-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_11/scaffold_11_2412281-2600987

-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 CodingQuarry_transcript_8000-T1
Valid prediction for GlimmerHMM_glimmerT_26700-T1
Valid prediction for snap_scaffold_11-snap.640-T1
Valid prediction for snap_scaffold_11-snap.650-T1
Valid prediction for snap_scaffold_11-snap.614-T1
Valid prediction for snap_scaffold_11-snap.648-T1
Valid prediction for GlimmerHMM_glimmerT_26689-T1
Valid prediction for Augustus_model.g17672.t1
Couldn't classify 96257, 96382
Sorry, prediction pasa_asmbl_6332.p1 fails validation.
(ATG)	 GA	93295-93405	GT	AGG
(AAA)	 AG	94495-94620	GT	AGG
(GTG)	 AG	94879-94962	GT	AGG
(GTG)	 AG	96257-96382	AG	CAA
-recovered pasa_asmbl_6332.p1, initial, 93295, 93405
-recovered pasa_asmbl_6332.p1, internal, 94495, 94620
-recovered pasa_asmbl_6332.p1, internal, 94879, 94962
Valid prediction for snap_scaffold_11-snap.619-T1
Couldn't classify 104074, 104108
Sorry, prediction pasa_asmbl_5370.p6 fails validation.
(CTG)	 AA	104074-104108	GT	GTG
(ACA)	 AG	104602-104688	GT	AGG
(CTT)	 AG	106039-106138	GT	TGG
(GCC)	 AG	106378-106437	GT	AGG
(CCA)	 AG	106596-106640	TT	GAT
-recovered pasa_asmbl_5370.p6, terminal, 106596, 106640
-recovered pasa_asmbl_5370.p6, internal, 104602, 104688
-recovered pasa_asmbl_5370.p6, internal, 106039, 106138
-recovered pasa_asmbl_5370.p6, internal, 106378, 106437
Valid prediction for Augustus_model.g17671.t1
Valid prediction for snap_scaffold_11-snap.634-T1
Valid prediction for snap_scaffold_11-snap.616-T1
Valid prediction for Augustus_model.g17674.t1
Valid prediction for snap_scaffold_11-snap.611-T1
Valid prediction for GlimmerHMM_glimmerT_26687-T1
Valid prediction for GlimmerHMM_glimmerT_26698-T1
Valid prediction for snap_scaffold_11-snap.629-T1
Valid prediction for Augustus_model.g17676.t1
Valid prediction for HiQ_model.g17666.t1
Valid prediction for snap_scaffold_11-snap.626-T1
Valid prediction for GlimmerHMM_glimmerT_26680-T1
Valid prediction for GlimmerHMM_glimmerT_26707-T1
Valid prediction for snap_scaffold_11-snap.624-T1
Valid prediction for snap_scaffold_11-snap.618-T1
Valid prediction for snap_scaffold_11-snap.621-T1
Valid prediction for GlimmerHMM_glimmerT_26702-T1
Couldn't classify 68825, 68944
Sorry, prediction pasa_asmbl_6311.p1 fails validation.
(ATG)	 AG	67805-68064	GT	GGG
(AGC)	 AG	68279-68392	GT	TGG
(GGG)	 AG	68619-68691	GT	AGG
(TCT)	 AG	68825-68944	GT	AGG
-recovered pasa_asmbl_6311.p1, initial, 67805, 68064
-recovered pasa_asmbl_6311.p1, internal, 67805, 68064
-recovered pasa_asmbl_6311.p1, internal, 68279, 68392
-recovered pasa_asmbl_6311.p1, internal, 68619, 68691
-recovered pasa_asmbl_6311.p1, internal, 68825, 68944
Valid prediction for Augustus_model.g17675.t1
Valid prediction for HiQ_model.g17669.t1
Valid prediction for GlimmerHMM_glimmerT_26697-T1
Valid prediction for GlimmerHMM_glimmerT_26708-T1
Valid prediction for GlimmerHMM_glimmerT_26683-T1
Valid prediction for snap_scaffold_11-snap.643-T1
Valid prediction for snap_scaffold_11-snap.651-T1
Valid prediction for snap_scaffold_11-snap.617-T1
Valid prediction for GlimmerHMM_glimmerT_26694-T1
Valid prediction for GlimmerHMM_glimmerT_26696-T1
Valid prediction for snap_scaffold_11-snap.636-T1
Valid prediction for HiQ_model.g17670.t1
Valid prediction for GlimmerHMM_glimmerT_26690-T1
Valid prediction for snap_scaffold_11-snap.623-T1
Valid prediction for snap_scaffold_11-snap.609-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 GlimmerHMM_glimmerT_26703-T1
Valid prediction for GlimmerHMM_glimmerT_26706-T1
Valid prediction for snap_scaffold_11-snap.622-T1
Valid prediction for snap_scaffold_11-snap.608-T1
Valid prediction for snap_scaffold_11-snap.627-T1
Valid prediction for snap_scaffold_11-snap.647-T1
Valid prediction for snap_scaffold_11-snap.620-T1
Valid prediction for snap_scaffold_11-snap.632-T1
Couldn't classify 171727, 171828
Couldn't classify 173672, 173923
Sorry, prediction pasa_asmbl_6498.p1 fails validation.
(GCG)	 AG	171727-171828	GT	AGG
(ATT)	 AG	172404-172601	GT	GGG
(GAG)	 AG	173672-173923	CT	CCC
-recovered pasa_asmbl_6498.p1, internal, 171727, 171828
-recovered pasa_asmbl_6498.p1, internal, 172404, 172601
Valid prediction for GlimmerHMM_glimmerT_26688-T1
Valid prediction for snap_scaffold_11-snap.631-T1
Valid prediction for GlimmerHMM_glimmerT_26699-T1
Valid prediction for GlimmerHMM_glimmerT_26705-T1
Valid prediction for Augustus_model.g17677.t1
Valid prediction for GlimmerHMM_glimmerT_26695-T1
Valid prediction for snap_scaffold_11-snap.644-T1
Valid prediction for CodingQuarry_transcript_7998-T1
Valid prediction for snap_scaffold_11-snap.645-T1
Valid prediction for pasa_asmbl_6496.p1
Valid prediction for Augustus_model.g17664.t1
Valid prediction for GlimmerHMM_glimmerT_26704-T1
Valid prediction for snap_scaffold_11-snap.639-T1
Valid prediction for snap_scaffold_11-snap.625-T1
Valid prediction for Augustus_model.g17661.t1
Valid prediction for snap_scaffold_11-snap.628-T1
Valid prediction for snap_scaffold_11-snap.642-T1
Couldn't classify 102558, 102593
Couldn't classify 102911, 103204
Sorry, prediction pasa_asmbl_7359.p1 fails validation.
(GAC)	 AT	102558-102593	GT	AAG
(AAA)	 AG	102911-103204	GA	TGG
Valid prediction for snap_scaffold_11-snap.646-T1
Valid prediction for snap_scaffold_11-snap.635-T1
Valid prediction for snap_scaffold_11-snap.633-T1
Valid prediction for snap_scaffold_11-snap.615-T1
Valid prediction for GlimmerHMM_glimmerT_26693-T1
Valid prediction for Augustus_model.g17665.t1
Valid prediction for snap_scaffold_11-snap.612-T1
Valid prediction for GlimmerHMM_glimmerT_26685-T1
Valid prediction for Augustus_model.g17667.t1
Couldn't classify 136408, 137062
Sorry, prediction pasa_asmbl_6501.p1 fails validation.
(AGA)	 GC	136408-137062	GT	TGG
(TGG)	 AG	137477-137638	GT	TGG
(CCC)	 AG	137919-138035	GT	AGG
(AGA)	 AG	138235-138359	GT	AGG
(TCC)	 AG	138466-138570	GT	AGG
(GAG)	 AG	139177-139308	GT	AGG
(TTC)	 AG	139416-139522	GT	AAG
(GCA)	 AG	139688-139820	GT	AGG
(GCT)	 AG	140506-140602	GT	AGG
(AGC)	 AG	141015-141199	GT	AGG
(GAG)	 AG	141317-141385	GT	AGG
(ACT)	 AG	141500-141537	GT	CTG
(GTT)	 AG	141611-141701	GT	AGG
(GCG)	 AG	142277-142345	GT	AGG
(ACT)	 AG	142491-142528	GT	AGG
(CGT)	 AG	143293-143383	GT	AGG
(GCT)	 AG	143570-143638	GT	AGG
(TCC)	 AG	143728-143765	GT	AAG
(GAT)	 AG	144825-144915	GT	AGG
(GCT)	 AG	145129-145238	GT	CAG
(GCT)	 AG	145342-145540	GT	AGG
(GTA)	 AG	145631-145671	GT	GTG
(GTT)	 AG	145785-145875	GT	ACG
(GAT)	 AG	147238-147324	GT	AGG
(GAG)	 AG	149765-149854	GC	AGG
(GAC)	 AG	149974-150102	GT	CGG
(GTT)	 AG	150203-150292	GT	CGG
(GAG)	 AG	150499-150591	GT	AGG
(ATG)	 AG	150678-150746	GT	ACG
(TTG)	 AG	150854-150937	GT	AGG
(CTG)	 AG	152933-153016	GT	AGG
(GCT)	 AG	153199-153291	GT	GGG
(GAG)	 AG	153658-153768	GT	GGG
(GAT)	 AG	153916-153945	GA	AGG
-recovered pasa_asmbl_6501.p1, initial, 150678, 150746
-recovered pasa_asmbl_6501.p1, terminal, 153916, 153945
-recovered pasa_asmbl_6501.p1, internal, 137477, 137638
-recovered pasa_asmbl_6501.p1, internal, 137919, 138035
-recovered pasa_asmbl_6501.p1, internal, 138235, 138359
-recovered pasa_asmbl_6501.p1, internal, 138466, 138570
-recovered pasa_asmbl_6501.p1, internal, 139177, 139308
-recovered pasa_asmbl_6501.p1, internal, 139416, 139522
-recovered pasa_asmbl_6501.p1, internal, 139688, 139820
-recovered pasa_asmbl_6501.p1, internal, 140506, 140602
-recovered pasa_asmbl_6501.p1, internal, 141015, 141199
-recovered pasa_asmbl_6501.p1, internal, 141317, 141385
-recovered pasa_asmbl_6501.p1, internal, 141500, 141537
-recovered pasa_asmbl_6501.p1, internal, 141611, 141701
-recovered pasa_asmbl_6501.p1, internal, 142277, 142345
-recovered pasa_asmbl_6501.p1, internal, 142491, 142528
-recovered pasa_asmbl_6501.p1, internal, 143293, 143383
-recovered pasa_asmbl_6501.p1, internal, 143570, 143638
-recovered pasa_asmbl_6501.p1, internal, 143728, 143765
-recovered pasa_asmbl_6501.p1, internal, 144825, 144915
-recovered pasa_asmbl_6501.p1, internal, 145129, 145238
-recovered pasa_asmbl_6501.p1, internal, 145342, 145540
-recovered pasa_asmbl_6501.p1, internal, 145631, 145671
-recovered pasa_asmbl_6501.p1, internal, 145785, 145875
-recovered pasa_asmbl_6501.p1, internal, 147238, 147324
-recovered pasa_asmbl_6501.p1, internal, 149765, 149854
-recovered pasa_asmbl_6501.p1, internal, 149974, 150102
-recovered pasa_asmbl_6501.p1, internal, 150203, 150292
-recovered pasa_asmbl_6501.p1, internal, 150499, 150591
-recovered pasa_asmbl_6501.p1, internal, 150678, 150746
-recovered pasa_asmbl_6501.p1, internal, 150854, 150937
-recovered pasa_asmbl_6501.p1, internal, 152933, 153016
-recovered pasa_asmbl_6501.p1, internal, 153199, 153291
-recovered pasa_asmbl_6501.p1, internal, 153658, 153768
Valid prediction for Augustus_model.g17662.t1
Valid prediction for GlimmerHMM_glimmerT_26684-T1
Valid prediction for Augustus_model.g17668.t1
Valid prediction for GlimmerHMM_glimmerT_26682-T1
Valid prediction for GlimmerHMM_glimmerT_26701-T1
Valid prediction for snap_scaffold_11-snap.610-T1
Valid prediction for Augustus_model.g17663.t1
Valid prediction for snap_scaffold_11-snap.613-T1
Valid prediction for pasa_asmbl_6506.p2
Couldn't classify 128576, 128783
Sorry, prediction pasa_asmbl_6505.p1 fails validation.
(TGC)	 GC	128576-128783	GT	CGG
(GTC)	 AG	128863-128951	GT	TGG
(ACA)	 AG	129826-130023	GT	GAG
-recovered pasa_asmbl_6505.p1, terminal, 129826, 130023
-recovered pasa_asmbl_6505.p1, internal, 128863, 128951
-recovered pasa_asmbl_6505.p1, internal, 129826, 130023
Valid prediction for Augustus_model.g17673.t1
Valid prediction for snap_scaffold_11-snap.641-T1
Valid prediction for HiQ_model.g17660.t1
Valid prediction for GlimmerHMM_glimmerT_26691-T1
Valid prediction for CodingQuarry_transcript_7999-T1
Valid prediction for snap_scaffold_11-snap.630-T1
Valid prediction for snap_scaffold_11-snap.638-T1
Valid prediction for GlimmerHMM_glimmerT_26681-T1
Valid prediction for snap_scaffold_11-snap.637-T1
Valid prediction for GlimmerHMM_glimmerT_26692-T1
Valid prediction for GlimmerHMM_glimmerT_26686-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 16344, rend_intergenic: 13474  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24418, rend_intergenic: 16887  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27044, rend_intergenic: 25282  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31923, rend_intergenic: 30434  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52594, rend_intergenic: 35170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60286, rend_intergenic: 58837  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60972, rend_intergenic: 60865  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77592, rend_intergenic: 74427  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111063, rend_intergenic: 88273  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124559, rend_intergenic: 120531  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133739, rend_intergenic: 124891  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154026, rend_intergenic: 148335  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155159, rend_intergenic: 154396  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166319, rend_intergenic: 155536  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170573, rend_intergenic: 166655  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 188707
-exon list size: 419


building trellis

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23.5    
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28.7    
29.0    
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29.9    
30.2    
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31.1    
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32.1    
32.3    
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33.0    
33.3    
33.5    
33.7    
34.0    
34.2    
34.4    
34.7    
34.9    
35.2    
35.4    
35.6    
35.9    
36.1    
36.3    
36.6    
36.8    
37.1    
37.3    
37.5    
37.8    
38.0    
38.2    
38.5    
38.7    
39.0    
39.2    
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39.7    
39.9    
40.1    
40.4    
40.6    
40.9    
41.1    
41.3    
41.6    
41.8    
42.0    
42.3    
42.5    
42.8    
43.0    
43.2    
43.5    
43.7    
43.9    
44.2    
44.4    
44.7    
44.9    
45.1    
45.4    
45.6    
45.8    
46.1    
46.3    
46.6    
46.8    
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48.0    
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80.0    
80.3    
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81.0    
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88.1    
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88.8    
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90.5    
90.7    
91.0    
91.2    
91.4    
91.7    
91.9    
92.2    
92.4    
92.6    
92.9    
93.1    
93.3    
93.6    
93.8    
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94.3    
94.5    
94.8    
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95.2    
95.5    
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96.0    
96.2    
96.4    
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96.9    
97.1    
97.4    
97.6    
97.9    
98.1    
98.3    
98.6    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 16344, rend_intergenic: 13474  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24418, rend_intergenic: 16887  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27044, rend_intergenic: 25282  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31923, rend_intergenic: 30434  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52594, rend_intergenic: 35170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60286, rend_intergenic: 58837  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60972, rend_intergenic: 60865  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77592, rend_intergenic: 74427  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111063, rend_intergenic: 88273  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124559, rend_intergenic: 120531  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133739, rend_intergenic: 124891  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154026, rend_intergenic: 148335  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155159, rend_intergenic: 154396  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166319, rend_intergenic: 155536  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170573, rend_intergenic: 166655  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

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