-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_4/scaffold_4_984636-1225904

-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 GeneMark_model.14570_t
Valid prediction for GeneMark_model.14528_t
Valid prediction for GeneMark_model.14573_t
Valid prediction for GlimmerHMM_glimmerT_8912-T1
Valid prediction for GeneMark_model.14554_t
Valid prediction for GlimmerHMM_glimmerT_8890-T1
Valid prediction for snap_scaffold_4-snap.270-T1
Valid prediction for GlimmerHMM_glimmerT_8913-T1
Valid prediction for snap_scaffold_4-snap.248-T1
Valid prediction for GeneMark_model.14500_t
Valid prediction for GeneMark_model.14577_t
Valid prediction for GeneMark_model.14520_t
Valid prediction for Augustus_model.g5816.t1
Valid prediction for Augustus_model.g5820.t1
Valid prediction for GeneMark_model.14505_t
Valid prediction for GlimmerHMM_glimmerT_8911-T1
Valid prediction for GeneMark_model.14541_t
Valid prediction for GlimmerHMM_glimmerT_8904-T1
Valid prediction for GlimmerHMM_glimmerT_8903-T1
Valid prediction for snap_scaffold_4-snap.227-T1
Valid prediction for snap_scaffold_4-snap.231-T1
Valid prediction for Augustus_model.g5817.t1
Valid prediction for GeneMark_model.14557_t
Valid prediction for snap_scaffold_4-snap.228-T1
Valid prediction for GeneMark_model.14559_t
Valid prediction for GlimmerHMM_glimmerT_8894-T1
Valid prediction for GlimmerHMM_glimmerT_8915-T1
Valid prediction for GlimmerHMM_glimmerT_8898-T1
Valid prediction for GeneMark_model.14576_t
Valid prediction for GeneMark_model.14518_t
Valid prediction for GeneMark_model.14547_t
Valid prediction for GeneMark_model.14561_t
Valid prediction for snap_scaffold_4-snap.251-T1
Valid prediction for GlimmerHMM_glimmerT_8884-T1
Valid prediction for Augustus_model.g5811.t1
Valid prediction for GlimmerHMM_glimmerT_8888-T1
Valid prediction for snap_scaffold_4-snap.246-T1
Valid prediction for GlimmerHMM_glimmerT_8887-T1
Valid prediction for GeneMark_model.14550_t
Valid prediction for snap_scaffold_4-snap.252-T1
Valid prediction for GlimmerHMM_glimmerT_8896-T1
Valid prediction for snap_scaffold_4-snap.267-T1
Valid prediction for GlimmerHMM_glimmerT_8905-T1
Valid prediction for GeneMark_model.14530_t
Valid prediction for snap_scaffold_4-snap.256-T1
Valid prediction for snap_scaffold_4-snap.237-T1
Valid prediction for snap_scaffold_4-snap.247-T1
Valid prediction for GeneMark_model.14545_t
Valid prediction for GeneMark_model.14510_t
Valid prediction for GeneMark_model.14565_t
Valid prediction for snap_scaffold_4-snap.215-T1
Valid prediction for GlimmerHMM_glimmerT_8889-T1
Valid prediction for GeneMark_model.14501_t
Valid prediction for GlimmerHMM_glimmerT_8885-T1
Valid prediction for GeneMark_model.14533_t
Valid prediction for snap_scaffold_4-snap.271-T1
Valid prediction for Augustus_model.g5813.t1
Valid prediction for GeneMark_model.14514_t
Valid prediction for Augustus_model.g5812.t1
Valid prediction for GeneMark_model.14563_t
Valid prediction for snap_scaffold_4-snap.238-T1
Valid prediction for snap_scaffold_4-snap.220-T1
Valid prediction for GlimmerHMM_glimmerT_8909-T1
Valid prediction for GeneMark_model.14526_t
Valid prediction for snap_scaffold_4-snap.234-T1
Valid prediction for snap_scaffold_4-snap.254-T1
Valid prediction for GeneMark_model.14512_t
Valid prediction for GeneMark_model.14516_t
Valid prediction for GlimmerHMM_glimmerT_8907-T1
Valid prediction for GeneMark_model.14552_t
Valid prediction for GeneMark_model.14521_t
Valid prediction for snap_scaffold_4-snap.241-T1
Valid prediction for GlimmerHMM_glimmerT_8897-T1
Valid prediction for GeneMark_model.14540_t
Valid prediction for GlimmerHMM_glimmerT_8891-T1
Valid prediction for snap_scaffold_4-snap.258-T1
Valid prediction for GeneMark_model.14538_t
Valid prediction for snap_scaffold_4-snap.217-T1
Valid prediction for snap_scaffold_4-snap.236-T1
Valid prediction for Augustus_model.g5814.t1
Valid prediction for GlimmerHMM_glimmerT_8916-T1
Couldn't classify 23830, 24010
Couldn't classify 24103, 24263
Sorry, prediction pasa_asmbl_43578.p2 fails validation.
(TTC)	 AC	23830-24010	GT	CGG
(CGG)	 AG	24103-24263	TA	GGT
Valid prediction for GlimmerHMM_glimmerT_8908-T1
Valid prediction for GeneMark_model.14571_t
Valid prediction for snap_scaffold_4-snap.230-T1
Valid prediction for GeneMark_model.14535_t
Valid prediction for GeneMark_model.14508_t
Valid prediction for Augustus_model.g5821.t1
Valid prediction for GeneMark_model.14549_t
Valid prediction for GeneMark_model.14532_t
Valid prediction for snap_scaffold_4-snap.260-T1
Valid prediction for GeneMark_model.14523_t
Valid prediction for GeneMark_model.14574_t
Valid prediction for snap_scaffold_4-snap.263-T1
Valid prediction for snap_scaffold_4-snap.243-T1
Valid prediction for snap_scaffold_4-snap.249-T1
Valid prediction for GeneMark_model.14543_t
Valid prediction for GlimmerHMM_glimmerT_8900-T1
Valid prediction for GeneMark_model.14555_t
Valid prediction for GeneMark_model.14503_t
Valid prediction for GlimmerHMM_glimmerT_8901-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 GeneMark_model.14509_t
Valid prediction for GeneMark_model.14553_t
Valid prediction for GeneMark_model.14531_t
Valid prediction for GlimmerHMM_glimmerT_8886-T1
Valid prediction for GlimmerHMM_glimmerT_8893-T1
Valid prediction for GeneMark_model.14558_t
Valid prediction for CodingQuarry_transcript_48780-T1
Valid prediction for GlimmerHMM_glimmerT_8882-T1
Valid prediction for GeneMark_model.14529_t
Valid prediction for GeneMark_model.14548_t
Valid prediction for snap_scaffold_4-snap.242-T1
Couldn't classify 165034, 165265
Sorry, prediction pasa_asmbl_41102.p2 fails validation.
(CAT)	 TG	165034-165265	GT	AGG
(AGC)	 AG	165980-166076	GT	AGG
(GAG)	 AG	167287-167350	CC	AGC
-recovered pasa_asmbl_41102.p2, terminal, 167287, 167350
-recovered pasa_asmbl_41102.p2, internal, 165980, 166076
Valid prediction for GlimmerHMM_glimmerT_8902-T1
Valid prediction for snap_scaffold_4-snap.253-T1
Valid prediction for snap_scaffold_4-snap.264-T1
Valid prediction for GlimmerHMM_glimmerT_8920-T1
Valid prediction for snap_scaffold_4-snap.219-T1
Valid prediction for GeneMark_model.14575_t
Valid prediction for GeneMark_model.14546_t
Valid prediction for CodingQuarry_transcript_48779-T1
Valid prediction for snap_scaffold_4-snap.223-T1
Valid prediction for GeneMark_model.14513_t
Valid prediction for GeneMark_model.14551_t
Valid prediction for GeneMark_model.14564_t
Valid prediction for snap_scaffold_4-snap.221-T1
Valid prediction for snap_scaffold_4-snap.214-T1
Valid prediction for GeneMark_model.14524_t
Valid prediction for snap_scaffold_4-snap.226-T1
Valid prediction for Augustus_model.g5818.t1
Valid prediction for GeneMark_model.14511_t
Valid prediction for GeneMark_model.14536_t
Valid prediction for GlimmerHMM_glimmerT_8917-T1
Valid prediction for snap_scaffold_4-snap.240-T1
Valid prediction for GeneMark_model.14534_t
Valid prediction for GlimmerHMM_glimmerT_8919-T1
Valid prediction for GlimmerHMM_glimmerT_8918-T1
Valid prediction for GlimmerHMM_glimmerT_8914-T1
Valid prediction for GeneMark_model.14560_t
Valid prediction for GeneMark_model.14527_t
Valid prediction for snap_scaffold_4-snap.235-T1
Valid prediction for HiQ_model.g5810.t1
Valid prediction for GeneMark_model.14572_t
Valid prediction for GeneMark_model.14502_t
Valid prediction for GlimmerHMM_glimmerT_8883-T1
Valid prediction for snap_scaffold_4-snap.266-T1
Valid prediction for Augustus_model.g5819.t1
Valid prediction for snap_scaffold_4-snap.262-T1
Valid prediction for snap_scaffold_4-snap.245-T1
Valid prediction for snap_scaffold_4-snap.222-T1
Valid prediction for GeneMark_model.14507_t
Valid prediction for snap_scaffold_4-snap.250-T1
Valid prediction for GeneMark_model.14504_t
Valid prediction for GeneMark_model.14517_t
Valid prediction for GeneMark_model.14578_t
Valid prediction for snap_scaffold_4-snap.255-T1
Valid prediction for snap_scaffold_4-snap.269-T1
Valid prediction for GlimmerHMM_glimmerT_8892-T1
Valid prediction for snap_scaffold_4-snap.257-T1
Couldn't classify 164634, 164710
Sorry, prediction pasa_asmbl_41103.p2 fails validation.
(ATG)	 GC	163109-163157	GT	GAG
(TGC)	 AG	164032-164217	GT	TGG
(GTA)	 AG	164634-164710	AG	ACA
-recovered pasa_asmbl_41103.p2, initial, 163109, 163157
-recovered pasa_asmbl_41103.p2, internal, 164032, 164217
Valid prediction for GlimmerHMM_glimmerT_8899-T1
Valid prediction for HiQ_model.g5809.t1
Valid prediction for snap_scaffold_4-snap.239-T1
Valid prediction for GeneMark_model.14519_t
Valid prediction for GlimmerHMM_glimmerT_8906-T1
Valid prediction for GeneMark_model.14537_t
Valid prediction for snap_scaffold_4-snap.265-T1
Valid prediction for GeneMark_model.14542_t
Valid prediction for CodingQuarry_transcript_48778-T1
Valid prediction for snap_scaffold_4-snap.244-T1
Valid prediction for pasa_asmbl_41100.p1
Valid prediction for GeneMark_model.14556_t
Valid prediction for GeneMark_model.14566_t
Valid prediction for snap_scaffold_4-snap.229-T1
Valid prediction for snap_scaffold_4-snap.261-T1
Valid prediction for GeneMark_model.14499_t
Valid prediction for snap_scaffold_4-snap.224-T1
Valid prediction for HiQ_model.g5822.t1
Valid prediction for Augustus_model.g5815.t1
Valid prediction for snap_scaffold_4-snap.233-T1
Valid prediction for GeneMark_model.14544_t
Valid prediction for snap_scaffold_4-snap.268-T1
Valid prediction for GeneMark_model.14539_t
Valid prediction for GeneMark_model.14568_t
Valid prediction for snap_scaffold_4-snap.259-T1
Valid prediction for GeneMark_model.14567_t
Valid prediction for GlimmerHMM_glimmerT_8910-T1
Valid prediction for snap_scaffold_4-snap.216-T1
Valid prediction for snap_scaffold_4-snap.218-T1
Valid prediction for GlimmerHMM_glimmerT_8895-T1
Valid prediction for GeneMark_model.14515_t
Valid prediction for GeneMark_model.14522_t
Valid prediction for snap_scaffold_4-snap.225-T1
Valid prediction for GeneMark_model.14525_t
Valid prediction for snap_scaffold_4-snap.272-T1
Valid prediction for GeneMark_model.14562_t
Valid prediction for snap_scaffold_4-snap.213-T1
Valid prediction for GeneMark_model.14506_t
Valid prediction for snap_scaffold_4-snap.232-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11502, rend_intergenic: 7847  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17637, rend_intergenic: 14453  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27907, rend_intergenic: 17694  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56470, rend_intergenic: 32426  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73550, rend_intergenic: 69724  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76649, rend_intergenic: 74479  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81789, rend_intergenic: 77084  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89226, rend_intergenic: 85938  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92686, rend_intergenic: 89855  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98550, rend_intergenic: 94523  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110938, rend_intergenic: 102919  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129918, rend_intergenic: 112006  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152062, rend_intergenic: 135953  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156798, rend_intergenic: 153240  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160176, rend_intergenic: 157113  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161369, rend_intergenic: 160246  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164634, rend_intergenic: 163554  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165651, rend_intergenic: 164635  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167404, rend_intergenic: 167119  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176377, rend_intergenic: 167746  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186428, rend_intergenic: 179445  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203962, rend_intergenic: 194821  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211933, rend_intergenic: 204015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 222751, rend_intergenic: 212661  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 238112, rend_intergenic: 235478  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 241269
-exon list size: 1292


building trellis

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55.0    
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55.2    
55.3    
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56.0    
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56.9    
57.0    
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62.0    
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62.9    
63.0    
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63.9    
64.0    
64.1    
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64.5    
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64.6    
64.7    
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64.9    
65.0    
65.1    
65.1    
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66.0    
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66.2    
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66.6    
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67.0    
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67.7    
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67.9    
68.0    
68.1    
68.2    
68.2    
68.3    
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68.6    
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68.8    
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68.9    
69.0    
69.1    
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70.0    
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72.0    
72.1    
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73.0    
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73.6    
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73.9    
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74.9    
75.0    
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76.0    
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77.0    
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78.0    
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78.1    
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80.0    
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82.0    
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86.0    
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88.0    
88.1    
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88.3    
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88.6    
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89.1    
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91.0    
91.0    
91.1    
91.2    
91.3    
91.3    
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91.5    
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91.9    
92.0    
92.0    
92.1    
92.2    
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92.9    
93.0    
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94.0    
94.1    
94.2    
94.3    
94.4    
94.4    
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95.0    
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95.1    
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98.0    
98.1    
98.1    
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99.0    
99.1    
99.1    
99.2    
99.3    
99.4    
99.5    
99.5    
99.6    
99.7    
99.8    
99.8    
99.9    
-found 59 predictions from path traversal
Error with prediction: snap lend_intergenic: 11502, rend_intergenic: 7847  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17637, rend_intergenic: 14453  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27907, rend_intergenic: 17694  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56470, rend_intergenic: 32426  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73550, rend_intergenic: 69724  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76649, rend_intergenic: 74479  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81789, rend_intergenic: 77084  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89226, rend_intergenic: 85938  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92686, rend_intergenic: 89855  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98550, rend_intergenic: 94523  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110938, rend_intergenic: 102919  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129918, rend_intergenic: 112006  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152062, rend_intergenic: 135953  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156798, rend_intergenic: 153240  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160176, rend_intergenic: 157113  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161369, rend_intergenic: 160246  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164634, rend_intergenic: 163554  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165651, rend_intergenic: 164635  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167404, rend_intergenic: 167119  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176377, rend_intergenic: 167746  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186428, rend_intergenic: 179445  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203962, rend_intergenic: 194821  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211933, rend_intergenic: 204015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 222751, rend_intergenic: 212661  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 238112, rend_intergenic: 235478  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 228357 - 241269
-exon list size: 30


building trellis

3.1    
6.2    
9.4    
12.5    
15.6    
18.8    
21.9    
25.0    
28.1    
31.2    
34.4    
37.5    
40.6    
43.8    
46.9    
50.0    
53.1    
56.2    
59.4    
62.5    
65.6    
68.8    
71.9    
75.0    
78.1    
81.2    
84.4    
87.5    
90.6    
93.8    
96.9    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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