-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_8393066-8595249

-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.1511-T1
Valid prediction for GlimmerHMM_glimmerT_1175-T1
Valid prediction for snap_scaffold_1-snap.1499-T1
Valid prediction for HiQ_model.g868.t1
Valid prediction for Augustus_model.g871.t1
Valid prediction for Augustus_model.g870.t1
Couldn't classify 80718, 80842
Sorry, prediction pasa_asmbl_2806.p1 fails validation.
(TTT)	 GG	80718-80842	GT	AGG
(TGA)	 AG	81489-81570	GT	TGG
(AGC)	 AG	81826-81924	GT	AGG
(AAG)	 AG	82310-82456	GT	AGG
(GCT)	 AG	82671-82752	GT	AGG
(ATG)	 AG	83049-83195	GT	CAG
(ACC)	 AG	83701-83882	CA	GAC
add_exon() Sorry, pasa_asmbl_2806.p1 83049-83195-initial-1 is invalid.
-recovered pasa_asmbl_2806.p1, initial, 83049, 83195
-recovered pasa_asmbl_2806.p1, terminal, 83701, 83882
-recovered pasa_asmbl_2806.p1, internal, 81489, 81570
-recovered pasa_asmbl_2806.p1, internal, 81826, 81924
-recovered pasa_asmbl_2806.p1, internal, 82310, 82456
-recovered pasa_asmbl_2806.p1, internal, 82671, 82752
-recovered pasa_asmbl_2806.p1, internal, 83049, 83195
Couldn't classify 192023, 192129
Sorry, prediction pasa_asmbl_1937.p1 fails validation.
(GGT)	 CA	192023-192129	GT	AGG
(GCT)	 AG	192252-192294	GT	TGG
(TAC)	 AG	192387-192477	GT	CAG
(CTT)	 AG	192925-193002	GT	AGG
(GTC)	 AG	193219-193253	GG	AGG
-recovered pasa_asmbl_1937.p1, terminal, 193219, 193253
-recovered pasa_asmbl_1937.p1, internal, 192252, 192294
-recovered pasa_asmbl_1937.p1, internal, 192387, 192477
-recovered pasa_asmbl_1937.p1, internal, 192925, 193002
Valid prediction for snap_scaffold_1-snap.1502-T1
Valid prediction for GlimmerHMM_glimmerT_1177-T1
Valid prediction for snap_scaffold_1-snap.1513-T1
Valid prediction for snap_scaffold_1-snap.1522-T1
Valid prediction for Augustus_model.g869.t1
Valid prediction for snap_scaffold_1-snap.1535-T1
Valid prediction for GlimmerHMM_glimmerT_1174-T1
Valid prediction for GlimmerHMM_glimmerT_1190-T1
Valid prediction for GlimmerHMM_glimmerT_1176-T1
Valid prediction for snap_scaffold_1-snap.1497-T1
Couldn't classify 77281, 77391
Couldn't classify 79836, 79951
Sorry, prediction pasa_asmbl_2811.p1 fails validation.
(CCA)	 CT	77281-77391	GT	AGG
(CCT)	 AG	78751-78841	GT	AGG
(AGT)	 AG	79008-79155	GT	AGG
(TCG)	 AG	79325-79542	GT	TGG
(TGA)	 AG	79836-79951	GT	AGG
-recovered pasa_asmbl_2811.p1, internal, 78751, 78841
-recovered pasa_asmbl_2811.p1, internal, 79008, 79155
-recovered pasa_asmbl_2811.p1, internal, 79325, 79542
-recovered pasa_asmbl_2811.p1, internal, 79836, 79951
Valid prediction for GlimmerHMM_glimmerT_1189-T1
Valid prediction for Augustus_model.g877.t1
Valid prediction for GlimmerHMM_glimmerT_1170-T1
Valid prediction for snap_scaffold_1-snap.1527-T1
Couldn't classify 52611, 52709
Couldn't classify 57688, 57720
Sorry, prediction pasa_asmbl_2727.p1 fails validation.
(ATT)	 GA	52611-52709	GT	GCG
(GTA)	 AG	55116-55283	GT	GGG
(TCA)	 AG	56889-56981	GT	CGG
(TTC)	 AG	57688-57720	GT	AGG
-recovered pasa_asmbl_2727.p1, internal, 55116, 55283
-recovered pasa_asmbl_2727.p1, internal, 56889, 56981
-recovered pasa_asmbl_2727.p1, internal, 57688, 57720
Valid prediction for snap_scaffold_1-snap.1498-T1
Couldn't classify 26608, 26856
Sorry, prediction pasa_asmbl_1932.p1 fails validation.
(GAT)	 CG	26608-26856	GT	AGG
(GTA)	 AG	28841-28979	GT	GAG
(CCC)	 AG	30966-31178	GT	GGG
(AAA)	 AG	32006-32130	GT	AGG
(ACA)	 AG	32476-32622	GT	AGG
(GTG)	 AG	33108-33173	GT	AGG
(TAT)	 AG	33521-33709	GT	CGG
(ACT)	 AG	33996-34138	GT	AGG
(CCT)	 AG	34763-34877	GT	AGG
(AGC)	 AG	36813-36923	GT	TTG
(GCT)	 AG	37169-37267	GT	AGG
(GCT)	 AG	37680-37757	GT	ATG
(TTC)	 AG	38274-38377	GT	CAG
(GTG)	 AG	38800-38910	GT	AAG
(AGC)	 AG	39074-39141	GT	AGG
(GGA)	 AG	39346-39536	GT	AGG
(GCT)	 AG	40308-40403	GT	AGG
(GTG)	 AG	40568-40744	TA	GAT
-recovered pasa_asmbl_1932.p1, terminal, 40568, 40744
-recovered pasa_asmbl_1932.p1, internal, 28841, 28979
-recovered pasa_asmbl_1932.p1, internal, 30966, 31178
-recovered pasa_asmbl_1932.p1, internal, 32006, 32130
-recovered pasa_asmbl_1932.p1, internal, 32476, 32622
-recovered pasa_asmbl_1932.p1, internal, 33108, 33173
-recovered pasa_asmbl_1932.p1, internal, 33521, 33709
-recovered pasa_asmbl_1932.p1, internal, 33996, 34138
-recovered pasa_asmbl_1932.p1, internal, 34763, 34877
-recovered pasa_asmbl_1932.p1, internal, 36813, 36923
-recovered pasa_asmbl_1932.p1, internal, 37169, 37267
-recovered pasa_asmbl_1932.p1, internal, 37680, 37757
-recovered pasa_asmbl_1932.p1, internal, 38274, 38377
-recovered pasa_asmbl_1932.p1, internal, 38800, 38910
-recovered pasa_asmbl_1932.p1, internal, 39074, 39141
-recovered pasa_asmbl_1932.p1, internal, 39346, 39536
-recovered pasa_asmbl_1932.p1, internal, 40308, 40403
Valid prediction for GlimmerHMM_glimmerT_1179-T1
Valid prediction for snap_scaffold_1-snap.1529-T1
Valid prediction for snap_scaffold_1-snap.1496-T1
Valid prediction for Augustus_model.g881.t1
Valid prediction for snap_scaffold_1-snap.1515-T1
Valid prediction for Augustus_model.g880.t1
Couldn't classify 187351, 187443
Couldn't classify 190346, 190425
Sorry, prediction pasa_asmbl_1936.p1 fails validation.
(AGC)	 CC	187351-187443	GT	AGG
(GAC)	 AG	188877-189008	GT	TGG
(TCA)	 AG	189124-189180	GT	AGG
(GGG)	 AG	189999-190113	GT	AGG
(TTT)	 AG	190346-190425	GT	TGG
-recovered pasa_asmbl_1936.p1, internal, 188877, 189008
-recovered pasa_asmbl_1936.p1, internal, 189124, 189180
-recovered pasa_asmbl_1936.p1, internal, 189999, 190113
-recovered pasa_asmbl_1936.p1, internal, 190346, 190425
Valid prediction for snap_scaffold_1-snap.1521-T1
Valid prediction for snap_scaffold_1-snap.1534-T1
Valid prediction for GlimmerHMM_glimmerT_1191-T1
Valid prediction for snap_scaffold_1-snap.1524-T1
Valid prediction for snap_scaffold_1-snap.1530-T1
Valid prediction for snap_scaffold_1-snap.1531-T1
Valid prediction for snap_scaffold_1-snap.1505-T1
Valid prediction for snap_scaffold_1-snap.1491-T1
Valid prediction for snap_scaffold_1-snap.1518-T1
Valid prediction for GlimmerHMM_glimmerT_1182-T1
Valid prediction for Augustus_model.g872.t1
Valid prediction for snap_scaffold_1-snap.1519-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_1180-T1
Valid prediction for Augustus_model.g879.t1
Valid prediction for snap_scaffold_1-snap.1510-T1
Valid prediction for snap_scaffold_1-snap.1490-T1
Valid prediction for snap_scaffold_1-snap.1533-T1
Valid prediction for Augustus_model.g867.t1
Couldn't classify 90064, 90597
Sorry, prediction pasa_asmbl_449.p1 fails validation.
(GAT)	 CC	90064-90597	GC	TGG
Valid prediction for snap_scaffold_1-snap.1501-T1
Valid prediction for Augustus_model.g874.t1
Valid prediction for snap_scaffold_1-snap.1506-T1
Valid prediction for Augustus_model.g878.t1
Valid prediction for snap_scaffold_1-snap.1507-T1
Valid prediction for GlimmerHMM_glimmerT_1184-T1
Valid prediction for Augustus_model.g875.t1
Valid prediction for snap_scaffold_1-snap.1528-T1
Valid prediction for snap_scaffold_1-snap.1503-T1
Valid prediction for GlimmerHMM_glimmerT_1172-T1
Valid prediction for snap_scaffold_1-snap.1516-T1
Valid prediction for snap_scaffold_1-snap.1512-T1
Valid prediction for GlimmerHMM_glimmerT_1185-T1
Valid prediction for snap_scaffold_1-snap.1495-T1
Valid prediction for snap_scaffold_1-snap.1526-T1
Valid prediction for GlimmerHMM_glimmerT_1171-T1
Valid prediction for snap_scaffold_1-snap.1494-T1
Valid prediction for snap_scaffold_1-snap.1493-T1
Valid prediction for snap_scaffold_1-snap.1509-T1
Valid prediction for snap_scaffold_1-snap.1508-T1
Valid prediction for Augustus_model.g866.t1
Valid prediction for snap_scaffold_1-snap.1523-T1
Valid prediction for snap_scaffold_1-snap.1514-T1
Valid prediction for Augustus_model.g876.t1
Valid prediction for Augustus_model.g873.t1
Valid prediction for snap_scaffold_1-snap.1525-T1
Valid prediction for GlimmerHMM_glimmerT_1183-T1
Valid prediction for snap_scaffold_1-snap.1492-T1
Valid prediction for GlimmerHMM_glimmerT_1181-T1
Valid prediction for GlimmerHMM_glimmerT_1186-T1
Valid prediction for snap_scaffold_1-snap.1500-T1
Valid prediction for GlimmerHMM_glimmerT_1187-T1
Valid prediction for snap_scaffold_1-snap.1504-T1
Valid prediction for snap_scaffold_1-snap.1532-T1
Valid prediction for GlimmerHMM_glimmerT_1173-T1
Couldn't classify 101319, 101364
Sorry, prediction pasa_asmbl_448.p1 fails validation.
(AAC)	 CT	101319-101364	GT	CGG
(GCG)	 AG	101467-101601	GT	CAG
(GTG)	 AG	101703-101851	GT	AGG
(GTG)	 AG	102037-102222	AC	AGA
-recovered pasa_asmbl_448.p1, terminal, 102037, 102222
-recovered pasa_asmbl_448.p1, internal, 101467, 101601
-recovered pasa_asmbl_448.p1, internal, 101703, 101851
Valid prediction for snap_scaffold_1-snap.1517-T1
Valid prediction for GlimmerHMM_glimmerT_1188-T1
Valid prediction for GlimmerHMM_glimmerT_1178-T1
Valid prediction for snap_scaffold_1-snap.1520-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 26900, rend_intergenic: 24193  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52218, rend_intergenic: 46394  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53818, rend_intergenic: 52623  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61280, rend_intergenic: 54228  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65645, rend_intergenic: 62658  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83882, rend_intergenic: 65808  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94003, rend_intergenic: 92134  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94786, rend_intergenic: 94317  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102501, rend_intergenic: 102110  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107373, rend_intergenic: 102687  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146353, rend_intergenic: 132680  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154700, rend_intergenic: 146903  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164937, rend_intergenic: 154887  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182481, rend_intergenic: 168238  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193253, rend_intergenic: 183809  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 202184
-exon list size: 419


building trellis

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-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 26900, rend_intergenic: 24193  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52218, rend_intergenic: 46394  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53818, rend_intergenic: 52623  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61280, rend_intergenic: 54228  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65645, rend_intergenic: 62658  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83882, rend_intergenic: 65808  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94003, rend_intergenic: 92134  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94786, rend_intergenic: 94317  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102501, rend_intergenic: 102110  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107373, rend_intergenic: 102687  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146353, rend_intergenic: 132680  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154700, rend_intergenic: 146903  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164937, rend_intergenic: 154887  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182481, rend_intergenic: 168238  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193253, rend_intergenic: 183809  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support