-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_19576543-19802506

-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.14151_t
Valid prediction for GeneMark_model.14134_t
Valid prediction for snap_scaffold_3-snap.3882-T1
Valid prediction for GeneMark_model.14130_t
Valid prediction for snap_scaffold_3-snap.3933-T1
Valid prediction for snap_scaffold_3-snap.3924-T1
Valid prediction for GlimmerHMM_glimmerT_8693-T1
Valid prediction for GeneMark_model.14154_t
Valid prediction for GlimmerHMM_glimmerT_8694-T1
Valid prediction for GeneMark_model.14136_t
Valid prediction for snap_scaffold_3-snap.3891-T1
Valid prediction for GlimmerHMM_glimmerT_8713-T1
Valid prediction for snap_scaffold_3-snap.3922-T1
Valid prediction for snap_scaffold_3-snap.3921-T1
Valid prediction for snap_scaffold_3-snap.3912-T1
Valid prediction for snap_scaffold_3-snap.3899-T1
Valid prediction for GlimmerHMM_glimmerT_8698-T1
Valid prediction for GlimmerHMM_glimmerT_8699-T1
Valid prediction for snap_scaffold_3-snap.3881-T1
Valid prediction for snap_scaffold_3-snap.3928-T1
Valid prediction for GeneMark_model.14125_t
Valid prediction for snap_scaffold_3-snap.3887-T1
Valid prediction for GeneMark_model.14133_t
Valid prediction for GeneMark_model.14141_t
Valid prediction for GlimmerHMM_glimmerT_8705-T1
Valid prediction for snap_scaffold_3-snap.3903-T1
Valid prediction for GeneMark_model.14160_t
Valid prediction for GeneMark_model.14128_t
Valid prediction for snap_scaffold_3-snap.3926-T1
Valid prediction for snap_scaffold_3-snap.3914-T1
Valid prediction for GlimmerHMM_glimmerT_8700-T1
Valid prediction for GeneMark_model.14131_t
Valid prediction for GlimmerHMM_glimmerT_8695-T1
Valid prediction for snap_scaffold_3-snap.3888-T1
Valid prediction for snap_scaffold_3-snap.3919-T1
Valid prediction for snap_scaffold_3-snap.3902-T1
Valid prediction for GeneMark_model.14156_t
Valid prediction for snap_scaffold_3-snap.3931-T1
Valid prediction for snap_scaffold_3-snap.3893-T1
Valid prediction for snap_scaffold_3-snap.3923-T1
Valid prediction for GeneMark_model.14144_t
Valid prediction for snap_scaffold_3-snap.3895-T1
Valid prediction for snap_scaffold_3-snap.3909-T1
Valid prediction for GlimmerHMM_glimmerT_8710-T1
Valid prediction for GeneMark_model.14149_t
Valid prediction for GlimmerHMM_glimmerT_8716-T1
Valid prediction for GlimmerHMM_glimmerT_8715-T1
Valid prediction for snap_scaffold_3-snap.3894-T1
Valid prediction for snap_scaffold_3-snap.3897-T1
Valid prediction for GeneMark_model.14148_t
Valid prediction for GlimmerHMM_glimmerT_8697-T1
Valid prediction for snap_scaffold_3-snap.3917-T1
Valid prediction for GlimmerHMM_glimmerT_8714-T1
Valid prediction for snap_scaffold_3-snap.3908-T1
Valid prediction for GlimmerHMM_glimmerT_8703-T1
Valid prediction for GeneMark_model.14123_t
Valid prediction for GeneMark_model.14145_t
Valid prediction for snap_scaffold_3-snap.3910-T1
Valid prediction for snap_scaffold_3-snap.3905-T1
Valid prediction for snap_scaffold_3-snap.3885-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_3-snap.3925-T1
Valid prediction for snap_scaffold_3-snap.3901-T1
Valid prediction for GeneMark_model.14161_t
Valid prediction for GeneMark_model.14143_t
Valid prediction for snap_scaffold_3-snap.3886-T1
Valid prediction for snap_scaffold_3-snap.3900-T1
Valid prediction for GeneMark_model.14159_t
Valid prediction for snap_scaffold_3-snap.3930-T1
Valid prediction for GeneMark_model.14146_t
Valid prediction for GeneMark_model.14126_t
Valid prediction for snap_scaffold_3-snap.3892-T1
Valid prediction for GlimmerHMM_glimmerT_8701-T1
Valid prediction for GeneMark_model.14139_t
Valid prediction for snap_scaffold_3-snap.3932-T1
Valid prediction for GeneMark_model.14124_t
Valid prediction for GeneMark_model.14157_t
Valid prediction for GeneMark_model.14140_t
Valid prediction for GlimmerHMM_glimmerT_8711-T1
Valid prediction for GlimmerHMM_glimmerT_8704-T1
Valid prediction for snap_scaffold_3-snap.3896-T1
Valid prediction for GeneMark_model.14147_t
Valid prediction for GeneMark_model.14135_t
Valid prediction for GlimmerHMM_glimmerT_8709-T1
Valid prediction for snap_scaffold_3-snap.3906-T1
Valid prediction for GlimmerHMM_glimmerT_8706-T1
Valid prediction for GlimmerHMM_glimmerT_8712-T1
Valid prediction for snap_scaffold_3-snap.3918-T1
Valid prediction for snap_scaffold_3-snap.3913-T1
Valid prediction for snap_scaffold_3-snap.3927-T1
Valid prediction for GeneMark_model.14142_t
Valid prediction for GeneMark_model.14132_t
Valid prediction for GeneMark_model.14158_t
Valid prediction for snap_scaffold_3-snap.3934-T1
Valid prediction for snap_scaffold_3-snap.3916-T1
Valid prediction for snap_scaffold_3-snap.3920-T1
Valid prediction for snap_scaffold_3-snap.3915-T1
Valid prediction for snap_scaffold_3-snap.3884-T1
Valid prediction for GeneMark_model.14129_t
Valid prediction for GeneMark_model.14138_t
Valid prediction for GeneMark_model.14152_t
Valid prediction for GlimmerHMM_glimmerT_8717-T1
Valid prediction for GeneMark_model.14150_t
Valid prediction for snap_scaffold_3-snap.3890-T1
Valid prediction for GlimmerHMM_glimmerT_8707-T1
Valid prediction for GeneMark_model.14155_t
Valid prediction for snap_scaffold_3-snap.3911-T1
Valid prediction for GeneMark_model.14137_t
Valid prediction for snap_scaffold_3-snap.3898-T1
Valid prediction for snap_scaffold_3-snap.3904-T1
Valid prediction for GeneMark_model.14153_t
Valid prediction for snap_scaffold_3-snap.3883-T1
Valid prediction for GlimmerHMM_glimmerT_8702-T1
Valid prediction for snap_scaffold_3-snap.3889-T1
Valid prediction for snap_scaffold_3-snap.3907-T1
Valid prediction for GlimmerHMM_glimmerT_8696-T1
Valid prediction for GeneMark_model.14127_t
Valid prediction for GlimmerHMM_glimmerT_8708-T1
Valid prediction for snap_scaffold_3-snap.3929-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 24169, rend_intergenic: 19070  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31889, rend_intergenic: 27988  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45592, rend_intergenic: 43910  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53682, rend_intergenic: 51052  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54618, rend_intergenic: 54128  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65636, rend_intergenic: 61286  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84524, rend_intergenic: 80725  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93441, rend_intergenic: 90309  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100188, rend_intergenic: 96965  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112890, rend_intergenic: 108526  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116117, rend_intergenic: 112958  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127280, rend_intergenic: 126045  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140135, rend_intergenic: 136462  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157159, rend_intergenic: 154612  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173842, rend_intergenic: 159670  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177393, rend_intergenic: 174034  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180713, rend_intergenic: 178405  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192818, rend_intergenic: 186476  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211580, rend_intergenic: 204442  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 225964
-exon list size: 648


building trellis

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27.8    
28.0    
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29.1    
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29.4    
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29.8    
30.0    
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30.8    
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31.1    
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91.8    
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92.8    
92.9    
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99.7    
99.8    
-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 24169, rend_intergenic: 19070  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31889, rend_intergenic: 27988  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45592, rend_intergenic: 43910  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53682, rend_intergenic: 51052  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54618, rend_intergenic: 54128  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65636, rend_intergenic: 61286  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84524, rend_intergenic: 80725  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93441, rend_intergenic: 90309  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100188, rend_intergenic: 96965  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112890, rend_intergenic: 108526  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116117, rend_intergenic: 112958  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127280, rend_intergenic: 126045  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140135, rend_intergenic: 136462  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157159, rend_intergenic: 154612  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173842, rend_intergenic: 159670  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177393, rend_intergenic: 174034  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180713, rend_intergenic: 178405  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192818, rend_intergenic: 186476  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211580, rend_intergenic: 204442  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support