-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_1022587-1225029

-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_1-snap.213-T1
Valid prediction for GlimmerHMM_glimmerT_162-T1
Valid prediction for GeneMark_model.192_t
Valid prediction for snap_scaffold_1-snap.193-T1
Valid prediction for GeneMark_model.179_t
Valid prediction for snap_scaffold_1-snap.210-T1
Valid prediction for snap_scaffold_1-snap.201-T1
Valid prediction for snap_scaffold_1-snap.214-T1
Valid prediction for snap_scaffold_1-snap.204-T1
Valid prediction for GlimmerHMM_glimmerT_170-T1
Valid prediction for GeneMark_model.173_t
Valid prediction for snap_scaffold_1-snap.199-T1
Valid prediction for GlimmerHMM_glimmerT_156-T1
Valid prediction for Augustus_model.g122.t1
Valid prediction for GlimmerHMM_glimmerT_161-T1
Valid prediction for snap_scaffold_1-snap.221-T1
Valid prediction for GlimmerHMM_glimmerT_151-T1
Valid prediction for GlimmerHMM_glimmerT_150-T1
Valid prediction for GeneMark_model.170_t
Valid prediction for snap_scaffold_1-snap.218-T1
Valid prediction for GeneMark_model.171_t
Valid prediction for GeneMark_model.162_t
Valid prediction for GlimmerHMM_glimmerT_163-T1
Valid prediction for Augustus_model.g125.t1
Valid prediction for snap_scaffold_1-snap.197-T1
Valid prediction for Augustus_model.g124.t1
Valid prediction for GeneMark_model.167_t
Valid prediction for GeneMark_model.182_t
Valid prediction for GlimmerHMM_glimmerT_139-T1
Valid prediction for GlimmerHMM_glimmerT_143-T1
Valid prediction for GeneMark_model.164_t
Valid prediction for GlimmerHMM_glimmerT_159-T1
Valid prediction for GeneMark_model.181_t
Valid prediction for snap_scaffold_1-snap.198-T1
Valid prediction for snap_scaffold_1-snap.224-T1
Valid prediction for snap_scaffold_1-snap.190-T1
Valid prediction for Augustus_model.g117.t1
Valid prediction for GlimmerHMM_glimmerT_149-T1
Valid prediction for Augustus_model.g114.t1
Valid prediction for snap_scaffold_1-snap.192-T1
Valid prediction for snap_scaffold_1-snap.202-T1
Valid prediction for snap_scaffold_1-snap.220-T1
Valid prediction for snap_scaffold_1-snap.225-T1
Valid prediction for GeneMark_model.169_t
Couldn't classify 17149, 17372
Sorry, prediction pasa_asmbl_1449.p2 fails validation.
(GAT)	 GG	17149-17372	GT	TGG
(GTA)	 AG	18895-19198	TC	GAT
-recovered pasa_asmbl_1449.p2, terminal, 18895, 19198
Couldn't classify 25389, 25473
Sorry, prediction pasa_asmbl_1452.p1 fails validation.
(GAA)	 AA	25389-25473	GT	AGG
(ATG)	 AG	28206-29143	AA	AAA
-recovered pasa_asmbl_1452.p1, terminal, 28206, 29143
Valid prediction for GeneMark_model.183_t
Valid prediction for Augustus_model.g130.t1
Valid prediction for snap_scaffold_1-snap.208-T1
Valid prediction for snap_scaffold_1-snap.226-T1
Valid prediction for GeneMark_model.190_t
Valid prediction for GlimmerHMM_glimmerT_148-T1
Valid prediction for GlimmerHMM_glimmerT_142-T1
Valid prediction for GeneMark_model.193_t
Valid prediction for GlimmerHMM_glimmerT_167-T1
Valid prediction for snap_scaffold_1-snap.212-T1
Valid prediction for snap_scaffold_1-snap.227-T1
Valid prediction for Augustus_model.g111.t1
Valid prediction for snap_scaffold_1-snap.205-T1
Valid prediction for Augustus_model.g116.t1
Valid prediction for snap_scaffold_1-snap.200-T1
Valid prediction for GlimmerHMM_glimmerT_146-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.g127.t1
Valid prediction for snap_scaffold_1-snap.195-T1
Valid prediction for GlimmerHMM_glimmerT_160-T1
Valid prediction for snap_scaffold_1-snap.194-T1
Valid prediction for snap_scaffold_1-snap.209-T1
Couldn't classify 43537, 43983
Sorry, prediction pasa_asmbl_1454.p1 fails validation.
(CTG)	 CT	43537-43983	GA	ATG
Valid prediction for GeneMark_model.168_t
Valid prediction for snap_scaffold_1-snap.219-T1
Valid prediction for GeneMark_model.185_t
Valid prediction for GlimmerHMM_glimmerT_154-T1
Valid prediction for HiQ_model.g131.t1
Valid prediction for GlimmerHMM_glimmerT_155-T1
Valid prediction for snap_scaffold_1-snap.207-T1
Sorry, intron length (4) is less than minimum required (10)
Sorry, intron length (4) is less than minimum required (10)
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.163_t
Valid prediction for GeneMark_model.176_t
Valid prediction for CodingQuarry_transcript_2519-T1
Valid prediction for GlimmerHMM_glimmerT_164-T1
Valid prediction for GeneMark_model.187_t
Valid prediction for GlimmerHMM_glimmerT_166-T1
Valid prediction for snap_scaffold_1-snap.217-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_147-T1
Valid prediction for pasa_asmbl_47.p1
Valid prediction for GeneMark_model.184_t
Valid prediction for Augustus_model.g113.t1
Valid prediction for GlimmerHMM_glimmerT_138-T1
Valid prediction for GlimmerHMM_glimmerT_136-T1
Valid prediction for GeneMark_model.188_t
Valid prediction for GeneMark_model.161_t
Valid prediction for Augustus_model.g128.t1
Valid prediction for GeneMark_model.165_t
Valid prediction for snap_scaffold_1-snap.189-T1
Valid prediction for GeneMark_model.177_t
Valid prediction for GlimmerHMM_glimmerT_158-T1
Valid prediction for GlimmerHMM_glimmerT_141-T1
Valid prediction for snap_scaffold_1-snap.203-T1
Valid prediction for Augustus_model.g123.t1
Valid prediction for GlimmerHMM_glimmerT_168-T1
Valid prediction for Augustus_model.g119.t1
Valid prediction for GlimmerHMM_glimmerT_153-T1
Valid prediction for GlimmerHMM_glimmerT_171-T1
Valid prediction for Augustus_model.g126.t1
Valid prediction for GeneMark_model.172_t
Valid prediction for GlimmerHMM_glimmerT_140-T1
Valid prediction for GeneMark_model.174_t
Valid prediction for Augustus_model.g112.t1
Valid prediction for snap_scaffold_1-snap.215-T1
Valid prediction for GeneMark_model.191_t
Valid prediction for CodingQuarry_transcript_2516-T1
Valid prediction for GlimmerHMM_glimmerT_165-T1
Valid prediction for Augustus_model.g120.t1
Valid prediction for GeneMark_model.166_t
Couldn't classify 189056, 189565
Sorry, prediction pasa_asmbl_1447.p1 fails validation.
(CCT)	 AC	189056-189565	GA	AGG
Valid prediction for GeneMark_model.175_t
Valid prediction for Augustus_model.g121.t1
Valid prediction for snap_scaffold_1-snap.223-T1
Valid prediction for Augustus_model.g110.t1
Valid prediction for snap_scaffold_1-snap.191-T1
Valid prediction for GeneMark_model.178_t
Valid prediction for Augustus_model.g118.t1
Valid prediction for GlimmerHMM_glimmerT_152-T1
Valid prediction for GlimmerHMM_glimmerT_144-T1
Valid prediction for snap_scaffold_1-snap.206-T1
Valid prediction for Augustus_model.g129.t1
Valid prediction for snap_scaffold_1-snap.211-T1
Valid prediction for GeneMark_model.189_t
Valid prediction for GlimmerHMM_glimmerT_157-T1
Valid prediction for snap_scaffold_1-snap.196-T1
Valid prediction for GlimmerHMM_glimmerT_137-T1
Valid prediction for snap_scaffold_1-snap.222-T1
Valid prediction for snap_scaffold_1-snap.216-T1
Valid prediction for GlimmerHMM_glimmerT_145-T1
Valid prediction for GeneMark_model.180_t
Valid prediction for GlimmerHMM_glimmerT_169-T1
Valid prediction for Augustus_model.g115.t1
Valid prediction for GeneMark_model.186_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7615, rend_intergenic: 6171  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53844, rend_intergenic: 52462  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101386, rend_intergenic: 91840  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157186, rend_intergenic: 154256  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158581, rend_intergenic: 157486  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162590, rend_intergenic: 158620  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184824, rend_intergenic: 182539  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 202443
-exon list size: 422


building trellis

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98.1    
98.3    
98.6    
98.8    
99.1    
99.3    
99.5    
99.8    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 7615, rend_intergenic: 6171  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53844, rend_intergenic: 52462  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101386, rend_intergenic: 91840  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157186, rend_intergenic: 154256  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158581, rend_intergenic: 157486  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162590, rend_intergenic: 158620  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184824, rend_intergenic: 182539  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 31 predictions persist after filtering for low support