-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_9/scaffold_9_12637685-12786223

-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_23587-T1
Valid prediction for snap_scaffold_9-snap.2521-T1
Valid prediction for GeneMark_model.40349_t
Valid prediction for GeneMark_model.40334_t
Valid prediction for snap_scaffold_9-snap.2524-T1
Valid prediction for GlimmerHMM_glimmerT_23579-T1
Valid prediction for Augustus_model.g15824.t1
Valid prediction for GeneMark_model.40347_t
Valid prediction for GeneMark_model.40320_t
Valid prediction for snap_scaffold_9-snap.2533-T1
Valid prediction for snap_scaffold_9-snap.2527-T1
Valid prediction for snap_scaffold_9-snap.2514-T1
Valid prediction for snap_scaffold_9-snap.2528-T1
Valid prediction for snap_scaffold_9-snap.2536-T1
Valid prediction for GeneMark_model.40321_t
Valid prediction for snap_scaffold_9-snap.2540-T1
Valid prediction for HiQ_model.g15823.t1
Valid prediction for GlimmerHMM_glimmerT_23578-T1
Valid prediction for GeneMark_model.40337_t
Valid prediction for GlimmerHMM_glimmerT_23588-T1
Valid prediction for CodingQuarry_transcript_62215-T1
Valid prediction for GeneMark_model.40307_t
Valid prediction for Augustus_model.g15816.t1
Valid prediction for GeneMark_model.40314_t
Valid prediction for GeneMark_model.40310_t
Valid prediction for GlimmerHMM_glimmerT_23580-T1
Valid prediction for GlimmerHMM_glimmerT_23585-T1
Valid prediction for GeneMark_model.40316_t
Valid prediction for Augustus_model.g15818.t1
Valid prediction for snap_scaffold_9-snap.2530-T1
Valid prediction for snap_scaffold_9-snap.2511-T1
Valid prediction for pasa_asmbl_54439.p1
Valid prediction for GeneMark_model.40346_t
Valid prediction for GeneMark_model.40318_t
Valid prediction for snap_scaffold_9-snap.2516-T1
Valid prediction for GeneMark_model.40312_t
Valid prediction for GeneMark_model.40327_t
Couldn't classify 67624, 69765
Sorry, prediction pasa_asmbl_54442.p1 fails validation.
(ATG)	 CG	67624-69765	AT	ACA
Valid prediction for GeneMark_model.40335_t
Valid prediction for CodingQuarry_transcript_62214-T1
Valid prediction for snap_scaffold_9-snap.2519-T1
Valid prediction for GlimmerHMM_glimmerT_23576-T1
Valid prediction for snap_scaffold_9-snap.2539-T1
Valid prediction for GeneMark_model.40330_t
Valid prediction for GlimmerHMM_glimmerT_23591-T1
Valid prediction for Augustus_model.g15819.t1
Valid prediction for GeneMark_model.40331_t
Valid prediction for GeneMark_model.40340_t
Valid prediction for GeneMark_model.40338_t
Valid prediction for GeneMark_model.40342_t
Valid prediction for GeneMark_model.40332_t
Valid prediction for GeneMark_model.40325_t
Couldn't classify 9490, 9681
Sorry, prediction pasa_asmbl_54438.p2 fails validation.
(CAG)	 CT	9490-9681	GT	AGG
(GTT)	 AG	9828-10094	AG	AGA
-recovered pasa_asmbl_54438.p2, terminal, 9828, 10094
Valid prediction for GeneMark_model.40323_t
Valid prediction for GlimmerHMM_glimmerT_23577-T1
Couldn't classify 70117, 70812
Sorry, prediction pasa_asmbl_54443.p1 fails validation.
(GCT)	 CT	70117-70812	GT	AGG
(GTG)	 AG	70915-71466	GT	AGG
(AAA)	 AG	73987-74125	GT	AGG
(GAC)	 AG	76582-76659	GT	GGG
(ACC)	 AG	77444-77575	GT	CAG
(AGA)	 AG	78468-78573	GT	AAG
(GGT)	 AG	78820-79345	AG	GAA
-recovered pasa_asmbl_54443.p1, terminal, 78820, 79345
-recovered pasa_asmbl_54443.p1, internal, 70915, 71466
-recovered pasa_asmbl_54443.p1, internal, 73987, 74125
-recovered pasa_asmbl_54443.p1, internal, 76582, 76659
-recovered pasa_asmbl_54443.p1, internal, 77444, 77575
-recovered pasa_asmbl_54443.p1, internal, 78468, 78573
Valid prediction for HiQ_model.g15821.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 GeneMark_model.40348_t
Valid prediction for snap_scaffold_9-snap.2517-T1
Valid prediction for CodingQuarry_transcript_62219-T1
Valid prediction for snap_scaffold_9-snap.2534-T1
Valid prediction for snap_scaffold_9-snap.2512-T1
Valid prediction for snap_scaffold_9-snap.2535-T1
Valid prediction for Augustus_model.g15827.t1
Valid prediction for CodingQuarry_transcript_62218-T1
Valid prediction for GlimmerHMM_glimmerT_23590-T1
Valid prediction for snap_scaffold_9-snap.2526-T1
Valid prediction for GlimmerHMM_glimmerT_23592-T1
Valid prediction for Augustus_model.g15817.t1
Valid prediction for GeneMark_model.40324_t
Valid prediction for snap_scaffold_9-snap.2538-T1
Valid prediction for GeneMark_model.40339_t
Valid prediction for GeneMark_model.40328_t
Valid prediction for GeneMark_model.40326_t
Valid prediction for GeneMark_model.40329_t
Valid prediction for GlimmerHMM_glimmerT_23581-T1
Valid prediction for pasa_asmbl_55364.p1
Valid prediction for snap_scaffold_9-snap.2531-T1
Valid prediction for GeneMark_model.40336_t
Valid prediction for HiQ_model.g15822.t1
Valid prediction for snap_scaffold_9-snap.2522-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.40309_t
Valid prediction for Augustus_model.g15826.t1
Valid prediction for snap_scaffold_9-snap.2518-T1
Valid prediction for GlimmerHMM_glimmerT_23583-T1
Valid prediction for snap_scaffold_9-snap.2541-T1
Valid prediction for CodingQuarry_transcript_62217-T1
Valid prediction for HiQ_model.g15825.t1
Valid prediction for snap_scaffold_9-snap.2515-T1
Valid prediction for snap_scaffold_9-snap.2523-T1
Valid prediction for pasa_asmbl_55361.p1
Valid prediction for GeneMark_model.40333_t
Valid prediction for GeneMark_model.40308_t
Valid prediction for GlimmerHMM_glimmerT_23582-T1
Valid prediction for GlimmerHMM_glimmerT_23586-T1
Valid prediction for CodingQuarry_transcript_62216-T1
Valid prediction for Augustus_model.g15820.t1
Valid prediction for GeneMark_model.40322_t
Valid prediction for GeneMark_model.40343_t
Valid prediction for snap_scaffold_9-snap.2520-T1
Valid prediction for GlimmerHMM_glimmerT_23584-T1
Valid prediction for GlimmerHMM_glimmerT_23589-T1
Valid prediction for GeneMark_model.40317_t
Valid prediction for GeneMark_model.40341_t
Valid prediction for snap_scaffold_9-snap.2537-T1
Valid prediction for GeneMark_model.40345_t
Valid prediction for GeneMark_model.40311_t
Valid prediction for snap_scaffold_9-snap.2513-T1
Valid prediction for GeneMark_model.40306_t
Valid prediction for GeneMark_model.40315_t
Valid prediction for snap_scaffold_9-snap.2529-T1
Valid prediction for GeneMark_model.40319_t
Valid prediction for snap_scaffold_9-snap.2532-T1
Valid prediction for snap_scaffold_9-snap.2525-T1
Valid prediction for GeneMark_model.40313_t
Valid prediction for GlimmerHMM_glimmerT_23593-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10094, rend_intergenic: 4052  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16951, rend_intergenic: 13655  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33325, rend_intergenic: 18451  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38888, rend_intergenic: 36384  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61787, rend_intergenic: 55859  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63688, rend_intergenic: 61993  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82119, rend_intergenic: 69187  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89999, rend_intergenic: 87638  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100533, rend_intergenic: 90047  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112935, rend_intergenic: 101838  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114443, rend_intergenic: 113326  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123324, rend_intergenic: 115040  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125465, rend_intergenic: 123364  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129951, rend_intergenic: 125534  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135444, rend_intergenic: 131665  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142547, rend_intergenic: 139821  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146630, rend_intergenic: 143871  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 148539
-exon list size: 612


building trellis

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98.2    
98.4    
98.5    
98.7    
98.9    
99.0    
99.2    
99.3    
99.5    
99.7    
99.8    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 10094, rend_intergenic: 4052  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16951, rend_intergenic: 13655  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33325, rend_intergenic: 18451  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38888, rend_intergenic: 36384  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61787, rend_intergenic: 55859  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63688, rend_intergenic: 61993  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82119, rend_intergenic: 69187  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89999, rend_intergenic: 87638  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100533, rend_intergenic: 90047  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112935, rend_intergenic: 101838  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114443, rend_intergenic: 113326  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123324, rend_intergenic: 115040  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125465, rend_intergenic: 123364  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129951, rend_intergenic: 125534  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135444, rend_intergenic: 131665  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142547, rend_intergenic: 139821  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146630, rend_intergenic: 143871  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support