-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_14/scaffold_14_12545666-12814010

-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_14-snap.2594-T1
Valid prediction for GlimmerHMM_glimmerT_34869-T1
Valid prediction for GlimmerHMM_glimmerT_34882-T1
Valid prediction for GlimmerHMM_glimmerT_34876-T1
Valid prediction for GlimmerHMM_glimmerT_34874-T1
Valid prediction for GlimmerHMM_glimmerT_34879-T1
Valid prediction for HiQ_model.g23326.t1
Valid prediction for GlimmerHMM_glimmerT_34891-T1
Valid prediction for GlimmerHMM_glimmerT_34890-T1
Valid prediction for snap_scaffold_14-snap.2577-T1
Valid prediction for snap_scaffold_14-snap.2596-T1
Valid prediction for GlimmerHMM_glimmerT_34887-T1
Valid prediction for GlimmerHMM_glimmerT_34871-T1
Valid prediction for snap_scaffold_14-snap.2576-T1
Valid prediction for snap_scaffold_14-snap.2571-T1
Valid prediction for snap_scaffold_14-snap.2609-T1
Valid prediction for snap_scaffold_14-snap.2587-T1
Valid prediction for snap_scaffold_14-snap.2603-T1
Valid prediction for snap_scaffold_14-snap.2581-T1
Valid prediction for snap_scaffold_14-snap.2590-T1
Valid prediction for pasa_asmbl_12433.p1
Valid prediction for Augustus_model.g23325.t1
Valid prediction for GlimmerHMM_glimmerT_34870-T1
Valid prediction for Augustus_model.g23331.t1
Valid prediction for snap_scaffold_14-snap.2575-T1
Valid prediction for CodingQuarry_transcript_15882-T1
Valid prediction for snap_scaffold_14-snap.2599-T1
Valid prediction for Augustus_model.g23338.t1
Valid prediction for snap_scaffold_14-snap.2579-T1
Valid prediction for snap_scaffold_14-snap.2574-T1
Valid prediction for snap_scaffold_14-snap.2604-T1
Valid prediction for snap_scaffold_14-snap.2606-T1
Valid prediction for snap_scaffold_14-snap.2585-T1
Valid prediction for GlimmerHMM_glimmerT_34867-T1
Valid prediction for HiQ_model.g23320.t1
Valid prediction for Augustus_model.g23319.t1
Valid prediction for CodingQuarry_transcript_15883-T1
Valid prediction for snap_scaffold_14-snap.2586-T1
Valid prediction for CodingQuarry_transcript_15889-T1
Valid prediction for GlimmerHMM_glimmerT_34888-T1
Valid prediction for snap_scaffold_14-snap.2573-T1
Valid prediction for Augustus_model.g23318.t1
Valid prediction for GlimmerHMM_glimmerT_34885-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_34873-T1
Couldn't classify 103402, 103708
Sorry, prediction pasa_asmbl_13590.p1 fails validation.
(GAG)	 AG	103402-103708	GT	TGG
(ATC)	 AG	104045-104107	GT	TGG
(CAC)	 AG	104224-104505	GT	GGG
(GTG)	 AG	104875-105072	GT	AGG
(GTA)	 AG	105432-105610	GT	AGG
(CTC)	 AG	105906-105927	GT	AGG
(GAC)	 AG	106225-106489	GT	AGG
(GAT)	 AG	106643-106799	AA	AAA
-recovered pasa_asmbl_13590.p1, terminal, 105906, 105927
-recovered pasa_asmbl_13590.p1, terminal, 106643, 106799
-recovered pasa_asmbl_13590.p1, internal, 103402, 103708
-recovered pasa_asmbl_13590.p1, internal, 104045, 104107
-recovered pasa_asmbl_13590.p1, internal, 104224, 104505
-recovered pasa_asmbl_13590.p1, internal, 104875, 105072
-recovered pasa_asmbl_13590.p1, internal, 105432, 105610
-recovered pasa_asmbl_13590.p1, internal, 105906, 105927
-recovered pasa_asmbl_13590.p1, internal, 106225, 106489
Couldn't classify 133491, 133586
Sorry, prediction pasa_asmbl_13861.p1 fails validation.
(AAC)	 AG	133491-133586	GT	AGG
(AAG)	 AG	133978-134110	GT	AGG
(GGG)	 AG	134326-134408	GT	CAG
(CAC)	 AG	134707-134813	GT	GGG
(ATC)	 AG	135032-135210	GT	AGG
(GGA)	 AG	135705-135814	GA	AGG
-recovered pasa_asmbl_13861.p1, terminal, 135705, 135814
-recovered pasa_asmbl_13861.p1, internal, 133491, 133586
-recovered pasa_asmbl_13861.p1, internal, 133978, 134110
-recovered pasa_asmbl_13861.p1, internal, 134326, 134408
-recovered pasa_asmbl_13861.p1, internal, 134707, 134813
-recovered pasa_asmbl_13861.p1, internal, 135032, 135210
Valid prediction for GlimmerHMM_glimmerT_34884-T1
Valid prediction for Augustus_model.g23339.t1
Valid prediction for snap_scaffold_14-snap.2600-T1
Valid prediction for snap_scaffold_14-snap.2602-T1
Valid prediction for GlimmerHMM_glimmerT_34883-T1
Valid prediction for snap_scaffold_14-snap.2580-T1
Valid prediction for Augustus_model.g23328.t1
Valid prediction for snap_scaffold_14-snap.2601-T1
Valid prediction for snap_scaffold_14-snap.2607-T1
Valid prediction for snap_scaffold_14-snap.2584-T1
Valid prediction for GlimmerHMM_glimmerT_34877-T1
Valid prediction for CodingQuarry_transcript_15890-T1
Valid prediction for GlimmerHMM_glimmerT_34868-T1
Valid prediction for GlimmerHMM_glimmerT_34886-T1
Valid prediction for snap_scaffold_14-snap.2592-T1
Valid prediction for GlimmerHMM_glimmerT_34875-T1
Valid prediction for snap_scaffold_14-snap.2578-T1
Valid prediction for Augustus_model.g23332.t1
Valid prediction for snap_scaffold_14-snap.2582-T1
Valid prediction for pasa_asmbl_13581.p1
Valid prediction for GlimmerHMM_glimmerT_34880-T1
Valid prediction for CodingQuarry_transcript_15886-T1
Valid prediction for CodingQuarry_transcript_15892-T1
Valid prediction for Augustus_model.g23322.t1
Valid prediction for snap_scaffold_14-snap.2608-T1
Valid prediction for Augustus_model.g23334.t1
Valid prediction for snap_scaffold_14-snap.2588-T1
Valid prediction for snap_scaffold_14-snap.2595-T1
Valid prediction for CodingQuarry_transcript_15885-T1
Valid prediction for snap_scaffold_14-snap.2572-T1
Valid prediction for GlimmerHMM_glimmerT_34878-T1
Valid prediction for snap_scaffold_14-snap.2593-T1
Valid prediction for HiQ_model.g23333.t1
Valid prediction for snap_scaffold_14-snap.2591-T1
Valid prediction for Augustus_model.g23336.t1
Valid prediction for Augustus_model.g23323.t1
Valid prediction for CodingQuarry_transcript_15888-T1
Valid prediction for pasa_asmbl_13593.p1
Valid prediction for snap_scaffold_14-snap.2597-T1
Valid prediction for snap_scaffold_14-snap.2610-T1
Valid prediction for GlimmerHMM_glimmerT_34881-T1
Valid prediction for Augustus_model.g23327.t1
Valid prediction for HiQ_model.g23337.t1
Valid prediction for GlimmerHMM_glimmerT_34889-T1
Valid prediction for pasa_asmbl_13596.p1
Valid prediction for Augustus_model.g23324.t1
Valid prediction for Augustus_model.g23329.t1
Valid prediction for Augustus_model.g23335.t1
Valid prediction for pasa_asmbl_13597.p1
Valid prediction for Augustus_model.g23330.t1
Valid prediction for snap_scaffold_14-snap.2598-T1
Valid prediction for CodingQuarry_transcript_15887-T1
Valid prediction for GlimmerHMM_glimmerT_34892-T1
Valid prediction for GlimmerHMM_glimmerT_34872-T1
Valid prediction for Augustus_model.g23321.t1
Valid prediction for snap_scaffold_14-snap.2605-T1
Valid prediction for snap_scaffold_14-snap.2583-T1
Valid prediction for snap_scaffold_14-snap.2589-T1
Valid prediction for snap_scaffold_14-snap.2570-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 3822, rend_intergenic: 2362  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 9410, rend_intergenic: 5869  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71787, rend_intergenic: 65773  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86383, rend_intergenic: 78220  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132198, rend_intergenic: 127981  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142680, rend_intergenic: 138849  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192191, rend_intergenic: 186387  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198046, rend_intergenic: 196558  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203161, rend_intergenic: 198349  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 226409, rend_intergenic: 219823  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 261082, rend_intergenic: 259306  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 268345
-exon list size: 504


building trellis

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0.4    
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1.0    
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1.4    
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30.0    
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31.0    
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31.4    
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31.8    
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32.6    
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33.2    
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33.6    
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35.8    
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37.4    
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37.9    
38.1    
38.3    
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38.7    
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75.3    
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76.1    
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78.9    
79.1    
79.2    
79.4    
79.6    
79.8    
80.0    
80.2    
80.4    
80.6    
80.8    
81.0    
81.2    
81.4    
81.6    
81.8    
82.0    
82.2    
82.4    
82.6    
82.8    
83.0    
83.2    
83.4    
83.6    
83.8    
84.0    
84.2    
84.4    
84.6    
84.8    
85.0    
85.2    
85.4    
85.6    
85.8    
86.0    
86.2    
86.4    
86.6    
86.8    
87.0    
87.2    
87.4    
87.5    
87.7    
87.9    
88.1    
88.3    
88.5    
88.7    
88.9    
89.1    
89.3    
89.5    
89.7    
89.9    
90.1    
90.3    
90.5    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
91.9    
92.1    
92.3    
92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.7    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.8    
98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 3822, rend_intergenic: 2362  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 9410, rend_intergenic: 5869  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71787, rend_intergenic: 65773  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86383, rend_intergenic: 78220  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132198, rend_intergenic: 127981  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142680, rend_intergenic: 138849  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192191, rend_intergenic: 186387  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198046, rend_intergenic: 196558  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203161, rend_intergenic: 198349  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 226409, rend_intergenic: 219823  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 261082, rend_intergenic: 259306  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support