-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_20/scaffold_20_6952520-7111295

-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 GlimmerHMM_glimmerT_47379-T1
Valid prediction for snap_scaffold_20-snap.1554-T1
Valid prediction for GlimmerHMM_glimmerT_47384-T1
Valid prediction for snap_scaffold_20-snap.1563-T1
Valid prediction for Augustus_model.g31593.t1
Valid prediction for GeneMark_model.82766_t
Couldn't classify 88018, 88032
Sorry, prediction pasa_asmbl_25849.p2 fails validation.
(GAC)	 AG	88018-88032	GT	TGG
(GAT)	 AG	88338-88646	GC	GAG
-recovered pasa_asmbl_25849.p2, terminal, 88338, 88646
-recovered pasa_asmbl_25849.p2, internal, 88018, 88032
-recovered pasa_asmbl_25849.p2, internal, 88338, 88646
Valid prediction for GlimmerHMM_glimmerT_47377-T1
Valid prediction for snap_scaffold_20-snap.1547-T1
Valid prediction for GeneMark_model.82749_t
Valid prediction for GlimmerHMM_glimmerT_47385-T1
Valid prediction for GeneMark_model.82751_t
Valid prediction for Augustus_model.g31587.t1
Valid prediction for CodingQuarry_transcript_30480-T1
Valid prediction for snap_scaffold_20-snap.1541-T1
Valid prediction for GeneMark_model.82747_t
Valid prediction for GeneMark_model.82762_t
Valid prediction for GeneMark_model.82755_t
Valid prediction for GeneMark_model.82757_t
Valid prediction for GlimmerHMM_glimmerT_47381-T1
Valid prediction for Augustus_model.g31586.t1
Valid prediction for Augustus_model.g31585.t1
Valid prediction for snap_scaffold_20-snap.1561-T1
Valid prediction for snap_scaffold_20-snap.1549-T1
Valid prediction for snap_scaffold_20-snap.1564-T1
Valid prediction for snap_scaffold_20-snap.1572-T1
Valid prediction for GeneMark_model.82776_t
Valid prediction for snap_scaffold_20-snap.1551-T1
Valid prediction for snap_scaffold_20-snap.1539-T1
Valid prediction for GeneMark_model.82778_t
Couldn't classify 23819, 23974
Sorry, prediction pasa_asmbl_25845.p1 fails validation.
(CCT)	 CC	23819-23974	GT	GCG
(ATG)	 AG	24664-24714	GT	TGG
(AGT)	 AG	25062-25205	AC	AGA
-recovered pasa_asmbl_25845.p1, initial, 24664, 24714
-recovered pasa_asmbl_25845.p1, terminal, 25062, 25205
-recovered pasa_asmbl_25845.p1, internal, 24664, 24714
Valid prediction for HiQ_model.g31601.t1
Valid prediction for Augustus_model.g31596.t1
Valid prediction for GlimmerHMM_glimmerT_47390-T1
Valid prediction for GlimmerHMM_glimmerT_47378-T1
Valid prediction for Augustus_model.g31594.t1
Valid prediction for GeneMark_model.82770_t
Valid prediction for GeneMark_model.82768_t
Valid prediction for GeneMark_model.82752_t
Valid prediction for pasa_asmbl_25850.p1
Valid prediction for snap_scaffold_20-snap.1556-T1
Valid prediction for GeneMark_model.82764_t
Valid prediction for snap_scaffold_20-snap.1568-T1
Valid prediction for GeneMark_model.82772_t
Valid prediction for GlimmerHMM_glimmerT_47383-T1
Valid prediction for GlimmerHMM_glimmerT_47386-T1
Valid prediction for snap_scaffold_20-snap.1558-T1
Valid prediction for Augustus_model.g31588.t1
Valid prediction for GlimmerHMM_glimmerT_47394-T1
Valid prediction for Augustus_model.g31598.t1
Valid prediction for GeneMark_model.82759_t
Valid prediction for snap_scaffold_20-snap.1548-T1
Valid prediction for CodingQuarry_transcript_30483-T1
Valid prediction for GeneMark_model.82774_t
Valid prediction for snap_scaffold_20-snap.1542-T1
Valid prediction for snap_scaffold_20-snap.1543-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.g31590.t1
Couldn't classify 43290, 43452
Sorry, prediction pasa_asmbl_26787.p2 fails validation.
(ATG)	 CC	37658-37766	GT	TGG
(AGT)	 AG	38463-38622	GT	AGG
(CAT)	 AG	39336-39496	GT	CGG
(GCA)	 AG	42037-42144	GT	ATG
(TGG)	 AG	42334-42453	GT	AGG
(GTG)	 AG	42622-42737	GT	AGG
(GTG)	 AG	42897-43066	GT	GGG
(AGA)	 AG	43290-43452	GT	AGG
-recovered pasa_asmbl_26787.p2, initial, 37658, 37766
-recovered pasa_asmbl_26787.p2, internal, 38463, 38622
-recovered pasa_asmbl_26787.p2, internal, 39336, 39496
-recovered pasa_asmbl_26787.p2, internal, 42037, 42144
-recovered pasa_asmbl_26787.p2, internal, 42334, 42453
-recovered pasa_asmbl_26787.p2, internal, 42622, 42737
-recovered pasa_asmbl_26787.p2, internal, 42897, 43066
-recovered pasa_asmbl_26787.p2, internal, 43290, 43452
Valid prediction for GlimmerHMM_glimmerT_47388-T1
Valid prediction for GlimmerHMM_glimmerT_47391-T1
Valid prediction for CodingQuarry_transcript_30485-T1
Valid prediction for GlimmerHMM_glimmerT_47380-T1
Valid prediction for snap_scaffold_20-snap.1555-T1
Valid prediction for snap_scaffold_20-snap.1566-T1
Valid prediction for GeneMark_model.82775_t
Valid prediction for snap_scaffold_20-snap.1565-T1
Valid prediction for GlimmerHMM_glimmerT_47396-T1
Valid prediction for snap_scaffold_20-snap.1557-T1
Valid prediction for GlimmerHMM_glimmerT_47392-T1
Valid prediction for Augustus_model.g31604.t1
Valid prediction for GeneMark_model.82765_t
Valid prediction for snap_scaffold_20-snap.1552-T1
Valid prediction for GlimmerHMM_glimmerT_47382-T1
Valid prediction for Augustus_model.g31602.t1
Valid prediction for snap_scaffold_20-snap.1559-T1
Valid prediction for snap_scaffold_20-snap.1544-T1
Valid prediction for Augustus_model.g31592.t1
Valid prediction for snap_scaffold_20-snap.1574-T1
Valid prediction for GlimmerHMM_glimmerT_47387-T1
Valid prediction for snap_scaffold_20-snap.1553-T1
Valid prediction for snap_scaffold_20-snap.1567-T1
Valid prediction for GeneMark_model.82758_t
Valid prediction for GeneMark_model.82773_t
Valid prediction for GeneMark_model.82771_t
Valid prediction for pasa_asmbl_26794.p1
Valid prediction for GeneMark_model.82777_t
Valid prediction for snap_scaffold_20-snap.1562-T1
Couldn't classify 13822, 13890
Sorry, prediction pasa_asmbl_27199.p1 fails validation.
(CAC)	 AG	13822-13890	GT	AGG
(GCC)	 AG	14119-14201	GT	AAG
(GAC)	 AG	14313-14422	GT	CGG
(GCG)	 AG	14522-14604	GT	AGG
(GCC)	 AG	14714-14854	GT	AGG
(GCG)	 AG	17202-17300	GT	CGG
(AAG)	 AG	17444-17508	GT	AGG
(CTA)	 AG	17664-17817	GT	AGG
(AGT)	 AG	17918-18012	GT	AGG
(GTG)	 AG	18251-18380	GT	AGG
(GAC)	 AG	18679-18754	GT	AGG
(ACA)	 AG	18979-19031	GT	CGG
(CCG)	 AG	19980-20207	AT	AAA
add_exon() Sorry, pasa_asmbl_27199.p1 17444-17508-terminal-2 is invalid.
-recovered pasa_asmbl_27199.p1, terminal, 17444, 17508
add_exon() Sorry, pasa_asmbl_27199.p1 17918-18012-terminal-2 is invalid.
-recovered pasa_asmbl_27199.p1, terminal, 17918, 18012
add_exon() Sorry, pasa_asmbl_27199.p1 18679-18754-terminal-3 is invalid.
-recovered pasa_asmbl_27199.p1, terminal, 18679, 18754
-recovered pasa_asmbl_27199.p1, terminal, 19980, 20207
-recovered pasa_asmbl_27199.p1, internal, 13822, 13890
-recovered pasa_asmbl_27199.p1, internal, 14119, 14201
-recovered pasa_asmbl_27199.p1, internal, 14313, 14422
-recovered pasa_asmbl_27199.p1, internal, 14522, 14604
-recovered pasa_asmbl_27199.p1, internal, 14714, 14854
-recovered pasa_asmbl_27199.p1, internal, 17202, 17300
-recovered pasa_asmbl_27199.p1, internal, 17444, 17508
-recovered pasa_asmbl_27199.p1, internal, 17664, 17817
-recovered pasa_asmbl_27199.p1, internal, 17918, 18012
-recovered pasa_asmbl_27199.p1, internal, 18251, 18380
-recovered pasa_asmbl_27199.p1, internal, 18679, 18754
-recovered pasa_asmbl_27199.p1, internal, 18979, 19031
Valid prediction for GeneMark_model.82780_t
Couldn't classify 33506, 34330
Sorry, prediction pasa_asmbl_26790.p1 fails validation.
(AAA)	 CC	33506-34330	AC	GCA
Valid prediction for GlimmerHMM_glimmerT_47397-T1
Couldn't classify 122708, 123148
Sorry, prediction pasa_asmbl_26783.p1 fails validation.
(TTT)	 CA	122708-123148	AA	CTA
Valid prediction for GeneMark_model.82745_t
Valid prediction for snap_scaffold_20-snap.1540-T1
Valid prediction for GeneMark_model.82781_t
Valid prediction for CodingQuarry_transcript_30484-T1
Valid prediction for GeneMark_model.82746_t
Valid prediction for snap_scaffold_20-snap.1573-T1
Valid prediction for snap_scaffold_20-snap.1569-T1
Valid prediction for GlimmerHMM_glimmerT_47398-T1
Valid prediction for GlimmerHMM_glimmerT_47393-T1
Valid prediction for Augustus_model.g31597.t1
Couldn't classify 43650, 43828
Sorry, prediction pasa_asmbl_27255.p1 fails validation.
(TCC)	 CT	43650-43828	GT	AGG
(GTA)	 AG	44452-44628	GT	AAG
(GTT)	 AG	45266-45371	GT	ATG
(GCC)	 AG	45849-45992	GT	AGG
(GCG)	 AG	46101-46307	GT	AGG
(GTT)	 AG	46585-46635	GC	GAG
-recovered pasa_asmbl_27255.p1, terminal, 46585, 46635
-recovered pasa_asmbl_27255.p1, internal, 44452, 44628
-recovered pasa_asmbl_27255.p1, internal, 45266, 45371
-recovered pasa_asmbl_27255.p1, internal, 45849, 45992
-recovered pasa_asmbl_27255.p1, internal, 46101, 46307
-recovered pasa_asmbl_27255.p1, internal, 46585, 46635
Valid prediction for GlimmerHMM_glimmerT_47376-T1
Valid prediction for GlimmerHMM_glimmerT_47395-T1
Valid prediction for GeneMark_model.82756_t
Valid prediction for GeneMark_model.82753_t
Valid prediction for Augustus_model.g31591.t1
Valid prediction for CodingQuarry_transcript_30481-T1
Valid prediction for snap_scaffold_20-snap.1560-T1
Valid prediction for GeneMark_model.82754_t
Valid prediction for snap_scaffold_20-snap.1546-T1
Valid prediction for Augustus_model.g31599.t1
Valid prediction for snap_scaffold_20-snap.1538-T1
Valid prediction for GeneMark_model.82779_t
Valid prediction for HiQ_model.g31603.t1
Valid prediction for pasa_asmbl_26796.p1
Valid prediction for GeneMark_model.82763_t
Valid prediction for snap_scaffold_20-snap.1545-T1
Couldn't classify 118692, 118897
Sorry, prediction pasa_asmbl_27248.p1 fails validation.
(ATG)	 TC	118235-118328	GT	GGG
(GAG)	 AG	118692-118897	TT	CCT
-recovered pasa_asmbl_27248.p1, initial, 118235, 118328
Valid prediction for Augustus_model.g31595.t1
Valid prediction for Augustus_model.g31600.t1
Valid prediction for GlimmerHMM_glimmerT_47389-T1
Valid prediction for GeneMark_model.82761_t
Valid prediction for GeneMark_model.82767_t
Valid prediction for snap_scaffold_20-snap.1550-T1
Valid prediction for GeneMark_model.82748_t
Valid prediction for Augustus_model.g31584.t1
Valid prediction for GeneMark_model.82769_t
Valid prediction for snap_scaffold_20-snap.1570-T1
Valid prediction for pasa_asmbl_26786.p2
Valid prediction for snap_scaffold_20-snap.1571-T1
Valid prediction for Augustus_model.g31589.t1
Valid prediction for GeneMark_model.82750_t
Couldn't classify 118787, 119000
Couldn't classify 119099, 119346
Sorry, prediction pasa_asmbl_27195.p1 fails validation.
(TTG)	 TC	118787-119000	GT	AGG
(GTG)	 AG	119099-119346	CA	GCC

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10014, rend_intergenic: 7007  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55585, rend_intergenic: 50841  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57102, rend_intergenic: 56356  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77615, rend_intergenic: 70313  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83159, rend_intergenic: 78196  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97219, rend_intergenic: 94298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99117, rend_intergenic: 97407  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145667, rend_intergenic: 142027  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 158776
-exon list size: 563


building trellis

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97.0    
97.2    
97.3    
97.5    
97.7    
97.9    
98.1    
98.2    
98.4    
98.6    
98.8    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 10014, rend_intergenic: 7007  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55585, rend_intergenic: 50841  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57102, rend_intergenic: 56356  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77615, rend_intergenic: 70313  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83159, rend_intergenic: 78196  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97219, rend_intergenic: 94298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99117, rend_intergenic: 97407  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145667, rend_intergenic: 142027  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support