-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_9/scaffold_9_13749654-13957675

-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_9-snap.2767-T1
Valid prediction for Augustus_model.g15491.t1
Valid prediction for snap_scaffold_9-snap.2763-T1
Valid prediction for Augustus_model.g15493.t1
Valid prediction for snap_scaffold_9-snap.2766-T1
Valid prediction for GlimmerHMM_glimmerT_23249-T1
Valid prediction for snap_scaffold_9-snap.2735-T1
Valid prediction for snap_scaffold_9-snap.2762-T1
Valid prediction for Augustus_model.g15487.t1
Valid prediction for GlimmerHMM_glimmerT_23243-T1
Valid prediction for GlimmerHMM_glimmerT_23247-T1
Valid prediction for Augustus_model.g15484.t1
Valid prediction for snap_scaffold_9-snap.2729-T1
Valid prediction for GlimmerHMM_glimmerT_23245-T1
Valid prediction for GlimmerHMM_glimmerT_23236-T1
Valid prediction for snap_scaffold_9-snap.2747-T1
Valid prediction for GlimmerHMM_glimmerT_23250-T1
Valid prediction for snap_scaffold_9-snap.2727-T1
Valid prediction for Augustus_model.g15495.t1
Valid prediction for Augustus_model.g15490.t1
Valid prediction for snap_scaffold_9-snap.2760-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_9-snap.2737-T1
Valid prediction for snap_scaffold_9-snap.2733-T1
Valid prediction for snap_scaffold_9-snap.2755-T1
Valid prediction for GlimmerHMM_glimmerT_23239-T1
Valid prediction for snap_scaffold_9-snap.2743-T1
Valid prediction for snap_scaffold_9-snap.2770-T1
Valid prediction for snap_scaffold_9-snap.2730-T1
Valid prediction for Augustus_model.g15486.t1
Valid prediction for GlimmerHMM_glimmerT_23237-T1
Valid prediction for Augustus_model.g15485.t1
Valid prediction for GlimmerHMM_glimmerT_23242-T1
Valid prediction for snap_scaffold_9-snap.2756-T1
Valid prediction for snap_scaffold_9-snap.2744-T1
Valid prediction for snap_scaffold_9-snap.2768-T1
Valid prediction for Augustus_model.g15483.t1
Valid prediction for GlimmerHMM_glimmerT_23253-T1
Valid prediction for snap_scaffold_9-snap.2739-T1
Valid prediction for Augustus_model.g15488.t1
Valid prediction for snap_scaffold_9-snap.2750-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_9-snap.2740-T1
Valid prediction for GlimmerHMM_glimmerT_23248-T1
Valid prediction for Augustus_model.g15499.t1
Valid prediction for snap_scaffold_9-snap.2769-T1
Valid prediction for snap_scaffold_9-snap.2742-T1
Valid prediction for HiQ_model.g15494.t1
Valid prediction for GlimmerHMM_glimmerT_23252-T1
Valid prediction for snap_scaffold_9-snap.2759-T1
Valid prediction for GlimmerHMM_glimmerT_23246-T1
Valid prediction for snap_scaffold_9-snap.2764-T1
Valid prediction for pasa_asmbl_55450.p1
Valid prediction for GlimmerHMM_glimmerT_23259-T1
Couldn't classify 5004, 5611
Sorry, prediction pasa_asmbl_55466.p1 fails validation.
(ACA)	 AG	5004-5611	GT	AGG
(GAA)	 AG	6114-6410	GT	AAG
(TCT)	 AG	7313-7399	GT	CAG
(GCT)	 AG	7957-8208	GT	CAG
(CCT)	 AG	8341-8548	GT	AGG
(GTG)	 AG	8650-8784	TG	AGT
-recovered pasa_asmbl_55466.p1, terminal, 8650, 8784
-recovered pasa_asmbl_55466.p1, internal, 5004, 5611
-recovered pasa_asmbl_55466.p1, internal, 6114, 6410
-recovered pasa_asmbl_55466.p1, internal, 7313, 7399
-recovered pasa_asmbl_55466.p1, internal, 7957, 8208
-recovered pasa_asmbl_55466.p1, internal, 8341, 8548
Valid prediction for snap_scaffold_9-snap.2749-T1
Couldn't classify 55359, 55703
Sorry, prediction pasa_asmbl_55460.p1 fails validation.
(GAC)	 CC	55359-55703	AC	AGA
Valid prediction for GlimmerHMM_glimmerT_23238-T1
Valid prediction for snap_scaffold_9-snap.2765-T1
Valid prediction for HiQ_model.g15492.t1
Valid prediction for GlimmerHMM_glimmerT_23254-T1
Valid prediction for snap_scaffold_9-snap.2771-T1
Valid prediction for GlimmerHMM_glimmerT_23258-T1
Valid prediction for snap_scaffold_9-snap.2746-T1
Valid prediction for Augustus_model.g15500.t1
Couldn't classify 54819, 55193
Sorry, prediction pasa_asmbl_55461.p1 fails validation.
(GTC)	 AG	54819-55193	CA	CCC
Valid prediction for HiQ_model.g15498.t1
Valid prediction for GlimmerHMM_glimmerT_23256-T1
Valid prediction for snap_scaffold_9-snap.2732-T1
Valid prediction for GlimmerHMM_glimmerT_23257-T1
Couldn't classify 51188, 51721
Sorry, prediction pasa_asmbl_55463.p2 fails validation.
(AGG)	 GG	51188-51721	AA	GGA
Valid prediction for snap_scaffold_9-snap.2751-T1
Valid prediction for snap_scaffold_9-snap.2738-T1
Valid prediction for GlimmerHMM_glimmerT_23255-T1
Valid prediction for pasa_asmbl_55464.p1
Valid prediction for Augustus_model.g15497.t1
Valid prediction for GlimmerHMM_glimmerT_23244-T1
Couldn't classify 4467, 4691
Sorry, prediction pasa_asmbl_55469.p1 fails validation.
(ATG)	 CA	3303-3420	GT	AGG
(ACC)	 AG	3656-4272	GT	AGG
(GCC)	 AG	4467-4691	CA	GCC
-recovered pasa_asmbl_55469.p1, initial, 3303, 3420
-recovered pasa_asmbl_55469.p1, internal, 3656, 4272
Valid prediction for snap_scaffold_9-snap.2734-T1
Valid prediction for snap_scaffold_9-snap.2758-T1
Valid prediction for snap_scaffold_9-snap.2754-T1
Valid prediction for snap_scaffold_9-snap.2748-T1
Couldn't classify 64911, 65116
Sorry, prediction pasa_asmbl_55452.p1 fails validation.
(CTG)	 GA	64911-65116	GT	AGG
(AAG)	 AG	66416-66657	GT	AGG
(GTG)	 AG	66827-67350	AG	AAA
-recovered pasa_asmbl_55452.p1, terminal, 66827, 67350
-recovered pasa_asmbl_55452.p1, internal, 66416, 66657
Valid prediction for GlimmerHMM_glimmerT_23240-T1
Valid prediction for snap_scaffold_9-snap.2741-T1
Valid prediction for Augustus_model.g15496.t1
Valid prediction for snap_scaffold_9-snap.2728-T1
Valid prediction for snap_scaffold_9-snap.2752-T1
Valid prediction for snap_scaffold_9-snap.2731-T1
Valid prediction for CodingQuarry_transcript_62397-T1
Valid prediction for GlimmerHMM_glimmerT_23241-T1
Valid prediction for snap_scaffold_9-snap.2757-T1
Valid prediction for snap_scaffold_9-snap.2761-T1
Valid prediction for snap_scaffold_9-snap.2736-T1
Couldn't classify 58229, 58311
Couldn't classify 59148, 59381
Sorry, prediction pasa_asmbl_55459.p1 fails validation.
(TTC)	 AC	58229-58311	GT	CGG
(GCG)	 AG	58570-58653	GT	AGG
(GTC)	 AG	58826-58955	GT	AGG
(GGG)	 AG	59148-59381	TG	CCT
-recovered pasa_asmbl_55459.p1, internal, 58570, 58653
-recovered pasa_asmbl_55459.p1, internal, 58826, 58955
Valid prediction for snap_scaffold_9-snap.2745-T1
Valid prediction for Augustus_model.g15489.t1
Valid prediction for snap_scaffold_9-snap.2753-T1
Valid prediction for GlimmerHMM_glimmerT_23251-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 24698, rend_intergenic: 23386  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36533, rend_intergenic: 25181  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49724, rend_intergenic: 38967  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51331, rend_intergenic: 50492  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56596, rend_intergenic: 51939  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63192, rend_intergenic: 57329  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71448, rend_intergenic: 64190  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96747, rend_intergenic: 82777  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106740, rend_intergenic: 102153  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110849, rend_intergenic: 107460  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118643, rend_intergenic: 118633  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122336, rend_intergenic: 119086  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131911, rend_intergenic: 127620  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143703, rend_intergenic: 141638  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157189, rend_intergenic: 153797  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162456, rend_intergenic: 157231  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175348, rend_intergenic: 162524  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190915, rend_intergenic: 182555  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196253, rend_intergenic: 192561  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198930, rend_intergenic: 196820  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200050, rend_intergenic: 199239  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 208022
-exon list size: 479


building trellis

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-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 24698, rend_intergenic: 23386  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36533, rend_intergenic: 25181  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49724, rend_intergenic: 38967  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51331, rend_intergenic: 50492  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56596, rend_intergenic: 51939  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63192, rend_intergenic: 57329  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71448, rend_intergenic: 64190  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96747, rend_intergenic: 82777  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106740, rend_intergenic: 102153  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110849, rend_intergenic: 107460  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118643, rend_intergenic: 118633  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122336, rend_intergenic: 119086  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131911, rend_intergenic: 127620  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143703, rend_intergenic: 141638  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157189, rend_intergenic: 153797  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162456, rend_intergenic: 157231  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175348, rend_intergenic: 162524  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190915, rend_intergenic: 182555  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196253, rend_intergenic: 192561  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198930, rend_intergenic: 196820  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200050, rend_intergenic: 199239  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 10548
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support