-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_7/scaffold_7_13602263-13884313

-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_7-snap.2554-T1
Valid prediction for snap_scaffold_7-snap.2590-T1
Valid prediction for snap_scaffold_7-snap.2557-T1
Valid prediction for GlimmerHMM_glimmerT_18429-T1
Couldn't classify 7836, 7888
Sorry, prediction pasa_asmbl_50365.p1 fails validation.
(GCC)	 CT	7836-7888	GT	AGG
(GTA)	 AG	7991-8108	GT	AGG
(GAG)	 AG	9540-9617	GT	GGG
(ATT)	 AG	9756-9823	GT	GAG
(GTC)	 AG	10094-10232	GT	AGG
(CCT)	 AG	11298-11384	GT	ATG
(AGC)	 AG	11832-11927	GT	AGG
(GCG)	 AG	12232-12433	GT	AGG
(AAA)	 AG	12817-12951	GT	AGG
(GAA)	 AG	13213-13331	CG	GAC
-recovered pasa_asmbl_50365.p1, terminal, 13213, 13331
-recovered pasa_asmbl_50365.p1, internal, 7991, 8108
-recovered pasa_asmbl_50365.p1, internal, 9540, 9617
-recovered pasa_asmbl_50365.p1, internal, 9756, 9823
-recovered pasa_asmbl_50365.p1, internal, 10094, 10232
-recovered pasa_asmbl_50365.p1, internal, 11298, 11384
-recovered pasa_asmbl_50365.p1, internal, 11832, 11927
-recovered pasa_asmbl_50365.p1, internal, 12232, 12433
-recovered pasa_asmbl_50365.p1, internal, 12817, 12951
Valid prediction for GlimmerHMM_glimmerT_18430-T1
Couldn't classify 93526, 93575
Sorry, prediction pasa_asmbl_50368.p1 fails validation.
(GCT)	 CA	93526-93575	GT	AGG
(CCT)	 AG	95690-95809	GT	AAG
(TAA)	 AG	96005-96107	GT	AGG
(ACC)	 AG	96251-96298	GT	AAG
(GTG)	 AG	96436-96504	GT	TGG
(GCC)	 AG	97963-98568	TG	GAT
-recovered pasa_asmbl_50368.p1, terminal, 95690, 95809
-recovered pasa_asmbl_50368.p1, terminal, 97963, 98568
-recovered pasa_asmbl_50368.p1, internal, 95690, 95809
-recovered pasa_asmbl_50368.p1, internal, 96005, 96107
-recovered pasa_asmbl_50368.p1, internal, 96251, 96298
-recovered pasa_asmbl_50368.p1, internal, 96436, 96504
Valid prediction for pasa_asmbl_50380.p1
Valid prediction for snap_scaffold_7-snap.2566-T1
Valid prediction for snap_scaffold_7-snap.2564-T1
Valid prediction for GlimmerHMM_glimmerT_18422-T1
Valid prediction for snap_scaffold_7-snap.2561-T1
Valid prediction for snap_scaffold_7-snap.2572-T1
Valid prediction for GlimmerHMM_glimmerT_18420-T1
Valid prediction for Augustus_model.g12421.t1
Valid prediction for Augustus_model.g12419.t1
Valid prediction for snap_scaffold_7-snap.2567-T1
Valid prediction for snap_scaffold_7-snap.2574-T1
Valid prediction for GlimmerHMM_glimmerT_18416-T1
Valid prediction for snap_scaffold_7-snap.2575-T1
Valid prediction for GlimmerHMM_glimmerT_18434-T1
Valid prediction for Augustus_model.g12426.t1
Valid prediction for GlimmerHMM_glimmerT_18424-T1
Valid prediction for Augustus_model.g12422.t1
Valid prediction for CodingQuarry_transcript_57705-T1
Valid prediction for snap_scaffold_7-snap.2588-T1
Valid prediction for Augustus_model.g12424.t1
Valid prediction for GlimmerHMM_glimmerT_18433-T1
Valid prediction for snap_scaffold_7-snap.2555-T1
Valid prediction for snap_scaffold_7-snap.2552-T1
Valid prediction for snap_scaffold_7-snap.2571-T1
Valid prediction for Augustus_model.g12417.t1
Valid prediction for snap_scaffold_7-snap.2582-T1
Valid prediction for snap_scaffold_7-snap.2584-T1
Valid prediction for snap_scaffold_7-snap.2581-T1
Valid prediction for snap_scaffold_7-snap.2558-T1
Valid prediction for pasa_asmbl_50375.p3
Valid prediction for CodingQuarry_transcript_57706-T1
Valid prediction for pasa_asmbl_51325.p1
Valid prediction for GlimmerHMM_glimmerT_18417-T1
Valid prediction for snap_scaffold_7-snap.2583-T1
Valid prediction for Augustus_model.g12425.t1
Valid prediction for HiQ_model.g12423.t1
Valid prediction for GlimmerHMM_glimmerT_18423-T1
Valid prediction for GlimmerHMM_glimmerT_18432-T1
Valid prediction for GlimmerHMM_glimmerT_18428-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 snap_scaffold_7-snap.2570-T1
Valid prediction for GlimmerHMM_glimmerT_18421-T1
Valid prediction for snap_scaffold_7-snap.2591-T1
Valid prediction for snap_scaffold_7-snap.2569-T1
Valid prediction for GlimmerHMM_glimmerT_18431-T1
Couldn't classify 10753, 10868
Sorry, prediction pasa_asmbl_51329.p1 fails validation.
(ATG)	 AT	6810-7500	GT	TTG
(ATG)	 AG	10166-10219	GC	AGG
(CAC)	 AG	10753-10868	GC	TGG
-recovered pasa_asmbl_51329.p1, initial, 6810, 7500
add_exon() Sorry, pasa_asmbl_51329.p1 10166-10219-initial-1 is invalid.
-recovered pasa_asmbl_51329.p1, initial, 10166, 10219
-recovered pasa_asmbl_51329.p1, internal, 10166, 10219
-recovered pasa_asmbl_51329.p1, internal, 10753, 10868
Valid prediction for snap_scaffold_7-snap.2576-T1
Valid prediction for snap_scaffold_7-snap.2563-T1
Valid prediction for Augustus_model.g12414.t1
Valid prediction for snap_scaffold_7-snap.2592-T1
Valid prediction for CodingQuarry_transcript_57707-T1
Valid prediction for GlimmerHMM_glimmerT_18425-T1
Valid prediction for snap_scaffold_7-snap.2586-T1
Valid prediction for snap_scaffold_7-snap.2559-T1
Valid prediction for snap_scaffold_7-snap.2546-T1
Valid prediction for snap_scaffold_7-snap.2579-T1
Valid prediction for snap_scaffold_7-snap.2547-T1
Valid prediction for Augustus_model.g12428.t1
Valid prediction for Augustus_model.g12418.t1
Valid prediction for snap_scaffold_7-snap.2568-T1
Valid prediction for snap_scaffold_7-snap.2549-T1
Valid prediction for HiQ_model.g12427.t1
Valid prediction for snap_scaffold_7-snap.2553-T1
Valid prediction for snap_scaffold_7-snap.2562-T1
Valid prediction for GlimmerHMM_glimmerT_18418-T1
Valid prediction for GlimmerHMM_glimmerT_18426-T1
Valid prediction for GlimmerHMM_glimmerT_18419-T1
Valid prediction for snap_scaffold_7-snap.2587-T1
Valid prediction for GlimmerHMM_glimmerT_18436-T1
Valid prediction for GlimmerHMM_glimmerT_18435-T1
Couldn't classify 11178, 12527
Sorry, prediction pasa_asmbl_51328.p1 fails validation.
(CCT)	 TC	11178-12527	GC	CTG
Valid prediction for pasa_asmbl_51318.p1
Valid prediction for Augustus_model.g12420.t1
Valid prediction for snap_scaffold_7-snap.2550-T1
Valid prediction for snap_scaffold_7-snap.2577-T1
Valid prediction for snap_scaffold_7-snap.2580-T1
Valid prediction for GlimmerHMM_glimmerT_18427-T1
Valid prediction for snap_scaffold_7-snap.2551-T1
Valid prediction for snap_scaffold_7-snap.2565-T1
Valid prediction for snap_scaffold_7-snap.2548-T1
Valid prediction for snap_scaffold_7-snap.2556-T1
Valid prediction for snap_scaffold_7-snap.2593-T1
Valid prediction for snap_scaffold_7-snap.2589-T1
Couldn't classify 210440, 210509
Sorry, prediction pasa_asmbl_51317.p1 fails validation.
(AAC)	 CA	210440-210509	GT	AGG
(TTC)	 AG	210885-210979	GT	AGG
(GAT)	 AG	211150-211306	GT	AGG
(GGG)	 AG	212138-212265	GC	AGG
-recovered pasa_asmbl_51317.p1, terminal, 212138, 212265
-recovered pasa_asmbl_51317.p1, internal, 210885, 210979
-recovered pasa_asmbl_51317.p1, internal, 211150, 211306
-recovered pasa_asmbl_51317.p1, internal, 212138, 212265
Valid prediction for Augustus_model.g12416.t1
Valid prediction for snap_scaffold_7-snap.2585-T1
Valid prediction for snap_scaffold_7-snap.2573-T1
Valid prediction for snap_scaffold_7-snap.2578-T1
Valid prediction for snap_scaffold_7-snap.2560-T1
Valid prediction for Augustus_model.g12415.t1
Valid prediction for Augustus_model.g12413.t1
Valid prediction for snap_scaffold_7-snap.2594-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 68423, rend_intergenic: 62991  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85687, rend_intergenic: 72086  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87419, rend_intergenic: 85720  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94245, rend_intergenic: 88330  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134398, rend_intergenic: 129473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137637, rend_intergenic: 135610  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141664, rend_intergenic: 137892  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148124, rend_intergenic: 145947  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160489, rend_intergenic: 150017  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164941, rend_intergenic: 160861  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168145, rend_intergenic: 167101  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177406, rend_intergenic: 168194  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209083, rend_intergenic: 178100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 229303, rend_intergenic: 215804  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 239890, rend_intergenic: 230593  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 243587, rend_intergenic: 240618  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 257720, rend_intergenic: 244525  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 282051
-exon list size: 482


building trellis

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28.3    
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29.3    
29.5    
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30.2    
30.4    
30.6    
30.8    
31.0    
31.2    
31.4    
31.6    
31.8    
32.0    
32.2    
32.4    
32.6    
32.9    
33.1    
33.3    
33.5    
33.7    
33.9    
34.1    
34.3    
34.5    
34.7    
34.9    
35.1    
35.3    
35.5    
35.7    
36.0    
36.2    
36.4    
36.6    
36.8    
37.0    
37.2    
37.4    
37.6    
37.8    
38.0    
38.2    
38.4    
38.6    
38.8    
39.0    
39.3    
39.5    
39.7    
39.9    
40.1    
40.3    
40.5    
40.7    
40.9    
41.1    
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42.8    
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44.8    
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49.6    
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64.3    
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88.4    
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88.8    
89.0    
89.3    
89.5    
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90.1    
90.3    
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90.9    
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91.3    
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92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
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96.9    
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97.3    
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97.9    
98.1    
98.3    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 68423, rend_intergenic: 62991  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85687, rend_intergenic: 72086  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87419, rend_intergenic: 85720  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94245, rend_intergenic: 88330  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134398, rend_intergenic: 129473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137637, rend_intergenic: 135610  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141664, rend_intergenic: 137892  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148124, rend_intergenic: 145947  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160489, rend_intergenic: 150017  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164941, rend_intergenic: 160861  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168145, rend_intergenic: 167101  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177406, rend_intergenic: 168194  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209083, rend_intergenic: 178100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 229303, rend_intergenic: 215804  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 239890, rend_intergenic: 230593  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 243587, rend_intergenic: 240618  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 257720, rend_intergenic: 244525  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support