-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_2/scaffold_2_13590916-13878634

-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_2-snap.2649-T1
Valid prediction for GlimmerHMM_glimmerT_4820-T1
Valid prediction for GlimmerHMM_glimmerT_4825-T1
Valid prediction for snap_scaffold_2-snap.2630-T1
Valid prediction for GlimmerHMM_glimmerT_4845-T1
Valid prediction for GlimmerHMM_glimmerT_4840-T1
Valid prediction for snap_scaffold_2-snap.2628-T1
Valid prediction for GlimmerHMM_glimmerT_4839-T1
Valid prediction for GlimmerHMM_glimmerT_4834-T1
Valid prediction for snap_scaffold_2-snap.2613-T1
Valid prediction for snap_scaffold_2-snap.2643-T1
Valid prediction for GlimmerHMM_glimmerT_4829-T1
Valid prediction for snap_scaffold_2-snap.2623-T1
Valid prediction for snap_scaffold_2-snap.2637-T1
Valid prediction for snap_scaffold_2-snap.2615-T1
Couldn't classify 196095, 196253
Sorry, prediction pasa_asmbl_24859.p1 fails validation.
(GCC)	 GA	196095-196253	GT	AGG
(TAT)	 AG	196874-196926	GT	AGG
(ATG)	 AG	197107-197230	GT	AGG
(ATC)	 AG	198173-198286	GT	AGG
(GAA)	 AG	200359-200484	GT	AGG
(GTT)	 AG	202595-202766	GT	CAG
(AGT)	 AG	202960-203138	GT	AGG
(GTG)	 AG	203508-203574	GT	AGG
(GAA)	 AG	204036-204191	GT	AGG
(CTG)	 AG	204503-204579	GT	TGG
(GCT)	 AG	205254-205382	GA	GAG
add_exon() Sorry, pasa_asmbl_24859.p1 197107-197230-initial-1 is invalid.
-recovered pasa_asmbl_24859.p1, initial, 197107, 197230
-recovered pasa_asmbl_24859.p1, terminal, 205254, 205382
-recovered pasa_asmbl_24859.p1, internal, 196874, 196926
-recovered pasa_asmbl_24859.p1, internal, 197107, 197230
-recovered pasa_asmbl_24859.p1, internal, 198173, 198286
-recovered pasa_asmbl_24859.p1, internal, 200359, 200484
-recovered pasa_asmbl_24859.p1, internal, 202595, 202766
-recovered pasa_asmbl_24859.p1, internal, 202960, 203138
-recovered pasa_asmbl_24859.p1, internal, 203508, 203574
-recovered pasa_asmbl_24859.p1, internal, 204036, 204191
-recovered pasa_asmbl_24859.p1, internal, 204503, 204579
Valid prediction for GlimmerHMM_glimmerT_4828-T1
Valid prediction for GlimmerHMM_glimmerT_4826-T1
Valid prediction for snap_scaffold_2-snap.2645-T1
Valid prediction for snap_scaffold_2-snap.2620-T1
Valid prediction for snap_scaffold_2-snap.2617-T1
Valid prediction for snap_scaffold_2-snap.2622-T1
Valid prediction for snap_scaffold_2-snap.2644-T1
Valid prediction for Augustus_model.g3240.t1
Valid prediction for snap_scaffold_2-snap.2642-T1
Valid prediction for GlimmerHMM_glimmerT_4836-T1
Valid prediction for snap_scaffold_2-snap.2635-T1
Valid prediction for Augustus_model.g3246.t1
Valid prediction for GlimmerHMM_glimmerT_4827-T1
Valid prediction for Augustus_model.g3241.t1
Valid prediction for GlimmerHMM_glimmerT_4823-T1
Valid prediction for snap_scaffold_2-snap.2638-T1
Valid prediction for snap_scaffold_2-snap.2652-T1
Valid prediction for GlimmerHMM_glimmerT_4830-T1
Valid prediction for HiQ_model.g3245.t1
Valid prediction for GlimmerHMM_glimmerT_4835-T1
Valid prediction for GlimmerHMM_glimmerT_4822-T1
Valid prediction for GlimmerHMM_glimmerT_4843-T1
Valid prediction for GlimmerHMM_glimmerT_4842-T1
Valid prediction for GlimmerHMM_glimmerT_4846-T1
Valid prediction for snap_scaffold_2-snap.2639-T1
Valid prediction for snap_scaffold_2-snap.2626-T1
Valid prediction for Augustus_model.g3244.t1
Valid prediction for snap_scaffold_2-snap.2640-T1
Valid prediction for snap_scaffold_2-snap.2625-T1
Valid prediction for Augustus_model.g3233.t1
Valid prediction for GlimmerHMM_glimmerT_4847-T1
Valid prediction for Augustus_model.g3242.t1
Valid prediction for GlimmerHMM_glimmerT_4832-T1
Valid prediction for snap_scaffold_2-snap.2624-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 Augustus_model.g3249.t1
Valid prediction for GlimmerHMM_glimmerT_4837-T1
Valid prediction for Augustus_model.g3231.t1
Valid prediction for snap_scaffold_2-snap.2634-T1
Valid prediction for Augustus_model.g3251.t1
Valid prediction for snap_scaffold_2-snap.2651-T1
Valid prediction for snap_scaffold_2-snap.2619-T1
Valid prediction for GlimmerHMM_glimmerT_4848-T1
Valid prediction for snap_scaffold_2-snap.2631-T1
Valid prediction for GlimmerHMM_glimmerT_4833-T1
Valid prediction for snap_scaffold_2-snap.2646-T1
Valid prediction for Augustus_model.g3235.t1
Couldn't classify 42691, 42872
Sorry, prediction pasa_asmbl_23529.p1 fails validation.
(ATG)	 AG	40366-40464	GT	AGG
(GAG)	 AG	41591-41762	GT	AGG
(ACA)	 AG	42691-42872	GT	AGG
-recovered pasa_asmbl_23529.p1, initial, 40366, 40464
add_exon() Sorry, pasa_asmbl_23529.p1 41591-41762-terminal-3 is invalid.
-recovered pasa_asmbl_23529.p1, terminal, 41591, 41762
-recovered pasa_asmbl_23529.p1, internal, 40366, 40464
-recovered pasa_asmbl_23529.p1, internal, 41591, 41762
-recovered pasa_asmbl_23529.p1, internal, 42691, 42872
Valid prediction for GlimmerHMM_glimmerT_4838-T1
Valid prediction for CodingQuarry_transcript_28700-T1
Valid prediction for pasa_asmbl_23524.p1
Valid prediction for HiQ_model.g3243.t1
Couldn't classify 22848, 22938
Couldn't classify 27281, 27349
Sorry, prediction pasa_asmbl_24017.p1 fails validation.
(GAG)	 TA	22848-22938	GT	AGG
(GTA)	 AG	25912-26084	GT	AGG
(ATC)	 AG	27281-27349	GT	AGG
-recovered pasa_asmbl_24017.p1, internal, 25912, 26084
-recovered pasa_asmbl_24017.p1, internal, 27281, 27349
Valid prediction for snap_scaffold_2-snap.2648-T1
Valid prediction for GlimmerHMM_glimmerT_4821-T1
Valid prediction for snap_scaffold_2-snap.2633-T1
Valid prediction for snap_scaffold_2-snap.2614-T1
Valid prediction for snap_scaffold_2-snap.2629-T1
Valid prediction for pasa_asmbl_23528.p1
Valid prediction for Augustus_model.g3230.t1
Valid prediction for snap_scaffold_2-snap.2632-T1
Valid prediction for Augustus_model.g3232.t1
Valid prediction for Augustus_model.g3238.t1
Valid prediction for snap_scaffold_2-snap.2627-T1
Valid prediction for snap_scaffold_2-snap.2636-T1
Valid prediction for Augustus_model.g3248.t1
Valid prediction for GlimmerHMM_glimmerT_4841-T1
Valid prediction for snap_scaffold_2-snap.2653-T1
Valid prediction for snap_scaffold_2-snap.2618-T1
Valid prediction for snap_scaffold_2-snap.2621-T1
Valid prediction for Augustus_model.g3237.t1
Valid prediction for Augustus_model.g3239.t1
Valid prediction for GlimmerHMM_glimmerT_4831-T1
Valid prediction for Augustus_model.g3250.t1
Valid prediction for Augustus_model.g3234.t1
Valid prediction for snap_scaffold_2-snap.2650-T1
Valid prediction for GlimmerHMM_glimmerT_4844-T1
Valid prediction for GlimmerHMM_glimmerT_4824-T1
Valid prediction for snap_scaffold_2-snap.2647-T1
Valid prediction for Augustus_model.g3236.t1
Couldn't classify 13437, 13646
Sorry, prediction pasa_asmbl_24037.p1 fails validation.
(ATG)	 GA	11817-12032	GT	CGG
(GAA)	 AG	13437-13646	GA	GTG
-recovered pasa_asmbl_24037.p1, initial, 11817, 12032
Valid prediction for snap_scaffold_2-snap.2641-T1
Valid prediction for snap_scaffold_2-snap.2616-T1
Valid prediction for HiQ_model.g3247.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7722, rend_intergenic: 5174  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25609, rend_intergenic: 8206  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34960, rend_intergenic: 31310  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37792, rend_intergenic: 36284  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44844, rend_intergenic: 42547  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47945, rend_intergenic: 46963  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77076, rend_intergenic: 48892  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83128, rend_intergenic: 79832  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83601, rend_intergenic: 83142  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86197, rend_intergenic: 84114  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90060, rend_intergenic: 86659  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127070, rend_intergenic: 124991  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134827, rend_intergenic: 133747  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 270598, rend_intergenic: 253198  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 287719
-exon list size: 326


building trellis

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98.8    
99.1    
99.4    
99.7    
-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 7722, rend_intergenic: 5174  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25609, rend_intergenic: 8206  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34960, rend_intergenic: 31310  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37792, rend_intergenic: 36284  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44844, rend_intergenic: 42547  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47945, rend_intergenic: 46963  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77076, rend_intergenic: 48892  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83128, rend_intergenic: 79832  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83601, rend_intergenic: 83142  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86197, rend_intergenic: 84114  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90060, rend_intergenic: 86659  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127070, rend_intergenic: 124991  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134827, rend_intergenic: 133747  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 270598, rend_intergenic: 253198  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 275904 - 287719
-exon list size: 1


building trellis

33.3    
66.7    
-found 1 predictions from path traversal

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