-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_14/scaffold_14_12240141-12419105

-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_14-snap.2557-T1
Valid prediction for GlimmerHMM_glimmerT_35586-T1
Valid prediction for GlimmerHMM_glimmerT_35592-T1
Valid prediction for snap_scaffold_14-snap.2524-T1
Valid prediction for snap_scaffold_14-snap.2551-T1
Valid prediction for snap_scaffold_14-snap.2540-T1
Valid prediction for GeneMark_model.60996_t
Valid prediction for GeneMark_model.61017_t
Valid prediction for snap_scaffold_14-snap.2556-T1
Valid prediction for GlimmerHMM_glimmerT_35582-T1
Valid prediction for snap_scaffold_14-snap.2533-T1
Valid prediction for GeneMark_model.61019_t
Valid prediction for snap_scaffold_14-snap.2531-T1
Valid prediction for GeneMark_model.61023_t
Valid prediction for GeneMark_model.61015_t
Valid prediction for GlimmerHMM_glimmerT_35595-T1
Valid prediction for GeneMark_model.61012_t
Valid prediction for CodingQuarry_transcript_15828-T1
Valid prediction for GeneMark_model.61025_t
Valid prediction for snap_scaffold_14-snap.2527-T1
Valid prediction for snap_scaffold_14-snap.2549-T1
Valid prediction for CodingQuarry_transcript_15826-T1
Valid prediction for GeneMark_model.61013_t
Valid prediction for GlimmerHMM_glimmerT_35594-T1
Valid prediction for GeneMark_model.61021_t
Valid prediction for snap_scaffold_14-snap.2528-T1
Valid prediction for HiQ_model.g23953.t1
Valid prediction for pasa_asmbl_12403.p1
Valid prediction for snap_scaffold_14-snap.2543-T1
Valid prediction for snap_scaffold_14-snap.2542-T1
Valid prediction for GeneMark_model.60998_t
Valid prediction for GlimmerHMM_glimmerT_35588-T1
Valid prediction for snap_scaffold_14-snap.2538-T1
Valid prediction for snap_scaffold_14-snap.2552-T1
Valid prediction for Augustus_model.g23961.t1
Valid prediction for Augustus_model.g23964.t1
Valid prediction for pasa_asmbl_12406.p1
Valid prediction for Augustus_model.g23960.t1
Valid prediction for GeneMark_model.61010_t
Valid prediction for snap_scaffold_14-snap.2555-T1
Valid prediction for GlimmerHMM_glimmerT_35580-T1
Valid prediction for Augustus_model.g23955.t1
Valid prediction for GlimmerHMM_glimmerT_35598-T1
Valid prediction for Augustus_model.g23949.t1
Valid prediction for CodingQuarry_transcript_15829-T1
Valid prediction for GeneMark_model.60997_t
Valid prediction for GlimmerHMM_glimmerT_35577-T1
Valid prediction for HiQ_model.g23958.t1
Valid prediction for Augustus_model.g23959.t1
Valid prediction for GlimmerHMM_glimmerT_35573-T1
Valid prediction for Augustus_model.g23946.t1
Valid prediction for GeneMark_model.61008_t
Valid prediction for GlimmerHMM_glimmerT_35590-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 GlimmerHMM_glimmerT_35584-T1
Couldn't classify 93397, 93567
Sorry, prediction pasa_asmbl_13548.p1 fails validation.
(AAA)	 TG	93397-93567	GT	AGG
(CGC)	 AG	93776-93964	TG	GAT
-recovered pasa_asmbl_13548.p1, terminal, 93776, 93964
Valid prediction for snap_scaffold_14-snap.2537-T1
Valid prediction for HiQ_model.g23951.t1
Valid prediction for snap_scaffold_14-snap.2534-T1
Valid prediction for snap_scaffold_14-snap.2548-T1
Valid prediction for Augustus_model.g23950.t1
Valid prediction for GlimmerHMM_glimmerT_35575-T1
Valid prediction for GlimmerHMM_glimmerT_35581-T1
Valid prediction for GeneMark_model.61005_t
Valid prediction for GeneMark_model.61002_t
Valid prediction for GlimmerHMM_glimmerT_35585-T1
Valid prediction for GlimmerHMM_glimmerT_35587-T1
Valid prediction for snap_scaffold_14-snap.2558-T1
Valid prediction for snap_scaffold_14-snap.2546-T1
Valid prediction for GeneMark_model.61004_t
Valid prediction for GeneMark_model.60999_t
Valid prediction for Augustus_model.g23948.t1
Valid prediction for GlimmerHMM_glimmerT_35576-T1
Valid prediction for GlimmerHMM_glimmerT_35591-T1
Valid prediction for GlimmerHMM_glimmerT_35597-T1
Valid prediction for Augustus_model.g23954.t1
Couldn't classify 74102, 74218
Couldn't classify 75079, 75174
Sorry, prediction pasa_asmbl_13837.p1 fails validation.
(GTG)	 AG	74102-74218	GT	AGG
(GTT)	 AG	74387-74517	GT	AAG
(GAC)	 AG	74611-74677	GT	AGG
(GGT)	 AG	74756-74847	GT	AAG
(GAA)	 AG	74937-74991	GT	AGG
(GAG)	 AG	75079-75174	TA	GGT
-recovered pasa_asmbl_13837.p1, internal, 74102, 74218
-recovered pasa_asmbl_13837.p1, internal, 74387, 74517
-recovered pasa_asmbl_13837.p1, internal, 74611, 74677
-recovered pasa_asmbl_13837.p1, internal, 74756, 74847
-recovered pasa_asmbl_13837.p1, internal, 74937, 74991
Valid prediction for pasa_asmbl_13838.p1
Valid prediction for Augustus_model.g23963.t1
Valid prediction for snap_scaffold_14-snap.2532-T1
Valid prediction for GlimmerHMM_glimmerT_35596-T1
Valid prediction for snap_scaffold_14-snap.2535-T1
Valid prediction for CodingQuarry_transcript_15827-T1
Valid prediction for GlimmerHMM_glimmerT_35589-T1
Valid prediction for GeneMark_model.61011_t
Valid prediction for snap_scaffold_14-snap.2553-T1
Valid prediction for GeneMark_model.61003_t
Valid prediction for GeneMark_model.61000_t
Valid prediction for CodingQuarry_transcript_15825-T1
Valid prediction for Augustus_model.g23945.t1
Valid prediction for pasa_asmbl_13545.p1
Valid prediction for GlimmerHMM_glimmerT_35599-T1
Valid prediction for snap_scaffold_14-snap.2523-T1
Valid prediction for GeneMark_model.61022_t
Valid prediction for snap_scaffold_14-snap.2547-T1
Couldn't classify 102397, 102936
Sorry, prediction pasa_asmbl_13546.p2 fails validation.
(GTG)	 AC	102397-102936	GC	GAG
Valid prediction for GlimmerHMM_glimmerT_35583-T1
Couldn't classify 73785, 73872
Sorry, prediction pasa_asmbl_13551.p1 fails validation.
(ATG)	 AC	72479-72517	GT	AGG
(TTT)	 AG	72962-73090	GT	AGG
(CCA)	 AG	73254-73413	GT	AGG
(GCC)	 AG	73641-73698	GT	TGG
(GGA)	 AG	73785-73872	GA	ACG
-recovered pasa_asmbl_13551.p1, initial, 72479, 72517
-recovered pasa_asmbl_13551.p1, internal, 72962, 73090
-recovered pasa_asmbl_13551.p1, internal, 73254, 73413
-recovered pasa_asmbl_13551.p1, internal, 73641, 73698
Valid prediction for pasa_asmbl_13552.p1
Valid prediction for GeneMark_model.61007_t
Valid prediction for snap_scaffold_14-snap.2536-T1
Valid prediction for HiQ_model.g23952.t1
Valid prediction for GlimmerHMM_glimmerT_35593-T1
Valid prediction for snap_scaffold_14-snap.2545-T1
Valid prediction for snap_scaffold_14-snap.2554-T1
Valid prediction for GlimmerHMM_glimmerT_35574-T1
Valid prediction for snap_scaffold_14-snap.2526-T1
Valid prediction for snap_scaffold_14-snap.2530-T1
Valid prediction for snap_scaffold_14-snap.2544-T1
Valid prediction for CodingQuarry_transcript_15823-T1
Valid prediction for GeneMark_model.61014_t
Valid prediction for GeneMark_model.61020_t
Valid prediction for HiQ_model.g23956.t1
Valid prediction for snap_scaffold_14-snap.2550-T1
Valid prediction for GeneMark_model.61018_t
Valid prediction for snap_scaffold_14-snap.2539-T1
Valid prediction for GeneMark_model.61024_t
Valid prediction for HiQ_model.g23957.t1
Valid prediction for GeneMark_model.61001_t
Valid prediction for snap_scaffold_14-snap.2525-T1
Valid prediction for CodingQuarry_transcript_15824-T1
Valid prediction for Augustus_model.g23962.t1
Valid prediction for GlimmerHMM_glimmerT_35579-T1
Valid prediction for snap_scaffold_14-snap.2541-T1
Valid prediction for GeneMark_model.61016_t
Valid prediction for HiQ_model.g23947.t1
Valid prediction for GeneMark_model.61026_t
Valid prediction for GlimmerHMM_glimmerT_35578-T1
Valid prediction for GeneMark_model.61009_t
Valid prediction for snap_scaffold_14-snap.2529-T1
Valid prediction for snap_scaffold_14-snap.2559-T1
Valid prediction for pasa_asmbl_13547.p1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 52154, rend_intergenic: 49696  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135671, rend_intergenic: 131740  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138958, rend_intergenic: 136159  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143359, rend_intergenic: 141931  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 178965
-exon list size: 450


building trellis

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-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 52154, rend_intergenic: 49696  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135671, rend_intergenic: 131740  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138958, rend_intergenic: 136159  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143359, rend_intergenic: 141931  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support