-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_3/scaffold_3_8275562-8524177

-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_3-snap.1701-T1
Valid prediction for snap_scaffold_3-snap.1688-T1
Valid prediction for Augustus_model.g4541.t1
Valid prediction for snap_scaffold_3-snap.1728-T1
Valid prediction for Augustus_model.g4528.t1
Valid prediction for GlimmerHMM_glimmerT_6953-T1
Valid prediction for Augustus_model.g4530.t1
Valid prediction for GlimmerHMM_glimmerT_6947-T1
Valid prediction for Augustus_model.g4543.t1
Valid prediction for Augustus_model.g4545.t1
Valid prediction for Augustus_model.g4554.t1
Valid prediction for Augustus_model.g4555.t1
Valid prediction for Augustus_model.g4540.t1
Valid prediction for snap_scaffold_3-snap.1705-T1
Valid prediction for GlimmerHMM_glimmerT_6942-T1
Valid prediction for snap_scaffold_3-snap.1696-T1
Valid prediction for GlimmerHMM_glimmerT_6943-T1
Valid prediction for Augustus_model.g4533.t1
Valid prediction for snap_scaffold_3-snap.1703-T1
Valid prediction for snap_scaffold_3-snap.1725-T1
Couldn't classify 145926, 145971
Sorry, prediction pasa_asmbl_40212.p1 fails validation.
(TGC)	 CC	145926-145971	GT	AGG
(TAA)	 AG	146990-147034	GT	AGG
(CAT)	 AG	147568-147773	GT	AGG
(ACC)	 AG	148858-149034	GA	GAG
-recovered pasa_asmbl_40212.p1, terminal, 148858, 149034
-recovered pasa_asmbl_40212.p1, internal, 146990, 147034
-recovered pasa_asmbl_40212.p1, internal, 147568, 147773
Valid prediction for GlimmerHMM_glimmerT_6964-T1
Valid prediction for snap_scaffold_3-snap.1685-T1
Valid prediction for GlimmerHMM_glimmerT_6962-T1
Valid prediction for Augustus_model.g4535.t1
Valid prediction for snap_scaffold_3-snap.1679-T1
Valid prediction for snap_scaffold_3-snap.1706-T1
Valid prediction for GlimmerHMM_glimmerT_6948-T1
Valid prediction for snap_scaffold_3-snap.1710-T1
Valid prediction for snap_scaffold_3-snap.1699-T1
Valid prediction for CodingQuarry_transcript_46226-T1
Couldn't classify 191805, 191861
Sorry, prediction pasa_asmbl_40216.p1 fails validation.
(AGG)	 GG	191805-191861	GT	AGG
(GTG)	 AG	192771-192854	GT	TGG
(GAA)	 AG	193312-193422	GT	AGG
(GAA)	 AG	193915-194451	AC	GAA
-recovered pasa_asmbl_40216.p1, terminal, 193915, 194451
-recovered pasa_asmbl_40216.p1, internal, 192771, 192854
-recovered pasa_asmbl_40216.p1, internal, 193312, 193422
Valid prediction for Augustus_model.g4544.t1
Valid prediction for Augustus_model.g4529.t1
Valid prediction for Augustus_model.g4549.t1
Valid prediction for snap_scaffold_3-snap.1697-T1
Valid prediction for Augustus_model.g4536.t1
Valid prediction for snap_scaffold_3-snap.1718-T1
Valid prediction for snap_scaffold_3-snap.1716-T1
Valid prediction for snap_scaffold_3-snap.1675-T1
Valid prediction for snap_scaffold_3-snap.1690-T1
Valid prediction for snap_scaffold_3-snap.1714-T1
Couldn't classify 132446, 132641
Couldn't classify 132915, 133027
Sorry, prediction pasa_asmbl_40820.p1 fails validation.
(GAT)	 TC	132446-132641	GT	AGG
(AGT)	 AG	132915-133027	CA	TAC
Valid prediction for snap_scaffold_3-snap.1677-T1
Valid prediction for snap_scaffold_3-snap.1689-T1
Valid prediction for GlimmerHMM_glimmerT_6945-T1
Valid prediction for Augustus_model.g4539.t1
Valid prediction for GlimmerHMM_glimmerT_6963-T1
Valid prediction for GlimmerHMM_glimmerT_6940-T1
Valid prediction for snap_scaffold_3-snap.1708-T1
Valid prediction for GlimmerHMM_glimmerT_6936-T1
Valid prediction for snap_scaffold_3-snap.1687-T1
Valid prediction for GlimmerHMM_glimmerT_6956-T1
Valid prediction for GlimmerHMM_glimmerT_6944-T1
Valid prediction for snap_scaffold_3-snap.1692-T1
Valid prediction for GlimmerHMM_glimmerT_6950-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_3-snap.1700-T1
Valid prediction for snap_scaffold_3-snap.1695-T1
Valid prediction for snap_scaffold_3-snap.1680-T1
Valid prediction for Augustus_model.g4547.t1
Valid prediction for Augustus_model.g4531.t1
Valid prediction for GlimmerHMM_glimmerT_6952-T1
Valid prediction for Augustus_model.g4553.t1
Couldn't classify 188531, 188613
Couldn't classify 201404, 201474
Sorry, prediction pasa_asmbl_39036.p1 fails validation.
(GAT)	 GA	188531-188613	GT	AAG
(GGA)	 AG	188704-188749	GT	AGG
(TCC)	 AG	189303-189395	GT	AGG
(GAC)	 AG	190329-190389	GT	CTG
(GGT)	 AG	190665-190732	GT	ATG
(GTG)	 AG	192095-192186	GT	CAG
(GAA)	 AG	194135-194206	GT	AAG
(CCC)	 AG	195706-195842	GT	CTG
(GGT)	 AG	198103-198173	GT	ACG
(AGC)	 AG	199113-199276	GT	AAG
(CCC)	 AG	199445-199575	GT	CTG
(GGT)	 AG	201404-201474	GT	AGG
-recovered pasa_asmbl_39036.p1, internal, 188704, 188749
-recovered pasa_asmbl_39036.p1, internal, 189303, 189395
-recovered pasa_asmbl_39036.p1, internal, 190329, 190389
-recovered pasa_asmbl_39036.p1, internal, 190665, 190732
-recovered pasa_asmbl_39036.p1, internal, 192095, 192186
-recovered pasa_asmbl_39036.p1, internal, 194135, 194206
-recovered pasa_asmbl_39036.p1, internal, 195706, 195842
-recovered pasa_asmbl_39036.p1, internal, 198103, 198173
-recovered pasa_asmbl_39036.p1, internal, 199113, 199276
-recovered pasa_asmbl_39036.p1, internal, 199445, 199575
-recovered pasa_asmbl_39036.p1, internal, 201404, 201474
Valid prediction for GlimmerHMM_glimmerT_6946-T1
Valid prediction for snap_scaffold_3-snap.1721-T1
Valid prediction for GlimmerHMM_glimmerT_6957-T1
Valid prediction for snap_scaffold_3-snap.1724-T1
Valid prediction for snap_scaffold_3-snap.1712-T1
Valid prediction for CodingQuarry_transcript_46225-T1
Valid prediction for Augustus_model.g4538.t1
Valid prediction for snap_scaffold_3-snap.1722-T1
Valid prediction for snap_scaffold_3-snap.1709-T1
Valid prediction for snap_scaffold_3-snap.1704-T1
Valid prediction for GlimmerHMM_glimmerT_6960-T1
Valid prediction for Augustus_model.g4537.t1
Couldn't classify 68166, 68433
Sorry, prediction pasa_asmbl_39038.p1 fails validation.
(TTT)	 GG	68166-68433	GT	AGG
(AGT)	 AG	69371-69555	GC	AGG
-recovered pasa_asmbl_39038.p1, terminal, 69371, 69555
-recovered pasa_asmbl_39038.p1, internal, 69371, 69555
Valid prediction for snap_scaffold_3-snap.1698-T1
Valid prediction for snap_scaffold_3-snap.1720-T1
Valid prediction for snap_scaffold_3-snap.1713-T1
Valid prediction for snap_scaffold_3-snap.1693-T1
Valid prediction for CodingQuarry_transcript_46227-T1
Valid prediction for GlimmerHMM_glimmerT_6938-T1
Valid prediction for GlimmerHMM_glimmerT_6941-T1
Valid prediction for pasa_asmbl_39042.p1
Valid prediction for snap_scaffold_3-snap.1694-T1
Valid prediction for snap_scaffold_3-snap.1727-T1
Valid prediction for CodingQuarry_transcript_46229-T1
Valid prediction for Augustus_model.g4548.t1
Valid prediction for HiQ_model.g4552.t1
Valid prediction for snap_scaffold_3-snap.1686-T1
Valid prediction for Augustus_model.g4542.t1
Valid prediction for snap_scaffold_3-snap.1715-T1
Valid prediction for GlimmerHMM_glimmerT_6955-T1
Valid prediction for Augustus_model.g4532.t1
Valid prediction for snap_scaffold_3-snap.1678-T1
Valid prediction for snap_scaffold_3-snap.1681-T1
Valid prediction for Augustus_model.g4550.t1
Valid prediction for Augustus_model.g4534.t1
Valid prediction for GlimmerHMM_glimmerT_6958-T1
Valid prediction for snap_scaffold_3-snap.1711-T1
Valid prediction for snap_scaffold_3-snap.1707-T1
Valid prediction for snap_scaffold_3-snap.1682-T1
Valid prediction for GlimmerHMM_glimmerT_6961-T1
Valid prediction for snap_scaffold_3-snap.1683-T1
Valid prediction for Augustus_model.g4546.t1
Valid prediction for snap_scaffold_3-snap.1719-T1
Valid prediction for snap_scaffold_3-snap.1676-T1
Valid prediction for GlimmerHMM_glimmerT_6939-T1
Valid prediction for snap_scaffold_3-snap.1723-T1
Valid prediction for GlimmerHMM_glimmerT_6954-T1
Valid prediction for Augustus_model.g4551.t1
Valid prediction for snap_scaffold_3-snap.1726-T1
Valid prediction for GlimmerHMM_glimmerT_6949-T1
Valid prediction for snap_scaffold_3-snap.1702-T1
Valid prediction for snap_scaffold_3-snap.1684-T1
Couldn't classify 41029, 41124
Sorry, prediction pasa_asmbl_39040.p1 fails validation.
(GGG)	 AA	41029-41124	GT	CGG
(ACG)	 AG	41233-41399	GT	CGG
(AAT)	 AG	41584-41665	GT	ATG
(ACC)	 AG	41780-41983	GT	GGG
(TTG)	 AG	42809-42970	TA	AGT
-recovered pasa_asmbl_39040.p1, terminal, 42809, 42970
-recovered pasa_asmbl_39040.p1, internal, 41233, 41399
-recovered pasa_asmbl_39040.p1, internal, 41584, 41665
-recovered pasa_asmbl_39040.p1, internal, 41780, 41983
Valid prediction for pasa_asmbl_39032.p1
Valid prediction for GlimmerHMM_glimmerT_6959-T1
Valid prediction for GlimmerHMM_glimmerT_6937-T1
Valid prediction for snap_scaffold_3-snap.1691-T1
Valid prediction for GlimmerHMM_glimmerT_6951-T1
Valid prediction for snap_scaffold_3-snap.1717-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 173492, rend_intergenic: 173489  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10171, rend_intergenic: 5345  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11002, rend_intergenic: 10402  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14220, rend_intergenic: 12610  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21874, rend_intergenic: 14438  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28655, rend_intergenic: 23942  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53484, rend_intergenic: 49936  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54559, rend_intergenic: 54068  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68022, rend_intergenic: 61520  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85172, rend_intergenic: 82619  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86751, rend_intergenic: 85202  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104428, rend_intergenic: 97487  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114209, rend_intergenic: 112739  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116764, rend_intergenic: 114648  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127076, rend_intergenic: 122225  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134669, rend_intergenic: 129282  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139488, rend_intergenic: 138447  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181387, rend_intergenic: 173397  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 239468, rend_intergenic: 223623  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 248616
-exon list size: 508


building trellis

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-found 37 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 173492, rend_intergenic: 173489  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10171, rend_intergenic: 5345  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11002, rend_intergenic: 10402  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14220, rend_intergenic: 12610  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21874, rend_intergenic: 14438  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28655, rend_intergenic: 23942  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53484, rend_intergenic: 49936  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54559, rend_intergenic: 54068  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68022, rend_intergenic: 61520  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85172, rend_intergenic: 82619  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86751, rend_intergenic: 85202  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104428, rend_intergenic: 97487  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114209, rend_intergenic: 112739  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116764, rend_intergenic: 114648  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127076, rend_intergenic: 122225  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134669, rend_intergenic: 129282  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139488, rend_intergenic: 138447  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181387, rend_intergenic: 173397  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 239468, rend_intergenic: 223623  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 26 predictions persist after filtering for low support