-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_23/scaffold_23_8696564-8816504

-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: +)Couldn't classify 58511, 58615
Sorry, prediction pasa_asmbl_31071.p1 fails validation.
(CTG)	 TC	58511-58615	GT	AGG
(AAC)	 AG	58959-59124	GT	CGG
(ACA)	 AG	59256-59368	GT	GGG
(GTG)	 AG	59802-59979	GT	TAG
(ACA)	 AG	60328-60492	GT	ACG
(TGT)	 AG	60986-61155	GT	AGG
(GTT)	 AG	61316-61407	GT	AGG
(CGT)	 AG	62132-62411	CG	AGC
-recovered pasa_asmbl_31071.p1, terminal, 62132, 62411
-recovered pasa_asmbl_31071.p1, internal, 58959, 59124
-recovered pasa_asmbl_31071.p1, internal, 59256, 59368
-recovered pasa_asmbl_31071.p1, internal, 59802, 59979
-recovered pasa_asmbl_31071.p1, internal, 60328, 60492
-recovered pasa_asmbl_31071.p1, internal, 60986, 61155
-recovered pasa_asmbl_31071.p1, internal, 61316, 61407
Valid prediction for snap_scaffold_23-snap.1698-T1
Valid prediction for GeneMark_model.91496_t
Valid prediction for GlimmerHMM_glimmerT_52774-T1
Valid prediction for GeneMark_model.91501_t
Valid prediction for Augustus_model.g35471.t1
Valid prediction for HiQ_model.g35478.t1
Valid prediction for snap_scaffold_23-snap.1692-T1
Valid prediction for GeneMark_model.91516_t
Valid prediction for snap_scaffold_23-snap.1684-T1
Valid prediction for snap_scaffold_23-snap.1676-T1
Valid prediction for GlimmerHMM_glimmerT_52778-T1
Valid prediction for GlimmerHMM_glimmerT_52781-T1
Valid prediction for GeneMark_model.91499_t
Valid prediction for GeneMark_model.91498_t
Valid prediction for GeneMark_model.91522_t
Valid prediction for GlimmerHMM_glimmerT_52770-T1
Valid prediction for GeneMark_model.91509_t
Valid prediction for GeneMark_model.91520_t
Valid prediction for GeneMark_model.91512_t
Valid prediction for GlimmerHMM_glimmerT_52772-T1
Valid prediction for snap_scaffold_23-snap.1682-T1
Valid prediction for snap_scaffold_23-snap.1695-T1
Valid prediction for GlimmerHMM_glimmerT_52771-T1
Valid prediction for GeneMark_model.91505_t
Valid prediction for GeneMark_model.91523_t
Valid prediction for Augustus_model.g35474.t1
Valid prediction for Augustus_model.g35473.t1
Valid prediction for Augustus_model.g35476.t1
Valid prediction for GlimmerHMM_glimmerT_52776-T1
Valid prediction for GlimmerHMM_glimmerT_52773-T1
Valid prediction for snap_scaffold_23-snap.1670-T1
Valid prediction for GeneMark_model.91507_t
Valid prediction for snap_scaffold_23-snap.1669-T1
Valid prediction for Augustus_model.g35472.t1
Valid prediction for GeneMark_model.91518_t
Valid prediction for GeneMark_model.91492_t
Valid prediction for GeneMark_model.91513_t
Valid prediction for GeneMark_model.91495_t
Valid prediction for snap_scaffold_23-snap.1679-T1
Couldn't classify 68370, 68602
Sorry, prediction pasa_asmbl_31073.p1 fails validation.
(GGG)	 CA	68370-68602	GT	AGG
(CCC)	 AG	69381-69459	GT	AGG
(TCA)	 AG	70249-70367	GT	AAG
(GGA)	 AG	70833-70982	GT	GGG
(GGT)	 AG	71708-71756	AG	GAA
-recovered pasa_asmbl_31073.p1, terminal, 71708, 71756
-recovered pasa_asmbl_31073.p1, internal, 69381, 69459
-recovered pasa_asmbl_31073.p1, internal, 70249, 70367
-recovered pasa_asmbl_31073.p1, internal, 70833, 70982
Valid prediction for snap_scaffold_23-snap.1674-T1
Valid prediction for snap_scaffold_23-snap.1689-T1
Valid prediction for snap_scaffold_23-snap.1675-T1
Valid prediction for pasa_asmbl_31078.p1
Valid prediction for snap_scaffold_23-snap.1668-T1
Valid prediction for GeneMark_model.91511_t
Valid prediction for CodingQuarry_transcript_35699-T1
Valid prediction for GlimmerHMM_glimmerT_52777-T1
Valid prediction for snap_scaffold_23-snap.1672-T1
Valid prediction for Augustus_model.g35475.t1
Valid prediction for snap_scaffold_23-snap.1686-T1
Valid prediction for GeneMark_model.91503_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.91525_t
Valid prediction for GeneMark_model.91510_t
Valid prediction for snap_scaffold_23-snap.1677-T1
Valid prediction for GeneMark_model.91526_t
Valid prediction for GlimmerHMM_glimmerT_52765-T1
Valid prediction for snap_scaffold_23-snap.1688-T1
Valid prediction for GlimmerHMM_glimmerT_52779-T1
Valid prediction for GlimmerHMM_glimmerT_52763-T1
Valid prediction for snap_scaffold_23-snap.1673-T1
Valid prediction for GeneMark_model.91517_t
Valid prediction for GeneMark_model.91493_t
Valid prediction for Augustus_model.g35477.t1
Valid prediction for GlimmerHMM_glimmerT_52761-T1
Valid prediction for snap_scaffold_23-snap.1693-T1
Valid prediction for snap_scaffold_23-snap.1678-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_23-snap.1691-T1
Valid prediction for GlimmerHMM_glimmerT_52762-T1
Valid prediction for GeneMark_model.91514_t
Valid prediction for GeneMark_model.91508_t
Valid prediction for GlimmerHMM_glimmerT_52767-T1
Valid prediction for snap_scaffold_23-snap.1697-T1
Valid prediction for GeneMark_model.91506_t
Valid prediction for GlimmerHMM_glimmerT_52769-T1
Valid prediction for snap_scaffold_23-snap.1680-T1
Valid prediction for GeneMark_model.91497_t
Valid prediction for GeneMark_model.91504_t
Valid prediction for GlimmerHMM_glimmerT_52768-T1
Valid prediction for Augustus_model.g35470.t1
Valid prediction for GlimmerHMM_glimmerT_52766-T1
Valid prediction for GeneMark_model.91500_t
Valid prediction for GeneMark_model.91519_t
Valid prediction for GeneMark_model.91524_t
Valid prediction for snap_scaffold_23-snap.1685-T1
Valid prediction for snap_scaffold_23-snap.1687-T1
Valid prediction for snap_scaffold_23-snap.1690-T1
Valid prediction for GeneMark_model.91515_t
Valid prediction for GeneMark_model.91494_t
Valid prediction for GlimmerHMM_glimmerT_52764-T1
Valid prediction for GlimmerHMM_glimmerT_52780-T1
Valid prediction for snap_scaffold_23-snap.1681-T1
Valid prediction for snap_scaffold_23-snap.1671-T1
Valid prediction for snap_scaffold_23-snap.1694-T1
Valid prediction for GlimmerHMM_glimmerT_52775-T1
Valid prediction for snap_scaffold_23-snap.1696-T1
Valid prediction for snap_scaffold_23-snap.1683-T1
Valid prediction for GeneMark_model.91502_t
Valid prediction for GeneMark_model.91521_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9597, rend_intergenic: 5933  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21255, rend_intergenic: 11731  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38564, rend_intergenic: 37204  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47604, rend_intergenic: 45741  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59821, rend_intergenic: 56841  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63571, rend_intergenic: 60924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68542, rend_intergenic: 65523  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71800, rend_intergenic: 68564  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88451, rend_intergenic: 84378  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98240, rend_intergenic: 88894  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 119941
-exon list size: 482


building trellis

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-found 22 predictions from path traversal
Error with prediction: snap lend_intergenic: 9597, rend_intergenic: 5933  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21255, rend_intergenic: 11731  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38564, rend_intergenic: 37204  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47604, rend_intergenic: 45741  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59821, rend_intergenic: 56841  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63571, rend_intergenic: 60924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68542, rend_intergenic: 65523  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71800, rend_intergenic: 68564  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88451, rend_intergenic: 84378  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98240, rend_intergenic: 88894  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 11 predictions persist after filtering for low support