-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_14601462-14778406

-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.2715_t
Couldn't classify 20755, 20844
Couldn't classify 21591, 21693
Sorry, prediction pasa_asmbl_2819.p1 fails validation.
(GCC)	 CA	20755-20844	GT	CTG
(GAG)	 AG	21116-21210	GT	AGG
(GTA)	 AG	21326-21430	GT	TGG
(GTA)	 AG	21591-21693	GC	ATG
-recovered pasa_asmbl_2819.p1, internal, 21116, 21210
-recovered pasa_asmbl_2819.p1, internal, 21326, 21430
-recovered pasa_asmbl_2819.p1, internal, 21591, 21693
Valid prediction for GeneMark_model.2728_t
Valid prediction for GlimmerHMM_glimmerT_1958-T1
Valid prediction for Augustus_model.g1462.t1
Valid prediction for snap_scaffold_1-snap.2535-T1
Valid prediction for GeneMark_model.2741_t
Valid prediction for GlimmerHMM_glimmerT_1962-T1
Valid prediction for snap_scaffold_1-snap.2531-T1
Valid prediction for CodingQuarry_transcript_2920-T1
Valid prediction for snap_scaffold_1-snap.2530-T1
Valid prediction for GlimmerHMM_glimmerT_1973-T1
Valid prediction for Augustus_model.g1472.t1
Valid prediction for GeneMark_model.2705_t
Valid prediction for snap_scaffold_1-snap.2556-T1
Valid prediction for GeneMark_model.2704_t
Valid prediction for GlimmerHMM_glimmerT_1976-T1
Valid prediction for GeneMark_model.2726_t
Valid prediction for GlimmerHMM_glimmerT_1960-T1
Valid prediction for GeneMark_model.2718_t
Valid prediction for GeneMark_model.2730_t
Valid prediction for snap_scaffold_1-snap.2545-T1
Valid prediction for GlimmerHMM_glimmerT_1974-T1
Valid prediction for Augustus_model.g1463.t1
Valid prediction for GeneMark_model.2708_t
Valid prediction for snap_scaffold_1-snap.2541-T1
Valid prediction for CodingQuarry_transcript_2919-T1
Couldn't classify 5853, 5869
Sorry, prediction pasa_asmbl_2380.p1 fails validation.
(GCG)	 TG	5853-5869	GT	CCG
(GAT)	 AG	6825-6945	GT	AGG
(ACT)	 AG	7068-7148	GT	TGG
(GCC)	 AG	7288-7370	GT	AGG
(ACC)	 AG	7465-7545	GT	CCG
(ACA)	 AG	7667-7710	GT	ACG
(AAT)	 AG	7797-7861	GT	TGG
(CTT)	 AG	7967-8122	GT	AGG
(ATC)	 AG	8243-8345	GT	AGG
(ATG)	 AG	8450-8563	GT	GGG
(GTG)	 AG	8837-8890	GT	TGG
(CGG)	 AG	9050-9086	GT	AGG
(TGC)	 AG	9196-9277	GT	AGG
(GAT)	 AG	9380-9480	GT	CTG
(ACA)	 AG	9622-9685	GT	AGG
(AGT)	 AG	9832-9886	GT	AGG
(AAC)	 AG	10453-10541	GA	AGG
add_exon() Sorry, pasa_asmbl_2380.p1 8450-8563-initial-1 is invalid.
-recovered pasa_asmbl_2380.p1, initial, 8450, 8563
-recovered pasa_asmbl_2380.p1, terminal, 10453, 10541
-recovered pasa_asmbl_2380.p1, internal, 6825, 6945
-recovered pasa_asmbl_2380.p1, internal, 7068, 7148
-recovered pasa_asmbl_2380.p1, internal, 7288, 7370
-recovered pasa_asmbl_2380.p1, internal, 7465, 7545
-recovered pasa_asmbl_2380.p1, internal, 7667, 7710
-recovered pasa_asmbl_2380.p1, internal, 7797, 7861
-recovered pasa_asmbl_2380.p1, internal, 7967, 8122
-recovered pasa_asmbl_2380.p1, internal, 8243, 8345
-recovered pasa_asmbl_2380.p1, internal, 8450, 8563
-recovered pasa_asmbl_2380.p1, internal, 8837, 8890
-recovered pasa_asmbl_2380.p1, internal, 9050, 9086
-recovered pasa_asmbl_2380.p1, internal, 9196, 9277
-recovered pasa_asmbl_2380.p1, internal, 9380, 9480
-recovered pasa_asmbl_2380.p1, internal, 9622, 9685
-recovered pasa_asmbl_2380.p1, internal, 9832, 9886
Valid prediction for GeneMark_model.2725_t
Valid prediction for snap_scaffold_1-snap.2548-T1
Valid prediction for Augustus_model.g1469.t1
Valid prediction for snap_scaffold_1-snap.2562-T1
Valid prediction for GeneMark_model.2731_t
Valid prediction for snap_scaffold_1-snap.2551-T1
Valid prediction for GeneMark_model.2703_t
Valid prediction for GeneMark_model.2720_t
Couldn't classify 13828, 13972
Sorry, prediction CodingQuarry_transcript_2921-T1 fails validation.
(ATG)	 GA	11658-11793	GT	CGG
(ATG)	 AG	11900-13278	GT	AGG
(GTG)	 AG	13496-13599	GT	GAG
(GAC)	 GG	13828-13972	GT	AGG
(GAG)	 AG	14054-14159	GT	GGG
(GTG)	 AG	14240-14382	GT	AGG
(GTT)	 AG	14710-14876	GT	AAG
(GGA)	 AG	15026-15182	GT	AGG
(GTA)	 AG	15278-15370	GT	AGG
(AGA)	 AG	15534-15690	GT	AGG
(TGG)	 AG	15802-15994	GT	AGG
(AGA)	 AG	16157-16226	GT	AGG
(CTT)	 AG	16310-16402	GT	AGG
(GAG)	 AG	16520-16642	GT	TGG
(GAT)	 AG	16744-16896	GT	AGG
(CTG)	 AG	17025-17150	GT	AGG
(GAC)	 AG	17423-17563	GC	AGG
-recovered CodingQuarry_transcript_2921-T1, initial, 11658, 11793
add_exon() Sorry, CodingQuarry_transcript_2921-T1 11900-13278-initial-1 is invalid.
-recovered CodingQuarry_transcript_2921-T1, initial, 11900, 13278
add_exon() Sorry, CodingQuarry_transcript_2921-T1 15534-15690-terminal-3 is invalid.
-recovered CodingQuarry_transcript_2921-T1, terminal, 15534, 15690
-recovered CodingQuarry_transcript_2921-T1, terminal, 17423, 17563
-recovered CodingQuarry_transcript_2921-T1, internal, 11900, 13278
-recovered CodingQuarry_transcript_2921-T1, internal, 13496, 13599
-recovered CodingQuarry_transcript_2921-T1, internal, 14054, 14159
-recovered CodingQuarry_transcript_2921-T1, internal, 14240, 14382
-recovered CodingQuarry_transcript_2921-T1, internal, 14710, 14876
-recovered CodingQuarry_transcript_2921-T1, internal, 15026, 15182
-recovered CodingQuarry_transcript_2921-T1, internal, 15278, 15370
-recovered CodingQuarry_transcript_2921-T1, internal, 15534, 15690
-recovered CodingQuarry_transcript_2921-T1, internal, 15802, 15994
-recovered CodingQuarry_transcript_2921-T1, internal, 16157, 16226
-recovered CodingQuarry_transcript_2921-T1, internal, 16310, 16402
-recovered CodingQuarry_transcript_2921-T1, internal, 16520, 16642
-recovered CodingQuarry_transcript_2921-T1, internal, 16744, 16896
-recovered CodingQuarry_transcript_2921-T1, internal, 17025, 17150
-recovered CodingQuarry_transcript_2921-T1, internal, 17423, 17563
Valid prediction for CodingQuarry_transcript_2923-T1
Valid prediction for HiQ_model.g1459.t1
Valid prediction for GlimmerHMM_glimmerT_1965-T1
Valid prediction for Augustus_model.g1460.t1
Valid prediction for snap_scaffold_1-snap.2538-T1
Valid prediction for snap_scaffold_1-snap.2549-T1
Valid prediction for GeneMark_model.2738_t
Valid prediction for snap_scaffold_1-snap.2532-T1
Valid prediction for GlimmerHMM_glimmerT_1978-T1
Valid prediction for snap_scaffold_1-snap.2550-T1
Valid prediction for snap_scaffold_1-snap.2558-T1
Valid prediction for HiQ_model.g1458.t1
Valid prediction for snap_scaffold_1-snap.2542-T1
Valid prediction for snap_scaffold_1-snap.2539-T1
Valid prediction for GeneMark_model.2702_t
Valid prediction for CodingQuarry_transcript_2922-T1
Valid prediction for GeneMark_model.2722_t
Valid prediction for GlimmerHMM_glimmerT_1967-T1
Valid prediction for GeneMark_model.2707_t
Valid prediction for GlimmerHMM_glimmerT_1959-T1
Valid prediction for pasa_asmbl_2383.p1
Couldn't classify 21845, 21892
Sorry, prediction pasa_asmbl_2387.p1 fails validation.
(ATC)	 AC	21845-21892	GT	CGG
(AGT)	 AG	22561-22653	GT	GGG
(GTG)	 AG	22849-22920	GT	TGG
(ATA)	 AG	23523-23609	GT	AGG
(GAG)	 AG	24652-24720	GT	AGG
(CTT)	 AG	24965-25026	GT	AAG
(GGA)	 AG	25296-25415	GT	CTG
(ATA)	 AG	25866-25968	GT	AGG
(GGC)	 AG	26256-26402	GT	AGG
-recovered pasa_asmbl_2387.p1, terminal, 26256, 26402
-recovered pasa_asmbl_2387.p1, internal, 22561, 22653
-recovered pasa_asmbl_2387.p1, internal, 22849, 22920
-recovered pasa_asmbl_2387.p1, internal, 23523, 23609
-recovered pasa_asmbl_2387.p1, internal, 24652, 24720
-recovered pasa_asmbl_2387.p1, internal, 24965, 25026
-recovered pasa_asmbl_2387.p1, internal, 25296, 25415
-recovered pasa_asmbl_2387.p1, internal, 25866, 25968
-recovered pasa_asmbl_2387.p1, internal, 26256, 26402
Valid prediction for GeneMark_model.2711_t
Valid prediction for snap_scaffold_1-snap.2547-T1
Valid prediction for Augustus_model.g1470.t1
Valid prediction for GeneMark_model.2737_t
Valid prediction for GlimmerHMM_glimmerT_1970-T1
Valid prediction for GeneMark_model.2735_t
Valid prediction for GeneMark_model.2713_t
Valid prediction for GeneMark_model.2742_t
Valid prediction for snap_scaffold_1-snap.2552-T1
Valid prediction for GeneMark_model.2724_t
Valid prediction for Augustus_model.g1467.t1
Valid prediction for Augustus_model.g1468.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_1963-T1
Valid prediction for GlimmerHMM_glimmerT_1975-T1
Valid prediction for GlimmerHMM_glimmerT_1971-T1
Valid prediction for Augustus_model.g1473.t1
Valid prediction for GeneMark_model.2734_t
Valid prediction for GeneMark_model.2729_t
Valid prediction for GeneMark_model.2740_t
Valid prediction for GeneMark_model.2714_t
Valid prediction for GlimmerHMM_glimmerT_1969-T1
Valid prediction for snap_scaffold_1-snap.2554-T1
Valid prediction for GeneMark_model.2709_t
Valid prediction for snap_scaffold_1-snap.2540-T1
Valid prediction for GlimmerHMM_glimmerT_1979-T1
Valid prediction for GeneMark_model.2719_t
Valid prediction for snap_scaffold_1-snap.2555-T1
Valid prediction for snap_scaffold_1-snap.2543-T1
Valid prediction for GlimmerHMM_glimmerT_1972-T1
Valid prediction for Augustus_model.g1461.t1
Valid prediction for GeneMark_model.2712_t
Valid prediction for GlimmerHMM_glimmerT_1980-T1
Valid prediction for Augustus_model.g1464.t1
Valid prediction for GlimmerHMM_glimmerT_1964-T1
Valid prediction for GeneMark_model.2739_t
Valid prediction for Augustus_model.g1466.t1
Valid prediction for snap_scaffold_1-snap.2561-T1
Valid prediction for snap_scaffold_1-snap.2553-T1
Valid prediction for snap_scaffold_1-snap.2557-T1
Valid prediction for GlimmerHMM_glimmerT_1968-T1
Valid prediction for GeneMark_model.2732_t
Valid prediction for GeneMark_model.2716_t
Valid prediction for Augustus_model.g1471.t1
Valid prediction for GeneMark_model.2733_t
Valid prediction for snap_scaffold_1-snap.2544-T1
Valid prediction for GlimmerHMM_glimmerT_1977-T1
Valid prediction for GeneMark_model.2721_t
Valid prediction for GlimmerHMM_glimmerT_1966-T1
Valid prediction for snap_scaffold_1-snap.2537-T1
Valid prediction for snap_scaffold_1-snap.2533-T1
Valid prediction for snap_scaffold_1-snap.2560-T1
Valid prediction for GeneMark_model.2717_t
Valid prediction for snap_scaffold_1-snap.2536-T1
Valid prediction for GeneMark_model.2736_t
Valid prediction for snap_scaffold_1-snap.2546-T1
Valid prediction for GlimmerHMM_glimmerT_1982-T1
Valid prediction for GeneMark_model.2706_t
Valid prediction for GlimmerHMM_glimmerT_1981-T1
Valid prediction for snap_scaffold_1-snap.2559-T1
Valid prediction for GlimmerHMM_glimmerT_1961-T1
Valid prediction for GeneMark_model.2723_t
Valid prediction for snap_scaffold_1-snap.2534-T1
Valid prediction for Augustus_model.g1465.t1
Valid prediction for GeneMark_model.2727_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 26402, rend_intergenic: 23774  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35948, rend_intergenic: 33115  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41741, rend_intergenic: 36167  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50243, rend_intergenic: 41766  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65752, rend_intergenic: 63845  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96908, rend_intergenic: 92878  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122833, rend_intergenic: 118808  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143099, rend_intergenic: 140406  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153001, rend_intergenic: 146492  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 176945
-exon list size: 534


building trellis

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96.5    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.8    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.3    
99.4    
99.6    
99.8    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 26402, rend_intergenic: 23774  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35948, rend_intergenic: 33115  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41741, rend_intergenic: 36167  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50243, rend_intergenic: 41766  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65752, rend_intergenic: 63845  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96908, rend_intergenic: 92878  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122833, rend_intergenic: 118808  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143099, rend_intergenic: 140406  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153001, rend_intergenic: 146492  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