-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_4/scaffold_4_8593470-8896462

-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 GlimmerHMM_glimmerT_9815-T1
Valid prediction for snap_scaffold_4-snap.1835-T1
Valid prediction for snap_scaffold_4-snap.1810-T1
Valid prediction for GlimmerHMM_glimmerT_9843-T1
Valid prediction for Augustus_model.g6397.t1
Valid prediction for snap_scaffold_4-snap.1864-T1
Valid prediction for snap_scaffold_4-snap.1862-T1
Valid prediction for GlimmerHMM_glimmerT_9832-T1
Valid prediction for HiQ_model.g6392.t1
Valid prediction for Augustus_model.g6394.t1
Valid prediction for snap_scaffold_4-snap.1829-T1
Valid prediction for snap_scaffold_4-snap.1865-T1
Valid prediction for snap_scaffold_4-snap.1858-T1
Valid prediction for Augustus_model.g6375.t1
Valid prediction for snap_scaffold_4-snap.1820-T1
Valid prediction for snap_scaffold_4-snap.1823-T1
Valid prediction for snap_scaffold_4-snap.1855-T1
Valid prediction for GlimmerHMM_glimmerT_9836-T1
Valid prediction for snap_scaffold_4-snap.1814-T1
Valid prediction for GlimmerHMM_glimmerT_9813-T1
Valid prediction for snap_scaffold_4-snap.1817-T1
Valid prediction for GlimmerHMM_glimmerT_9827-T1
Valid prediction for GlimmerHMM_glimmerT_9829-T1
Valid prediction for Augustus_model.g6398.t1
Valid prediction for snap_scaffold_4-snap.1859-T1
Valid prediction for snap_scaffold_4-snap.1844-T1
Valid prediction for Augustus_model.g6395.t1
Valid prediction for pasa_asmbl_41574.p1
Couldn't classify 275190, 275229
Sorry, prediction pasa_asmbl_41591.p1 fails validation.
(TCT)	 AC	275190-275229	GT	AGG
(GCC)	 AG	275374-275557	GT	AGG
(GCT)	 AG	275896-276064	GT	AGG
(GTG)	 AG	276432-276570	GT	TAG
(GCC)	 AG	276891-277102	CG	GAC
-recovered pasa_asmbl_41591.p1, terminal, 276891, 277102
-recovered pasa_asmbl_41591.p1, internal, 275374, 275557
-recovered pasa_asmbl_41591.p1, internal, 275896, 276064
-recovered pasa_asmbl_41591.p1, internal, 276432, 276570
Valid prediction for pasa_asmbl_41585.p1
Valid prediction for snap_scaffold_4-snap.1847-T1
Valid prediction for CodingQuarry_transcript_49087-T1
Valid prediction for GlimmerHMM_glimmerT_9821-T1
Valid prediction for snap_scaffold_4-snap.1856-T1
Couldn't classify 178552, 178645
Sorry, prediction pasa_asmbl_41579.p1 fails validation.
(ATG)	 CG	176968-177110	GT	AGG
(TTC)	 AG	177329-177431	GT	AAG
(CAG)	 AG	177522-177589	GT	AAG
(ATG)	 AG	178234-178299	GT	AGG
(GTC)	 AG	178552-178645	AG	TTA
-recovered pasa_asmbl_41579.p1, initial, 176968, 177110
-recovered pasa_asmbl_41579.p1, initial, 178234, 178299
-recovered pasa_asmbl_41579.p1, internal, 177329, 177431
-recovered pasa_asmbl_41579.p1, internal, 177522, 177589
-recovered pasa_asmbl_41579.p1, internal, 178234, 178299
Valid prediction for Augustus_model.g6399.t1
Valid prediction for GlimmerHMM_glimmerT_9845-T1
Valid prediction for snap_scaffold_4-snap.1832-T1
Valid prediction for Augustus_model.g6401.t1
Valid prediction for CodingQuarry_transcript_49092-T1
Valid prediction for GlimmerHMM_glimmerT_9841-T1
Valid prediction for Augustus_model.g6381.t1
Valid prediction for CodingQuarry_transcript_49084-T1
Valid prediction for Augustus_model.g6386.t1
Valid prediction for HiQ_model.g6374.t1
Valid prediction for Augustus_model.g6385.t1
Valid prediction for snap_scaffold_4-snap.1827-T1
Valid prediction for snap_scaffold_4-snap.1861-T1
Valid prediction for GlimmerHMM_glimmerT_9808-T1
Valid prediction for GlimmerHMM_glimmerT_9844-T1
Valid prediction for GlimmerHMM_glimmerT_9828-T1
Valid prediction for Augustus_model.g6388.t1
Valid prediction for GlimmerHMM_glimmerT_9824-T1
Valid prediction for pasa_asmbl_41587.p1
Valid prediction for GlimmerHMM_glimmerT_9840-T1
Valid prediction for GlimmerHMM_glimmerT_9831-T1
Valid prediction for snap_scaffold_4-snap.1853-T1
Valid prediction for snap_scaffold_4-snap.1840-T1
Couldn't classify 42017, 42111
Sorry, prediction pasa_asmbl_41570.p1 fails validation.
(ATG)	 GA	39454-39561	GT	ATG
(CTC)	 AG	39698-39825	GT	TGG
(GCA)	 AG	40258-40336	GT	AGG
(AAC)	 AG	40464-40626	GT	TGG
(ATA)	 AG	42017-42111	GT	TGG
-recovered pasa_asmbl_41570.p1, initial, 39454, 39561
-recovered pasa_asmbl_41570.p1, internal, 39698, 39825
-recovered pasa_asmbl_41570.p1, internal, 40258, 40336
-recovered pasa_asmbl_41570.p1, internal, 40464, 40626
-recovered pasa_asmbl_41570.p1, internal, 42017, 42111
Valid prediction for GlimmerHMM_glimmerT_9816-T1
Valid prediction for snap_scaffold_4-snap.1843-T1
Valid prediction for snap_scaffold_4-snap.1846-T1
Valid prediction for GlimmerHMM_glimmerT_9842-T1
Valid prediction for Augustus_model.g6382.t1
Valid prediction for snap_scaffold_4-snap.1863-T1
Valid prediction for GlimmerHMM_glimmerT_9830-T1
Valid prediction for snap_scaffold_4-snap.1808-T1
Valid prediction for GlimmerHMM_glimmerT_9838-T1
Couldn't classify 273061, 273184
Couldn't classify 273945, 274129
Sorry, prediction pasa_asmbl_41590.p2 fails validation.
(TGG)	 GC	273061-273184	GT	TGG
(TTG)	 AG	273771-273794	GT	AGG
(GCC)	 AG	273945-274129	GG	CAG
-recovered pasa_asmbl_41590.p2, internal, 273771, 273794
Valid prediction for Augustus_model.g6372.t1
Valid prediction for snap_scaffold_4-snap.1841-T1
Valid prediction for Augustus_model.g6400.t1
Valid prediction for snap_scaffold_4-snap.1866-T1
Valid prediction for snap_scaffold_4-snap.1809-T1
Valid prediction for snap_scaffold_4-snap.1857-T1
Valid prediction for Augustus_model.g6387.t1
Valid prediction for Augustus_model.g6396.t1
Valid prediction for snap_scaffold_4-snap.1845-T1
Valid prediction for snap_scaffold_4-snap.1842-T1
Couldn't classify 152759, 153006
Sorry, prediction pasa_asmbl_41576.p3 fails validation.
(AGC)	 GC	152759-153006	GT	AGG
(GGA)	 AG	153097-153175	TT	GAT
-recovered pasa_asmbl_41576.p3, terminal, 153097, 153175
Valid prediction for snap_scaffold_4-snap.1813-T1
Valid prediction for snap_scaffold_4-snap.1854-T1
Valid prediction for snap_scaffold_4-snap.1806-T1
Valid prediction for snap_scaffold_4-snap.1819-T1
Valid prediction for CodingQuarry_transcript_49085-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_4-snap.1830-T1
Valid prediction for GlimmerHMM_glimmerT_9814-T1
Valid prediction for GlimmerHMM_glimmerT_9820-T1
Valid prediction for HiQ_model.g6384.t1
Valid prediction for GlimmerHMM_glimmerT_9818-T1
Valid prediction for snap_scaffold_4-snap.1812-T1
Valid prediction for GlimmerHMM_glimmerT_9833-T1
Valid prediction for snap_scaffold_4-snap.1815-T1
Valid prediction for Augustus_model.g6371.t1
Valid prediction for snap_scaffold_4-snap.1833-T1
Valid prediction for pasa_asmbl_42793.p1
Valid prediction for GlimmerHMM_glimmerT_9822-T1
Valid prediction for snap_scaffold_4-snap.1821-T1
Valid prediction for GlimmerHMM_glimmerT_9823-T1
Valid prediction for snap_scaffold_4-snap.1838-T1
Valid prediction for snap_scaffold_4-snap.1828-T1
Valid prediction for pasa_asmbl_42788.p1
Valid prediction for Augustus_model.g6370.t1
Valid prediction for GlimmerHMM_glimmerT_9809-T1
Valid prediction for GlimmerHMM_glimmerT_9837-T1
Valid prediction for snap_scaffold_4-snap.1851-T1
Valid prediction for snap_scaffold_4-snap.1831-T1
Valid prediction for Augustus_model.g6380.t1
Valid prediction for snap_scaffold_4-snap.1836-T1
Valid prediction for Augustus_model.g6369.t1
Valid prediction for Augustus_model.g6377.t1
Couldn't classify 96700, 97533
Sorry, prediction pasa_asmbl_42790.p1 fails validation.
(ACT)	 AC	96700-97533	GG	GAG
Valid prediction for GlimmerHMM_glimmerT_9834-T1
Valid prediction for Augustus_model.g6389.t1
Valid prediction for snap_scaffold_4-snap.1825-T1
Valid prediction for GlimmerHMM_glimmerT_9811-T1
Valid prediction for GlimmerHMM_glimmerT_9817-T1
Valid prediction for snap_scaffold_4-snap.1849-T1
Valid prediction for GlimmerHMM_glimmerT_9819-T1
Valid prediction for CodingQuarry_transcript_49086-T1
Valid prediction for GlimmerHMM_glimmerT_9807-T1
Valid prediction for snap_scaffold_4-snap.1850-T1
Valid prediction for Augustus_model.g6379.t1
Valid prediction for Augustus_model.g6391.t1
Valid prediction for GlimmerHMM_glimmerT_9835-T1
Valid prediction for snap_scaffold_4-snap.1848-T1
Valid prediction for GlimmerHMM_glimmerT_9826-T1
Valid prediction for Augustus_model.g6393.t1
Valid prediction for snap_scaffold_4-snap.1826-T1
Valid prediction for Augustus_model.g6383.t1
Valid prediction for snap_scaffold_4-snap.1839-T1
Valid prediction for Augustus_model.g6376.t1
Valid prediction for GlimmerHMM_glimmerT_9812-T1
Valid prediction for CodingQuarry_transcript_49083-T1
Valid prediction for snap_scaffold_4-snap.1816-T1
Valid prediction for GlimmerHMM_glimmerT_9810-T1
Valid prediction for GlimmerHMM_glimmerT_9839-T1
Valid prediction for snap_scaffold_4-snap.1852-T1
Valid prediction for snap_scaffold_4-snap.1834-T1
Valid prediction for Augustus_model.g6390.t1
Valid prediction for pasa_asmbl_42780.p1
Valid prediction for snap_scaffold_4-snap.1860-T1
Valid prediction for snap_scaffold_4-snap.1807-T1
Valid prediction for CodingQuarry_transcript_49090-T1
Valid prediction for pasa_asmbl_42784.p1
Valid prediction for Augustus_model.g6378.t1
Valid prediction for HiQ_model.g6373.t1
Valid prediction for Augustus_model.g6368.t1
Valid prediction for snap_scaffold_4-snap.1822-T1
Valid prediction for GlimmerHMM_glimmerT_9825-T1
Valid prediction for snap_scaffold_4-snap.1824-T1
Valid prediction for snap_scaffold_4-snap.1818-T1
Valid prediction for snap_scaffold_4-snap.1837-T1
Valid prediction for snap_scaffold_4-snap.1811-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7936, rend_intergenic: 4501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19131, rend_intergenic: 8270  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30614, rend_intergenic: 26311  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35720, rend_intergenic: 32616  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52543, rend_intergenic: 46783  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56760, rend_intergenic: 52547  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64193, rend_intergenic: 62418  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71795, rend_intergenic: 64332  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86736, rend_intergenic: 83053  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97257, rend_intergenic: 86975  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105962, rend_intergenic: 97749  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113621, rend_intergenic: 107195  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115327, rend_intergenic: 114714  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130268, rend_intergenic: 128724  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135228, rend_intergenic: 130973  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 272974, rend_intergenic: 270588  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 302993
-exon list size: 536


building trellis

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-found 46 predictions from path traversal
Error with prediction: snap lend_intergenic: 7936, rend_intergenic: 4501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19131, rend_intergenic: 8270  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30614, rend_intergenic: 26311  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35720, rend_intergenic: 32616  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52543, rend_intergenic: 46783  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56760, rend_intergenic: 52547  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64193, rend_intergenic: 62418  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71795, rend_intergenic: 64332  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86736, rend_intergenic: 83053  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97257, rend_intergenic: 86975  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105962, rend_intergenic: 97749  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113621, rend_intergenic: 107195  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115327, rend_intergenic: 114714  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130268, rend_intergenic: 128724  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135228, rend_intergenic: 130973  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 272974, rend_intergenic: 270588  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 37 predictions persist after filtering for low support