl_30946.p2, terminal, 85569, 85595
-recovered pasa_asmbl_30946.p2, internal, 84637, 84752
-recovered pasa_asmbl_30946.p2, internal, 85087, 85186
Valid prediction for GlimmerHMM_glimmerT_51095-T1
Valid prediction for GlimmerHMM_glimmerT_51086-T1
Valid prediction for snap_scaffold_23-snap.1053-T1
Valid prediction for snap_scaffold_23-snap.1047-T1
Valid prediction for HiQ_model.g34176.t1
Valid prediction for CodingQuarry_transcript_35672-T1
Valid prediction for pasa_asmbl_30949.p1
Couldn't classify 82260, 82419
Couldn't classify 84046, 84240
Sorry, prediction pasa_asmbl_30947.p1 fails validation.
(GCG)	 GC	82260-82419	GT	TGG
(CGG)	 AG	82898-83013	GT	AGG
(GAG)	 AG	84046-84240	TA	GGT
-recovered pasa_asmbl_30947.p1, internal, 82898, 83013
Valid prediction for GlimmerHMM_glimmerT_51072-T1
Valid prediction for CodingQuarry_transcript_35671-T1
Valid prediction for snap_scaffold_23-snap.1060-T1
Valid prediction for snap_scaffold_23-snap.1034-T1
Valid prediction for Augustus_model.g34175.t1
Valid prediction for GlimmerHMM_glimmerT_51094-T1
Valid prediction for GlimmerHMM_glimmerT_51091-T1
Valid prediction for CodingQuarry_transcript_35669-T1
Valid prediction for snap_scaffold_23-snap.1043-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17280, rend_intergenic: 14439  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85247, rend_intergenic: 75733  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157201, rend_intergenic: 154366  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167405, rend_intergenic: 161726  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172850, rend_intergenic: 169135  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180380, rend_intergenic: 177955  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 187857
-exon list size: 447


building trellis

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-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 17280, rend_intergenic: 14439  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85247, rend_intergenic: 75733  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157201, rend_intergenic: 154366  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167405, rend_intergenic: 161726  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172850, rend_intergenic: 169135  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180380, rend_intergenic: 177955  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support