-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_12081639-12303755

-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_11-snap.2566-T1
Valid prediction for snap_scaffold_11-snap.2607-T1
Valid prediction for snap_scaffold_11-snap.2583-T1
Valid prediction for GlimmerHMM_glimmerT_27989-T1
Valid prediction for GlimmerHMM_glimmerT_27978-T1
Valid prediction for Augustus_model.g18555.t1
Valid prediction for Augustus_model.g18554.t1
Valid prediction for GlimmerHMM_glimmerT_28003-T1
Valid prediction for snap_scaffold_11-snap.2571-T1
Couldn't classify 140846, 140984
Couldn't classify 145929, 146003
Sorry, prediction pasa_asmbl_6014.p1 fails validation.
(GAC)	 TA	140846-140984	GT	AGG
(CCT)	 AG	142982-143014	GT	AGG
(GGA)	 AG	144617-144842	GT	GGG
(GTG)	 AG	145465-145567	GT	AGG
(TAC)	 AG	145929-146003	GA	ACG
-recovered pasa_asmbl_6014.p1, internal, 142982, 143014
-recovered pasa_asmbl_6014.p1, internal, 144617, 144842
-recovered pasa_asmbl_6014.p1, internal, 145465, 145567
Valid prediction for GlimmerHMM_glimmerT_27991-T1
Valid prediction for snap_scaffold_11-snap.2605-T1
Valid prediction for GlimmerHMM_glimmerT_27992-T1
Valid prediction for Augustus_model.g18542.t1
Valid prediction for GlimmerHMM_glimmerT_28008-T1
Valid prediction for Augustus_model.g18553.t1
Valid prediction for Augustus_model.g18550.t1
Valid prediction for GlimmerHMM_glimmerT_28009-T1
Couldn't classify 96199, 96594
Sorry, prediction pasa_asmbl_6009.p1 fails validation.
(GAG)	 AT	96199-96594	GA	TGG
Valid prediction for GlimmerHMM_glimmerT_27983-T1
Valid prediction for GlimmerHMM_glimmerT_27999-T1
Valid prediction for GlimmerHMM_glimmerT_27980-T1
Valid prediction for snap_scaffold_11-snap.2565-T1
Valid prediction for snap_scaffold_11-snap.2581-T1
Valid prediction for snap_scaffold_11-snap.2590-T1
Valid prediction for Augustus_model.g18539.t1
Valid prediction for Augustus_model.g18551.t1
Valid prediction for GlimmerHMM_glimmerT_28013-T1
Valid prediction for snap_scaffold_11-snap.2587-T1
Valid prediction for Augustus_model.g18552.t1
Valid prediction for snap_scaffold_11-snap.2576-T1
Valid prediction for GlimmerHMM_glimmerT_28005-T1
Valid prediction for GlimmerHMM_glimmerT_28000-T1
Valid prediction for GlimmerHMM_glimmerT_27994-T1
Valid prediction for Augustus_model.g18558.t1
Couldn't classify 201338, 201469
Couldn't classify 201650, 201820
Sorry, prediction pasa_asmbl_6232.p1 fails validation.
(GTA)	 CA	201338-201469	GT	AAG
(GAC)	 AG	201650-201820	CA	AGC
Valid prediction for GlimmerHMM_glimmerT_28002-T1
Valid prediction for snap_scaffold_11-snap.2569-T1
Valid prediction for GlimmerHMM_glimmerT_28004-T1
Valid prediction for GlimmerHMM_glimmerT_27988-T1
Valid prediction for snap_scaffold_11-snap.2586-T1
Valid prediction for snap_scaffold_11-snap.2604-T1
Valid prediction for Augustus_model.g18544.t1
Valid prediction for GlimmerHMM_glimmerT_27998-T1
Valid prediction for GlimmerHMM_glimmerT_27986-T1
Valid prediction for snap_scaffold_11-snap.2598-T1
Valid prediction for snap_scaffold_11-snap.2574-T1
Valid prediction for GlimmerHMM_glimmerT_28011-T1
Valid prediction for GlimmerHMM_glimmerT_27990-T1
Valid prediction for Augustus_model.g18549.t1
Couldn't classify 111289, 111338
Sorry, prediction pasa_asmbl_6010.p1 fails validation.
(AGC)	 TC	111289-111338	GT	AGG
(GCT)	 AG	111590-111665	GT	AGG
(GTG)	 AG	111860-112009	GT	TGG
(GCC)	 AG	112146-112383	GT	GGG
(GTG)	 AG	113178-113378	GT	ACG
(TGG)	 AG	113782-113966	AC	AAA
-recovered pasa_asmbl_6010.p1, terminal, 113782, 113966
-recovered pasa_asmbl_6010.p1, internal, 111590, 111665
-recovered pasa_asmbl_6010.p1, internal, 111860, 112009
-recovered pasa_asmbl_6010.p1, internal, 112146, 112383
-recovered pasa_asmbl_6010.p1, internal, 113178, 113378
Valid prediction for snap_scaffold_11-snap.2579-T1
Valid prediction for Augustus_model.g18557.t1
Valid prediction for snap_scaffold_11-snap.2584-T1
Valid prediction for snap_scaffold_11-snap.2568-T1
Valid prediction for GlimmerHMM_glimmerT_27979-T1
Valid prediction for GlimmerHMM_glimmerT_27996-T1
Valid prediction for snap_scaffold_11-snap.2578-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_11-snap.2600-T1
Valid prediction for snap_scaffold_11-snap.2603-T1
Valid prediction for GlimmerHMM_glimmerT_28012-T1
Valid prediction for snap_scaffold_11-snap.2594-T1
Valid prediction for snap_scaffold_11-snap.2606-T1
Valid prediction for GlimmerHMM_glimmerT_28010-T1
Valid prediction for snap_scaffold_11-snap.2593-T1
Valid prediction for Augustus_model.g18545.t1
Valid prediction for GlimmerHMM_glimmerT_27993-T1
Valid prediction for GlimmerHMM_glimmerT_27984-T1
Valid prediction for Augustus_model.g18546.t1
Valid prediction for snap_scaffold_11-snap.2596-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_28001-T1
Valid prediction for snap_scaffold_11-snap.2608-T1
Valid prediction for snap_scaffold_11-snap.2588-T1
Valid prediction for snap_scaffold_11-snap.2585-T1
Valid prediction for GlimmerHMM_glimmerT_27981-T1
Valid prediction for snap_scaffold_11-snap.2567-T1
Valid prediction for snap_scaffold_11-snap.2580-T1
Valid prediction for snap_scaffold_11-snap.2595-T1
Couldn't classify 178366, 178393
Sorry, prediction pasa_asmbl_7079.p1 fails validation.
(AAT)	 CC	178366-178393	GT	AGG
(AAC)	 AG	181251-182122	CT	AGC
-recovered pasa_asmbl_7079.p1, terminal, 181251, 182122
Valid prediction for snap_scaffold_11-snap.2599-T1
Valid prediction for snap_scaffold_11-snap.2592-T1
Valid prediction for snap_scaffold_11-snap.2597-T1
Valid prediction for GlimmerHMM_glimmerT_27977-T1
Valid prediction for snap_scaffold_11-snap.2577-T1
Valid prediction for snap_scaffold_11-snap.2572-T1
Valid prediction for snap_scaffold_11-snap.2601-T1
Valid prediction for GlimmerHMM_glimmerT_27997-T1
Valid prediction for Augustus_model.g18541.t1
Valid prediction for Augustus_model.g18547.t1
Valid prediction for snap_scaffold_11-snap.2575-T1
Valid prediction for snap_scaffold_11-snap.2582-T1
Valid prediction for GlimmerHMM_glimmerT_28007-T1
Valid prediction for GlimmerHMM_glimmerT_28006-T1
Valid prediction for snap_scaffold_11-snap.2573-T1
Valid prediction for GlimmerHMM_glimmerT_27982-T1
Valid prediction for Augustus_model.g18543.t1
Valid prediction for Augustus_model.g18548.t1
Valid prediction for snap_scaffold_11-snap.2570-T1
Valid prediction for snap_scaffold_11-snap.2589-T1
Valid prediction for Augustus_model.g18556.t1
Valid prediction for GlimmerHMM_glimmerT_27985-T1
Valid prediction for snap_scaffold_11-snap.2591-T1
Valid prediction for GlimmerHMM_glimmerT_27987-T1
Valid prediction for snap_scaffold_11-snap.2602-T1
Valid prediction for GlimmerHMM_glimmerT_27995-T1
Valid prediction for Augustus_model.g18540.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6750, rend_intergenic: 3734  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 9925, rend_intergenic: 6783  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14487, rend_intergenic: 11109  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21193, rend_intergenic: 16242  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31957, rend_intergenic: 26864  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34416, rend_intergenic: 32001  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47209, rend_intergenic: 40081  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55316, rend_intergenic: 52827  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64910, rend_intergenic: 59169  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76997, rend_intergenic: 65939  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77746, rend_intergenic: 77071  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81944, rend_intergenic: 78232  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94673, rend_intergenic: 85044  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113966, rend_intergenic: 99511  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127957, rend_intergenic: 123787  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134799, rend_intergenic: 128553  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143991, rend_intergenic: 135711  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155241, rend_intergenic: 149915  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182085, rend_intergenic: 172715  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 222117
-exon list size: 404


building trellis

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34.5    
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36.9    
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37.4    
37.7    
37.9    
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38.4    
38.7    
38.9    
39.2    
39.4    
39.7    
39.9    
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40.9    
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42.6    
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44.6    
44.8    
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48.3    
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53.9    
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55.9    
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83.3    
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86.9    
87.2    
87.4    
87.7    
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88.2    
88.4    
88.7    
88.9    
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89.4    
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90.4    
90.6    
90.9    
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91.4    
91.6    
91.9    
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92.4    
92.6    
92.9    
93.1    
93.3    
93.6    
93.8    
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96.8    
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97.3    
97.5    
97.8    
98.0    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 6750, rend_intergenic: 3734  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 9925, rend_intergenic: 6783  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14487, rend_intergenic: 11109  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21193, rend_intergenic: 16242  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31957, rend_intergenic: 26864  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34416, rend_intergenic: 32001  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47209, rend_intergenic: 40081  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55316, rend_intergenic: 52827  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64910, rend_intergenic: 59169  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76997, rend_intergenic: 65939  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77746, rend_intergenic: 77071  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81944, rend_intergenic: 78232  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94673, rend_intergenic: 85044  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113966, rend_intergenic: 99511  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127957, rend_intergenic: 123787  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134799, rend_intergenic: 128553  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143991, rend_intergenic: 135711  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155241, rend_intergenic: 149915  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182085, rend_intergenic: 172715  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support