-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_9891325-10069848

-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 GeneMark_model.12075_t
Valid prediction for Augustus_model.g4788.t1
Valid prediction for GeneMark_model.12070_t
Valid prediction for Augustus_model.g4796.t1
Valid prediction for GlimmerHMM_glimmerT_7300-T1
Valid prediction for GlimmerHMM_glimmerT_7289-T1
Valid prediction for snap_scaffold_3-snap.1970-T1
Valid prediction for GlimmerHMM_glimmerT_7296-T1
Valid prediction for GeneMark_model.12106_t
Valid prediction for GeneMark_model.12062_t
Couldn't classify 86220, 86304
Couldn't classify 87985, 88037
Sorry, prediction pasa_asmbl_40199.p1 fails validation.
(TCC)	 CC	86220-86304	GT	CTG
(CAT)	 AG	86427-86529	GT	AGG
(GTT)	 AG	87206-87270	GT	CCG
(TCC)	 AG	87985-88037	AG	CCA
-recovered pasa_asmbl_40199.p1, internal, 86427, 86529
-recovered pasa_asmbl_40199.p1, internal, 87206, 87270
Valid prediction for GlimmerHMM_glimmerT_7304-T1
Valid prediction for Augustus_model.g4784.t1
Valid prediction for GeneMark_model.12077_t
Valid prediction for GlimmerHMM_glimmerT_7309-T1
Valid prediction for snap_scaffold_3-snap.1965-T1
Valid prediction for snap_scaffold_3-snap.1981-T1
Valid prediction for GeneMark_model.12082_t
Valid prediction for GeneMark_model.12098_t
Valid prediction for GeneMark_model.12112_t
Valid prediction for snap_scaffold_3-snap.2001-T1
Valid prediction for GeneMark_model.12104_t
Valid prediction for GlimmerHMM_glimmerT_7303-T1
Valid prediction for snap_scaffold_3-snap.1986-T1
Valid prediction for Augustus_model.g4800.t1
Valid prediction for snap_scaffold_3-snap.1973-T1
Valid prediction for snap_scaffold_3-snap.1980-T1
Valid prediction for snap_scaffold_3-snap.1972-T1
Valid prediction for Augustus_model.g4797.t1
Valid prediction for Augustus_model.g4799.t1
Valid prediction for GeneMark_model.12117_t
Valid prediction for GeneMark_model.12061_t
Valid prediction for GeneMark_model.12087_t
Valid prediction for GeneMark_model.12096_t
Valid prediction for GeneMark_model.12090_t
Valid prediction for GeneMark_model.12108_t
Valid prediction for GlimmerHMM_glimmerT_7299-T1
Valid prediction for Augustus_model.g4789.t1
Valid prediction for snap_scaffold_3-snap.1991-T1
Valid prediction for GlimmerHMM_glimmerT_7312-T1
Valid prediction for GlimmerHMM_glimmerT_7297-T1
Valid prediction for GeneMark_model.12100_t
Valid prediction for snap_scaffold_3-snap.1993-T1
Valid prediction for GlimmerHMM_glimmerT_7313-T1
Valid prediction for GlimmerHMM_glimmerT_7310-T1
Valid prediction for snap_scaffold_3-snap.1971-T1
Valid prediction for Augustus_model.g4791.t1
Valid prediction for GeneMark_model.12088_t
Valid prediction for snap_scaffold_3-snap.1987-T1
Valid prediction for Augustus_model.g4780.t1
Valid prediction for GeneMark_model.12068_t
Valid prediction for Augustus_model.g4792.t1
Valid prediction for GeneMark_model.12114_t
Valid prediction for GeneMark_model.12083_t
Valid prediction for GeneMark_model.12072_t
Valid prediction for Augustus_model.g4790.t1
Valid prediction for snap_scaffold_3-snap.1996-T1
Valid prediction for snap_scaffold_3-snap.1995-T1
Valid prediction for snap_scaffold_3-snap.1984-T1
Valid prediction for GeneMark_model.12092_t
Valid prediction for GlimmerHMM_glimmerT_7287-T1
Valid prediction for snap_scaffold_3-snap.2002-T1
Valid prediction for GeneMark_model.12076_t
Valid prediction for GeneMark_model.12102_t
Valid prediction for snap_scaffold_3-snap.2004-T1
Valid prediction for snap_scaffold_3-snap.1968-T1
Valid prediction for GlimmerHMM_glimmerT_7291-T1
Valid prediction for snap_scaffold_3-snap.1967-T1
Valid prediction for GeneMark_model.12078_t
Valid prediction for snap_scaffold_3-snap.1978-T1
Valid prediction for GeneMark_model.12066_t
Valid prediction for GeneMark_model.12094_t
Valid prediction for snap_scaffold_3-snap.1994-T1
Valid prediction for GeneMark_model.12073_t
Valid prediction for GeneMark_model.12109_t
Valid prediction for GlimmerHMM_glimmerT_7306-T1
Valid prediction for snap_scaffold_3-snap.1997-T1
Valid prediction for GlimmerHMM_glimmerT_7295-T1
Valid prediction for GeneMark_model.12064_t
Valid prediction for GeneMark_model.12071_t
Valid prediction for GlimmerHMM_glimmerT_7302-T1
Valid prediction for GeneMark_model.12080_t
Valid prediction for GeneMark_model.12063_t
Valid prediction for Augustus_model.g4794.t1
Valid prediction for GeneMark_model.12085_t

-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 GeneMark_model.12103_t
Valid prediction for snap_scaffold_3-snap.1990-T1
Valid prediction for Augustus_model.g4795.t1
Valid prediction for Augustus_model.g4785.t1
Valid prediction for GeneMark_model.12089_t
Valid prediction for GlimmerHMM_glimmerT_7314-T1
Valid prediction for GlimmerHMM_glimmerT_7292-T1
Valid prediction for Augustus_model.g4782.t1
Valid prediction for snap_scaffold_3-snap.1983-T1
Valid prediction for GlimmerHMM_glimmerT_7307-T1
Valid prediction for GeneMark_model.12074_t
Valid prediction for GlimmerHMM_glimmerT_7290-T1
Valid prediction for snap_scaffold_3-snap.1979-T1
Valid prediction for GeneMark_model.12081_t
Valid prediction for Augustus_model.g4801.t1
Valid prediction for GlimmerHMM_glimmerT_7305-T1
Valid prediction for Augustus_model.g4786.t1
Valid prediction for GlimmerHMM_glimmerT_7298-T1
Valid prediction for snap_scaffold_3-snap.1998-T1
Valid prediction for GeneMark_model.12067_t
Valid prediction for GeneMark_model.12079_t
Valid prediction for GlimmerHMM_glimmerT_7288-T1
Valid prediction for Augustus_model.g4787.t1
Valid prediction for GlimmerHMM_glimmerT_7294-T1
Valid prediction for snap_scaffold_3-snap.1989-T1
Valid prediction for GeneMark_model.12095_t
Valid prediction for GeneMark_model.12099_t
Valid prediction for snap_scaffold_3-snap.1982-T1
Valid prediction for GeneMark_model.12118_t
Valid prediction for snap_scaffold_3-snap.1975-T1
Valid prediction for snap_scaffold_3-snap.2000-T1
Valid prediction for snap_scaffold_3-snap.1977-T1
Valid prediction for GeneMark_model.12110_t
Valid prediction for Augustus_model.g4781.t1
Valid prediction for GeneMark_model.12069_t
Valid prediction for GeneMark_model.12084_t
Valid prediction for snap_scaffold_3-snap.1966-T1
Valid prediction for GeneMark_model.12093_t
Valid prediction for GeneMark_model.12097_t
Valid prediction for GeneMark_model.12107_t
Valid prediction for snap_scaffold_3-snap.1988-T1
Valid prediction for GeneMark_model.12116_t
Valid prediction for GeneMark_model.12105_t
Valid prediction for GlimmerHMM_glimmerT_7301-T1
Valid prediction for GeneMark_model.12113_t
Valid prediction for GlimmerHMM_glimmerT_7311-T1
Valid prediction for Augustus_model.g4793.t1
Valid prediction for Augustus_model.g4798.t1
Valid prediction for GeneMark_model.12115_t
Valid prediction for GeneMark_model.12065_t
Valid prediction for snap_scaffold_3-snap.1976-T1
Valid prediction for GeneMark_model.12086_t
Valid prediction for snap_scaffold_3-snap.1985-T1
Valid prediction for Augustus_model.g4783.t1
Valid prediction for GlimmerHMM_glimmerT_7308-T1
Valid prediction for snap_scaffold_3-snap.1999-T1
Valid prediction for snap_scaffold_3-snap.1992-T1
Valid prediction for GlimmerHMM_glimmerT_7293-T1
Valid prediction for GeneMark_model.12101_t
Valid prediction for GeneMark_model.12111_t
Valid prediction for snap_scaffold_3-snap.2003-T1
Valid prediction for snap_scaffold_3-snap.1974-T1
Valid prediction for snap_scaffold_3-snap.1969-T1
Valid prediction for GeneMark_model.12091_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7515, rend_intergenic: 3544  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13894, rend_intergenic: 8741  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25109, rend_intergenic: 22753  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28674, rend_intergenic: 25970  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72004, rend_intergenic: 41654  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73709, rend_intergenic: 72855  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80070, rend_intergenic: 74288  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89112, rend_intergenic: 80720  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100044, rend_intergenic: 91829  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105820, rend_intergenic: 105679  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110976, rend_intergenic: 106102  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127054, rend_intergenic: 125335  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130446, rend_intergenic: 127298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134718, rend_intergenic: 133103  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147713, rend_intergenic: 145841  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172017, rend_intergenic: 169787  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176213, rend_intergenic: 173796  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 178524
-exon list size: 686


building trellis

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-found 43 predictions from path traversal
Error with prediction: snap lend_intergenic: 7515, rend_intergenic: 3544  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13894, rend_intergenic: 8741  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25109, rend_intergenic: 22753  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28674, rend_intergenic: 25970  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72004, rend_intergenic: 41654  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73709, rend_intergenic: 72855  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80070, rend_intergenic: 74288  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89112, rend_intergenic: 80720  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100044, rend_intergenic: 91829  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105820, rend_intergenic: 105679  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110976, rend_intergenic: 106102  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127054, rend_intergenic: 125335  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130446, rend_intergenic: 127298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134718, rend_intergenic: 133103  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147713, rend_intergenic: 145841  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172017, rend_intergenic: 169787  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176213, rend_intergenic: 173796  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support