-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_3823334-4011619

-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_26908-T1
Valid prediction for snap_scaffold_11-snap.961-T1
Valid prediction for snap_scaffold_11-snap.955-T1
Valid prediction for pasa_asmbl_5462.p1
Valid prediction for Augustus_model.g17815.t1
Valid prediction for snap_scaffold_11-snap.963-T1
Valid prediction for GlimmerHMM_glimmerT_26907-T1
Valid prediction for GlimmerHMM_glimmerT_26924-T1
Valid prediction for GlimmerHMM_glimmerT_26928-T1
Valid prediction for snap_scaffold_11-snap.951-T1
Valid prediction for snap_scaffold_11-snap.969-T1
Valid prediction for snap_scaffold_11-snap.980-T1
Valid prediction for snap_scaffold_11-snap.972-T1
Valid prediction for CodingQuarry_transcript_8032-T1
Valid prediction for snap_scaffold_11-snap.981-T1
Valid prediction for GlimmerHMM_glimmerT_26910-T1
Valid prediction for Augustus_model.g17812.t1
Valid prediction for GlimmerHMM_glimmerT_26909-T1
Valid prediction for snap_scaffold_11-snap.946-T1
Valid prediction for snap_scaffold_11-snap.948-T1
Valid prediction for GlimmerHMM_glimmerT_26919-T1
Valid prediction for Augustus_model.g17814.t1
Valid prediction for Augustus_model.g17807.t1
Valid prediction for HiQ_model.g17804.t1
Valid prediction for Augustus_model.g17809.t1
Couldn't classify 123956, 124274
Sorry, prediction pasa_asmbl_5470.p1 fails validation.
(GCT)	 AG	123956-124274	GT	TGG
(GTG)	 AG	124818-125112	GT	AGG
(CTC)	 AG	125315-125435	TC	AGT
-recovered pasa_asmbl_5470.p1, terminal, 125315, 125435
-recovered pasa_asmbl_5470.p1, internal, 123956, 124274
-recovered pasa_asmbl_5470.p1, internal, 124818, 125112
Valid prediction for GlimmerHMM_glimmerT_26913-T1
Valid prediction for snap_scaffold_11-snap.944-T1
Valid prediction for CodingQuarry_transcript_8031-T1
Valid prediction for GlimmerHMM_glimmerT_26915-T1
Valid prediction for snap_scaffold_11-snap.960-T1
Valid prediction for snap_scaffold_11-snap.943-T1
Valid prediction for snap_scaffold_11-snap.939-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_11-snap.942-T1
Valid prediction for HiQ_model.g17808.t1
Valid prediction for Augustus_model.g17805.t1
Valid prediction for snap_scaffold_11-snap.966-T1
Couldn't classify 75915, 75945
Sorry, prediction pasa_asmbl_5469.p1 fails validation.
(TTA)	 GC	75915-75945	GT	GGG
(CGG)	 AG	76294-76445	GT	AGG
(TAC)	 AG	76574-76640	GT	AGG
(ACA)	 AG	76763-76855	GT	AAG
(GAG)	 AG	77207-77319	TG	AAT
-recovered pasa_asmbl_5469.p1, terminal, 77207, 77319
-recovered pasa_asmbl_5469.p1, internal, 76294, 76445
-recovered pasa_asmbl_5469.p1, internal, 76574, 76640
-recovered pasa_asmbl_5469.p1, internal, 76763, 76855
Valid prediction for GlimmerHMM_glimmerT_26923-T1
Valid prediction for GlimmerHMM_glimmerT_26916-T1
Valid prediction for snap_scaffold_11-snap.956-T1
Valid prediction for snap_scaffold_11-snap.983-T1
Valid prediction for GlimmerHMM_glimmerT_26930-T1
Valid prediction for snap_scaffold_11-snap.958-T1
Valid prediction for snap_scaffold_11-snap.976-T1
Valid prediction for snap_scaffold_11-snap.945-T1
Valid prediction for GlimmerHMM_glimmerT_26922-T1
Valid prediction for snap_scaffold_11-snap.974-T1
Valid prediction for CodingQuarry_transcript_8033-T1
Couldn't classify 54620, 54796
Sorry, prediction pasa_asmbl_5466.p1 fails validation.
(CAG)	 TG	54620-54796	GT	AGG
(GTC)	 AG	55990-56161	GT	AGG
(GTG)	 AG	57666-57820	AG	AGA
-recovered pasa_asmbl_5466.p1, terminal, 57666, 57820
-recovered pasa_asmbl_5466.p1, internal, 55990, 56161
Valid prediction for snap_scaffold_11-snap.978-T1
Valid prediction for Augustus_model.g17806.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 snap_scaffold_11-snap.962-T1
Valid prediction for GlimmerHMM_glimmerT_26926-T1
Valid prediction for snap_scaffold_11-snap.977-T1
Valid prediction for snap_scaffold_11-snap.947-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for Augustus_model.g17810.t1
Valid prediction for GlimmerHMM_glimmerT_26914-T1
Valid prediction for GlimmerHMM_glimmerT_26931-T1
Valid prediction for snap_scaffold_11-snap.941-T1
Valid prediction for snap_scaffold_11-snap.985-T1
Valid prediction for snap_scaffold_11-snap.967-T1
Valid prediction for GlimmerHMM_glimmerT_26921-T1
Valid prediction for GlimmerHMM_glimmerT_26912-T1
Valid prediction for snap_scaffold_11-snap.984-T1
Valid prediction for snap_scaffold_11-snap.952-T1
Valid prediction for GlimmerHMM_glimmerT_26927-T1
Couldn't classify 90908, 91003
Sorry, prediction pasa_asmbl_7345.p1 fails validation.
(GAC)	 CA	90908-91003	GT	AGG
(TGC)	 AG	91678-91819	GT	TGG
(GTA)	 AG	92110-92293	GT	AGG
(AGA)	 AG	92421-92592	GC	GAG
-recovered pasa_asmbl_7345.p1, terminal, 92421, 92592
-recovered pasa_asmbl_7345.p1, internal, 91678, 91819
-recovered pasa_asmbl_7345.p1, internal, 92110, 92293
-recovered pasa_asmbl_7345.p1, internal, 92421, 92592
Valid prediction for snap_scaffold_11-snap.979-T1
Valid prediction for GlimmerHMM_glimmerT_26920-T1
Valid prediction for HiQ_model.g17811.t1
Valid prediction for snap_scaffold_11-snap.950-T1
Valid prediction for GlimmerHMM_glimmerT_26918-T1
Valid prediction for snap_scaffold_11-snap.982-T1
Valid prediction for snap_scaffold_11-snap.965-T1
Valid prediction for Augustus_model.g17816.t1
Valid prediction for Augustus_model.g17817.t1
Valid prediction for snap_scaffold_11-snap.940-T1
Valid prediction for snap_scaffold_11-snap.968-T1
Valid prediction for snap_scaffold_11-snap.949-T1
Valid prediction for snap_scaffold_11-snap.957-T1
Valid prediction for GlimmerHMM_glimmerT_26917-T1
Valid prediction for snap_scaffold_11-snap.973-T1
Valid prediction for snap_scaffold_11-snap.953-T1
Couldn't classify 98325, 98369
Sorry, prediction pasa_asmbl_6587.p1 fails validation.
(GCA)	 TA	98325-98369	GT	AGG
(GCA)	 AG	98562-98705	GT	CGG
(GAC)	 AG	98838-99147	GT	AAG
(GTT)	 AG	99491-99612	GT	AGG
(TAC)	 AG	99818-99853	AA	AAA
-recovered pasa_asmbl_6587.p1, terminal, 99818, 99853
-recovered pasa_asmbl_6587.p1, internal, 98562, 98705
-recovered pasa_asmbl_6587.p1, internal, 98838, 99147
-recovered pasa_asmbl_6587.p1, internal, 99491, 99612
Valid prediction for GlimmerHMM_glimmerT_26929-T1
Valid prediction for snap_scaffold_11-snap.970-T1
Valid prediction for Augustus_model.g17813.t1
Valid prediction for snap_scaffold_11-snap.959-T1
Valid prediction for snap_scaffold_11-snap.954-T1
Valid prediction for GlimmerHMM_glimmerT_26911-T1
Valid prediction for snap_scaffold_11-snap.964-T1
Valid prediction for GlimmerHMM_glimmerT_26925-T1
Valid prediction for snap_scaffold_11-snap.971-T1
Valid prediction for Augustus_model.g17803.t1
Valid prediction for snap_scaffold_11-snap.975-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 18085, rend_intergenic: 11983  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21980, rend_intergenic: 18575  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40843, rend_intergenic: 34267  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53863, rend_intergenic: 43400  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64986, rend_intergenic: 54649  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67782, rend_intergenic: 66113  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78431, rend_intergenic: 76302  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82561, rend_intergenic: 79020  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88218, rend_intergenic: 86758  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100484, rend_intergenic: 95765  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125435, rend_intergenic: 110559  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131186, rend_intergenic: 126184  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137754, rend_intergenic: 133225  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144607, rend_intergenic: 138052  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151096, rend_intergenic: 146778  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152482, rend_intergenic: 151117  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154975, rend_intergenic: 152782  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156263, rend_intergenic: 155233  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170002, rend_intergenic: 156529  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171942, rend_intergenic: 170574  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185557, rend_intergenic: 174591  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 188286
-exon list size: 413


building trellis

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28.9    
29.2    
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29.9    
30.1    
30.4    
30.6    
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31.6    
31.8    
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33.3    
33.5    
33.7    
34.0    
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34.9    
35.2    
35.4    
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36.6    
36.9    
37.1    
37.3    
37.6    
37.8    
38.1    
38.3    
38.6    
38.8    
39.0    
39.3    
39.5    
39.8    
40.0    
40.2    
40.5    
40.7    
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41.2    
41.4    
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41.9    
42.2    
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42.7    
42.9    
43.1    
43.4    
43.6    
43.9    
44.1    
44.3    
44.6    
44.8    
45.1    
45.3    
45.5    
45.8    
46.0    
46.3    
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46.7    
47.0    
47.2    
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48.0    
48.2    
48.4    
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48.9    
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93.3    
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94.9    
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96.6    
96.9    
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97.3    
97.6    
97.8    
98.1    
98.3    
98.6    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 18085, rend_intergenic: 11983  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21980, rend_intergenic: 18575  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40843, rend_intergenic: 34267  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53863, rend_intergenic: 43400  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64986, rend_intergenic: 54649  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67782, rend_intergenic: 66113  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78431, rend_intergenic: 76302  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82561, rend_intergenic: 79020  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88218, rend_intergenic: 86758  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100484, rend_intergenic: 95765  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125435, rend_intergenic: 110559  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131186, rend_intergenic: 126184  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137754, rend_intergenic: 133225  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144607, rend_intergenic: 138052  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151096, rend_intergenic: 146778  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152482, rend_intergenic: 151117  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154975, rend_intergenic: 152782  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156263, rend_intergenic: 155233  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170002, rend_intergenic: 156529  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171942, rend_intergenic: 170574  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185557, rend_intergenic: 174591  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support