-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_11/scaffold_11_11908683-12133050

-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_28553-T1
Valid prediction for GeneMark_model.49301_t
Valid prediction for GlimmerHMM_glimmerT_28577-T1
Valid prediction for snap_scaffold_11-snap.2583-T1
Valid prediction for Augustus_model.g19079.t1
Valid prediction for GeneMark_model.49318_t
Valid prediction for GlimmerHMM_glimmerT_28573-T1
Valid prediction for GlimmerHMM_glimmerT_28574-T1
Valid prediction for snap_scaffold_11-snap.2589-T1
Valid prediction for snap_scaffold_11-snap.2581-T1
Valid prediction for GeneMark_model.49297_t
Valid prediction for GeneMark_model.49328_t
Valid prediction for GeneMark_model.49303_t
Valid prediction for snap_scaffold_11-snap.2567-T1
Valid prediction for GlimmerHMM_glimmerT_28547-T1
Valid prediction for snap_scaffold_11-snap.2596-T1
Valid prediction for Augustus_model.g19063.t1
Valid prediction for Augustus_model.g19058.t1
Valid prediction for GeneMark_model.49319_t
Valid prediction for snap_scaffold_11-snap.2561-T1
Valid prediction for GeneMark_model.49298_t
Valid prediction for HiQ_model.g19075.t1
Valid prediction for snap_scaffold_11-snap.2577-T1
Valid prediction for GeneMark_model.49310_t
Valid prediction for snap_scaffold_11-snap.2560-T1
Valid prediction for Augustus_model.g19071.t1
Valid prediction for pasa_asmbl_5970.p1
Valid prediction for GlimmerHMM_glimmerT_28570-T1
Valid prediction for GeneMark_model.49331_t
Valid prediction for HiQ_model.g19059.t1
Valid prediction for GeneMark_model.49315_t
Valid prediction for GeneMark_model.49286_t
Valid prediction for snap_scaffold_11-snap.2595-T1
Valid prediction for GeneMark_model.49313_t
Valid prediction for GlimmerHMM_glimmerT_28564-T1
Valid prediction for Augustus_model.g19057.t1
Valid prediction for GeneMark_model.49312_t
Valid prediction for GlimmerHMM_glimmerT_28568-T1
Valid prediction for GeneMark_model.49284_t
Valid prediction for GlimmerHMM_glimmerT_28549-T1
Valid prediction for GeneMark_model.49322_t
Valid prediction for GeneMark_model.49294_t
Valid prediction for CodingQuarry_transcript_8232-T1
Valid prediction for snap_scaffold_11-snap.2559-T1
Valid prediction for GeneMark_model.49285_t
Valid prediction for pasa_asmbl_5973.p1
Valid prediction for GeneMark_model.49326_t
Valid prediction for GeneMark_model.49287_t
Valid prediction for snap_scaffold_11-snap.2592-T1
Valid prediction for GeneMark_model.49333_t
Valid prediction for snap_scaffold_11-snap.2562-T1
Valid prediction for GeneMark_model.49321_t
Valid prediction for GlimmerHMM_glimmerT_28557-T1
Valid prediction for GeneMark_model.49308_t
Valid prediction for GeneMark_model.49283_t
Valid prediction for GeneMark_model.49325_t
Valid prediction for CodingQuarry_transcript_8221-T1
Valid prediction for snap_scaffold_11-snap.2587-T1
Valid prediction for snap_scaffold_11-snap.2590-T1
Valid prediction for GlimmerHMM_glimmerT_28548-T1
Valid prediction for GlimmerHMM_glimmerT_28579-T1
Valid prediction for Augustus_model.g19080.t1
Valid prediction for GlimmerHMM_glimmerT_28552-T1
Valid prediction for GeneMark_model.49292_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 GlimmerHMM_glimmerT_28569-T1
Valid prediction for Augustus_model.g19064.t1
Valid prediction for Augustus_model.g19072.t1
Valid prediction for GeneMark_model.49293_t
Valid prediction for GeneMark_model.49307_t
Valid prediction for GlimmerHMM_glimmerT_28550-T1
Valid prediction for GeneMark_model.49320_t
Valid prediction for CodingQuarry_transcript_8225-T1
Couldn't classify 7661, 7688
Sorry, prediction pasa_asmbl_7059.p1 fails validation.
(AAT)	 CC	7661-7688	GT	AGG
(AAC)	 AG	10546-11417	CT	AGC
-recovered pasa_asmbl_7059.p1, terminal, 10546, 11417
Valid prediction for GeneMark_model.49289_t
Valid prediction for GlimmerHMM_glimmerT_28551-T1
Valid prediction for GeneMark_model.49332_t
Valid prediction for GeneMark_model.49311_t
Valid prediction for snap_scaffold_11-snap.2578-T1
Valid prediction for GeneMark_model.49324_t
Valid prediction for snap_scaffold_11-snap.2588-T1
Valid prediction for GlimmerHMM_glimmerT_28578-T1
Valid prediction for GlimmerHMM_glimmerT_28572-T1
Valid prediction for HiQ_model.g19078.t1
Valid prediction for GeneMark_model.49327_t
Couldn't classify 111643, 111874
Sorry, prediction pasa_asmbl_7044.p1 fails validation.
(GGT)	 CA	111643-111874	GT	GTG
(GTA)	 AG	112001-112105	GT	AGG
(GCC)	 AG	112206-112277	GT	AGG
(GCC)	 AG	112445-112596	GT	AGG
(GTT)	 AG	112894-113028	GT	AGG
(ATC)	 AG	113263-113367	AC	GAA
-recovered pasa_asmbl_7044.p1, terminal, 113263, 113367
-recovered pasa_asmbl_7044.p1, internal, 112001, 112105
-recovered pasa_asmbl_7044.p1, internal, 112206, 112277
-recovered pasa_asmbl_7044.p1, internal, 112445, 112596
-recovered pasa_asmbl_7044.p1, internal, 112894, 113028
Valid prediction for CodingQuarry_transcript_8223-T1
Valid prediction for GeneMark_model.49296_t
Valid prediction for GlimmerHMM_glimmerT_28556-T1
Valid prediction for CodingQuarry_transcript_8224-T1
Valid prediction for GeneMark_model.49317_t
Valid prediction for GeneMark_model.49304_t
Valid prediction for CodingQuarry_transcript_8228-T1
Valid prediction for GlimmerHMM_glimmerT_28562-T1
Valid prediction for snap_scaffold_11-snap.2570-T1
Valid prediction for snap_scaffold_11-snap.2585-T1
Valid prediction for CodingQuarry_transcript_8233-T1
Valid prediction for CodingQuarry_transcript_8222-T1
Valid prediction for snap_scaffold_11-snap.2563-T1
Valid prediction for Augustus_model.g19060.t1
Valid prediction for GeneMark_model.49291_t
Valid prediction for snap_scaffold_11-snap.2569-T1
Valid prediction for GlimmerHMM_glimmerT_28576-T1
Valid prediction for snap_scaffold_11-snap.2582-T1
Valid prediction for GeneMark_model.49300_t
Couldn't classify 118039, 118183
Couldn't classify 118892, 119384
Sorry, prediction pasa_asmbl_7043.p1 fails validation.
(AAG)	 CC	118039-118183	GT	CGG
(GTG)	 AG	118302-118411	GT	AGG
(GTA)	 AG	118536-118612	GT	AAG
(ATA)	 AG	118892-119384	AC	GAA
add_exon() Sorry, pasa_asmbl_7043.p1 118536-118612-terminal-2 is invalid.
-recovered pasa_asmbl_7043.p1, terminal, 118536, 118612
-recovered pasa_asmbl_7043.p1, internal, 118302, 118411
-recovered pasa_asmbl_7043.p1, internal, 118536, 118612
Valid prediction for Augustus_model.g19077.t1
Valid prediction for Augustus_model.g19066.t1
Valid prediction for snap_scaffold_11-snap.2564-T1
Valid prediction for GlimmerHMM_glimmerT_28566-T1
Valid prediction for Augustus_model.g19074.t1
Valid prediction for Augustus_model.g19081.t1
Valid prediction for snap_scaffold_11-snap.2580-T1
Valid prediction for GeneMark_model.49295_t
Valid prediction for HiQ_model.g19070.t1
Couldn't classify 76348, 76512
Sorry, prediction pasa_asmbl_7048.p1 fails validation.
(GAT)	 TG	76348-76512	GT	TGG
(GCC)	 AG	76849-77047	GT	CGG
(GCT)	 AG	77321-77467	GT	TGG
(AAA)	 AG	78718-78834	GT	AGG
(GAA)	 AG	80095-80621	TG	GAT
-recovered pasa_asmbl_7048.p1, terminal, 80095, 80621
-recovered pasa_asmbl_7048.p1, internal, 76849, 77047
-recovered pasa_asmbl_7048.p1, internal, 77321, 77467
-recovered pasa_asmbl_7048.p1, internal, 78718, 78834
Valid prediction for snap_scaffold_11-snap.2597-T1
Valid prediction for Augustus_model.g19062.t1
Valid prediction for Augustus_model.g19076.t1
Valid prediction for GeneMark_model.49323_t
Valid prediction for Augustus_model.g19083.t1
Valid prediction for GlimmerHMM_glimmerT_28559-T1
Valid prediction for snap_scaffold_11-snap.2576-T1
Valid prediction for GeneMark_model.49316_t
Valid prediction for CodingQuarry_transcript_8229-T1
Valid prediction for snap_scaffold_11-snap.2566-T1
Valid prediction for snap_scaffold_11-snap.2591-T1
Valid prediction for GeneMark_model.49305_t
Valid prediction for GeneMark_model.49306_t
Valid prediction for GeneMark_model.49290_t
Valid prediction for snap_scaffold_11-snap.2572-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_11-snap.2593-T1
Valid prediction for snap_scaffold_11-snap.2574-T1
Valid prediction for GlimmerHMM_glimmerT_28565-T1
Valid prediction for Augustus_model.g19084.t1
Valid prediction for GlimmerHMM_glimmerT_28571-T1
Valid prediction for snap_scaffold_11-snap.2586-T1
Valid prediction for CodingQuarry_transcript_8227-T1
Valid prediction for Augustus_model.g19068.t1
Valid prediction for GlimmerHMM_glimmerT_28554-T1
Valid prediction for snap_scaffold_11-snap.2571-T1
Valid prediction for GlimmerHMM_glimmerT_28561-T1
Valid prediction for Augustus_model.g19082.t1
Valid prediction for GeneMark_model.49288_t
Valid prediction for pasa_asmbl_7057.p1
Valid prediction for Augustus_model.g19061.t1
Valid prediction for GlimmerHMM_glimmerT_28567-T1
Valid prediction for HiQ_model.g19067.t1
Valid prediction for GeneMark_model.49314_t
Valid prediction for CodingQuarry_transcript_8230-T1
Valid prediction for snap_scaffold_11-snap.2579-T1
Valid prediction for GeneMark_model.49330_t
Valid prediction for snap_scaffold_11-snap.2573-T1
Valid prediction for snap_scaffold_11-snap.2565-T1
Valid prediction for Augustus_model.g19069.t1
Valid prediction for GlimmerHMM_glimmerT_28558-T1
Valid prediction for pasa_asmbl_7019.p1
Valid prediction for GlimmerHMM_glimmerT_28560-T1
Valid prediction for GeneMark_model.49302_t
Valid prediction for GlimmerHMM_glimmerT_28580-T1
Valid prediction for pasa_asmbl_7039.p1
Valid prediction for CodingQuarry_transcript_8234-T1
Valid prediction for GlimmerHMM_glimmerT_28575-T1
Valid prediction for snap_scaffold_11-snap.2584-T1
Valid prediction for GeneMark_model.49309_t
Valid prediction for GlimmerHMM_glimmerT_28555-T1
Valid prediction for snap_scaffold_11-snap.2594-T1
Valid prediction for GlimmerHMM_glimmerT_28563-T1
Valid prediction for pasa_asmbl_7034.p1
Valid prediction for CodingQuarry_transcript_8226-T1
Valid prediction for HiQ_model.g19073.t1
Valid prediction for snap_scaffold_11-snap.2575-T1
Valid prediction for Augustus_model.g19065.t1
Valid prediction for snap_scaffold_11-snap.2568-T1
Sorry, intron length (4) is less than minimum required (10)

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 119604, rend_intergenic: 109635  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142581, rend_intergenic: 137065  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147559, rend_intergenic: 143748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179706, rend_intergenic: 176690  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183737, rend_intergenic: 179739  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187443, rend_intergenic: 184065  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194149, rend_intergenic: 189198  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206639, rend_intergenic: 199820  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 224368
-exon list size: 722


building trellis

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85.5    
85.6    
85.8    
85.9    
86.0    
86.2    
86.3    
86.5    
86.6    
86.7    
86.9    
87.0    
87.2    
87.3    
87.4    
87.6    
87.7    
87.8    
88.0    
88.1    
88.3    
88.4    
88.5    
88.7    
88.8    
89.0    
89.1    
89.2    
89.4    
89.5    
89.6    
89.8    
89.9    
90.1    
90.2    
90.3    
90.5    
90.6    
90.7    
90.9    
91.0    
91.2    
91.3    
91.4    
91.6    
91.7    
91.9    
92.0    
92.1    
92.3    
92.4    
92.5    
92.7    
92.8    
93.0    
93.1    
93.2    
93.4    
93.5    
93.6    
93.8    
93.9    
94.1    
94.2    
94.3    
94.5    
94.6    
94.8    
94.9    
95.0    
95.2    
95.3    
95.4    
95.6    
95.7    
95.9    
96.0    
96.1    
96.3    
96.4    
96.5    
96.7    
96.8    
97.0    
97.1    
97.2    
97.4    
97.5    
97.7    
97.8    
97.9    
98.1    
98.2    
98.3    
98.5    
98.6    
98.8    
98.9    
99.0    
99.2    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 119604, rend_intergenic: 109635  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142581, rend_intergenic: 137065  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147559, rend_intergenic: 143748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179706, rend_intergenic: 176690  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183737, rend_intergenic: 179739  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187443, rend_intergenic: 184065  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194149, rend_intergenic: 189198  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206639, rend_intergenic: 199820  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 29 predictions persist after filtering for low support