-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_15/scaffold_15_209806-413438

-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_35451-T1
Valid prediction for snap_scaffold_15-snap.74-T1
Valid prediction for snap_scaffold_15-snap.48-T1
Valid prediction for snap_scaffold_15-snap.75-T1
Valid prediction for Augustus_model.g23684.t1
Valid prediction for GlimmerHMM_glimmerT_35446-T1
Valid prediction for snap_scaffold_15-snap.79-T1
Valid prediction for snap_scaffold_15-snap.83-T1
Valid prediction for GlimmerHMM_glimmerT_35442-T1
Valid prediction for snap_scaffold_15-snap.52-T1
Valid prediction for snap_scaffold_15-snap.81-T1
Valid prediction for GlimmerHMM_glimmerT_35472-T1
Valid prediction for CodingQuarry_transcript_17890-T1
Valid prediction for snap_scaffold_15-snap.84-T1
Valid prediction for GlimmerHMM_glimmerT_35466-T1
Valid prediction for GlimmerHMM_glimmerT_35458-T1
Valid prediction for snap_scaffold_15-snap.80-T1
Valid prediction for snap_scaffold_15-snap.72-T1
Valid prediction for Augustus_model.g23678.t1
Valid prediction for GlimmerHMM_glimmerT_35470-T1
Valid prediction for GlimmerHMM_glimmerT_35467-T1
Valid prediction for GlimmerHMM_glimmerT_35460-T1
Valid prediction for GlimmerHMM_glimmerT_35448-T1
Valid prediction for snap_scaffold_15-snap.44-T1
Valid prediction for GlimmerHMM_glimmerT_35471-T1
Valid prediction for HiQ_model.g23687.t1
Valid prediction for snap_scaffold_15-snap.45-T1
Valid prediction for snap_scaffold_15-snap.53-T1
Valid prediction for snap_scaffold_15-snap.71-T1
Valid prediction for snap_scaffold_15-snap.65-T1
Valid prediction for GlimmerHMM_glimmerT_35457-T1
Valid prediction for GlimmerHMM_glimmerT_35456-T1
Valid prediction for Augustus_model.g23674.t1
Valid prediction for GlimmerHMM_glimmerT_35462-T1
Valid prediction for snap_scaffold_15-snap.50-T1
Valid prediction for Augustus_model.g23681.t1
Valid prediction for pasa_asmbl_14974.p1
Valid prediction for Augustus_model.g23676.t1
Valid prediction for GlimmerHMM_glimmerT_35476-T1
Valid prediction for GlimmerHMM_glimmerT_35449-T1
Valid prediction for snap_scaffold_15-snap.57-T1
Valid prediction for snap_scaffold_15-snap.59-T1
Valid prediction for GlimmerHMM_glimmerT_35452-T1
Valid prediction for GlimmerHMM_glimmerT_35444-T1
Valid prediction for snap_scaffold_15-snap.55-T1
Valid prediction for snap_scaffold_15-snap.58-T1
Valid prediction for Augustus_model.g23680.t1
Valid prediction for CodingQuarry_transcript_17889-T1
Couldn't classify 133191, 133351
Couldn't classify 137685, 137766
Sorry, prediction pasa_asmbl_14960.p1 fails validation.
(GGA)	 CA	133191-133351	GT	TGG
(GTA)	 AG	133531-133684	GT	CCG
(GTG)	 AG	133832-133939	GC	AGG
(AAC)	 AG	134638-134690	GT	AGG
(CAT)	 AG	135896-135991	GT	AGG
(GTT)	 AG	137685-137766	GT	AGG
-recovered pasa_asmbl_14960.p1, internal, 133531, 133684
-recovered pasa_asmbl_14960.p1, internal, 133832, 133939
-recovered pasa_asmbl_14960.p1, internal, 134638, 134690
-recovered pasa_asmbl_14960.p1, internal, 135896, 135991
-recovered pasa_asmbl_14960.p1, internal, 137685, 137766
Couldn't classify 140055, 140184
Couldn't classify 149351, 149607
Sorry, prediction pasa_asmbl_14961.p1 fails validation.
(AGG)	 CC	140055-140184	GT	AGG
(GCA)	 AG	140329-140465	GT	AGG
(GGT)	 AG	141824-141929	GT	TGG
(GGA)	 AG	143465-143622	GT	AGG
(GTG)	 AG	145350-145527	GT	AGG
(CTT)	 AG	145965-145982	GT	AGG
(AGT)	 AG	146353-146530	GT	AGG
(CAT)	 AG	146619-146787	GT	AGG
(GGG)	 AG	146942-147127	GT	CGG
(GTA)	 AG	147994-148099	GT	AGG
(AGC)	 AG	149351-149607	TG	GGT
-recovered pasa_asmbl_14961.p1, internal, 140329, 140465
-recovered pasa_asmbl_14961.p1, internal, 141824, 141929
-recovered pasa_asmbl_14961.p1, internal, 143465, 143622
-recovered pasa_asmbl_14961.p1, internal, 145350, 145527
-recovered pasa_asmbl_14961.p1, internal, 145965, 145982
-recovered pasa_asmbl_14961.p1, internal, 146353, 146530
-recovered pasa_asmbl_14961.p1, internal, 146619, 146787
-recovered pasa_asmbl_14961.p1, internal, 146942, 147127
-recovered pasa_asmbl_14961.p1, internal, 147994, 148099
Valid prediction for CodingQuarry_transcript_17887-T1
Valid prediction for GlimmerHMM_glimmerT_35474-T1
Valid prediction for GlimmerHMM_glimmerT_35445-T1
Valid prediction for GlimmerHMM_glimmerT_35465-T1
Valid prediction for snap_scaffold_15-snap.46-T1
Valid prediction for Augustus_model.g23677.t1
Valid prediction for snap_scaffold_15-snap.76-T1
Valid prediction for pasa_asmbl_14973.p1
Valid prediction for snap_scaffold_15-snap.67-T1
Valid prediction for CodingQuarry_transcript_17886-T1
Valid prediction for GlimmerHMM_glimmerT_35475-T1
Valid prediction for GlimmerHMM_glimmerT_35453-T1
Valid prediction for GlimmerHMM_glimmerT_35454-T1
Valid prediction for snap_scaffold_15-snap.68-T1
Valid prediction for pasa_asmbl_14963.p1
Valid prediction for GlimmerHMM_glimmerT_35477-T1
Couldn't classify 171053, 171331
Sorry, prediction pasa_asmbl_14966.p1 fails validation.
(GAG)	 GA	171053-171331	GT	GGG
(GTG)	 AG	172677-173259	GT	TGG
(GTG)	 AG	173608-173790	GT	AGG
(GAT)	 AG	174012-174118	GT	AGG
(GTG)	 AG	174213-174731	CG	AGC
-recovered pasa_asmbl_14966.p1, terminal, 174213, 174731
-recovered pasa_asmbl_14966.p1, internal, 172677, 173259
-recovered pasa_asmbl_14966.p1, internal, 173608, 173790
-recovered pasa_asmbl_14966.p1, internal, 174012, 174118
Valid prediction for pasa_asmbl_14971.p1
Valid prediction for HiQ_model.g23685.t1
Valid prediction for snap_scaffold_15-snap.43-T1
Valid prediction for Augustus_model.g23679.t1
Valid prediction for Augustus_model.g23688.t1
Valid prediction for snap_scaffold_15-snap.77-T1
Valid prediction for GlimmerHMM_glimmerT_35459-T1
Valid prediction for snap_scaffold_15-snap.60-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_35464-T1
Valid prediction for GlimmerHMM_glimmerT_35469-T1
Valid prediction for GlimmerHMM_glimmerT_35455-T1
Valid prediction for HiQ_model.g23683.t1
Couldn't classify 125832, 126025
Couldn't classify 131044, 131212
Sorry, prediction pasa_asmbl_14958.p1 fails validation.
(ACG)	 AG	125832-126025	GT	TGG
(CCA)	 AG	127785-127953	GT	AGG
(GAC)	 AG	128611-128717	GT	AGG
(GAG)	 AG	131044-131212	TG	GTT
-recovered pasa_asmbl_14958.p1, terminal, 128611, 128717
-recovered pasa_asmbl_14958.p1, internal, 125832, 126025
-recovered pasa_asmbl_14958.p1, internal, 127785, 127953
-recovered pasa_asmbl_14958.p1, internal, 128611, 128717
Valid prediction for snap_scaffold_15-snap.49-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_15-snap.82-T1
Valid prediction for snap_scaffold_15-snap.64-T1
Valid prediction for snap_scaffold_15-snap.51-T1
Valid prediction for snap_scaffold_15-snap.42-T1
Valid prediction for GlimmerHMM_glimmerT_35461-T1
Valid prediction for GlimmerHMM_glimmerT_35447-T1
Valid prediction for snap_scaffold_15-snap.70-T1
Valid prediction for snap_scaffold_15-snap.61-T1
Valid prediction for snap_scaffold_15-snap.54-T1
Valid prediction for snap_scaffold_15-snap.63-T1
Valid prediction for GlimmerHMM_glimmerT_35450-T1
Valid prediction for HiQ_model.g23686.t1
Valid prediction for GlimmerHMM_glimmerT_35468-T1
Valid prediction for Augustus_model.g23675.t1
Valid prediction for GlimmerHMM_glimmerT_35473-T1
Valid prediction for HiQ_model.g23682.t1
Valid prediction for snap_scaffold_15-snap.66-T1
Valid prediction for CodingQuarry_transcript_17888-T1
Valid prediction for pasa_asmbl_13916.p1
Valid prediction for snap_scaffold_15-snap.73-T1
Valid prediction for snap_scaffold_15-snap.69-T1
Valid prediction for pasa_asmbl_13919.p1
Valid prediction for snap_scaffold_15-snap.56-T1
Valid prediction for GlimmerHMM_glimmerT_35443-T1
Valid prediction for snap_scaffold_15-snap.47-T1
Valid prediction for snap_scaffold_15-snap.62-T1
Valid prediction for snap_scaffold_15-snap.78-T1
Valid prediction for GlimmerHMM_glimmerT_35463-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 48424, rend_intergenic: 3087  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55979, rend_intergenic: 52928  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73542, rend_intergenic: 68009  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82457, rend_intergenic: 80786  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105920, rend_intergenic: 85828  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125335, rend_intergenic: 112622  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129436, rend_intergenic: 127858  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132019, rend_intergenic: 129582  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151715, rend_intergenic: 133670  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 203633
-exon list size: 403


building trellis

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35.3    
35.6    
35.8    
36.0    
36.3    
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37.3    
37.5    
37.8    
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38.5    
38.8    
39.0    
39.3    
39.5    
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40.0    
40.2    
40.5    
40.7    
41.0    
41.2    
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42.0    
42.2    
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44.2    
44.4    
44.7    
44.9    
45.2    
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45.9    
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46.9    
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48.1    
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48.6    
48.9    
49.1    
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50.1    
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50.6    
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54.6    
54.8    
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55.6    
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56.0    
56.3    
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57.3    
57.5    
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58.3    
58.5    
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59.3    
59.5    
59.8    
60.0    
60.2    
60.5    
60.7    
61.0    
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64.0    
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80.0    
80.2    
80.5    
80.7    
81.0    
81.2    
81.5    
81.7    
82.0    
82.2    
82.5    
82.7    
83.0    
83.2    
83.5    
83.7    
84.0    
84.2    
84.4    
84.7    
84.9    
85.2    
85.4    
85.7    
85.9    
86.2    
86.4    
86.7    
86.9    
87.2    
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87.9    
88.1    
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88.6    
88.9    
89.1    
89.4    
89.6    
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90.1    
90.4    
90.6    
90.9    
91.1    
91.4    
91.6    
91.9    
92.1    
92.3    
92.6    
92.8    
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93.3    
93.6    
93.8    
94.1    
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95.1    
95.3    
95.6    
95.8    
96.0    
96.3    
96.5    
96.8    
97.0    
97.3    
97.5    
97.8    
98.0    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 48424, rend_intergenic: 3087  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55979, rend_intergenic: 52928  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73542, rend_intergenic: 68009  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82457, rend_intergenic: 80786  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105920, rend_intergenic: 85828  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125335, rend_intergenic: 112622  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129436, rend_intergenic: 127858  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132019, rend_intergenic: 129582  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151715, rend_intergenic: 133670  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 12181
-exon list size: 14


building trellis

6.2    
12.5    
18.8    
25.0    
31.2    
37.5    
43.8    
50.0    
56.2    
62.5    
68.8    
75.0    
81.2    
87.5    
93.8    
-found 2 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support