-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_27/scaffold_27_3129880-3261852

-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_27-snap.770-T1
Valid prediction for snap_scaffold_27-snap.755-T1
Valid prediction for GeneMark_model.101471_t
Valid prediction for GlimmerHMM_glimmerT_58361-T1
Valid prediction for Augustus_model.g38876.t1
Valid prediction for Augustus_model.g38880.t1
Valid prediction for GeneMark_model.101489_t
Valid prediction for Augustus_model.g38871.t1
Valid prediction for GeneMark_model.101462_t
Valid prediction for Augustus_model.g38881.t1
Valid prediction for GlimmerHMM_glimmerT_58364-T1
Valid prediction for snap_scaffold_27-snap.748-T1
Valid prediction for GlimmerHMM_glimmerT_58340-T1
Valid prediction for GlimmerHMM_glimmerT_58349-T1
Couldn't classify 3231, 3338
Sorry, prediction CodingQuarry_transcript_41758-T1 fails validation.
(ATG)	 TG	381-432	GT	CTG
(ATG)	 AG	1304-1339	GT	AGG
(ATC)	 AG	1645-1713	GT	CGG
(GTG)	 AG	1817-2073	GT	GGG
(GTG)	 AG	2160-2281	GT	TGG
(TGT)	 AG	2751-2952	GT	AGG
(GTC)	 AG	3058-3115	GT	GAG
(GTG)	 GG	3231-3338	GT	AAG
(GCG)	 AG	3425-3483	CA	AAC
-recovered CodingQuarry_transcript_41758-T1, initial, 381, 432
-recovered CodingQuarry_transcript_41758-T1, initial, 1304, 1339
-recovered CodingQuarry_transcript_41758-T1, terminal, 3425, 3483
-recovered CodingQuarry_transcript_41758-T1, internal, 1304, 1339
-recovered CodingQuarry_transcript_41758-T1, internal, 1645, 1713
-recovered CodingQuarry_transcript_41758-T1, internal, 1817, 2073
-recovered CodingQuarry_transcript_41758-T1, internal, 2160, 2281
-recovered CodingQuarry_transcript_41758-T1, internal, 2751, 2952
-recovered CodingQuarry_transcript_41758-T1, internal, 3058, 3115
Valid prediction for GeneMark_model.101478_t
Valid prediction for GlimmerHMM_glimmerT_58343-T1
Valid prediction for GlimmerHMM_glimmerT_58358-T1
Valid prediction for snap_scaffold_27-snap.772-T1
Valid prediction for snap_scaffold_27-snap.761-T1
Valid prediction for GeneMark_model.101481_t
Valid prediction for GlimmerHMM_glimmerT_58354-T1
Valid prediction for GlimmerHMM_glimmerT_58366-T1
Valid prediction for GlimmerHMM_glimmerT_58347-T1
Valid prediction for GeneMark_model.101474_t
Valid prediction for GlimmerHMM_glimmerT_58351-T1
Valid prediction for GeneMark_model.101470_t
Valid prediction for GlimmerHMM_glimmerT_58363-T1
Valid prediction for GeneMark_model.101483_t
Valid prediction for GeneMark_model.101479_t
Valid prediction for GeneMark_model.101472_t
Valid prediction for GeneMark_model.101476_t
Valid prediction for snap_scaffold_27-snap.762-T1
Valid prediction for GlimmerHMM_glimmerT_58355-T1
Valid prediction for GlimmerHMM_glimmerT_58348-T1
Valid prediction for GlimmerHMM_glimmerT_58360-T1
Valid prediction for snap_scaffold_27-snap.742-T1
Valid prediction for GlimmerHMM_glimmerT_58357-T1
Valid prediction for GeneMark_model.101484_t
Valid prediction for Augustus_model.g38878.t1
Valid prediction for snap_scaffold_27-snap.775-T1
Valid prediction for snap_scaffold_27-snap.773-T1
Valid prediction for snap_scaffold_27-snap.745-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for snap_scaffold_27-snap.768-T1
Valid prediction for Augustus_model.g38875.t1
Valid prediction for snap_scaffold_27-snap.746-T1
Valid prediction for GeneMark_model.101467_t
Valid prediction for GeneMark_model.101491_t
Valid prediction for snap_scaffold_27-snap.767-T1
Valid prediction for GeneMark_model.101487_t
Valid prediction for snap_scaffold_27-snap.766-T1
Valid prediction for GeneMark_model.101469_t
Valid prediction for pasa_asmbl_36149.p1
Valid prediction for GlimmerHMM_glimmerT_58352-T1
Valid prediction for GlimmerHMM_glimmerT_58353-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_27-snap.774-T1
Valid prediction for snap_scaffold_27-snap.763-T1
Valid prediction for snap_scaffold_27-snap.760-T1
Valid prediction for GeneMark_model.101473_t
Valid prediction for GeneMark_model.101488_t
Valid prediction for Augustus_model.g38879.t1
Valid prediction for GeneMark_model.101477_t
Valid prediction for Augustus_model.g38877.t1
Valid prediction for GeneMark_model.101482_t
Valid prediction for snap_scaffold_27-snap.751-T1
Valid prediction for GlimmerHMM_glimmerT_58342-T1
Valid prediction for snap_scaffold_27-snap.754-T1
Valid prediction for Augustus_model.g38873.t1
Valid prediction for GlimmerHMM_glimmerT_58341-T1
Valid prediction for GlimmerHMM_glimmerT_58365-T1
Valid prediction for GlimmerHMM_glimmerT_58344-T1
Valid prediction for snap_scaffold_27-snap.753-T1
Valid prediction for GeneMark_model.101468_t
Valid prediction for snap_scaffold_27-snap.764-T1
Valid prediction for Augustus_model.g38870.t1
Valid prediction for snap_scaffold_27-snap.747-T1
Valid prediction for GeneMark_model.101486_t
Valid prediction for snap_scaffold_27-snap.744-T1
Valid prediction for GeneMark_model.101466_t
Valid prediction for Augustus_model.g38882.t1
Valid prediction for Augustus_model.g38884.t1
Couldn't classify 94951, 95331
Sorry, prediction GlimmerHMM_glimmerT_58346-T1 fails validation.
(ATG)	 AG	92195-92317	GT	AGG
(NNN)	 AN	94951-95331	GA	GAG
-recovered GlimmerHMM_glimmerT_58346-T1, initial, 92195, 92317
-recovered GlimmerHMM_glimmerT_58346-T1, internal, 92195, 92317
Valid prediction for snap_scaffold_27-snap.771-T1
Valid prediction for GeneMark_model.101480_t
Valid prediction for Augustus_model.g38872.t1
Valid prediction for snap_scaffold_27-snap.752-T1
Valid prediction for GeneMark_model.101490_t
Valid prediction for GeneMark_model.101475_t
Valid prediction for snap_scaffold_27-snap.749-T1
Valid prediction for snap_scaffold_27-snap.769-T1
Valid prediction for GlimmerHMM_glimmerT_58356-T1
Valid prediction for Augustus_model.g38874.t1
Valid prediction for GlimmerHMM_glimmerT_58362-T1
Valid prediction for snap_scaffold_27-snap.750-T1
Valid prediction for snap_scaffold_27-snap.743-T1
Valid prediction for GlimmerHMM_glimmerT_58350-T1
Valid prediction for snap_scaffold_27-snap.776-T1
Valid prediction for GeneMark_model.101485_t
Valid prediction for GlimmerHMM_glimmerT_58345-T1
Valid prediction for Augustus_model.g38883.t1
Valid prediction for GlimmerHMM_glimmerT_58359-T1
Valid prediction for GeneMark_model.101492_t
Valid prediction for snap_scaffold_27-snap.758-T1
Valid prediction for snap_scaffold_27-snap.765-T1
Valid prediction for snap_scaffold_27-snap.759-T1
Valid prediction for snap_scaffold_27-snap.756-T1
Valid prediction for snap_scaffold_27-snap.757-T1
Valid prediction for GeneMark_model.101463_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12383, rend_intergenic: 7381  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95790, rend_intergenic: 90557  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122381, rend_intergenic: 118621  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130243, rend_intergenic: 128324  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 131973
-exon list size: 443


building trellis

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2.9    
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29.7    
29.9    
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30.6    
30.8    
31.0    
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31.5    
31.7    
31.9    
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32.8    
33.0    
33.3    
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33.7    
33.9    
34.2    
34.4    
34.6    
34.8    
35.1    
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35.7    
36.0    
36.2    
36.4    
36.6    
36.9    
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38.0    
38.2    
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40.9    
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42.9    
43.1    
43.4    
43.6    
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44.0    
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44.5    
44.7    
44.9    
45.2    
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45.6    
45.8    
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47.0    
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47.6    
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51.9    
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55.7    
56.0    
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56.9    
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64.0    
64.3    
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65.2    
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67.0    
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73.0    
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73.9    
74.2    
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79.1    
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83.1    
83.4    
83.6    
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84.3    
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84.7    
84.9    
85.2    
85.4    
85.6    
85.8    
86.1    
86.3    
86.5    
86.7    
87.0    
87.2    
87.4    
87.6    
87.9    
88.1    
88.3    
88.5    
88.8    
89.0    
89.2    
89.4    
89.7    
89.9    
90.1    
90.3    
90.6    
90.8    
91.0    
91.2    
91.5    
91.7    
91.9    
92.1    
92.4    
92.6    
92.8    
93.0    
93.3    
93.5    
93.7    
93.9    
94.2    
94.4    
94.6    
94.8    
95.1    
95.3    
95.5    
95.7    
96.0    
96.2    
96.4    
96.6    
96.9    
97.1    
97.3    
97.5    
97.8    
98.0    
98.2    
98.4    
98.7    
98.9    
99.1    
99.3    
99.6    
99.8    
-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 12383, rend_intergenic: 7381  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95790, rend_intergenic: 90557  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122381, rend_intergenic: 118621  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130243, rend_intergenic: 128324  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 15 predictions persist after filtering for low support