-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_20/scaffold_20_8574372-8719076

-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 pasa_asmbl_25950.p1
Valid prediction for GeneMark_model.83155_t
Valid prediction for snap_scaffold_20-snap.1907-T1
Valid prediction for pasa_asmbl_25952.p1
Valid prediction for snap_scaffold_20-snap.1917-T1
Valid prediction for Augustus_model.g31786.t1
Valid prediction for snap_scaffold_20-snap.1909-T1
Valid prediction for snap_scaffold_20-snap.1908-T1
Valid prediction for CodingQuarry_transcript_30521-T1
Valid prediction for Augustus_model.g31781.t1
Valid prediction for GeneMark_model.83161_t
Valid prediction for GlimmerHMM_glimmerT_47650-T1
Valid prediction for snap_scaffold_20-snap.1893-T1
Valid prediction for GlimmerHMM_glimmerT_47645-T1
Valid prediction for GeneMark_model.83154_t
Valid prediction for Augustus_model.g31785.t1
Valid prediction for GeneMark_model.83139_t
Valid prediction for GlimmerHMM_glimmerT_47647-T1
Valid prediction for GeneMark_model.83145_t
Valid prediction for GlimmerHMM_glimmerT_47634-T1
Valid prediction for GeneMark_model.83156_t
Valid prediction for snap_scaffold_20-snap.1920-T1
Valid prediction for snap_scaffold_20-snap.1904-T1
Valid prediction for Augustus_model.g31783.t1
Valid prediction for GeneMark_model.83165_t
Valid prediction for snap_scaffold_20-snap.1918-T1
Valid prediction for GeneMark_model.83143_t
Valid prediction for GeneMark_model.83141_t
Valid prediction for GlimmerHMM_glimmerT_47641-T1
Valid prediction for GeneMark_model.83163_t
Valid prediction for GlimmerHMM_glimmerT_47635-T1
Valid prediction for GlimmerHMM_glimmerT_47646-T1
Valid prediction for snap_scaffold_20-snap.1913-T1
Valid prediction for GlimmerHMM_glimmerT_47648-T1
Valid prediction for Augustus_model.g31778.t1
Valid prediction for snap_scaffold_20-snap.1898-T1
Valid prediction for GeneMark_model.83150_t
Valid prediction for snap_scaffold_20-snap.1912-T1
Valid prediction for GlimmerHMM_glimmerT_47633-T1
Valid prediction for GeneMark_model.83147_t
Valid prediction for GlimmerHMM_glimmerT_47636-T1
Valid prediction for GlimmerHMM_glimmerT_47637-T1
Valid prediction for GlimmerHMM_glimmerT_47638-T1
Valid prediction for snap_scaffold_20-snap.1900-T1
Valid prediction for GeneMark_model.83142_t
Valid prediction for Augustus_model.g31788.t1
Valid prediction for GeneMark_model.83140_t
Valid prediction for GlimmerHMM_glimmerT_47644-T1
Valid prediction for HiQ_model.g31787.t1
Valid prediction for GeneMark_model.83152_t
Valid prediction for GlimmerHMM_glimmerT_47652-T1
Valid prediction for snap_scaffold_20-snap.1896-T1
Valid prediction for Augustus_model.g31780.t1
Valid prediction for snap_scaffold_20-snap.1906-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for snap_scaffold_20-snap.1903-T1
Valid prediction for snap_scaffold_20-snap.1911-T1
Valid prediction for snap_scaffold_20-snap.1897-T1
Valid prediction for snap_scaffold_20-snap.1891-T1
Couldn't classify 40687, 40864
Sorry, prediction pasa_asmbl_25948.p1 fails validation.
(TCC)	 CC	40687-40864	GT	TGG
(GAC)	 AG	41175-41223	GT	GTG
(GGT)	 AG	41390-41496	GT	AGG
(GTG)	 AG	41760-41847	GT	AGG
(AGA)	 AG	42018-42174	GG	GAG
-recovered pasa_asmbl_25948.p1, terminal, 42018, 42174
-recovered pasa_asmbl_25948.p1, internal, 41175, 41223
-recovered pasa_asmbl_25948.p1, internal, 41390, 41496
-recovered pasa_asmbl_25948.p1, internal, 41760, 41847
Valid prediction for Augustus_model.g31779.t1
Valid prediction for GlimmerHMM_glimmerT_47651-T1
Valid prediction for snap_scaffold_20-snap.1922-T1
Valid prediction for GlimmerHMM_glimmerT_47632-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 GeneMark_model.83160_t
Valid prediction for snap_scaffold_20-snap.1895-T1
Valid prediction for GeneMark_model.83164_t
Valid prediction for Augustus_model.g31791.t1
Valid prediction for GlimmerHMM_glimmerT_47653-T1
Valid prediction for snap_scaffold_20-snap.1921-T1
Valid prediction for GeneMark_model.83149_t
Valid prediction for GlimmerHMM_glimmerT_47654-T1
Valid prediction for GeneMark_model.83146_t
Valid prediction for snap_scaffold_20-snap.1914-T1
Valid prediction for GlimmerHMM_glimmerT_47655-T1
Valid prediction for snap_scaffold_20-snap.1902-T1
Valid prediction for Augustus_model.g31782.t1
Valid prediction for GlimmerHMM_glimmerT_47656-T1
Valid prediction for snap_scaffold_20-snap.1901-T1
Valid prediction for GlimmerHMM_glimmerT_47642-T1
Valid prediction for snap_scaffold_20-snap.1899-T1
Valid prediction for GeneMark_model.83138_t
Valid prediction for Augustus_model.g31777.t1
Valid prediction for GeneMark_model.83162_t
Valid prediction for GlimmerHMM_glimmerT_47640-T1
Valid prediction for GlimmerHMM_glimmerT_47639-T1
Valid prediction for GlimmerHMM_glimmerT_47643-T1
Valid prediction for snap_scaffold_20-snap.1889-T1
Valid prediction for GlimmerHMM_glimmerT_47649-T1
Valid prediction for GeneMark_model.83144_t
Valid prediction for GlimmerHMM_glimmerT_47631-T1
Valid prediction for snap_scaffold_20-snap.1916-T1
Valid prediction for Augustus_model.g31784.t1
Valid prediction for GlimmerHMM_glimmerT_47630-T1
Couldn't classify 16502, 17119
Sorry, prediction pasa_asmbl_26931.p1 fails validation.
(GGC)	 AT	16502-17119	GG	AAG
Valid prediction for GeneMark_model.83158_t
Valid prediction for snap_scaffold_20-snap.1919-T1
Valid prediction for snap_scaffold_20-snap.1905-T1
Valid prediction for Augustus_model.g31790.t1
Couldn't classify 141113, 141207
Sorry, prediction pasa_asmbl_26920.p1 fails validation.
(ATG)	 AA	136205-136510	GT	GGG
(GTG)	 AG	137592-137837	GT	AGG
(GTG)	 AG	138906-139582	GT	AGG
(ATA)	 AG	140107-140312	GT	AGG
(GCG)	 AG	140659-140835	GT	GGG
(GCG)	 AG	141113-141207	AG	GGA
-recovered pasa_asmbl_26920.p1, initial, 136205, 136510
-recovered pasa_asmbl_26920.p1, internal, 137592, 137837
-recovered pasa_asmbl_26920.p1, internal, 138906, 139582
-recovered pasa_asmbl_26920.p1, internal, 140107, 140312
-recovered pasa_asmbl_26920.p1, internal, 140659, 140835
Valid prediction for GeneMark_model.83157_t
Valid prediction for HiQ_model.g31776.t1
Valid prediction for snap_scaffold_20-snap.1915-T1
Valid prediction for Augustus_model.g31789.t1
Valid prediction for GeneMark_model.83153_t
Valid prediction for GeneMark_model.83151_t
Valid prediction for snap_scaffold_20-snap.1892-T1
Valid prediction for snap_scaffold_20-snap.1890-T1
Valid prediction for GeneMark_model.83136_t
Valid prediction for snap_scaffold_20-snap.1894-T1
Valid prediction for snap_scaffold_20-snap.1910-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 28167, rend_intergenic: 25652  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62079, rend_intergenic: 60166  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67797, rend_intergenic: 64620  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72637, rend_intergenic: 72194  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82975, rend_intergenic: 73581  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112668, rend_intergenic: 107838  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121902, rend_intergenic: 119626  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129499, rend_intergenic: 126769  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133664, rend_intergenic: 130013  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139194, rend_intergenic: 135718  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 144705
-exon list size: 436


building trellis

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-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 28167, rend_intergenic: 25652  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62079, rend_intergenic: 60166  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67797, rend_intergenic: 64620  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72637, rend_intergenic: 72194  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82975, rend_intergenic: 73581  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112668, rend_intergenic: 107838  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121902, rend_intergenic: 119626  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129499, rend_intergenic: 126769  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133664, rend_intergenic: 130013  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139194, rend_intergenic: 135718  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 133665 - 144705
-exon list size: 27


building trellis

3.4    
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27.6    
31.0    
34.5    
37.9    
41.4    
44.8    
48.3    
51.7    
55.2    
58.6    
62.1    
65.5    
69.0    
72.4    
75.9    
79.3    
82.8    
86.2    
89.7    
93.1    
96.6    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support