-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_620513-841054

-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.9910_t
Valid prediction for CodingQuarry_transcript_45952-T1
Valid prediction for snap_scaffold_3-snap.166-T1
Valid prediction for snap_scaffold_3-snap.201-T1
Valid prediction for GeneMark_model.9902_t
Valid prediction for GeneMark_model.9895_t
Valid prediction for GeneMark_model.9885_t
Valid prediction for snap_scaffold_3-snap.170-T1
Valid prediction for GeneMark_model.9896_t
Valid prediction for GeneMark_model.9912_t
Valid prediction for GlimmerHMM_glimmerT_6043-T1
Valid prediction for GlimmerHMM_glimmerT_6040-T1
Valid prediction for GeneMark_model.9889_t
Valid prediction for GlimmerHMM_glimmerT_6027-T1
Valid prediction for GeneMark_model.9930_t
Valid prediction for snap_scaffold_3-snap.189-T1
Valid prediction for GeneMark_model.9882_t
Valid prediction for GlimmerHMM_glimmerT_6031-T1
Valid prediction for snap_scaffold_3-snap.198-T1
Valid prediction for snap_scaffold_3-snap.194-T1
Valid prediction for GeneMark_model.9868_t
Valid prediction for GeneMark_model.9924_t
Valid prediction for GeneMark_model.9866_t
Valid prediction for GlimmerHMM_glimmerT_6054-T1
Valid prediction for GeneMark_model.9892_t
Valid prediction for Augustus_model.g3968.t1
Valid prediction for GlimmerHMM_glimmerT_6051-T1
Valid prediction for snap_scaffold_3-snap.195-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_3-snap.174-T1
Valid prediction for GeneMark_model.9918_t
Valid prediction for snap_scaffold_3-snap.181-T1
Valid prediction for snap_scaffold_3-snap.182-T1
Valid prediction for snap_scaffold_3-snap.208-T1
Valid prediction for snap_scaffold_3-snap.172-T1
Valid prediction for GeneMark_model.9876_t
Valid prediction for GlimmerHMM_glimmerT_6046-T1
Valid prediction for snap_scaffold_3-snap.160-T1
Valid prediction for snap_scaffold_3-snap.192-T1
Valid prediction for snap_scaffold_3-snap.167-T1
Valid prediction for GlimmerHMM_glimmerT_6038-T1
Valid prediction for GeneMark_model.9872_t
Valid prediction for GeneMark_model.9915_t
Valid prediction for GeneMark_model.9874_t
Valid prediction for GeneMark_model.9904_t
Valid prediction for GeneMark_model.9922_t
Valid prediction for GlimmerHMM_glimmerT_6044-T1
Valid prediction for GeneMark_model.9907_t
Valid prediction for GlimmerHMM_glimmerT_6042-T1
Valid prediction for snap_scaffold_3-snap.171-T1
Valid prediction for GeneMark_model.9928_t
Valid prediction for GeneMark_model.9913_t
Valid prediction for GeneMark_model.9917_t
Valid prediction for GeneMark_model.9873_t
Valid prediction for GeneMark_model.9878_t
Valid prediction for snap_scaffold_3-snap.176-T1
Valid prediction for snap_scaffold_3-snap.184-T1
Valid prediction for snap_scaffold_3-snap.205-T1
Valid prediction for snap_scaffold_3-snap.197-T1
Valid prediction for GeneMark_model.9887_t
Valid prediction for snap_scaffold_3-snap.187-T1
Valid prediction for GeneMark_model.9900_t
Valid prediction for snap_scaffold_3-snap.161-T1
Valid prediction for Augustus_model.g3978.t1
Valid prediction for snap_scaffold_3-snap.188-T1
Valid prediction for GlimmerHMM_glimmerT_6049-T1
Valid prediction for GeneMark_model.9926_t
Valid prediction for GlimmerHMM_glimmerT_6036-T1
Valid prediction for GeneMark_model.9908_t
Valid prediction for GeneMark_model.9880_t
Valid prediction for GeneMark_model.9865_t
Valid prediction for Augustus_model.g3973.t1
Valid prediction for snap_scaffold_3-snap.191-T1
Valid prediction for snap_scaffold_3-snap.164-T1
Valid prediction for GeneMark_model.9898_t
Valid prediction for snap_scaffold_3-snap.178-T1
Valid prediction for snap_scaffold_3-snap.183-T1
Valid prediction for GeneMark_model.9870_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.9903_t
Valid prediction for snap_scaffold_3-snap.199-T1
Valid prediction for GeneMark_model.9921_t
Valid prediction for snap_scaffold_3-snap.175-T1
Valid prediction for GlimmerHMM_glimmerT_6053-T1
Valid prediction for Augustus_model.g3979.t1
Valid prediction for GeneMark_model.9909_t
Valid prediction for GlimmerHMM_glimmerT_6048-T1
Valid prediction for GlimmerHMM_glimmerT_6028-T1
Valid prediction for Augustus_model.g3964.t1
Valid prediction for GlimmerHMM_glimmerT_6045-T1
Valid prediction for GlimmerHMM_glimmerT_6035-T1
Valid prediction for snap_scaffold_3-snap.209-T1
Valid prediction for snap_scaffold_3-snap.185-T1
Valid prediction for GeneMark_model.9923_t
Valid prediction for Augustus_model.g3976.t1
Valid prediction for Augustus_model.g3967.t1
Valid prediction for GeneMark_model.9869_t
Valid prediction for Augustus_model.g3965.t1
Valid prediction for GeneMark_model.9875_t
Valid prediction for snap_scaffold_3-snap.202-T1
Valid prediction for GeneMark_model.9888_t
Valid prediction for GeneMark_model.9931_t
Valid prediction for GlimmerHMM_glimmerT_6034-T1
Valid prediction for GlimmerHMM_glimmerT_6037-T1
Valid prediction for GlimmerHMM_glimmerT_6056-T1
Valid prediction for snap_scaffold_3-snap.163-T1
Valid prediction for snap_scaffold_3-snap.204-T1
Valid prediction for GeneMark_model.9890_t
Valid prediction for pasa_asmbl_38630.p1
Valid prediction for GeneMark_model.9919_t
Valid prediction for GlimmerHMM_glimmerT_6030-T1
Valid prediction for GlimmerHMM_glimmerT_6033-T1
Valid prediction for GeneMark_model.9897_t
Valid prediction for GeneMark_model.9883_t
Valid prediction for GeneMark_model.9911_t
Valid prediction for snap_scaffold_3-snap.190-T1
Valid prediction for snap_scaffold_3-snap.210-T1
Valid prediction for GeneMark_model.9920_t
Valid prediction for Augustus_model.g3977.t1
Valid prediction for Augustus_model.g3963.t1
Valid prediction for GeneMark_model.9927_t
Valid prediction for pasa_asmbl_38634.p1
Valid prediction for snap_scaffold_3-snap.196-T1
Valid prediction for snap_scaffold_3-snap.207-T1
Valid prediction for GeneMark_model.9925_t
Valid prediction for snap_scaffold_3-snap.168-T1
Valid prediction for GeneMark_model.9891_t
Valid prediction for GeneMark_model.9916_t
Valid prediction for GlimmerHMM_glimmerT_6029-T1
Valid prediction for snap_scaffold_3-snap.180-T1
Valid prediction for GeneMark_model.9914_t
Valid prediction for CodingQuarry_transcript_45953-T1
Valid prediction for GeneMark_model.9929_t
Valid prediction for GlimmerHMM_glimmerT_6047-T1
Valid prediction for Augustus_model.g3961.t1
Valid prediction for snap_scaffold_3-snap.203-T1
Couldn't classify 59285, 59457
Couldn't classify 59699, 59906
Sorry, prediction pasa_asmbl_38629.p2 fails validation.
(GAA)	 CG	59285-59457	GT	AGG
(CCG)	 AG	59699-59906	GG	GGG
Valid prediction for snap_scaffold_3-snap.206-T1
Valid prediction for snap_scaffold_3-snap.177-T1
Valid prediction for snap_scaffold_3-snap.169-T1
Valid prediction for GlimmerHMM_glimmerT_6057-T1
Valid prediction for GeneMark_model.9906_t
Valid prediction for GeneMark_model.9867_t
Valid prediction for Augustus_model.g3971.t1
Valid prediction for GeneMark_model.9886_t
Valid prediction for Augustus_model.g3970.t1
Valid prediction for GeneMark_model.9877_t
Valid prediction for GlimmerHMM_glimmerT_6032-T1
Valid prediction for GlimmerHMM_glimmerT_6041-T1
Valid prediction for snap_scaffold_3-snap.193-T1
Valid prediction for snap_scaffold_3-snap.173-T1
Valid prediction for GeneMark_model.9899_t
Valid prediction for GlimmerHMM_glimmerT_6039-T1
Valid prediction for Augustus_model.g3974.t1
Valid prediction for GeneMark_model.9871_t
Valid prediction for Augustus_model.g3966.t1
Valid prediction for HiQ_model.g3975.t1
Valid prediction for GeneMark_model.9894_t
Valid prediction for GeneMark_model.9893_t
Valid prediction for GeneMark_model.9879_t
Valid prediction for CodingQuarry_transcript_45951-T1
Valid prediction for GeneMark_model.9901_t
Valid prediction for GlimmerHMM_glimmerT_6050-T1
Valid prediction for Augustus_model.g3972.t1
Valid prediction for GeneMark_model.9864_t
Valid prediction for snap_scaffold_3-snap.179-T1
Valid prediction for GeneMark_model.9884_t
Valid prediction for snap_scaffold_3-snap.200-T1
Valid prediction for snap_scaffold_3-snap.186-T1
Valid prediction for Augustus_model.g3962.t1
Valid prediction for snap_scaffold_3-snap.165-T1
Valid prediction for Augustus_model.g3969.t1
Valid prediction for snap_scaffold_3-snap.162-T1
Valid prediction for GlimmerHMM_glimmerT_6052-T1
Valid prediction for GeneMark_model.9905_t
Valid prediction for GeneMark_model.9881_t
Valid prediction for GlimmerHMM_glimmerT_6055-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6927, rend_intergenic: 4996  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11081, rend_intergenic: 8579  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16378, rend_intergenic: 15723  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22306, rend_intergenic: 18276  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24513, rend_intergenic: 23483  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38439, rend_intergenic: 28954  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42412, rend_intergenic: 41690  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67471, rend_intergenic: 63530  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101348, rend_intergenic: 76460  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118136, rend_intergenic: 101661  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142403, rend_intergenic: 132286  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152720, rend_intergenic: 144567  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155168, rend_intergenic: 154010  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166286, rend_intergenic: 159618  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172737, rend_intergenic: 169414  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192191, rend_intergenic: 182415  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196790, rend_intergenic: 192590  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211708, rend_intergenic: 208404  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 213583, rend_intergenic: 211916  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 220542
-exon list size: 875


building trellis

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74.3    
74.5    
74.6    
74.7    
74.8    
74.9    
75.0    
75.1    
75.3    
75.4    
75.5    
75.6    
75.7    
75.8    
75.9    
76.1    
76.2    
76.3    
76.4    
76.5    
76.6    
76.7    
76.9    
77.0    
77.1    
77.2    
77.3    
77.4    
77.5    
77.7    
77.8    
77.9    
78.0    
78.1    
78.2    
78.3    
78.4    
78.6    
78.7    
78.8    
78.9    
79.0    
79.1    
79.2    
79.4    
79.5    
79.6    
79.7    
79.8    
79.9    
80.0    
80.2    
80.3    
80.4    
80.5    
80.6    
80.7    
80.8    
81.0    
81.1    
81.2    
81.3    
81.4    
81.5    
81.6    
81.8    
81.9    
82.0    
82.1    
82.2    
82.3    
82.4    
82.6    
82.7    
82.8    
82.9    
83.0    
83.1    
83.2    
83.4    
83.5    
83.6    
83.7    
83.8    
83.9    
84.0    
84.2    
84.3    
84.4    
84.5    
84.6    
84.7    
84.8    
84.9    
85.1    
85.2    
85.3    
85.4    
85.5    
85.6    
85.7    
85.9    
86.0    
86.1    
86.2    
86.3    
86.4    
86.5    
86.7    
86.8    
86.9    
87.0    
87.1    
87.2    
87.3    
87.5    
87.6    
87.7    
87.8    
87.9    
88.0    
88.1    
88.3    
88.4    
88.5    
88.6    
88.7    
88.8    
88.9    
89.1    
89.2    
89.3    
89.4    
89.5    
89.6    
89.7    
89.9    
90.0    
90.1    
90.2    
90.3    
90.4    
90.5    
90.6    
90.8    
90.9    
91.0    
91.1    
91.2    
91.3    
91.4    
91.6    
91.7    
91.8    
91.9    
92.0    
92.1    
92.2    
92.4    
92.5    
92.6    
92.7    
92.8    
92.9    
93.0    
93.2    
93.3    
93.4    
93.5    
93.6    
93.7    
93.8    
94.0    
94.1    
94.2    
94.3    
94.4    
94.5    
94.6    
94.8    
94.9    
95.0    
95.1    
95.2    
95.3    
95.4    
95.6    
95.7    
95.8    
95.9    
96.0    
96.1    
96.2    
96.4    
96.5    
96.6    
96.7    
96.8    
96.9    
97.0    
97.1    
97.3    
97.4    
97.5    
97.6    
97.7    
97.8    
97.9    
98.1    
98.2    
98.3    
98.4    
98.5    
98.6    
98.7    
98.9    
99.0    
99.1    
99.2    
99.3    
99.4    
99.5    
99.7    
99.8    
99.9    
-found 49 predictions from path traversal
Error with prediction: snap lend_intergenic: 6927, rend_intergenic: 4996  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11081, rend_intergenic: 8579  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16378, rend_intergenic: 15723  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22306, rend_intergenic: 18276  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24513, rend_intergenic: 23483  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38439, rend_intergenic: 28954  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42412, rend_intergenic: 41690  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67471, rend_intergenic: 63530  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101348, rend_intergenic: 76460  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118136, rend_intergenic: 101661  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142403, rend_intergenic: 132286  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152720, rend_intergenic: 144567  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155168, rend_intergenic: 154010  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166286, rend_intergenic: 159618  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172737, rend_intergenic: 169414  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192191, rend_intergenic: 182415  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196790, rend_intergenic: 192590  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211708, rend_intergenic: 208404  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 213583, rend_intergenic: 211916  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support