-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_18/scaffold_18_11204981-11496553

-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_43125-T1
Valid prediction for snap_scaffold_18-snap.2421-T1
Valid prediction for snap_scaffold_18-snap.2412-T1
Valid prediction for GlimmerHMM_glimmerT_43129-T1
Valid prediction for snap_scaffold_18-snap.2416-T1
Valid prediction for snap_scaffold_18-snap.2401-T1
Valid prediction for GlimmerHMM_glimmerT_43128-T1
Valid prediction for snap_scaffold_18-snap.2434-T1
Valid prediction for snap_scaffold_18-snap.2406-T1
Valid prediction for snap_scaffold_18-snap.2419-T1
Valid prediction for snap_scaffold_18-snap.2383-T1
Valid prediction for CodingQuarry_transcript_23903-T1
Valid prediction for GlimmerHMM_glimmerT_43119-T1
Valid prediction for CodingQuarry_transcript_23904-T1
Valid prediction for snap_scaffold_18-snap.2410-T1
Valid prediction for Augustus_model.g28731.t1
Valid prediction for Augustus_model.g28738.t1
Valid prediction for snap_scaffold_18-snap.2404-T1
Valid prediction for GlimmerHMM_glimmerT_43144-T1
Valid prediction for Augustus_model.g28741.t1
Valid prediction for snap_scaffold_18-snap.2415-T1
Valid prediction for Augustus_model.g28739.t1
Valid prediction for snap_scaffold_18-snap.2382-T1
Valid prediction for Augustus_model.g28740.t1
Valid prediction for snap_scaffold_18-snap.2444-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g28743.t1
Valid prediction for snap_scaffold_18-snap.2396-T1
Valid prediction for snap_scaffold_18-snap.2386-T1
Valid prediction for GlimmerHMM_glimmerT_43115-T1
Valid prediction for GlimmerHMM_glimmerT_43132-T1
Valid prediction for snap_scaffold_18-snap.2422-T1
Valid prediction for GlimmerHMM_glimmerT_43121-T1
Valid prediction for snap_scaffold_18-snap.2435-T1
Valid prediction for snap_scaffold_18-snap.2438-T1
Valid prediction for snap_scaffold_18-snap.2439-T1
Valid prediction for GlimmerHMM_glimmerT_43126-T1
Valid prediction for snap_scaffold_18-snap.2393-T1
Valid prediction for CodingQuarry_transcript_23905-T1
Valid prediction for GlimmerHMM_glimmerT_43123-T1
Valid prediction for GlimmerHMM_glimmerT_43139-T1
Valid prediction for snap_scaffold_18-snap.2403-T1
Valid prediction for snap_scaffold_18-snap.2399-T1
Valid prediction for snap_scaffold_18-snap.2405-T1
Valid prediction for snap_scaffold_18-snap.2431-T1
Valid prediction for snap_scaffold_18-snap.2384-T1
Valid prediction for GlimmerHMM_glimmerT_43133-T1
Valid prediction for snap_scaffold_18-snap.2442-T1
Valid prediction for HiQ_model.g28747.t1
Valid prediction for snap_scaffold_18-snap.2395-T1
Valid prediction for Augustus_model.g28736.t1
Valid prediction for Augustus_model.g28734.t1
Valid prediction for GlimmerHMM_glimmerT_43130-T1
Valid prediction for snap_scaffold_18-snap.2400-T1
Valid prediction for snap_scaffold_18-snap.2427-T1
Valid prediction for GlimmerHMM_glimmerT_43120-T1
Valid prediction for GlimmerHMM_glimmerT_43135-T1
Valid prediction for snap_scaffold_18-snap.2392-T1
Valid prediction for GlimmerHMM_glimmerT_43124-T1
Valid prediction for snap_scaffold_18-snap.2418-T1
Valid prediction for snap_scaffold_18-snap.2388-T1
Valid prediction for Augustus_model.g28733.t1
Valid prediction for pasa_asmbl_20945.p1
Valid prediction for snap_scaffold_18-snap.2390-T1
Valid prediction for Augustus_model.g28735.t1
Valid prediction for pasa_asmbl_20943.p1

-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_18-snap.2407-T1
Valid prediction for snap_scaffold_18-snap.2432-T1
Valid prediction for snap_scaffold_18-snap.2441-T1
Valid prediction for snap_scaffold_18-snap.2411-T1
Valid prediction for snap_scaffold_18-snap.2398-T1
Valid prediction for GlimmerHMM_glimmerT_43134-T1
Valid prediction for Augustus_model.g28745.t1
Valid prediction for Augustus_model.g28749.t1
Valid prediction for snap_scaffold_18-snap.2429-T1
Valid prediction for snap_scaffold_18-snap.2417-T1
Valid prediction for snap_scaffold_18-snap.2409-T1
Valid prediction for GlimmerHMM_glimmerT_43145-T1
Valid prediction for GlimmerHMM_glimmerT_43143-T1
Valid prediction for GlimmerHMM_glimmerT_43122-T1
Valid prediction for snap_scaffold_18-snap.2413-T1
Valid prediction for snap_scaffold_18-snap.2402-T1
Valid prediction for snap_scaffold_18-snap.2436-T1
Valid prediction for snap_scaffold_18-snap.2420-T1
Valid prediction for GlimmerHMM_glimmerT_43136-T1
Valid prediction for snap_scaffold_18-snap.2414-T1
Valid prediction for snap_scaffold_18-snap.2423-T1
Valid prediction for GlimmerHMM_glimmerT_43147-T1
Valid prediction for GlimmerHMM_glimmerT_43142-T1
Valid prediction for GlimmerHMM_glimmerT_43117-T1
Valid prediction for snap_scaffold_18-snap.2430-T1
Valid prediction for snap_scaffold_18-snap.2425-T1
Valid prediction for snap_scaffold_18-snap.2397-T1
Valid prediction for snap_scaffold_18-snap.2391-T1
Valid prediction for Augustus_model.g28748.t1
Valid prediction for snap_scaffold_18-snap.2428-T1
Valid prediction for snap_scaffold_18-snap.2381-T1
Valid prediction for Augustus_model.g28744.t1
Valid prediction for snap_scaffold_18-snap.2424-T1
Valid prediction for Augustus_model.g28732.t1
Valid prediction for Augustus_model.g28746.t1
Couldn't classify 37721, 37821
Sorry, prediction pasa_asmbl_20133.p1 fails validation.
(ATG)	 TT	35672-35717	GT	AGG
(GTC)	 AG	36306-36418	GT	AGG
(TTT)	 AG	36618-36755	GT	AGG
(GGA)	 AG	37019-37121	GT	TGG
(GCG)	 AG	37721-37821	GT	CGG
-recovered pasa_asmbl_20133.p1, initial, 35672, 35717
-recovered pasa_asmbl_20133.p1, internal, 36306, 36418
-recovered pasa_asmbl_20133.p1, internal, 36618, 36755
-recovered pasa_asmbl_20133.p1, internal, 37019, 37121
-recovered pasa_asmbl_20133.p1, internal, 37721, 37821
Valid prediction for Augustus_model.g28737.t1
Couldn't classify 28645, 28823
Sorry, prediction pasa_asmbl_20136.p1 fails validation.
(ATG)	 CC	27354-27552	GT	AGG
(GTG)	 AG	28645-28823	CG	ACC
-recovered pasa_asmbl_20136.p1, initial, 27354, 27552
Valid prediction for GlimmerHMM_glimmerT_43127-T1
Valid prediction for Augustus_model.g28742.t1
Valid prediction for snap_scaffold_18-snap.2443-T1
Valid prediction for GlimmerHMM_glimmerT_43138-T1
Valid prediction for snap_scaffold_18-snap.2408-T1
Valid prediction for GlimmerHMM_glimmerT_43141-T1
Valid prediction for snap_scaffold_18-snap.2426-T1
Valid prediction for GlimmerHMM_glimmerT_43137-T1
Valid prediction for GlimmerHMM_glimmerT_43146-T1
Valid prediction for GlimmerHMM_glimmerT_43116-T1
Valid prediction for snap_scaffold_18-snap.2433-T1
Valid prediction for snap_scaffold_18-snap.2387-T1
Valid prediction for snap_scaffold_18-snap.2394-T1
Valid prediction for snap_scaffold_18-snap.2389-T1
Valid prediction for snap_scaffold_18-snap.2440-T1
Valid prediction for GlimmerHMM_glimmerT_43118-T1
Valid prediction for snap_scaffold_18-snap.2445-T1
Valid prediction for snap_scaffold_18-snap.2437-T1
Valid prediction for snap_scaffold_18-snap.2385-T1
Valid prediction for GlimmerHMM_glimmerT_43131-T1
Valid prediction for GlimmerHMM_glimmerT_43140-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15283, rend_intergenic: 5121  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25072, rend_intergenic: 17327  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34906, rend_intergenic: 32069  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37829, rend_intergenic: 36381  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40151, rend_intergenic: 38091  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57332, rend_intergenic: 40375  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74150, rend_intergenic: 62247  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79540, rend_intergenic: 74239  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89991, rend_intergenic: 83404  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115510, rend_intergenic: 107195  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147139, rend_intergenic: 142228  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150601, rend_intergenic: 149018  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152453, rend_intergenic: 150758  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167871, rend_intergenic: 167201  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175968, rend_intergenic: 168755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187276, rend_intergenic: 184484  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189531, rend_intergenic: 187288  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211268, rend_intergenic: 189608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 216494, rend_intergenic: 213846  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 233472, rend_intergenic: 231850  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 241146, rend_intergenic: 233730  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 252042, rend_intergenic: 248133  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 264301, rend_intergenic: 253426  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 276521, rend_intergenic: 275130  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 282063, rend_intergenic: 280626  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 286665, rend_intergenic: 284730  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 289711, rend_intergenic: 288820  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 170490, rend_intergenic: 170487  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 291573
-exon list size: 434


building trellis

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31.2    
31.4    
31.7    
31.9    
32.1    
32.3    
32.6    
32.8    
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33.3    
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34.2    
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34.6    
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35.8    
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36.7    
36.9    
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37.8    
38.1    
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38.8    
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41.7    
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42.4    
42.7    
42.9    
43.1    
43.3    
43.6    
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99.5    
99.8    
-found 42 predictions from path traversal
Error with prediction: snap lend_intergenic: 15283, rend_intergenic: 5121  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25072, rend_intergenic: 17327  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34906, rend_intergenic: 32069  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37829, rend_intergenic: 36381  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40151, rend_intergenic: 38091  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57332, rend_intergenic: 40375  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74150, rend_intergenic: 62247  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79540, rend_intergenic: 74239  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89991, rend_intergenic: 83404  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115510, rend_intergenic: 107195  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147139, rend_intergenic: 142228  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150601, rend_intergenic: 149018  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152453, rend_intergenic: 150758  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167871, rend_intergenic: 167201  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175968, rend_intergenic: 168755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187276, rend_intergenic: 184484  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189531, rend_intergenic: 187288  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211268, rend_intergenic: 189608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 216494, rend_intergenic: 213846  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 233472, rend_intergenic: 231850  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 241146, rend_intergenic: 233730  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 252042, rend_intergenic: 248133  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 264301, rend_intergenic: 253426  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 276521, rend_intergenic: 275130  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 282063, rend_intergenic: 280626  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 286665, rend_intergenic: 284730  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 289711, rend_intergenic: 288820  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 170490, rend_intergenic: 170487  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support