-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_12748849-12982595

-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.12664_t
Valid prediction for GlimmerHMM_glimmerT_7678-T1
Valid prediction for GlimmerHMM_glimmerT_7672-T1
Valid prediction for snap_scaffold_3-snap.2492-T1
Valid prediction for GeneMark_model.12685_t
Valid prediction for GlimmerHMM_glimmerT_7667-T1
Valid prediction for GeneMark_model.12657_t
Valid prediction for snap_scaffold_3-snap.2489-T1
Valid prediction for snap_scaffold_3-snap.2485-T1
Valid prediction for snap_scaffold_3-snap.2524-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.12655_t
Valid prediction for GeneMark_model.12653_t
Valid prediction for GeneMark_model.12662_t
Valid prediction for snap_scaffold_3-snap.2522-T1
Valid prediction for GlimmerHMM_glimmerT_7659-T1
Valid prediction for snap_scaffold_3-snap.2518-T1
Valid prediction for GlimmerHMM_glimmerT_7680-T1
Valid prediction for GeneMark_model.12676_t
Valid prediction for snap_scaffold_3-snap.2479-T1
Valid prediction for snap_scaffold_3-snap.2477-T1
Valid prediction for GeneMark_model.12683_t
Valid prediction for GlimmerHMM_glimmerT_7668-T1
Valid prediction for snap_scaffold_3-snap.2525-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for Augustus_model.g5031.t1
Valid prediction for snap_scaffold_3-snap.2514-T1
Valid prediction for snap_scaffold_3-snap.2506-T1
Valid prediction for GlimmerHMM_glimmerT_7681-T1
Valid prediction for Augustus_model.g5033.t1
Valid prediction for GlimmerHMM_glimmerT_7656-T1
Valid prediction for snap_scaffold_3-snap.2496-T1
Valid prediction for GeneMark_model.12667_t
Valid prediction for CodingQuarry_transcript_46200-T1
Valid prediction for CodingQuarry_transcript_46201-T1
Valid prediction for GeneMark_model.12670_t
Valid prediction for GeneMark_model.12665_t
Valid prediction for CodingQuarry_transcript_46202-T1
Valid prediction for snap_scaffold_3-snap.2519-T1
Valid prediction for snap_scaffold_3-snap.2521-T1
Valid prediction for Augustus_model.g5048.t1
Valid prediction for snap_scaffold_3-snap.2490-T1
Valid prediction for pasa_asmbl_40368.p1
Valid prediction for snap_scaffold_3-snap.2482-T1
Valid prediction for Augustus_model.g5039.t1
Valid prediction for snap_scaffold_3-snap.2486-T1
Valid prediction for GlimmerHMM_glimmerT_7663-T1
Valid prediction for Augustus_model.g5045.t1
Valid prediction for GlimmerHMM_glimmerT_7661-T1
Valid prediction for snap_scaffold_3-snap.2493-T1
Couldn't classify 81546, 81595
Couldn't classify 83247, 83283
Sorry, prediction pasa_asmbl_40747.p1 fails validation.
(ATC)	 TG	81546-81595	GT	AGG
(GCC)	 AG	81737-81876	GT	AGG
(CCT)	 AG	82403-82539	GT	AGG
(ACC)	 AG	82679-82759	GT	CGG
(GAT)	 AG	82935-83062	GT	AGG
(GAT)	 AG	83247-83283	AG	AGA
-recovered pasa_asmbl_40747.p1, internal, 81737, 81876
-recovered pasa_asmbl_40747.p1, internal, 82403, 82539
-recovered pasa_asmbl_40747.p1, internal, 82679, 82759
-recovered pasa_asmbl_40747.p1, internal, 82935, 83062
Valid prediction for Augustus_model.g5030.t1
Valid prediction for GlimmerHMM_glimmerT_7655-T1
Valid prediction for snap_scaffold_3-snap.2491-T1
Valid prediction for snap_scaffold_3-snap.2487-T1
Couldn't classify 88509, 88547
Sorry, prediction pasa_asmbl_40371.p1 fails validation.
(ACC)	 CC	88509-88547	GT	AGG
(GGC)	 AG	90813-90874	GT	AGG
(GGT)	 AG	91261-91318	GT	AGG
(ATC)	 AG	91761-91835	GT	AGG
(ATA)	 AG	93074-93248	GT	AGG
(AGC)	 AG	93542-93665	GT	TGG
(TGC)	 AG	95185-95437	AC	AGA
-recovered pasa_asmbl_40371.p1, terminal, 95185, 95437
-recovered pasa_asmbl_40371.p1, internal, 90813, 90874
-recovered pasa_asmbl_40371.p1, internal, 91261, 91318
-recovered pasa_asmbl_40371.p1, internal, 91761, 91835
-recovered pasa_asmbl_40371.p1, internal, 93074, 93248
-recovered pasa_asmbl_40371.p1, internal, 93542, 93665
Valid prediction for snap_scaffold_3-snap.2503-T1
Valid prediction for GlimmerHMM_glimmerT_7660-T1
Valid prediction for GlimmerHMM_glimmerT_7665-T1
Valid prediction for GeneMark_model.12679_t
Valid prediction for GlimmerHMM_glimmerT_7657-T1
Valid prediction for GeneMark_model.12656_t
Valid prediction for GeneMark_model.12669_t
Valid prediction for snap_scaffold_3-snap.2523-T1
Valid prediction for snap_scaffold_3-snap.2480-T1
Valid prediction for snap_scaffold_3-snap.2498-T1
Valid prediction for Augustus_model.g5041.t1
Valid prediction for GeneMark_model.12660_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 Augustus_model.g5043.t1
Valid prediction for CodingQuarry_transcript_46203-T1
Valid prediction for Augustus_model.g5044.t1
Valid prediction for GeneMark_model.12674_t
Valid prediction for GlimmerHMM_glimmerT_7664-T1
Valid prediction for GeneMark_model.12678_t
Valid prediction for GlimmerHMM_glimmerT_7684-T1
Valid prediction for GeneMark_model.12668_t
Valid prediction for GeneMark_model.12654_t
Valid prediction for GlimmerHMM_glimmerT_7658-T1
Valid prediction for GlimmerHMM_glimmerT_7666-T1
Valid prediction for GeneMark_model.12686_t
Valid prediction for Augustus_model.g5046.t1
Valid prediction for Augustus_model.g5049.t1
Valid prediction for GlimmerHMM_glimmerT_7673-T1
Valid prediction for Augustus_model.g5042.t1
Valid prediction for snap_scaffold_3-snap.2500-T1
Valid prediction for snap_scaffold_3-snap.2513-T1
Valid prediction for snap_scaffold_3-snap.2520-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for Augustus_model.g5037.t1
Valid prediction for CodingQuarry_transcript_46204-T1
Valid prediction for snap_scaffold_3-snap.2517-T1
Valid prediction for GeneMark_model.12677_t
Valid prediction for GlimmerHMM_glimmerT_7679-T1
Valid prediction for snap_scaffold_3-snap.2483-T1
Valid prediction for GeneMark_model.12666_t
Valid prediction for snap_scaffold_3-snap.2478-T1
Valid prediction for CodingQuarry_transcript_46206-T1
Valid prediction for GlimmerHMM_glimmerT_7669-T1
Valid prediction for Augustus_model.g5038.t1
Valid prediction for snap_scaffold_3-snap.2512-T1
Valid prediction for snap_scaffold_3-snap.2511-T1
Valid prediction for snap_scaffold_3-snap.2504-T1
Valid prediction for Augustus_model.g5047.t1
Valid prediction for GeneMark_model.12658_t
Valid prediction for GeneMark_model.12672_t
Valid prediction for Augustus_model.g5035.t1
Valid prediction for snap_scaffold_3-snap.2484-T1
Valid prediction for GeneMark_model.12661_t
Valid prediction for GeneMark_model.12652_t
Valid prediction for pasa_asmbl_39193.p1
Valid prediction for GlimmerHMM_glimmerT_7676-T1
Valid prediction for GeneMark_model.12671_t
Valid prediction for GlimmerHMM_glimmerT_7683-T1
Valid prediction for snap_scaffold_3-snap.2495-T1
Valid prediction for GeneMark_model.12684_t
Valid prediction for snap_scaffold_3-snap.2502-T1
Valid prediction for GlimmerHMM_glimmerT_7675-T1
Valid prediction for GeneMark_model.12682_t
Valid prediction for GeneMark_model.12673_t
Valid prediction for GlimmerHMM_glimmerT_7654-T1
Valid prediction for pasa_asmbl_39189.p1
Valid prediction for snap_scaffold_3-snap.2497-T1
Valid prediction for snap_scaffold_3-snap.2505-T1
Couldn't classify 2324, 2662
Sorry, prediction pasa_asmbl_39631.p1 fails validation.
(CAG)	 GC	2324-2662	GG	AGG
Valid prediction for GeneMark_model.12659_t
Valid prediction for GlimmerHMM_glimmerT_7671-T1
Valid prediction for Augustus_model.g5036.t1
Valid prediction for GeneMark_model.12680_t
Valid prediction for snap_scaffold_3-snap.2476-T1
Valid prediction for snap_scaffold_3-snap.2499-T1
Valid prediction for snap_scaffold_3-snap.2494-T1
Valid prediction for GlimmerHMM_glimmerT_7682-T1
Valid prediction for Augustus_model.g5032.t1
Valid prediction for GeneMark_model.12688_t
Valid prediction for snap_scaffold_3-snap.2510-T1
Valid prediction for snap_scaffold_3-snap.2515-T1
Valid prediction for snap_scaffold_3-snap.2516-T1
Valid prediction for snap_scaffold_3-snap.2488-T1
Valid prediction for CodingQuarry_transcript_46205-T1
Valid prediction for Augustus_model.g5034.t1
Valid prediction for GeneMark_model.12663_t
Valid prediction for GlimmerHMM_glimmerT_7662-T1
Valid prediction for GeneMark_model.12681_t
Valid prediction for snap_scaffold_3-snap.2507-T1
Valid prediction for GlimmerHMM_glimmerT_7677-T1
Valid prediction for GlimmerHMM_glimmerT_7674-T1
Valid prediction for snap_scaffold_3-snap.2508-T1
Valid prediction for GlimmerHMM_glimmerT_7670-T1
Valid prediction for snap_scaffold_3-snap.2501-T1
Valid prediction for snap_scaffold_3-snap.2509-T1
Valid prediction for HiQ_model.g5040.t1
Valid prediction for snap_scaffold_3-snap.2481-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13149, rend_intergenic: 5461  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46359, rend_intergenic: 33842  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52946, rend_intergenic: 48573  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60136, rend_intergenic: 53409  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75905, rend_intergenic: 75833  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86086, rend_intergenic: 75909  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 116330, rend_intergenic: 116327  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 233747
-exon list size: 577


building trellis

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98.4    
98.6    
98.8    
99.0    
99.1    
99.3    
99.5    
99.7    
99.8    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 13149, rend_intergenic: 5461  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46359, rend_intergenic: 33842  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52946, rend_intergenic: 48573  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60136, rend_intergenic: 53409  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75905, rend_intergenic: 75833  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86086, rend_intergenic: 75909  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 116330, rend_intergenic: 116327  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 26 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 11803
-exon list size: 38


building trellis

2.5    
5.0    
7.5    
10.0    
12.5    
15.0    
17.5    
20.0    
22.5    
25.0    
27.5    
30.0    
32.5    
35.0    
37.5    
40.0    
42.5    
45.0    
47.5    
50.0    
52.5    
55.0    
57.5    
60.0    
62.5    
65.0    
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70.0    
72.5    
75.0    
77.5    
80.0    
82.5    
85.0    
87.5    
90.0    
92.5    
95.0    
97.5    
-found 2 predictions from path traversal

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