-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_6/scaffold_6_11086505-11402811

-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_15503-T1
Valid prediction for snap_scaffold_6-snap.2421-T1
Valid prediction for snap_scaffold_6-snap.2400-T1
Valid prediction for GlimmerHMM_glimmerT_15488-T1
Valid prediction for GlimmerHMM_glimmerT_15508-T1
Valid prediction for Augustus_model.g10331.t1
Valid prediction for Augustus_model.g10329.t1
Valid prediction for snap_scaffold_6-snap.2389-T1
Valid prediction for snap_scaffold_6-snap.2397-T1
Valid prediction for snap_scaffold_6-snap.2384-T1
Valid prediction for snap_scaffold_6-snap.2413-T1
Valid prediction for snap_scaffold_6-snap.2417-T1
Valid prediction for snap_scaffold_6-snap.2386-T1
Valid prediction for snap_scaffold_6-snap.2419-T1
Valid prediction for Augustus_model.g10330.t1
Valid prediction for snap_scaffold_6-snap.2420-T1
Valid prediction for snap_scaffold_6-snap.2418-T1
Valid prediction for snap_scaffold_6-snap.2398-T1
Valid prediction for GlimmerHMM_glimmerT_15496-T1
Valid prediction for GlimmerHMM_glimmerT_15506-T1
Valid prediction for GlimmerHMM_glimmerT_15499-T1
Valid prediction for HiQ_model.g10321.t1
Valid prediction for snap_scaffold_6-snap.2409-T1
Valid prediction for snap_scaffold_6-snap.2426-T1
Valid prediction for snap_scaffold_6-snap.2424-T1
Valid prediction for snap_scaffold_6-snap.2377-T1
Valid prediction for snap_scaffold_6-snap.2387-T1
Valid prediction for snap_scaffold_6-snap.2391-T1
Valid prediction for Augustus_model.g10328.t1
Valid prediction for GlimmerHMM_glimmerT_15500-T1
Valid prediction for Augustus_model.g10326.t1
Valid prediction for snap_scaffold_6-snap.2429-T1
Valid prediction for snap_scaffold_6-snap.2378-T1
Valid prediction for snap_scaffold_6-snap.2427-T1
Valid prediction for GlimmerHMM_glimmerT_15501-T1
Valid prediction for GlimmerHMM_glimmerT_15490-T1
Valid prediction for Augustus_model.g10325.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.g10315.t1
Valid prediction for snap_scaffold_6-snap.2390-T1
Valid prediction for Augustus_model.g10314.t1
Valid prediction for snap_scaffold_6-snap.2408-T1
Valid prediction for snap_scaffold_6-snap.2385-T1
Valid prediction for Augustus_model.g10316.t1
Valid prediction for snap_scaffold_6-snap.2379-T1
Valid prediction for snap_scaffold_6-snap.2393-T1
Valid prediction for Augustus_model.g10319.t1
Valid prediction for snap_scaffold_6-snap.2402-T1
Valid prediction for snap_scaffold_6-snap.2381-T1
Valid prediction for snap_scaffold_6-snap.2415-T1
Valid prediction for snap_scaffold_6-snap.2403-T1
Valid prediction for snap_scaffold_6-snap.2422-T1
Valid prediction for snap_scaffold_6-snap.2406-T1
Valid prediction for Augustus_model.g10317.t1
Valid prediction for GlimmerHMM_glimmerT_15484-T1
Valid prediction for Augustus_model.g10313.t1
Valid prediction for pasa_asmbl_48742.p1
Valid prediction for GlimmerHMM_glimmerT_15498-T1
Valid prediction for Augustus_model.g10323.t1
Valid prediction for GlimmerHMM_glimmerT_15489-T1
Valid prediction for snap_scaffold_6-snap.2412-T1
Valid prediction for snap_scaffold_6-snap.2394-T1
Valid prediction for GlimmerHMM_glimmerT_15487-T1
Valid prediction for GlimmerHMM_glimmerT_15485-T1
Valid prediction for GlimmerHMM_glimmerT_15504-T1
Valid prediction for Augustus_model.g10320.t1
Valid prediction for snap_scaffold_6-snap.2382-T1
Valid prediction for CodingQuarry_transcript_55222-T1
Valid prediction for snap_scaffold_6-snap.2380-T1
Valid prediction for GlimmerHMM_glimmerT_15497-T1
Valid prediction for Augustus_model.g10310.t1
Valid prediction for Augustus_model.g10312.t1
Valid prediction for snap_scaffold_6-snap.2423-T1
Valid prediction for GlimmerHMM_glimmerT_15495-T1
Valid prediction for snap_scaffold_6-snap.2396-T1
Valid prediction for snap_scaffold_6-snap.2395-T1
Valid prediction for GlimmerHMM_glimmerT_15493-T1
Valid prediction for snap_scaffold_6-snap.2414-T1
Valid prediction for snap_scaffold_6-snap.2410-T1
Valid prediction for GlimmerHMM_glimmerT_15491-T1
Valid prediction for Augustus_model.g10307.t1
Valid prediction for snap_scaffold_6-snap.2388-T1
Couldn't classify 268636, 268717
Couldn't classify 271065, 271124
Sorry, prediction pasa_asmbl_48746.p1 fails validation.
(TTT)	 AC	268636-268717	GT	AGG
(TCC)	 AG	269911-270110	GT	CTG
(ACC)	 AG	270454-270601	GT	TGG
(ACG)	 AG	270834-270961	GT	AGG
(GAC)	 AG	271065-271124	CG	AGC
-recovered pasa_asmbl_48746.p1, internal, 269911, 270110
-recovered pasa_asmbl_48746.p1, internal, 270454, 270601
-recovered pasa_asmbl_48746.p1, internal, 270834, 270961
Valid prediction for GlimmerHMM_glimmerT_15481-T1
Valid prediction for Augustus_model.g10311.t1
Valid prediction for GlimmerHMM_glimmerT_15494-T1
Valid prediction for snap_scaffold_6-snap.2392-T1
Valid prediction for Augustus_model.g10322.t1
Valid prediction for Augustus_model.g10308.t1
Valid prediction for snap_scaffold_6-snap.2428-T1
Valid prediction for GlimmerHMM_glimmerT_15502-T1
Valid prediction for GlimmerHMM_glimmerT_15505-T1
Valid prediction for Augustus_model.g10309.t1
Valid prediction for CodingQuarry_transcript_55223-T1
Valid prediction for Augustus_model.g10318.t1
Valid prediction for snap_scaffold_6-snap.2407-T1
Couldn't classify 98509, 98868
Sorry, prediction pasa_asmbl_48751.p1 fails validation.
(ATC)	 TC	98509-98868	TG	GAT
Valid prediction for GlimmerHMM_glimmerT_15507-T1
Valid prediction for Augustus_model.g10327.t1
Valid prediction for GlimmerHMM_glimmerT_15482-T1
Valid prediction for snap_scaffold_6-snap.2416-T1
Valid prediction for snap_scaffold_6-snap.2383-T1
Valid prediction for GlimmerHMM_glimmerT_15486-T1
Valid prediction for GlimmerHMM_glimmerT_15492-T1
Couldn't classify 284876, 284884
Sorry, prediction pasa_asmbl_48743.p1 fails validation.
(ATG)	 GT	283998-284438	GT	CTG
(TTG)	 AG	284876-284884	CC	ATC
-recovered pasa_asmbl_48743.p1, initial, 283998, 284438
Couldn't classify 133910, 134064
Couldn't classify 138220, 138300
Sorry, prediction pasa_asmbl_49389.p1 fails validation.
(GAG)	 AG	133910-134064	GT	CGG
(GAA)	 AG	134561-134690	GT	AGG
(GCC)	 AG	135039-135131	GT	GGG
(GAC)	 AG	135309-135368	GT	AGG
(GTG)	 AG	138220-138300	TA	GGT
-recovered pasa_asmbl_49389.p1, internal, 133910, 134064
-recovered pasa_asmbl_49389.p1, internal, 134561, 134690
-recovered pasa_asmbl_49389.p1, internal, 135039, 135131
-recovered pasa_asmbl_49389.p1, internal, 135309, 135368
Valid prediction for snap_scaffold_6-snap.2404-T1
Valid prediction for GlimmerHMM_glimmerT_15483-T1
Valid prediction for snap_scaffold_6-snap.2401-T1
Valid prediction for snap_scaffold_6-snap.2425-T1
Valid prediction for Augustus_model.g10324.t1
Valid prediction for CodingQuarry_transcript_55221-T1
Valid prediction for snap_scaffold_6-snap.2376-T1
Valid prediction for snap_scaffold_6-snap.2399-T1
Valid prediction for snap_scaffold_6-snap.2411-T1
Valid prediction for snap_scaffold_6-snap.2405-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12608, rend_intergenic: 9803  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15323, rend_intergenic: 14602  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70089, rend_intergenic: 69690  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72508, rend_intergenic: 70089  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89035, rend_intergenic: 85650  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101035, rend_intergenic: 89075  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114224, rend_intergenic: 110749  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140406, rend_intergenic: 133219  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158619, rend_intergenic: 153215  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 258272, rend_intergenic: 256089  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 293938, rend_intergenic: 289731  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 305476, rend_intergenic: 303302  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 316307
-exon list size: 443


building trellis

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27.9    
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29.7    
29.9    
30.1    
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30.6    
30.8    
31.0    
31.2    
31.5    
31.7    
31.9    
32.1    
32.4    
32.6    
32.8    
33.0    
33.3    
33.5    
33.7    
33.9    
34.2    
34.4    
34.6    
34.8    
35.1    
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35.5    
35.7    
36.0    
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36.9    
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37.8    
38.0    
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38.7    
38.9    
39.1    
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39.6    
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40.0    
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40.4    
40.7    
40.9    
41.1    
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41.6    
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42.0    
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42.9    
43.1    
43.4    
43.6    
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44.0    
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44.5    
44.7    
44.9    
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89.4    
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89.9    
90.1    
90.3    
90.6    
90.8    
91.0    
91.2    
91.5    
91.7    
91.9    
92.1    
92.4    
92.6    
92.8    
93.0    
93.3    
93.5    
93.7    
93.9    
94.2    
94.4    
94.6    
94.8    
95.1    
95.3    
95.5    
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96.0    
96.2    
96.4    
96.6    
96.9    
97.1    
97.3    
97.5    
97.8    
98.0    
98.2    
98.4    
98.7    
98.9    
99.1    
99.3    
99.6    
99.8    
-found 37 predictions from path traversal
Error with prediction: snap lend_intergenic: 12608, rend_intergenic: 9803  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15323, rend_intergenic: 14602  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70089, rend_intergenic: 69690  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72508, rend_intergenic: 70089  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89035, rend_intergenic: 85650  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101035, rend_intergenic: 89075  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114224, rend_intergenic: 110749  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140406, rend_intergenic: 133219  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158619, rend_intergenic: 153215  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 258272, rend_intergenic: 256089  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 293938, rend_intergenic: 289731  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 305476, rend_intergenic: 303302  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