-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_21/scaffold_21_2639033-2819828

-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.84162_t
Valid prediction for GeneMark_model.84155_t
Valid prediction for GlimmerHMM_glimmerT_48463-T1
Valid prediction for snap_scaffold_21-snap.497-T1
Valid prediction for snap_scaffold_21-snap.500-T1
Valid prediction for snap_scaffold_21-snap.492-T1
Valid prediction for snap_scaffold_21-snap.495-T1
Valid prediction for snap_scaffold_21-snap.488-T1
Valid prediction for GeneMark_model.84146_t
Valid prediction for Augustus_model.g32419.t1
Valid prediction for GlimmerHMM_glimmerT_48465-T1
Valid prediction for GeneMark_model.84151_t
Valid prediction for GeneMark_model.84166_t
Valid prediction for GeneMark_model.84149_t
Valid prediction for GlimmerHMM_glimmerT_48447-T1
Valid prediction for GlimmerHMM_glimmerT_48467-T1
Valid prediction for snap_scaffold_21-snap.490-T1
Valid prediction for GlimmerHMM_glimmerT_48469-T1
Valid prediction for Augustus_model.g32417.t1
Valid prediction for GlimmerHMM_glimmerT_48462-T1
Valid prediction for snap_scaffold_21-snap.482-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_21-snap.476-T1
Valid prediction for GeneMark_model.84172_t
Valid prediction for Augustus_model.g32414.t1
Valid prediction for GlimmerHMM_glimmerT_48455-T1
Valid prediction for Augustus_model.g32416.t1
Valid prediction for snap_scaffold_21-snap.480-T1
Valid prediction for GlimmerHMM_glimmerT_48468-T1
Valid prediction for GlimmerHMM_glimmerT_48458-T1
Valid prediction for Augustus_model.g32418.t1
Valid prediction for GlimmerHMM_glimmerT_48466-T1
Valid prediction for snap_scaffold_21-snap.485-T1
Valid prediction for GeneMark_model.84167_t
Valid prediction for Augustus_model.g32408.t1
Valid prediction for Augustus_model.g32412.t1
Valid prediction for snap_scaffold_21-snap.506-T1
Valid prediction for GeneMark_model.84147_t
Valid prediction for GeneMark_model.84174_t
Valid prediction for GeneMark_model.84182_t
Valid prediction for GeneMark_model.84153_t
Valid prediction for Augustus_model.g32415.t1
Valid prediction for snap_scaffold_21-snap.505-T1
Valid prediction for GeneMark_model.84163_t
Valid prediction for GeneMark_model.84175_t
Valid prediction for Augustus_model.g32420.t1
Valid prediction for GeneMark_model.84144_t
Valid prediction for GeneMark_model.84161_t
Valid prediction for snap_scaffold_21-snap.481-T1
Valid prediction for snap_scaffold_21-snap.508-T1
Valid prediction for snap_scaffold_21-snap.501-T1
Valid prediction for snap_scaffold_21-snap.502-T1
Valid prediction for GeneMark_model.84170_t
Valid prediction for GeneMark_model.84179_t
Valid prediction for snap_scaffold_21-snap.507-T1
Valid prediction for CodingQuarry_transcript_32415-T1
Valid prediction for GlimmerHMM_glimmerT_48450-T1
Valid prediction for GeneMark_model.84168_t
Valid prediction for GeneMark_model.84177_t
Valid prediction for pasa_asmbl_28440.p1
Valid prediction for GlimmerHMM_glimmerT_48464-T1
Valid prediction for GlimmerHMM_glimmerT_48451-T1
Valid prediction for Augustus_model.g32410.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 GlimmerHMM_glimmerT_48461-T1
Valid prediction for Augustus_model.g32413.t1
Valid prediction for GlimmerHMM_glimmerT_48470-T1
Valid prediction for snap_scaffold_21-snap.503-T1
Valid prediction for snap_scaffold_21-snap.477-T1
Valid prediction for snap_scaffold_21-snap.478-T1
Valid prediction for GeneMark_model.84148_t
Valid prediction for GlimmerHMM_glimmerT_48457-T1
Valid prediction for GeneMark_model.84150_t
Valid prediction for GlimmerHMM_glimmerT_48453-T1
Valid prediction for GeneMark_model.84173_t
Valid prediction for GlimmerHMM_glimmerT_48459-T1
Valid prediction for GeneMark_model.84158_t
Valid prediction for snap_scaffold_21-snap.493-T1
Valid prediction for GeneMark_model.84145_t
Valid prediction for GlimmerHMM_glimmerT_48446-T1
Valid prediction for GeneMark_model.84169_t
Valid prediction for GeneMark_model.84159_t
Valid prediction for Augustus_model.g32411.t1
Valid prediction for GlimmerHMM_glimmerT_48471-T1
Valid prediction for GlimmerHMM_glimmerT_48456-T1
Valid prediction for GeneMark_model.84176_t
Valid prediction for Augustus_model.g32409.t1
Valid prediction for snap_scaffold_21-snap.475-T1
Valid prediction for snap_scaffold_21-snap.494-T1
Valid prediction for GeneMark_model.84154_t
Valid prediction for snap_scaffold_21-snap.504-T1
Valid prediction for GlimmerHMM_glimmerT_48454-T1
Valid prediction for GlimmerHMM_glimmerT_48460-T1
Valid prediction for GeneMark_model.84157_t
Valid prediction for GlimmerHMM_glimmerT_48452-T1
Valid prediction for snap_scaffold_21-snap.491-T1
Valid prediction for snap_scaffold_21-snap.499-T1
Valid prediction for GeneMark_model.84156_t
Couldn't classify 162892, 163020
Sorry, prediction pasa_asmbl_27509.p1 fails validation.
(TCC)	 GC	162892-163020	GT	TGG
(GCA)	 AG	163723-163812	GT	AGG
(GCC)	 AG	164132-164207	GT	GGG
(GTC)	 AG	164293-164397	GT	AGG
(GTA)	 AG	164699-164777	GT	GAG
(GAT)	 AG	164925-164973	GT	AGG
(GTC)	 AG	165484-165588	AG	AAA
-recovered pasa_asmbl_27509.p1, terminal, 165484, 165588
-recovered pasa_asmbl_27509.p1, internal, 163723, 163812
-recovered pasa_asmbl_27509.p1, internal, 164132, 164207
-recovered pasa_asmbl_27509.p1, internal, 164293, 164397
-recovered pasa_asmbl_27509.p1, internal, 164699, 164777
-recovered pasa_asmbl_27509.p1, internal, 164925, 164973
Valid prediction for snap_scaffold_21-snap.484-T1
Valid prediction for GeneMark_model.84178_t
Valid prediction for snap_scaffold_21-snap.479-T1
Valid prediction for GeneMark_model.84180_t
Valid prediction for GeneMark_model.84164_t
Valid prediction for snap_scaffold_21-snap.486-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GeneMark_model.84181_t
Valid prediction for GeneMark_model.84160_t
Valid prediction for snap_scaffold_21-snap.498-T1
Valid prediction for GeneMark_model.84171_t
Valid prediction for snap_scaffold_21-snap.483-T1
Valid prediction for GeneMark_model.84165_t
Valid prediction for snap_scaffold_21-snap.496-T1
Valid prediction for GeneMark_model.84152_t
Valid prediction for snap_scaffold_21-snap.487-T1
Valid prediction for GlimmerHMM_glimmerT_48448-T1
Valid prediction for GlimmerHMM_glimmerT_48449-T1
Valid prediction for snap_scaffold_21-snap.489-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 53970, rend_intergenic: 37442  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62205, rend_intergenic: 59379  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86172, rend_intergenic: 82879  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90279, rend_intergenic: 86472  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98672, rend_intergenic: 92983  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103862, rend_intergenic: 99171  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117672, rend_intergenic: 111401  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124339, rend_intergenic: 119085  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155615, rend_intergenic: 148766  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 180796
-exon list size: 603


building trellis

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98.3    
98.5    
98.7    
98.8    
99.0    
99.2    
99.3    
99.5    
99.7    
99.8    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 53970, rend_intergenic: 37442  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62205, rend_intergenic: 59379  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86172, rend_intergenic: 82879  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90279, rend_intergenic: 86472  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98672, rend_intergenic: 92983  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103862, rend_intergenic: 99171  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117672, rend_intergenic: 111401  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124339, rend_intergenic: 119085  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155615, rend_intergenic: 148766  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

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