-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_7/scaffold_7_9367048-9638284

-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_18317-T1
Valid prediction for GlimmerHMM_glimmerT_18321-T1
Valid prediction for Augustus_model.g12326.t1
Valid prediction for GeneMark_model.30713_t
Valid prediction for snap_scaffold_7-snap.1865-T1
Valid prediction for Augustus_model.g12327.t1
Valid prediction for GeneMark_model.30700_t
Valid prediction for GeneMark_model.30734_t
Valid prediction for GeneMark_model.30711_t
Valid prediction for Augustus_model.g12341.t1
Valid prediction for GeneMark_model.30742_t
Valid prediction for snap_scaffold_7-snap.1852-T1
Valid prediction for GeneMark_model.30722_t
Valid prediction for GlimmerHMM_glimmerT_18318-T1
Valid prediction for GeneMark_model.30723_t
Valid prediction for snap_scaffold_7-snap.1869-T1
Valid prediction for snap_scaffold_7-snap.1864-T1
Valid prediction for Augustus_model.g12342.t1
Valid prediction for snap_scaffold_7-snap.1856-T1
Valid prediction for GlimmerHMM_glimmerT_18324-T1
Valid prediction for snap_scaffold_7-snap.1870-T1
Valid prediction for Augustus_model.g12339.t1
Valid prediction for snap_scaffold_7-snap.1871-T1
Valid prediction for GlimmerHMM_glimmerT_18320-T1
Valid prediction for GeneMark_model.30718_t
Valid prediction for GlimmerHMM_glimmerT_18311-T1
Valid prediction for GeneMark_model.30706_t
Valid prediction for snap_scaffold_7-snap.1866-T1
Valid prediction for snap_scaffold_7-snap.1861-T1
Valid prediction for GeneMark_model.30719_t
Valid prediction for snap_scaffold_7-snap.1843-T1
Valid prediction for GeneMark_model.30726_t
Valid prediction for GeneMark_model.30715_t
Valid prediction for snap_scaffold_7-snap.1854-T1
Valid prediction for GlimmerHMM_glimmerT_18314-T1
Valid prediction for Augustus_model.g12330.t1
Valid prediction for GeneMark_model.30702_t
Valid prediction for GeneMark_model.30707_t
Valid prediction for Augustus_model.g12343.t1
Valid prediction for GeneMark_model.30717_t
Valid prediction for GeneMark_model.30736_t
Valid prediction for GeneMark_model.30721_t
Valid prediction for Augustus_model.g12333.t1
Valid prediction for Augustus_model.g12338.t1
Valid prediction for GeneMark_model.30714_t
Couldn't classify 25433, 25477
Couldn't classify 26773, 26810
Sorry, prediction pasa_asmbl_50963.p1 fails validation.
(GCT)	 CC	25433-25477	GT	AGG
(GAG)	 AG	25751-25922	GT	AGG
(TGG)	 AG	26165-26350	GT	AAG
(TTA)	 AG	26773-26810	CA	CCC
-recovered pasa_asmbl_50963.p1, internal, 25751, 25922
-recovered pasa_asmbl_50963.p1, internal, 26165, 26350
Valid prediction for snap_scaffold_7-snap.1845-T1
Valid prediction for snap_scaffold_7-snap.1858-T1
Valid prediction for Augustus_model.g12332.t1
Valid prediction for Augustus_model.g12336.t1
Valid prediction for GeneMark_model.30738_t
Valid prediction for GeneMark_model.30733_t
Valid prediction for GeneMark_model.30725_t
Valid prediction for Augustus_model.g12340.t1
Valid prediction for snap_scaffold_7-snap.1872-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_18325-T1
Valid prediction for GeneMark_model.30731_t
Valid prediction for GeneMark_model.30737_t
Valid prediction for GlimmerHMM_glimmerT_18312-T1
Valid prediction for snap_scaffold_7-snap.1846-T1
Valid prediction for GlimmerHMM_glimmerT_18309-T1
Valid prediction for GeneMark_model.30728_t

-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_7-snap.1847-T1
Valid prediction for GlimmerHMM_glimmerT_18323-T1
Valid prediction for GeneMark_model.30730_t
Valid prediction for GlimmerHMM_glimmerT_18319-T1
Valid prediction for GeneMark_model.30732_t
Valid prediction for CodingQuarry_transcript_57439-T1
Valid prediction for snap_scaffold_7-snap.1862-T1
Valid prediction for CodingQuarry_transcript_57438-T1
Valid prediction for Augustus_model.g12328.t1
Valid prediction for snap_scaffold_7-snap.1853-T1
Valid prediction for GeneMark_model.30705_t
Valid prediction for GeneMark_model.30727_t
Valid prediction for GlimmerHMM_glimmerT_18316-T1
Valid prediction for snap_scaffold_7-snap.1868-T1
Valid prediction for GlimmerHMM_glimmerT_18322-T1
Valid prediction for GeneMark_model.30709_t
Valid prediction for GeneMark_model.30739_t
Valid prediction for GeneMark_model.30735_t
Valid prediction for GeneMark_model.30708_t
Valid prediction for Augustus_model.g12331.t1
Valid prediction for GeneMark_model.30743_t
Valid prediction for Augustus_model.g12329.t1
Valid prediction for GlimmerHMM_glimmerT_18308-T1
Valid prediction for snap_scaffold_7-snap.1844-T1
Valid prediction for GeneMark_model.30710_t
Valid prediction for GeneMark_model.30703_t
Valid prediction for GlimmerHMM_glimmerT_18313-T1
Valid prediction for GlimmerHMM_glimmerT_18326-T1
Valid prediction for GeneMark_model.30724_t
Valid prediction for Augustus_model.g12334.t1
Valid prediction for snap_scaffold_7-snap.1863-T1
Valid prediction for GeneMark_model.30720_t
Valid prediction for Augustus_model.g12337.t1
Valid prediction for snap_scaffold_7-snap.1859-T1
Valid prediction for GeneMark_model.30740_t
Valid prediction for Augustus_model.g12335.t1
Valid prediction for snap_scaffold_7-snap.1860-T1
Valid prediction for GlimmerHMM_glimmerT_18310-T1
Valid prediction for snap_scaffold_7-snap.1850-T1
Valid prediction for snap_scaffold_7-snap.1851-T1
Valid prediction for snap_scaffold_7-snap.1855-T1
Valid prediction for GeneMark_model.30741_t
Valid prediction for snap_scaffold_7-snap.1848-T1
Valid prediction for snap_scaffold_7-snap.1867-T1
Valid prediction for GlimmerHMM_glimmerT_18315-T1
Valid prediction for GeneMark_model.30704_t
Valid prediction for snap_scaffold_7-snap.1857-T1
Valid prediction for GeneMark_model.30712_t
Valid prediction for GeneMark_model.30701_t
Valid prediction for GeneMark_model.30716_t
Valid prediction for snap_scaffold_7-snap.1849-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 104793, rend_intergenic: 100066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130673, rend_intergenic: 128449  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 230879, rend_intergenic: 226661  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 239440, rend_intergenic: 237100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 271237
-exon list size: 461


building trellis

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29.8    
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30.2    
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30.9    
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31.7    
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32.6    
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33.3    
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34.6    
34.8    
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38.9    
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84.9    
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85.3    
85.5    
85.7    
86.0    
86.2    
86.4    
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86.8    
87.0    
87.3    
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87.9    
88.1    
88.3    
88.6    
88.8    
89.0    
89.2    
89.4    
89.6    
89.8    
90.1    
90.3    
90.5    
90.7    
90.9    
91.1    
91.4    
91.6    
91.8    
92.0    
92.2    
92.4    
92.7    
92.9    
93.1    
93.3    
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93.7    
94.0    
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94.6    
94.8    
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95.9    
96.1    
96.3    
96.5    
96.8    
97.0    
97.2    
97.4    
97.6    
97.8    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.4    
99.6    
99.8    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 104793, rend_intergenic: 100066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130673, rend_intergenic: 128449  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 230879, rend_intergenic: 226661  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 239440, rend_intergenic: 237100  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