-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_7/scaffold_7_1521544-1678591

-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 snap_scaffold_7-snap.382-T1
Valid prediction for GeneMark_model.29134_t
Valid prediction for GlimmerHMM_glimmerT_17297-T1
Valid prediction for snap_scaffold_7-snap.393-T1
Valid prediction for GeneMark_model.29115_t
Valid prediction for snap_scaffold_7-snap.383-T1
Valid prediction for GlimmerHMM_glimmerT_17311-T1
Valid prediction for GeneMark_model.29143_t
Valid prediction for GeneMark_model.29114_t
Valid prediction for snap_scaffold_7-snap.386-T1
Valid prediction for GeneMark_model.29145_t
Valid prediction for GlimmerHMM_glimmerT_17303-T1
Valid prediction for GeneMark_model.29140_t
Valid prediction for snap_scaffold_7-snap.371-T1
Valid prediction for snap_scaffold_7-snap.375-T1
Valid prediction for snap_scaffold_7-snap.364-T1
Valid prediction for Augustus_model.g11597.t1
Valid prediction for GlimmerHMM_glimmerT_17310-T1
Valid prediction for GeneMark_model.29132_t
Valid prediction for Augustus_model.g11591.t1
Valid prediction for snap_scaffold_7-snap.394-T1
Valid prediction for GlimmerHMM_glimmerT_17293-T1
Valid prediction for GeneMark_model.29130_t
Valid prediction for GlimmerHMM_glimmerT_17292-T1
Valid prediction for GeneMark_model.29123_t
Valid prediction for Augustus_model.g11595.t1
Valid prediction for GeneMark_model.29125_t
Valid prediction for GeneMark_model.29113_t
Valid prediction for GeneMark_model.29136_t
Valid prediction for GlimmerHMM_glimmerT_17300-T1
Valid prediction for snap_scaffold_7-snap.396-T1
Valid prediction for snap_scaffold_7-snap.368-T1
Valid prediction for GeneMark_model.29138_t
Valid prediction for GeneMark_model.29117_t
Valid prediction for GlimmerHMM_glimmerT_17291-T1
Valid prediction for GeneMark_model.29151_t
Valid prediction for snap_scaffold_7-snap.384-T1
Valid prediction for snap_scaffold_7-snap.366-T1
Valid prediction for GeneMark_model.29121_t
Valid prediction for snap_scaffold_7-snap.387-T1
Valid prediction for snap_scaffold_7-snap.391-T1
Valid prediction for snap_scaffold_7-snap.388-T1
Valid prediction for GeneMark_model.29155_t
Valid prediction for GlimmerHMM_glimmerT_17307-T1
Valid prediction for GlimmerHMM_glimmerT_17299-T1
Valid prediction for GeneMark_model.29127_t
Valid prediction for GeneMark_model.29119_t
Valid prediction for GeneMark_model.29147_t
Valid prediction for GeneMark_model.29149_t
Valid prediction for GeneMark_model.29129_t
Valid prediction for GlimmerHMM_glimmerT_17298-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 Augustus_model.g11589.t1
Valid prediction for GeneMark_model.29146_t
Valid prediction for GeneMark_model.29112_t
Valid prediction for GlimmerHMM_glimmerT_17305-T1
Valid prediction for Augustus_model.g11593.t1
Valid prediction for GlimmerHMM_glimmerT_17302-T1
Valid prediction for GeneMark_model.29137_t
Valid prediction for Augustus_model.g11599.t1
Valid prediction for snap_scaffold_7-snap.381-T1
Valid prediction for GlimmerHMM_glimmerT_17290-T1
Valid prediction for snap_scaffold_7-snap.395-T1
Valid prediction for snap_scaffold_7-snap.373-T1
Valid prediction for snap_scaffold_7-snap.376-T1
Valid prediction for Augustus_model.g11601.t1
Couldn't classify 153914, 154002
Sorry, prediction pasa_asmbl_49557.p1 fails validation.
(ATG)	 CC	151726-151880	GT	CTG
(GGT)	 AG	152445-152530	GT	GGG
(GAG)	 AG	152736-152892	GT	AAG
(CGA)	 AG	153361-153443	GT	GGG
(TTT)	 AG	153725-153817	GT	AGG
(GTG)	 AG	153914-154002	AC	GGA
-recovered pasa_asmbl_49557.p1, initial, 151726, 151880
add_exon() Sorry, pasa_asmbl_49557.p1 153725-153817-terminal-1 is invalid.
-recovered pasa_asmbl_49557.p1, terminal, 153725, 153817
-recovered pasa_asmbl_49557.p1, internal, 152445, 152530
-recovered pasa_asmbl_49557.p1, internal, 152736, 152892
-recovered pasa_asmbl_49557.p1, internal, 153361, 153443
-recovered pasa_asmbl_49557.p1, internal, 153725, 153817
Valid prediction for Augustus_model.g11592.t1
Valid prediction for GeneMark_model.29153_t
Valid prediction for GlimmerHMM_glimmerT_17301-T1
Valid prediction for GeneMark_model.29118_t
Valid prediction for snap_scaffold_7-snap.367-T1
Valid prediction for GeneMark_model.29133_t
Valid prediction for GeneMark_model.29126_t
Valid prediction for GeneMark_model.29135_t
Valid prediction for snap_scaffold_7-snap.380-T1
Valid prediction for GlimmerHMM_glimmerT_17295-T1
Valid prediction for GlimmerHMM_glimmerT_17308-T1
Valid prediction for snap_scaffold_7-snap.392-T1
Valid prediction for GlimmerHMM_glimmerT_17296-T1
Valid prediction for GlimmerHMM_glimmerT_17312-T1
Valid prediction for GeneMark_model.29139_t
Valid prediction for snap_scaffold_7-snap.370-T1
Valid prediction for GeneMark_model.29131_t
Valid prediction for snap_scaffold_7-snap.385-T1
Valid prediction for GeneMark_model.29116_t
Valid prediction for snap_scaffold_7-snap.374-T1
Valid prediction for Augustus_model.g11594.t1
Valid prediction for snap_scaffold_7-snap.378-T1
Valid prediction for snap_scaffold_7-snap.377-T1
Valid prediction for GeneMark_model.29122_t
Valid prediction for GeneMark_model.29150_t
Valid prediction for GlimmerHMM_glimmerT_17309-T1
Valid prediction for snap_scaffold_7-snap.379-T1
Valid prediction for Augustus_model.g11596.t1
Valid prediction for GeneMark_model.29142_t
Valid prediction for GeneMark_model.29152_t
Valid prediction for snap_scaffold_7-snap.365-T1
Valid prediction for GeneMark_model.29154_t
Valid prediction for GlimmerHMM_glimmerT_17306-T1
Valid prediction for GeneMark_model.29144_t
Valid prediction for snap_scaffold_7-snap.372-T1
Valid prediction for GeneMark_model.29141_t
Valid prediction for GeneMark_model.29148_t
Valid prediction for snap_scaffold_7-snap.369-T1
Valid prediction for GlimmerHMM_glimmerT_17294-T1
Valid prediction for Augustus_model.g11598.t1
Valid prediction for snap_scaffold_7-snap.389-T1
Valid prediction for HiQ_model.g11590.t1
Valid prediction for GeneMark_model.29120_t
Valid prediction for Augustus_model.g11600.t1
Valid prediction for GeneMark_model.29124_t
Valid prediction for GeneMark_model.29128_t
Valid prediction for GlimmerHMM_glimmerT_17289-T1
Valid prediction for snap_scaffold_7-snap.390-T1
Valid prediction for GlimmerHMM_glimmerT_17304-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 58798, rend_intergenic: 58795  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 5894, rend_intergenic: 2374  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10261, rend_intergenic: 8757  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11189, rend_intergenic: 10663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13759, rend_intergenic: 13649  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22490, rend_intergenic: 19746  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34440, rend_intergenic: 33677  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55107, rend_intergenic: 34753  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78339, rend_intergenic: 76438  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119928, rend_intergenic: 111775  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 157048
-exon list size: 514


building trellis

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34.9    
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85.3    
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85.7    
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86.0    
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86.4    
86.6    
86.8    
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87.2    
87.4    
87.6    
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88.0    
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88.4    
88.6    
88.8    
89.0    
89.1    
89.3    
89.5    
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89.9    
90.1    
90.3    
90.5    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
91.9    
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92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
94.0    
94.2    
94.4    
94.6    
94.8    
95.0    
95.2    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 28 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 58798, rend_intergenic: 58795  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 5894, rend_intergenic: 2374  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10261, rend_intergenic: 8757  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11189, rend_intergenic: 10663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13759, rend_intergenic: 13649  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22490, rend_intergenic: 19746  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34440, rend_intergenic: 33677  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55107, rend_intergenic: 34753  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78339, rend_intergenic: 76438  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119928, rend_intergenic: 111775  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support