-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_4/scaffold_4_4639120-4829644

-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_9473-T1
Valid prediction for CodingQuarry_transcript_48863-T1
Valid prediction for GeneMark_model.15569_t
Valid prediction for GlimmerHMM_glimmerT_9468-T1
Valid prediction for GeneMark_model.15549_t
Valid prediction for Augustus_model.g6165.t1
Valid prediction for GlimmerHMM_glimmerT_9492-T1
Valid prediction for GlimmerHMM_glimmerT_9474-T1
Valid prediction for snap_scaffold_4-snap.1084-T1
Valid prediction for snap_scaffold_4-snap.1063-T1
Valid prediction for snap_scaffold_4-snap.1076-T1
Valid prediction for Augustus_model.g6164.t1
Valid prediction for Augustus_model.g6161.t1
Valid prediction for GeneMark_model.15553_t
Valid prediction for snap_scaffold_4-snap.1088-T1
Valid prediction for Augustus_model.g6160.t1
Valid prediction for GlimmerHMM_glimmerT_9484-T1
Valid prediction for GeneMark_model.15542_t
Valid prediction for GlimmerHMM_glimmerT_9493-T1
Valid prediction for GeneMark_model.15559_t
Valid prediction for snap_scaffold_4-snap.1070-T1
Valid prediction for snap_scaffold_4-snap.1082-T1
Valid prediction for Augustus_model.g6156.t1
Valid prediction for GeneMark_model.15555_t
Valid prediction for GeneMark_model.15540_t
Valid prediction for GeneMark_model.15538_t
Valid prediction for Augustus_model.g6166.t1
Valid prediction for Augustus_model.g6173.t1
Valid prediction for snap_scaffold_4-snap.1092-T1
Couldn't classify 40309, 40454
Sorry, prediction pasa_asmbl_42625.p1 fails validation.
(CTC)	 CC	40309-40454	GT	AGG
(GTA)	 AG	41180-41387	CT	GAC
-recovered pasa_asmbl_42625.p1, terminal, 41180, 41387
Valid prediction for snap_scaffold_4-snap.1067-T1
Valid prediction for Augustus_model.g6158.t1
Valid prediction for GeneMark_model.15566_t
Valid prediction for GeneMark_model.15544_t
Valid prediction for snap_scaffold_4-snap.1065-T1
Valid prediction for GlimmerHMM_glimmerT_9475-T1
Valid prediction for snap_scaffold_4-snap.1066-T1
Valid prediction for GeneMark_model.15546_t
Valid prediction for snap_scaffold_4-snap.1085-T1
Valid prediction for GeneMark_model.15562_t
Valid prediction for Augustus_model.g6157.t1
Valid prediction for snap_scaffold_4-snap.1064-T1
Valid prediction for snap_scaffold_4-snap.1094-T1
Valid prediction for GlimmerHMM_glimmerT_9472-T1
Valid prediction for snap_scaffold_4-snap.1093-T1
Valid prediction for GlimmerHMM_glimmerT_9491-T1
Valid prediction for GlimmerHMM_glimmerT_9486-T1
Valid prediction for GlimmerHMM_glimmerT_9476-T1
Valid prediction for GeneMark_model.15560_t
Valid prediction for GlimmerHMM_glimmerT_9483-T1
Valid prediction for Augustus_model.g6171.t1
Valid prediction for Augustus_model.g6159.t1
Couldn't classify 47393, 47481
Couldn't classify 47807, 47951
Sorry, prediction pasa_asmbl_42627.p1 fails validation.
(TGT)	 CT	47393-47481	AT	CAA
(CTA)	 AC	47807-47951	GT	AGG
(AGC)	 AG	48055-48152	GT	CAG
(CAC)	 AG	50201-50231	GT	GGG
(ACC)	 AG	50435-50513	GT	AGG
(TGC)	 AG	50873-51022	GT	AGG
(GGA)	 AG	51437-51534	GT	TGG
(AAC)	 AG	51750-51872	GT	AGG
(CAA)	 AG	52030-52208	GT	CAG
(TTG)	 AG	52440-52530	GT	AGG
(AAA)	 AG	52703-52753	GT	CGG
(GAC)	 AG	53010-53097	GT	AGG
(ATA)	 AG	53239-53303	GT	TGG
(CAC)	 AG	53408-53462	GT	GGG
(GAA)	 AG	53834-53952	AC	AGA
-recovered pasa_asmbl_42627.p1, terminal, 53834, 53952
-recovered pasa_asmbl_42627.p1, internal, 48055, 48152
-recovered pasa_asmbl_42627.p1, internal, 50201, 50231
-recovered pasa_asmbl_42627.p1, internal, 50435, 50513
-recovered pasa_asmbl_42627.p1, internal, 50873, 51022
-recovered pasa_asmbl_42627.p1, internal, 51437, 51534
-recovered pasa_asmbl_42627.p1, internal, 51750, 51872
-recovered pasa_asmbl_42627.p1, internal, 52030, 52208
-recovered pasa_asmbl_42627.p1, internal, 52440, 52530
-recovered pasa_asmbl_42627.p1, internal, 52703, 52753
-recovered pasa_asmbl_42627.p1, internal, 53010, 53097
-recovered pasa_asmbl_42627.p1, internal, 53239, 53303
-recovered pasa_asmbl_42627.p1, internal, 53408, 53462
Valid prediction for GeneMark_model.15565_t
Valid prediction for GlimmerHMM_glimmerT_9469-T1
Valid prediction for GlimmerHMM_glimmerT_9470-T1
Valid prediction for GlimmerHMM_glimmerT_9490-T1
Valid prediction for Augustus_model.g6170.t1
Valid prediction for snap_scaffold_4-snap.1068-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for snap_scaffold_4-snap.1091-T1
Valid prediction for GeneMark_model.15567_t
Valid prediction for GlimmerHMM_glimmerT_9471-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_4-snap.1081-T1
Valid prediction for GeneMark_model.15539_t
Valid prediction for GeneMark_model.15558_t
Valid prediction for snap_scaffold_4-snap.1078-T1
Valid prediction for GeneMark_model.15547_t
Valid prediction for GeneMark_model.15557_t
Valid prediction for snap_scaffold_4-snap.1090-T1
Valid prediction for Augustus_model.g6155.t1
Valid prediction for Augustus_model.g6172.t1
Valid prediction for GlimmerHMM_glimmerT_9467-T1
Valid prediction for snap_scaffold_4-snap.1069-T1
Valid prediction for GlimmerHMM_glimmerT_9481-T1
Valid prediction for GeneMark_model.15556_t
Valid prediction for snap_scaffold_4-snap.1071-T1
Valid prediction for GlimmerHMM_glimmerT_9487-T1
Valid prediction for Augustus_model.g6162.t1
Valid prediction for GlimmerHMM_glimmerT_9464-T1
Valid prediction for snap_scaffold_4-snap.1074-T1
Valid prediction for snap_scaffold_4-snap.1075-T1
Valid prediction for snap_scaffold_4-snap.1086-T1
Valid prediction for GlimmerHMM_glimmerT_9485-T1
Valid prediction for Augustus_model.g6169.t1
Valid prediction for snap_scaffold_4-snap.1073-T1
Valid prediction for Augustus_model.g6154.t1
Valid prediction for GlimmerHMM_glimmerT_9479-T1
Valid prediction for GeneMark_model.15568_t
Valid prediction for snap_scaffold_4-snap.1060-T1
Valid prediction for snap_scaffold_4-snap.1083-T1
Valid prediction for GeneMark_model.15543_t
Valid prediction for Augustus_model.g6168.t1
Valid prediction for GlimmerHMM_glimmerT_9482-T1
Valid prediction for GlimmerHMM_glimmerT_9480-T1
Valid prediction for pasa_asmbl_41271.p1
Valid prediction for GeneMark_model.15548_t
Valid prediction for Augustus_model.g6167.t1
Valid prediction for CodingQuarry_transcript_48860-T1
Valid prediction for snap_scaffold_4-snap.1077-T1
Valid prediction for snap_scaffold_4-snap.1079-T1
Valid prediction for GlimmerHMM_glimmerT_9488-T1
Valid prediction for GlimmerHMM_glimmerT_9478-T1
Valid prediction for snap_scaffold_4-snap.1062-T1
Valid prediction for snap_scaffold_4-snap.1087-T1
Valid prediction for GlimmerHMM_glimmerT_9463-T1
Valid prediction for snap_scaffold_4-snap.1080-T1
Valid prediction for GeneMark_model.15564_t
Valid prediction for GeneMark_model.15551_t
Valid prediction for GlimmerHMM_glimmerT_9489-T1
Valid prediction for GeneMark_model.15561_t
Valid prediction for GeneMark_model.15563_t
Valid prediction for GeneMark_model.15554_t
Valid prediction for Augustus_model.g6163.t1
Valid prediction for snap_scaffold_4-snap.1061-T1
Valid prediction for GlimmerHMM_glimmerT_9477-T1
Couldn't classify 126867, 126954
Couldn't classify 128368, 128505
Sorry, prediction pasa_asmbl_42390.p1 fails validation.
(AAG)	 AT	126867-126954	GT	AGG
(GAT)	 AG	127119-127246	GT	AGG
(AAC)	 AG	127842-128069	GT	AGG
(GAC)	 AG	128368-128505	GA	GAG
-recovered pasa_asmbl_42390.p1, internal, 127119, 127246
-recovered pasa_asmbl_42390.p1, internal, 127842, 128069
Valid prediction for GeneMark_model.15550_t
Valid prediction for GlimmerHMM_glimmerT_9465-T1
Valid prediction for GlimmerHMM_glimmerT_9466-T1
Valid prediction for snap_scaffold_4-snap.1059-T1
Valid prediction for snap_scaffold_4-snap.1072-T1
Valid prediction for snap_scaffold_4-snap.1089-T1
Valid prediction for GeneMark_model.15545_t
Valid prediction for GeneMark_model.15537_t
Valid prediction for GeneMark_model.15541_t
Valid prediction for snap_scaffold_4-snap.1058-T1
Valid prediction for GeneMark_model.15552_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 43829, rend_intergenic: 37354  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53952, rend_intergenic: 48563  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79019, rend_intergenic: 76246  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80752, rend_intergenic: 79313  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 190525
-exon list size: 554


building trellis

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48.0    
48.2    
48.4    
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48.7    
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53.6    
53.8    
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54.7    
54.9    
55.0    
55.2    
55.4    
55.6    
55.8    
55.9    
56.1    
56.3    
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57.0    
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58.1    
58.3    
58.5    
58.6    
58.8    
59.0    
59.2    
59.4    
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60.3    
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60.8    
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66.2    
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69.8    
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70.9    
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71.2    
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73.2    
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74.3    
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74.6    
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76.1    
76.3    
76.4    
76.6    
76.8    
77.0    
77.2    
77.3    
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78.1    
78.2    
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78.6    
78.8    
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79.1    
79.3    
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80.0    
80.2    
80.4    
80.6    
80.8    
80.9    
81.1    
81.3    
81.5    
81.7    
81.8    
82.0    
82.2    
82.4    
82.6    
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82.9    
83.1    
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83.5    
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84.2    
84.4    
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84.9    
85.1    
85.3    
85.4    
85.6    
85.8    
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86.2    
86.3    
86.5    
86.7    
86.9    
87.1    
87.2    
87.4    
87.6    
87.8    
87.9    
88.1    
88.3    
88.5    
88.7    
88.8    
89.0    
89.2    
89.4    
89.6    
89.7    
89.9    
90.1    
90.3    
90.5    
90.6    
90.8    
91.0    
91.2    
91.4    
91.5    
91.7    
91.9    
92.1    
92.3    
92.4    
92.6    
92.8    
93.0    
93.2    
93.3    
93.5    
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93.9    
94.1    
94.2    
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94.6    
94.8    
95.0    
95.1    
95.3    
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95.7    
95.9    
96.0    
96.2    
96.4    
96.6    
96.8    
96.9    
97.1    
97.3    
97.5    
97.7    
97.8    
98.0    
98.2    
98.4    
98.6    
98.7    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 43829, rend_intergenic: 37354  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53952, rend_intergenic: 48563  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79019, rend_intergenic: 76246  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80752, rend_intergenic: 79313  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 27 predictions persist after filtering for low support