-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_15/scaffold_15_6405225-6687210

-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_37105-T1
Valid prediction for GeneMark_model.63851_t
Valid prediction for GeneMark_model.63890_t
Valid prediction for GeneMark_model.63858_t
Valid prediction for GlimmerHMM_glimmerT_37128-T1
Valid prediction for snap_scaffold_15-snap.1390-T1
Valid prediction for GeneMark_model.63901_t
Valid prediction for GeneMark_model.63866_t
Valid prediction for GlimmerHMM_glimmerT_37117-T1
Valid prediction for snap_scaffold_15-snap.1402-T1
Couldn't classify 123715, 124045
Couldn't classify 125454, 125464
Sorry, prediction pasa_asmbl_14197.p1 fails validation.
(ATT)	 CC	123715-124045	GT	CGG
(AGA)	 AG	125083-125223	GT	AGG
(ATG)	 AG	125454-125464	AC	ACA
-recovered pasa_asmbl_14197.p1, internal, 125083, 125223
Valid prediction for GeneMark_model.63884_t
Valid prediction for Augustus_model.g24884.t1
Valid prediction for snap_scaffold_15-snap.1394-T1
Valid prediction for GlimmerHMM_glimmerT_37129-T1
Valid prediction for GlimmerHMM_glimmerT_37123-T1
Couldn't classify 250717, 250827
Couldn't classify 251005, 251205
Sorry, prediction pasa_asmbl_14900.p1 fails validation.
(CAG)	 TC	250717-250827	GT	AAG
(GAG)	 AG	251005-251205	AG	ACA
Valid prediction for GeneMark_model.63891_t
Valid prediction for GeneMark_model.63880_t
Valid prediction for snap_scaffold_15-snap.1393-T1
Valid prediction for GlimmerHMM_glimmerT_37102-T1
Valid prediction for snap_scaffold_15-snap.1397-T1
Valid prediction for GlimmerHMM_glimmerT_37131-T1
Valid prediction for GlimmerHMM_glimmerT_37112-T1
Valid prediction for GeneMark_model.63869_t
Valid prediction for GeneMark_model.63874_t
Valid prediction for GeneMark_model.63896_t
Valid prediction for GeneMark_model.63889_t
Valid prediction for snap_scaffold_15-snap.1388-T1
Valid prediction for GeneMark_model.63853_t
Valid prediction for CodingQuarry_transcript_17984-T1
Valid prediction for GeneMark_model.63886_t
Valid prediction for HiQ_model.g24887.t1
Valid prediction for GeneMark_model.63878_t
Valid prediction for GlimmerHMM_glimmerT_37113-T1
Valid prediction for snap_scaffold_15-snap.1406-T1
Valid prediction for GlimmerHMM_glimmerT_37111-T1
Valid prediction for GeneMark_model.63898_t
Valid prediction for snap_scaffold_15-snap.1413-T1
Valid prediction for snap_scaffold_15-snap.1410-T1
Valid prediction for snap_scaffold_15-snap.1386-T1
Valid prediction for snap_scaffold_15-snap.1382-T1
Valid prediction for snap_scaffold_15-snap.1409-T1
Valid prediction for GlimmerHMM_glimmerT_37115-T1
Valid prediction for GlimmerHMM_glimmerT_37122-T1
Valid prediction for GlimmerHMM_glimmerT_37132-T1
Valid prediction for snap_scaffold_15-snap.1379-T1
Valid prediction for Augustus_model.g24888.t1
Valid prediction for GlimmerHMM_glimmerT_37119-T1
Valid prediction for snap_scaffold_15-snap.1404-T1
Valid prediction for GeneMark_model.63862_t
Valid prediction for GeneMark_model.63872_t
Valid prediction for GlimmerHMM_glimmerT_37127-T1
Valid prediction for GlimmerHMM_glimmerT_37103-T1
Valid prediction for GeneMark_model.63860_t
Valid prediction for pasa_asmbl_14194.p1
Valid prediction for GeneMark_model.63854_t
Valid prediction for GlimmerHMM_glimmerT_37126-T1
Valid prediction for snap_scaffold_15-snap.1407-T1
Valid prediction for HiQ_model.g24886.t1
Valid prediction for GlimmerHMM_glimmerT_37114-T1
Valid prediction for GeneMark_model.63882_t
Valid prediction for GeneMark_model.63876_t
Valid prediction for snap_scaffold_15-snap.1385-T1
Valid prediction for Augustus_model.g24892.t1
Valid prediction for snap_scaffold_15-snap.1384-T1
Valid prediction for snap_scaffold_15-snap.1396-T1
Valid prediction for GeneMark_model.63864_t
Valid prediction for Augustus_model.g24893.t1
Valid prediction for GlimmerHMM_glimmerT_37106-T1
Valid prediction for GeneMark_model.63856_t
Valid prediction for snap_scaffold_15-snap.1380-T1
Valid prediction for GeneMark_model.63904_t
Valid prediction for pasa_asmbl_14195.p1
Valid prediction for GeneMark_model.63867_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 GeneMark_model.63855_t
Valid prediction for GlimmerHMM_glimmerT_37118-T1
Valid prediction for GeneMark_model.63857_t
Valid prediction for GlimmerHMM_glimmerT_37108-T1
Valid prediction for snap_scaffold_15-snap.1401-T1
Valid prediction for snap_scaffold_15-snap.1392-T1
Valid prediction for GeneMark_model.63881_t
Valid prediction for GeneMark_model.63895_t
Valid prediction for GeneMark_model.63852_t
Valid prediction for GeneMark_model.63897_t
Valid prediction for GlimmerHMM_glimmerT_37125-T1
Valid prediction for snap_scaffold_15-snap.1398-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.63888_t
Valid prediction for GlimmerHMM_glimmerT_37109-T1
Valid prediction for GlimmerHMM_glimmerT_37130-T1
Valid prediction for Augustus_model.g24891.t1
Valid prediction for snap_scaffold_15-snap.1403-T1
Valid prediction for GeneMark_model.63900_t
Valid prediction for Augustus_model.g24889.t1
Valid prediction for snap_scaffold_15-snap.1381-T1
Valid prediction for GlimmerHMM_glimmerT_37101-T1
Valid prediction for GeneMark_model.63877_t
Valid prediction for GeneMark_model.63873_t
Valid prediction for snap_scaffold_15-snap.1395-T1
Valid prediction for GeneMark_model.63861_t
Valid prediction for GeneMark_model.63859_t
Valid prediction for snap_scaffold_15-snap.1408-T1
Valid prediction for snap_scaffold_15-snap.1383-T1
Valid prediction for snap_scaffold_15-snap.1399-T1
Valid prediction for GlimmerHMM_glimmerT_37104-T1
Valid prediction for snap_scaffold_15-snap.1387-T1
Valid prediction for snap_scaffold_15-snap.1391-T1
Valid prediction for GeneMark_model.63850_t
Valid prediction for snap_scaffold_15-snap.1412-T1
Valid prediction for GeneMark_model.63899_t
Valid prediction for GlimmerHMM_glimmerT_37116-T1
Valid prediction for GlimmerHMM_glimmerT_37107-T1
Valid prediction for GeneMark_model.63885_t
Valid prediction for snap_scaffold_15-snap.1400-T1
Valid prediction for Augustus_model.g24890.t1
Valid prediction for GeneMark_model.63883_t
Valid prediction for Augustus_model.g24885.t1
Valid prediction for snap_scaffold_15-snap.1405-T1
Valid prediction for GlimmerHMM_glimmerT_37110-T1
Valid prediction for GeneMark_model.63865_t
Valid prediction for snap_scaffold_15-snap.1411-T1
Valid prediction for GlimmerHMM_glimmerT_37121-T1
Valid prediction for GeneMark_model.63879_t
Valid prediction for GeneMark_model.63875_t
Valid prediction for GeneMark_model.63868_t
Valid prediction for GlimmerHMM_glimmerT_37124-T1
Valid prediction for GeneMark_model.63887_t
Valid prediction for GlimmerHMM_glimmerT_37120-T1
Valid prediction for GeneMark_model.63870_t
Valid prediction for GeneMark_model.63871_t
Valid prediction for GeneMark_model.63863_t
Valid prediction for snap_scaffold_15-snap.1389-T1
Valid prediction for GeneMark_model.63902_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 52970, rend_intergenic: 48201  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65779, rend_intergenic: 53105  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68071, rend_intergenic: 65873  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77387, rend_intergenic: 69392  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79129, rend_intergenic: 77681  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81589, rend_intergenic: 81216  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83373, rend_intergenic: 82820  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96254, rend_intergenic: 92718  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115718, rend_intergenic: 111053  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124371, rend_intergenic: 123004  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 281986
-exon list size: 577


building trellis

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27.8    
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43.0    
43.2    
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44.2    
44.4    
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47.0    
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48.0    
48.2    
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48.9    
49.1    
49.2    
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50.3    
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53.2    
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53.9    
54.1    
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54.6    
54.7    
54.9    
55.1    
55.3    
55.4    
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55.8    
56.0    
56.1    
56.3    
56.5    
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57.0    
57.2    
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58.0    
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58.4    
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59.2    
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60.1    
60.3    
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61.1    
61.3    
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62.0    
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63.4    
63.6    
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64.2    
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65.3    
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66.0    
66.1    
66.3    
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66.8    
67.0    
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69.3    
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70.3    
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75.3    
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80.3    
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85.1    
85.3    
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85.7    
85.8    
86.0    
86.2    
86.4    
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86.9    
87.0    
87.2    
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88.3    
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88.8    
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89.1    
89.3    
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90.3    
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90.7    
90.8    
91.0    
91.2    
91.4    
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91.9    
92.1    
92.2    
92.4    
92.6    
92.7    
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93.3    
93.4    
93.6    
93.8    
94.0    
94.1    
94.3    
94.5    
94.6    
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95.0    
95.2    
95.3    
95.5    
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95.9    
96.0    
96.2    
96.4    
96.5    
96.7    
96.9    
97.1    
97.2    
97.4    
97.6    
97.8    
97.9    
98.1    
98.3    
98.4    
98.6    
98.8    
99.0    
99.1    
99.3    
99.5    
99.7    
99.8    
-found 41 predictions from path traversal
Error with prediction: snap lend_intergenic: 52970, rend_intergenic: 48201  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65779, rend_intergenic: 53105  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68071, rend_intergenic: 65873  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77387, rend_intergenic: 69392  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79129, rend_intergenic: 77681  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81589, rend_intergenic: 81216  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83373, rend_intergenic: 82820  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96254, rend_intergenic: 92718  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115718, rend_intergenic: 111053  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124371, rend_intergenic: 123004  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support