-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_11/scaffold_11_12816386-13058800

-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.49573_t
Valid prediction for snap_scaffold_11-snap.2780-T1
Valid prediction for snap_scaffold_11-snap.2793-T1
Valid prediction for GlimmerHMM_glimmerT_28714-T1
Valid prediction for snap_scaffold_11-snap.2767-T1
Valid prediction for GeneMark_model.49553_t
Valid prediction for GeneMark_model.49552_t
Valid prediction for GeneMark_model.49557_t
Valid prediction for GlimmerHMM_glimmerT_28707-T1
Couldn't classify 77970, 78074
Sorry, prediction pasa_asmbl_5992.p1 fails validation.
(ATG)	 CA	75431-75468	GT	GGG
(CTA)	 AG	75701-75849	GT	AGG
(AGG)	 AG	75934-76062	GT	ATG
(TGT)	 AG	76155-76348	GT	AGG
(ATA)	 AG	76603-76683	GT	GGG
(GAG)	 AG	77030-77146	GC	AGG
(GAG)	 AG	77475-77642	GT	AGG
(ATC)	 AG	77970-78074	TG	GCT
-recovered pasa_asmbl_5992.p1, initial, 75431, 75468
-recovered pasa_asmbl_5992.p1, internal, 75701, 75849
-recovered pasa_asmbl_5992.p1, internal, 75934, 76062
-recovered pasa_asmbl_5992.p1, internal, 76155, 76348
-recovered pasa_asmbl_5992.p1, internal, 76603, 76683
-recovered pasa_asmbl_5992.p1, internal, 77030, 77146
-recovered pasa_asmbl_5992.p1, internal, 77475, 77642
Valid prediction for snap_scaffold_11-snap.2778-T1
Valid prediction for Augustus_model.g19150.t1
Valid prediction for GeneMark_model.49582_t
Valid prediction for GeneMark_model.49548_t
Valid prediction for snap_scaffold_11-snap.2762-T1
Valid prediction for GeneMark_model.49585_t
Valid prediction for GlimmerHMM_glimmerT_28694-T1
Valid prediction for snap_scaffold_11-snap.2786-T1
Valid prediction for GeneMark_model.49562_t
Valid prediction for GlimmerHMM_glimmerT_28695-T1
Valid prediction for snap_scaffold_11-snap.2774-T1
Valid prediction for GlimmerHMM_glimmerT_28712-T1
Valid prediction for GeneMark_model.49555_t
Valid prediction for GeneMark_model.49541_t
Valid prediction for Augustus_model.g19154.t1
Valid prediction for snap_scaffold_11-snap.2759-T1
Valid prediction for snap_scaffold_11-snap.2784-T1
Valid prediction for GlimmerHMM_glimmerT_28704-T1
Valid prediction for GeneMark_model.49544_t
Valid prediction for snap_scaffold_11-snap.2761-T1
Valid prediction for GeneMark_model.49550_t
Valid prediction for GlimmerHMM_glimmerT_28719-T1
Couldn't classify 212708, 213046
Sorry, prediction pasa_asmbl_6218.p1 fails validation.
(GCA)	 TG	212708-213046	GT	GTG
(GCT)	 AG	213299-213351	GT	TCG
(CAT)	 AG	213734-213836	TT	AGT
-recovered pasa_asmbl_6218.p1, terminal, 213734, 213836
-recovered pasa_asmbl_6218.p1, internal, 213299, 213351
Valid prediction for Augustus_model.g19148.t1
Valid prediction for snap_scaffold_11-snap.2787-T1
Valid prediction for snap_scaffold_11-snap.2785-T1
Valid prediction for GeneMark_model.49543_t
Valid prediction for snap_scaffold_11-snap.2770-T1
Valid prediction for GeneMark_model.49566_t
Valid prediction for GeneMark_model.49560_t
Valid prediction for GlimmerHMM_glimmerT_28699-T1
Valid prediction for snap_scaffold_11-snap.2771-T1
Valid prediction for GeneMark_model.49576_t
Valid prediction for GeneMark_model.49567_t
Valid prediction for GeneMark_model.49559_t
Valid prediction for snap_scaffold_11-snap.2764-T1
Valid prediction for GlimmerHMM_glimmerT_28696-T1
Valid prediction for GeneMark_model.49546_t
Valid prediction for GeneMark_model.49565_t
Valid prediction for CodingQuarry_transcript_8241-T1
Valid prediction for GlimmerHMM_glimmerT_28705-T1
Valid prediction for snap_scaffold_11-snap.2772-T1
Valid prediction for snap_scaffold_11-snap.2765-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g19151.t1
Valid prediction for Augustus_model.g19149.t1
Valid prediction for GlimmerHMM_glimmerT_28698-T1
Valid prediction for Augustus_model.g19155.t1
Valid prediction for snap_scaffold_11-snap.2788-T1
Valid prediction for GlimmerHMM_glimmerT_28691-T1
Valid prediction for Augustus_model.g19163.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 pasa_asmbl_7083.p1
Valid prediction for GeneMark_model.49542_t
Valid prediction for snap_scaffold_11-snap.2777-T1
Valid prediction for GeneMark_model.49558_t
Valid prediction for snap_scaffold_11-snap.2789-T1
Valid prediction for GeneMark_model.49583_t
Valid prediction for HiQ_model.g19164.t1
Valid prediction for GlimmerHMM_glimmerT_28720-T1
Couldn't classify 109064, 109603
Sorry, prediction pasa_asmbl_7090.p1 fails validation.
(ACA)	 CA	109064-109603	GC	GAG
Valid prediction for GlimmerHMM_glimmerT_28723-T1
Valid prediction for Augustus_model.g19157.t1
Valid prediction for HiQ_model.g19153.t1
Valid prediction for snap_scaffold_11-snap.2779-T1
Valid prediction for GlimmerHMM_glimmerT_28709-T1
Valid prediction for snap_scaffold_11-snap.2776-T1
Valid prediction for GlimmerHMM_glimmerT_28697-T1
Valid prediction for GlimmerHMM_glimmerT_28700-T1
Valid prediction for GeneMark_model.49584_t
Valid prediction for GlimmerHMM_glimmerT_28702-T1
Valid prediction for GeneMark_model.49545_t
Valid prediction for pasa_asmbl_7094.p1
Valid prediction for GeneMark_model.49547_t
Valid prediction for snap_scaffold_11-snap.2775-T1
Valid prediction for snap_scaffold_11-snap.2796-T1
Valid prediction for pasa_asmbl_7100.p1
Valid prediction for GeneMark_model.49568_t
Valid prediction for GeneMark_model.49551_t
Valid prediction for snap_scaffold_11-snap.2763-T1
Valid prediction for GlimmerHMM_glimmerT_28701-T1
Valid prediction for GlimmerHMM_glimmerT_28706-T1
Valid prediction for GlimmerHMM_glimmerT_28725-T1
Valid prediction for CodingQuarry_transcript_8244-T1
Valid prediction for GeneMark_model.49580_t
Valid prediction for GeneMark_model.49556_t
Valid prediction for Augustus_model.g19162.t1
Valid prediction for Augustus_model.g19159.t1
Valid prediction for Augustus_model.g19165.t1
Valid prediction for snap_scaffold_11-snap.2792-T1
Valid prediction for GeneMark_model.49554_t
Valid prediction for snap_scaffold_11-snap.2783-T1
Valid prediction for GeneMark_model.49581_t
Valid prediction for Augustus_model.g19166.t1
Valid prediction for CodingQuarry_transcript_8243-T1
Valid prediction for snap_scaffold_11-snap.2756-T1
Valid prediction for CodingQuarry_transcript_8245-T1
Valid prediction for snap_scaffold_11-snap.2769-T1
Valid prediction for snap_scaffold_11-snap.2790-T1
Valid prediction for snap_scaffold_11-snap.2795-T1
Valid prediction for GlimmerHMM_glimmerT_28710-T1
Valid prediction for GeneMark_model.49561_t
Valid prediction for GlimmerHMM_glimmerT_28693-T1
Couldn't classify 144609, 145034
Sorry, prediction pasa_asmbl_7087.p1 fails validation.
(ATG)	 GA	143780-143814	GT	GAG
(GGA)	 AG	143996-144073	GT	AGG
(GGT)	 AG	144273-144330	GT	AGG
(GAT)	 AG	144609-145034	GG	ATG
-recovered pasa_asmbl_7087.p1, initial, 143780, 143814
-recovered pasa_asmbl_7087.p1, internal, 143996, 144073
-recovered pasa_asmbl_7087.p1, internal, 144273, 144330
Valid prediction for GeneMark_model.49577_t
Valid prediction for GeneMark_model.49564_t
Valid prediction for GlimmerHMM_glimmerT_28721-T1
Valid prediction for GeneMark_model.49549_t
Valid prediction for snap_scaffold_11-snap.2781-T1
Valid prediction for snap_scaffold_11-snap.2757-T1
Valid prediction for Augustus_model.g19156.t1
Valid prediction for snap_scaffold_11-snap.2760-T1
Valid prediction for snap_scaffold_11-snap.2773-T1
Valid prediction for Augustus_model.g19158.t1
Valid prediction for snap_scaffold_11-snap.2758-T1
Valid prediction for Augustus_model.g19161.t1
Valid prediction for GlimmerHMM_glimmerT_28716-T1
Couldn't classify 107556, 107617
Couldn't classify 108568, 108970
Sorry, prediction pasa_asmbl_7091.p1 fails validation.
(GGA)	 AA	107556-107617	GT	AGG
(CCT)	 AG	108568-108970	CA	TCC
Valid prediction for GlimmerHMM_glimmerT_28708-T1
Valid prediction for GeneMark_model.49587_t
Valid prediction for snap_scaffold_11-snap.2791-T1
Valid prediction for GlimmerHMM_glimmerT_28690-T1
Valid prediction for GlimmerHMM_glimmerT_28713-T1
Valid prediction for pasa_asmbl_7082.p1
Valid prediction for GeneMark_model.49579_t
Valid prediction for CodingQuarry_transcript_8242-T1
Valid prediction for HiQ_model.g19152.t1
Valid prediction for GlimmerHMM_glimmerT_28692-T1
Valid prediction for snap_scaffold_11-snap.2768-T1
Valid prediction for GeneMark_model.49578_t
Valid prediction for snap_scaffold_11-snap.2794-T1
Valid prediction for Augustus_model.g19147.t1
Valid prediction for snap_scaffold_11-snap.2754-T1
Valid prediction for Augustus_model.g19160.t1
Valid prediction for snap_scaffold_11-snap.2766-T1
Valid prediction for GlimmerHMM_glimmerT_28722-T1
Valid prediction for GlimmerHMM_glimmerT_28718-T1
Valid prediction for GeneMark_model.49586_t
Valid prediction for GlimmerHMM_glimmerT_28703-T1
Valid prediction for GlimmerHMM_glimmerT_28724-T1
Valid prediction for GeneMark_model.49575_t
Valid prediction for GlimmerHMM_glimmerT_28717-T1
Valid prediction for GeneMark_model.49563_t
Valid prediction for GlimmerHMM_glimmerT_28715-T1
Valid prediction for GlimmerHMM_glimmerT_28711-T1
Valid prediction for snap_scaffold_11-snap.2782-T1
Valid prediction for snap_scaffold_11-snap.2755-T1
Valid prediction for GeneMark_model.49574_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 47008, rend_intergenic: 37861  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61814, rend_intergenic: 55627  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70954, rend_intergenic: 62122  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94706, rend_intergenic: 85362  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180743, rend_intergenic: 178164  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 230458, rend_intergenic: 228927  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 233279, rend_intergenic: 231196  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 242415
-exon list size: 604


building trellis

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-found 40 predictions from path traversal
Error with prediction: snap lend_intergenic: 47008, rend_intergenic: 37861  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61814, rend_intergenic: 55627  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70954, rend_intergenic: 62122  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94706, rend_intergenic: 85362  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180743, rend_intergenic: 178164  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 230458, rend_intergenic: 228927  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 233279, rend_intergenic: 231196  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 17017
-exon list size: 14


building trellis

6.2    
12.5    
18.8    
25.0    
31.2    
37.5    
43.8    
50.0    
56.2    
62.5    
68.8    
75.0    
81.2    
87.5    
93.8    
-found 1 predictions from path traversal

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

-building DP trellis

-building trellis in range 1 - 16181
-exon list size: 12


building trellis

7.1    
14.3    
21.4    
28.6    
35.7    
42.9    
50.0    
57.1    
64.3    
71.4    
78.6    
85.7    
92.9    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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

-building DP trellis

-building trellis in range 1 - 15578
-exon list size: 10


building trellis

8.3    
16.7    
25.0    
33.3    
41.7    
50.0    
58.3    
66.7    
75.0    
83.3    
91.7    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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

-building DP trellis

-building trellis in range 1 - 11786
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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