-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_1/scaffold_1_4832514-5022532

-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_1-snap.732-T1
Valid prediction for GlimmerHMM_glimmerT_573-T1
Valid prediction for snap_scaffold_1-snap.709-T1
Valid prediction for snap_scaffold_1-snap.741-T1
Valid prediction for Augustus_model.g457.t1
Valid prediction for GlimmerHMM_glimmerT_580-T1
Valid prediction for snap_scaffold_1-snap.724-T1
Couldn't classify 36502, 37006
Couldn't classify 37844, 37953
Sorry, prediction pasa_asmbl_1687.p2 fails validation.
(GAG)	 TC	36502-37006	GT	AGG
(GCG)	 AG	37441-37536	GT	AGG
(GTC)	 AG	37844-37953	CT	CCC
-recovered pasa_asmbl_1687.p2, internal, 37441, 37536
Valid prediction for Augustus_model.g444.t1
Valid prediction for Augustus_model.g456.t1
Valid prediction for GlimmerHMM_glimmerT_592-T1
Valid prediction for GlimmerHMM_glimmerT_581-T1
Valid prediction for GlimmerHMM_glimmerT_561-T1
Valid prediction for GlimmerHMM_glimmerT_571-T1
Valid prediction for GlimmerHMM_glimmerT_563-T1
Valid prediction for snap_scaffold_1-snap.748-T1
Valid prediction for snap_scaffold_1-snap.743-T1
Valid prediction for Augustus_model.g452.t1
Valid prediction for GlimmerHMM_glimmerT_560-T1
Valid prediction for snap_scaffold_1-snap.745-T1
Valid prediction for snap_scaffold_1-snap.723-T1
Valid prediction for Augustus_model.g438.t1
Valid prediction for snap_scaffold_1-snap.735-T1
Valid prediction for snap_scaffold_1-snap.739-T1
Valid prediction for snap_scaffold_1-snap.727-T1
Valid prediction for GlimmerHMM_glimmerT_562-T1
Valid prediction for GlimmerHMM_glimmerT_588-T1
Valid prediction for Augustus_model.g446.t1
Valid prediction for Augustus_model.g454.t1
Valid prediction for GlimmerHMM_glimmerT_572-T1
Valid prediction for snap_scaffold_1-snap.715-T1
Valid prediction for GlimmerHMM_glimmerT_589-T1
Valid prediction for Augustus_model.g458.t1
Valid prediction for snap_scaffold_1-snap.726-T1
Valid prediction for Augustus_model.g448.t1
Valid prediction for Augustus_model.g441.t1
Valid prediction for GlimmerHMM_glimmerT_590-T1
Valid prediction for GlimmerHMM_glimmerT_565-T1
Valid prediction for snap_scaffold_1-snap.707-T1
Valid prediction for CodingQuarry_transcript_2600-T1
Couldn't classify 77618, 77728
Sorry, prediction pasa_asmbl_2707.p1 fails validation.
(CCC)	 CC	77618-77728	GT	AGG
(CGT)	 AG	77885-77968	GT	AGG
(GAC)	 AG	80147-80236	GT	AGG
(GAA)	 AG	81601-81659	GT	AGG
(CAC)	 AG	82611-82771	GT	AGG
(GCC)	 AG	83054-83168	GT	AGG
(GCC)	 AG	83339-83460	GT	AGG
(GGA)	 AG	83751-83851	GT	AGG
(AAG)	 AG	84038-84118	GA	AGG
-recovered pasa_asmbl_2707.p1, terminal, 84038, 84118
-recovered pasa_asmbl_2707.p1, internal, 77885, 77968
-recovered pasa_asmbl_2707.p1, internal, 80147, 80236
-recovered pasa_asmbl_2707.p1, internal, 81601, 81659
-recovered pasa_asmbl_2707.p1, internal, 82611, 82771
-recovered pasa_asmbl_2707.p1, internal, 83054, 83168
-recovered pasa_asmbl_2707.p1, internal, 83339, 83460
-recovered pasa_asmbl_2707.p1, internal, 83751, 83851
Valid prediction for snap_scaffold_1-snap.706-T1
Valid prediction for snap_scaffold_1-snap.736-T1
Valid prediction for snap_scaffold_1-snap.710-T1
Valid prediction for snap_scaffold_1-snap.750-T1
Valid prediction for snap_scaffold_1-snap.722-T1
Valid prediction for GlimmerHMM_glimmerT_579-T1
Valid prediction for snap_scaffold_1-snap.734-T1
Valid prediction for Augustus_model.g455.t1
Valid prediction for GlimmerHMM_glimmerT_586-T1
Valid prediction for GlimmerHMM_glimmerT_569-T1
Couldn't classify 180949, 181082
Sorry, prediction pasa_asmbl_1694.p1 fails validation.
(CAG)	 CC	180949-181082	GT	AGG
(GCT)	 AG	181606-181802	GT	AGG
(CCT)	 AG	182544-182731	GT	TTG
(CAA)	 AG	183007-183099	TG	GAT
-recovered pasa_asmbl_1694.p1, terminal, 183007, 183099
-recovered pasa_asmbl_1694.p1, internal, 181606, 181802
-recovered pasa_asmbl_1694.p1, internal, 182544, 182731
Valid prediction for GlimmerHMM_glimmerT_584-T1
Valid prediction for Augustus_model.g461.t1
Valid prediction for Augustus_model.g460.t1
Valid prediction for snap_scaffold_1-snap.740-T1
Valid prediction for snap_scaffold_1-snap.730-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_575-T1
Valid prediction for snap_scaffold_1-snap.744-T1
Valid prediction for snap_scaffold_1-snap.712-T1
Valid prediction for snap_scaffold_1-snap.718-T1
Valid prediction for CodingQuarry_transcript_2601-T1
Valid prediction for snap_scaffold_1-snap.731-T1
Valid prediction for GlimmerHMM_glimmerT_567-T1
Valid prediction for snap_scaffold_1-snap.717-T1
Couldn't classify 100017, 100062
Sorry, prediction pasa_asmbl_225.p1 fails validation.
(TAC)	 CG	100017-100062	GT	CGG
(AGG)	 AG	100155-100273	GT	AGG
(TAT)	 AG	100595-100723	GT	TGG
(ATT)	 AG	101054-101231	GT	AGG
(TCA)	 AG	101430-101565	GT	TGG
(GAA)	 AG	101645-101748	GT	AGG
(GGG)	 AG	101876-102115	GT	AGG
(CTC)	 AG	102379-102438	GT	AGG
(GTT)	 AG	102631-102840	GT	AGG
(TCA)	 AG	103093-103250	GT	AGG
(GTT)	 AG	103666-103802	GT	AGG
(GAT)	 AG	104225-104378	AC	AGA
-recovered pasa_asmbl_225.p1, terminal, 104225, 104378
-recovered pasa_asmbl_225.p1, internal, 100155, 100273
-recovered pasa_asmbl_225.p1, internal, 100595, 100723
-recovered pasa_asmbl_225.p1, internal, 101054, 101231
-recovered pasa_asmbl_225.p1, internal, 101430, 101565
-recovered pasa_asmbl_225.p1, internal, 101645, 101748
-recovered pasa_asmbl_225.p1, internal, 101876, 102115
-recovered pasa_asmbl_225.p1, internal, 102379, 102438
-recovered pasa_asmbl_225.p1, internal, 102631, 102840
-recovered pasa_asmbl_225.p1, internal, 103093, 103250
-recovered pasa_asmbl_225.p1, internal, 103666, 103802
Valid prediction for Augustus_model.g445.t1
Valid prediction for snap_scaffold_1-snap.711-T1
Valid prediction for GlimmerHMM_glimmerT_587-T1
Valid prediction for GlimmerHMM_glimmerT_576-T1
Valid prediction for GlimmerHMM_glimmerT_583-T1
Valid prediction for Augustus_model.g440.t1
Valid prediction for snap_scaffold_1-snap.746-T1
Valid prediction for Augustus_model.g439.t1
Valid prediction for snap_scaffold_1-snap.737-T1
Valid prediction for Augustus_model.g443.t1
Valid prediction for GlimmerHMM_glimmerT_568-T1
Valid prediction for snap_scaffold_1-snap.716-T1
Valid prediction for snap_scaffold_1-snap.725-T1
Valid prediction for snap_scaffold_1-snap.742-T1
Valid prediction for snap_scaffold_1-snap.713-T1
Valid prediction for GlimmerHMM_glimmerT_591-T1
Valid prediction for GlimmerHMM_glimmerT_570-T1
Valid prediction for Augustus_model.g442.t1
Valid prediction for Augustus_model.g447.t1
Valid prediction for snap_scaffold_1-snap.721-T1
Valid prediction for GlimmerHMM_glimmerT_566-T1
Valid prediction for Augustus_model.g459.t1
Valid prediction for GlimmerHMM_glimmerT_577-T1
Valid prediction for GlimmerHMM_glimmerT_574-T1
Valid prediction for snap_scaffold_1-snap.749-T1
Valid prediction for snap_scaffold_1-snap.738-T1
Valid prediction for HiQ_model.g450.t1
Valid prediction for GlimmerHMM_glimmerT_578-T1
Valid prediction for GlimmerHMM_glimmerT_564-T1
Couldn't classify 87966, 88107
Sorry, prediction pasa_asmbl_230.p1 fails validation.
(ATG)	 CC	86316-86340	GT	TGG
(TCC)	 AG	86556-86697	GT	GTG
(AAT)	 AG	86922-87046	GT	ATG
(TGT)	 AG	87536-87667	GT	CGG
(CTG)	 AG	87791-87839	GT	AGG
(GTC)	 AG	87966-88107	CC	GGC
-recovered pasa_asmbl_230.p1, initial, 86316, 86340
-recovered pasa_asmbl_230.p1, internal, 86556, 86697
-recovered pasa_asmbl_230.p1, internal, 86922, 87046
-recovered pasa_asmbl_230.p1, internal, 87536, 87667
-recovered pasa_asmbl_230.p1, internal, 87791, 87839
Valid prediction for CodingQuarry_transcript_2599-T1
Valid prediction for Augustus_model.g449.t1
Valid prediction for snap_scaffold_1-snap.714-T1
Valid prediction for snap_scaffold_1-snap.708-T1
Valid prediction for pasa_asmbl_226.p1
Valid prediction for snap_scaffold_1-snap.728-T1
Valid prediction for GlimmerHMM_glimmerT_585-T1
Couldn't classify 54459, 54572
Couldn't classify 57547, 57619
Sorry, prediction pasa_asmbl_232.p1 fails validation.
(GGC)	 GC	54459-54572	GT	TGG
(AAT)	 AG	54811-54900	GT	AGG
(GCA)	 AG	57146-57327	GT	AGG
(AGG)	 AG	57547-57619	AG	TCA
-recovered pasa_asmbl_232.p1, internal, 54811, 54900
-recovered pasa_asmbl_232.p1, internal, 57146, 57327
Valid prediction for snap_scaffold_1-snap.733-T1
Valid prediction for Augustus_model.g451.t1
Valid prediction for snap_scaffold_1-snap.747-T1
Couldn't classify 149166, 149244
Sorry, prediction pasa_asmbl_220.p1 fails validation.
(ATG)	 GC	146670-146738	GT	AGG
(GTT)	 AG	147063-147157	GT	AGG
(GCT)	 AG	147334-147427	GT	AGG
(GAT)	 AG	147609-147748	GT	AGG
(GTT)	 AG	149166-149244	GT	AGG
-recovered pasa_asmbl_220.p1, initial, 146670, 146738
-recovered pasa_asmbl_220.p1, internal, 147063, 147157
-recovered pasa_asmbl_220.p1, internal, 147334, 147427
-recovered pasa_asmbl_220.p1, internal, 147609, 147748
-recovered pasa_asmbl_220.p1, internal, 149166, 149244
Valid prediction for Augustus_model.g453.t1
Couldn't classify 93799, 94287
Sorry, prediction pasa_asmbl_229.p1 fails validation.
(TCT)	 TC	93799-94287	CG	AGC
Valid prediction for snap_scaffold_1-snap.720-T1
Couldn't classify 88506, 88597
Sorry, prediction pasa_asmbl_1318.p1 fails validation.
(CAG)	 CG	88506-88597	GT	GGG
(CTG)	 AG	88809-88904	GT	GGG
(GTG)	 AG	89069-89243	GT	GGG
(CTC)	 AG	89445-89514	GT	GGG
(AGA)	 AG	89670-89754	GT	GGG
(GTT)	 AG	89901-90029	GT	CTG
(GGA)	 AG	90200-90272	GT	AGG
(CAA)	 AG	90398-90469	GT	AAG
(ATC)	 AG	90716-90804	GT	AGG
(GGA)	 AG	90919-91078	GT	TGG
(GCT)	 AG	91239-91372	GT	AAG
(AGA)	 AG	91533-91673	GT	AGG
(GCT)	 AG	91761-91881	GT	AGG
(GTG)	 AG	91999-92103	GT	AGG
(TTT)	 AG	92277-92373	GT	GGG
(GGA)	 AG	92802-92878	GT	GAG
-recovered pasa_asmbl_1318.p1, terminal, 92802, 92878
-recovered pasa_asmbl_1318.p1, internal, 88809, 88904
-recovered pasa_asmbl_1318.p1, internal, 89069, 89243
-recovered pasa_asmbl_1318.p1, internal, 89445, 89514
-recovered pasa_asmbl_1318.p1, internal, 89670, 89754
-recovered pasa_asmbl_1318.p1, internal, 89901, 90029
-recovered pasa_asmbl_1318.p1, internal, 90200, 90272
-recovered pasa_asmbl_1318.p1, internal, 90398, 90469
-recovered pasa_asmbl_1318.p1, internal, 90716, 90804
-recovered pasa_asmbl_1318.p1, internal, 90919, 91078
-recovered pasa_asmbl_1318.p1, internal, 91239, 91372
-recovered pasa_asmbl_1318.p1, internal, 91533, 91673
-recovered pasa_asmbl_1318.p1, internal, 91761, 91881
-recovered pasa_asmbl_1318.p1, internal, 91999, 92103
-recovered pasa_asmbl_1318.p1, internal, 92277, 92373
-recovered pasa_asmbl_1318.p1, internal, 92802, 92878
Valid prediction for GlimmerHMM_glimmerT_582-T1
Valid prediction for snap_scaffold_1-snap.719-T1
Valid prediction for snap_scaffold_1-snap.729-T1
Valid prediction for CodingQuarry_transcript_2597-T1
Couldn't classify 57683, 57797
Sorry, prediction pasa_asmbl_231.p2 fails validation.
(CCC)	 CG	57683-57797	GT	AGG
(GCA)	 AG	59588-59673	GT	ATG
(GTG)	 AG	59987-60170	GT	CGG
(ACT)	 AG	61124-61192	GT	AGG
(AAG)	 AG	61395-61585	GT	AGG
(TGT)	 AG	61732-62052	GA	AGG
-recovered pasa_asmbl_231.p2, terminal, 61732, 62052
-recovered pasa_asmbl_231.p2, internal, 59588, 59673
-recovered pasa_asmbl_231.p2, internal, 59987, 60170
-recovered pasa_asmbl_231.p2, internal, 61124, 61192
-recovered pasa_asmbl_231.p2, internal, 61395, 61585

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 84118, rend_intergenic: 84115  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14169, rend_intergenic: 11384  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58172, rend_intergenic: 56101  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78063, rend_intergenic: 75288  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98671, rend_intergenic: 95733  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145903, rend_intergenic: 130641  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170581, rend_intergenic: 169794  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183789, rend_intergenic: 180690  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 190019
-exon list size: 424


building trellis

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99.8    
-found 38 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 84118, rend_intergenic: 84115  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14169, rend_intergenic: 11384  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58172, rend_intergenic: 56101  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78063, rend_intergenic: 75288  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98671, rend_intergenic: 95733  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145903, rend_intergenic: 130641  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170581, rend_intergenic: 169794  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183789, rend_intergenic: 180690  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

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