-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_6/scaffold_6_4528488-4633871

-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.25192_t
Valid prediction for GlimmerHMM_glimmerT_14861-T1
Valid prediction for GeneMark_model.25176_t
Valid prediction for GlimmerHMM_glimmerT_14864-T1
Valid prediction for GeneMark_model.25178_t
Valid prediction for GeneMark_model.25172_t
Valid prediction for GlimmerHMM_glimmerT_14872-T1
Valid prediction for snap_scaffold_6-snap.1090-T1
Valid prediction for GeneMark_model.25169_t
Couldn't classify 68958, 68993
Sorry, prediction pasa_asmbl_46834.p1 fails validation.
(GTG)	 AC	68958-68993	GT	GGG
(TCT)	 AG	69096-69170	GT	AGG
(GGT)	 AG	69662-69756	GT	AGG
(AAC)	 AG	69904-69972	GT	AGG
(TAC)	 AG	70069-70164	GT	AGG
(TGA)	 AG	70500-70626	GT	AGG
(TTG)	 AG	70878-70952	GT	CGG
(CAG)	 AG	72023-72153	GT	AGG
(AAT)	 AG	72278-72338	GT	GGG
(AAC)	 AG	72437-72481	GT	AGG
(ATC)	 AG	72625-72681	GT	TGG
(AGC)	 AG	72776-72988	GT	GGG
(ACT)	 AG	73127-73234	TG	GAT
-recovered pasa_asmbl_46834.p1, terminal, 73127, 73234
-recovered pasa_asmbl_46834.p1, internal, 69096, 69170
-recovered pasa_asmbl_46834.p1, internal, 69662, 69756
-recovered pasa_asmbl_46834.p1, internal, 69904, 69972
-recovered pasa_asmbl_46834.p1, internal, 70069, 70164
-recovered pasa_asmbl_46834.p1, internal, 70500, 70626
-recovered pasa_asmbl_46834.p1, internal, 70878, 70952
-recovered pasa_asmbl_46834.p1, internal, 72023, 72153
-recovered pasa_asmbl_46834.p1, internal, 72278, 72338
-recovered pasa_asmbl_46834.p1, internal, 72437, 72481
-recovered pasa_asmbl_46834.p1, internal, 72625, 72681
-recovered pasa_asmbl_46834.p1, internal, 72776, 72988
Valid prediction for snap_scaffold_6-snap.1088-T1
Valid prediction for GeneMark_model.25185_t
Valid prediction for Augustus_model.g9897.t1
Valid prediction for GeneMark_model.25179_t
Valid prediction for GeneMark_model.25166_t
Valid prediction for GlimmerHMM_glimmerT_14870-T1
Valid prediction for Augustus_model.g9892.t1
Valid prediction for snap_scaffold_6-snap.1084-T1
Valid prediction for Augustus_model.g9893.t1
Valid prediction for Augustus_model.g9898.t1
Valid prediction for snap_scaffold_6-snap.1075-T1
Valid prediction for GeneMark_model.25168_t
Valid prediction for GeneMark_model.25181_t
Valid prediction for GeneMark_model.25189_t
Valid prediction for snap_scaffold_6-snap.1078-T1
Valid prediction for snap_scaffold_6-snap.1092-T1
Valid prediction for GeneMark_model.25171_t
Valid prediction for snap_scaffold_6-snap.1073-T1
Valid prediction for GeneMark_model.25164_t
Valid prediction for GlimmerHMM_glimmerT_14862-T1
Valid prediction for snap_scaffold_6-snap.1080-T1
Valid prediction for snap_scaffold_6-snap.1076-T1
Valid prediction for snap_scaffold_6-snap.1081-T1
Valid prediction for snap_scaffold_6-snap.1086-T1
Valid prediction for GlimmerHMM_glimmerT_14873-T1
Valid prediction for snap_scaffold_6-snap.1071-T1
Valid prediction for GeneMark_model.25174_t
Valid prediction for GlimmerHMM_glimmerT_14865-T1
Valid prediction for GlimmerHMM_glimmerT_14859-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_14871-T1
Valid prediction for GeneMark_model.25187_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 CodingQuarry_transcript_54878-T1
Valid prediction for GeneMark_model.25163_t
Valid prediction for snap_scaffold_6-snap.1089-T1
Couldn't classify 42560, 43759
Sorry, prediction pasa_asmbl_48289.p1 fails validation.
(ATG)	 GA	42560-43759	CG	CCC
Valid prediction for GeneMark_model.25173_t
Valid prediction for GlimmerHMM_glimmerT_14869-T1
Valid prediction for snap_scaffold_6-snap.1094-T1
Valid prediction for snap_scaffold_6-snap.1070-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g9895.t1
Valid prediction for GeneMark_model.25167_t
Valid prediction for GlimmerHMM_glimmerT_14858-T1
Valid prediction for GeneMark_model.25177_t
Valid prediction for GeneMark_model.25170_t
Valid prediction for snap_scaffold_6-snap.1077-T1
Valid prediction for GlimmerHMM_glimmerT_14867-T1
Valid prediction for GeneMark_model.25184_t
Valid prediction for GlimmerHMM_glimmerT_14866-T1
Valid prediction for snap_scaffold_6-snap.1082-T1
Valid prediction for GeneMark_model.25180_t
Valid prediction for snap_scaffold_6-snap.1093-T1
Couldn't classify 46040, 46083
Sorry, prediction pasa_asmbl_48286.p1 fails validation.
(CGG)	 AG	46040-46083	GT	AAG
(GTT)	 AG	46196-46335	GT	TGG
(GTG)	 AG	46471-46641	GT	AGG
(GAG)	 AG	46766-46955	GT	AGG
(CGG)	 AG	47075-47131	GT	AGG
(TCG)	 AG	47274-47375	GT	GGG
(GTG)	 AG	47499-47576	GT	AGG
(CCG)	 AG	47864-47980	GT	TTG
(TCT)	 AG	48222-48353	GT	GAG
(TCT)	 AG	48451-48674	GT	AGG
(GGC)	 AG	48813-49273	GG	AGG
-recovered pasa_asmbl_48286.p1, terminal, 48813, 49273
-recovered pasa_asmbl_48286.p1, internal, 46040, 46083
-recovered pasa_asmbl_48286.p1, internal, 46196, 46335
-recovered pasa_asmbl_48286.p1, internal, 46471, 46641
-recovered pasa_asmbl_48286.p1, internal, 46766, 46955
-recovered pasa_asmbl_48286.p1, internal, 47075, 47131
-recovered pasa_asmbl_48286.p1, internal, 47274, 47375
-recovered pasa_asmbl_48286.p1, internal, 47499, 47576
-recovered pasa_asmbl_48286.p1, internal, 47864, 47980
-recovered pasa_asmbl_48286.p1, internal, 48222, 48353
-recovered pasa_asmbl_48286.p1, internal, 48451, 48674
Valid prediction for snap_scaffold_6-snap.1069-T1
Valid prediction for GeneMark_model.25190_t
Valid prediction for GeneMark_model.25175_t
Couldn't classify 52615, 52935
Sorry, prediction pasa_asmbl_48284.p1 fails validation.
(ATG)	 TC	52615-52935	CT	CCC
Valid prediction for snap_scaffold_6-snap.1087-T1
Couldn't classify 95416, 95499
Sorry, prediction pasa_asmbl_48281.p1 fails validation.
(ATA)	 AG	95416-95499	GT	AGG
(TGG)	 AG	95664-95739	GT	AGG
(CCG)	 AG	97274-97453	GT	TGG
(ATC)	 AG	98323-98495	TA	GAT
-recovered pasa_asmbl_48281.p1, terminal, 98323, 98495
-recovered pasa_asmbl_48281.p1, internal, 95416, 95499
-recovered pasa_asmbl_48281.p1, internal, 95664, 95739
-recovered pasa_asmbl_48281.p1, internal, 97274, 97453
Valid prediction for GeneMark_model.25186_t
Valid prediction for Augustus_model.g9896.t1
Valid prediction for Augustus_model.g9889.t1
Valid prediction for GlimmerHMM_glimmerT_14863-T1
Valid prediction for GeneMark_model.25188_t
Valid prediction for GlimmerHMM_glimmerT_14874-T1
Valid prediction for Augustus_model.g9894.t1
Valid prediction for GeneMark_model.25193_t
Valid prediction for GlimmerHMM_glimmerT_14860-T1
Valid prediction for snap_scaffold_6-snap.1079-T1
Valid prediction for snap_scaffold_6-snap.1091-T1
Valid prediction for GeneMark_model.25182_t
Valid prediction for snap_scaffold_6-snap.1083-T1
Valid prediction for snap_scaffold_6-snap.1085-T1
Valid prediction for GeneMark_model.25162_t
Valid prediction for GlimmerHMM_glimmerT_14868-T1
Valid prediction for CodingQuarry_transcript_54877-T1
Valid prediction for Augustus_model.g9890.t1
Valid prediction for snap_scaffold_6-snap.1074-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for GeneMark_model.25165_t
Valid prediction for GlimmerHMM_glimmerT_14857-T1
Valid prediction for Augustus_model.g9891.t1
Valid prediction for GeneMark_model.25191_t
Valid prediction for HiQ_model.g9888.t1
Valid prediction for snap_scaffold_6-snap.1072-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15766, rend_intergenic: 14723  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20016, rend_intergenic: 17299  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20962, rend_intergenic: 20801  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23805, rend_intergenic: 21295  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28010, rend_intergenic: 24775  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38803, rend_intergenic: 36408  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40041, rend_intergenic: 38950  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47480, rend_intergenic: 40158  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53214, rend_intergenic: 50357  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60512, rend_intergenic: 55468  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73697, rend_intergenic: 72740  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90018, rend_intergenic: 88495  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97347, rend_intergenic: 91608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102489, rend_intergenic: 99315  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 105384
-exon list size: 461


building trellis

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25.9    
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27.4    
27.6    
27.9    
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28.3    
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29.8    
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30.2    
30.5    
30.7    
30.9    
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31.5    
31.7    
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32.2    
32.4    
32.6    
32.8    
33.0    
33.3    
33.5    
33.7    
33.9    
34.1    
34.3    
34.6    
34.8    
35.0    
35.2    
35.4    
35.6    
35.9    
36.1    
36.3    
36.5    
36.7    
36.9    
37.1    
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37.8    
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38.4    
38.7    
38.9    
39.1    
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39.5    
39.7    
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40.6    
40.8    
41.0    
41.3    
41.5    
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45.4    
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64.6    
64.8    
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65.9    
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68.0    
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88.8    
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91.6    
91.8    
92.0    
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92.4    
92.7    
92.9    
93.1    
93.3    
93.5    
93.7    
94.0    
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94.4    
94.6    
94.8    
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95.5    
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95.9    
96.1    
96.3    
96.5    
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97.2    
97.4    
97.6    
97.8    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.4    
99.6    
99.8    
-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 15766, rend_intergenic: 14723  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20016, rend_intergenic: 17299  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20962, rend_intergenic: 20801  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23805, rend_intergenic: 21295  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28010, rend_intergenic: 24775  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38803, rend_intergenic: 36408  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40041, rend_intergenic: 38950  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47480, rend_intergenic: 40158  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53214, rend_intergenic: 50357  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60512, rend_intergenic: 55468  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73697, rend_intergenic: 72740  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90018, rend_intergenic: 88495  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97347, rend_intergenic: 91608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102489, rend_intergenic: 99315  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 12 predictions persist after filtering for low support