-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_20/scaffold_20_8039462-8207575

-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 Augustus_model.g31734.t1
Valid prediction for HiQ_model.g31730.t1
Valid prediction for snap_scaffold_20-snap.1814-T1
Valid prediction for Augustus_model.g31719.t1
Valid prediction for GlimmerHMM_glimmerT_47563-T1
Valid prediction for GeneMark_model.83059_t
Valid prediction for GeneMark_model.83017_t
Valid prediction for GlimmerHMM_glimmerT_47578-T1
Valid prediction for snap_scaffold_20-snap.1808-T1
Valid prediction for snap_scaffold_20-snap.1790-T1
Valid prediction for GlimmerHMM_glimmerT_47561-T1
Valid prediction for snap_scaffold_20-snap.1812-T1
Valid prediction for GeneMark_model.83029_t
Valid prediction for GlimmerHMM_glimmerT_47576-T1
Valid prediction for snap_scaffold_20-snap.1797-T1
Valid prediction for GlimmerHMM_glimmerT_47558-T1
Valid prediction for GeneMark_model.83057_t
Valid prediction for GeneMark_model.83049_t
Valid prediction for GeneMark_model.83028_t
Valid prediction for snap_scaffold_20-snap.1813-T1
Valid prediction for GeneMark_model.83052_t
Valid prediction for GeneMark_model.83033_t
Valid prediction for GeneMark_model.83026_t
Couldn't classify 162461, 162671
Sorry, prediction pasa_asmbl_25907.p1 fails validation.
(ATG)	 AA	161730-162166	GT	CGG
(GCT)	 AG	162461-162671	CA	GCC
-recovered pasa_asmbl_25907.p1, initial, 161730, 162166
Valid prediction for snap_scaffold_20-snap.1791-T1
Valid prediction for GeneMark_model.83047_t
Valid prediction for GlimmerHMM_glimmerT_47570-T1
Valid prediction for Augustus_model.g31733.t1
Valid prediction for GeneMark_model.83043_t
Valid prediction for Augustus_model.g31732.t1
Valid prediction for GlimmerHMM_glimmerT_47572-T1
Valid prediction for snap_scaffold_20-snap.1816-T1
Valid prediction for GeneMark_model.83055_t
Valid prediction for GlimmerHMM_glimmerT_47564-T1
Valid prediction for snap_scaffold_20-snap.1815-T1
Valid prediction for snap_scaffold_20-snap.1796-T1
Valid prediction for GeneMark_model.83035_t
Valid prediction for GlimmerHMM_glimmerT_47560-T1
Valid prediction for Augustus_model.g31721.t1
Valid prediction for GeneMark_model.83037_t
Valid prediction for snap_scaffold_20-snap.1784-T1
Valid prediction for GeneMark_model.83024_t
Valid prediction for GlimmerHMM_glimmerT_47579-T1
Valid prediction for snap_scaffold_20-snap.1793-T1
Couldn't classify 128025, 128186
Sorry, prediction pasa_asmbl_25903.p1 fails validation.
(CTA)	 CA	128025-128186	GT	AAG
(ACG)	 AG	128619-128756	AG	AAA
-recovered pasa_asmbl_25903.p1, terminal, 128619, 128756
Valid prediction for snap_scaffold_20-snap.1783-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for Augustus_model.g31727.t1
Valid prediction for GeneMark_model.83039_t
Valid prediction for GeneMark_model.83022_t
Valid prediction for Augustus_model.g31718.t1
Valid prediction for snap_scaffold_20-snap.1785-T1
Valid prediction for GeneMark_model.83031_t
Valid prediction for GeneMark_model.83020_t

-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 snap_scaffold_20-snap.1782-T1
Valid prediction for snap_scaffold_20-snap.1794-T1
Valid prediction for Augustus_model.g31728.t1
Valid prediction for GlimmerHMM_glimmerT_47577-T1
Valid prediction for snap_scaffold_20-snap.1817-T1
Valid prediction for GeneMark_model.83023_t
Valid prediction for GlimmerHMM_glimmerT_47575-T1
Valid prediction for snap_scaffold_20-snap.1810-T1
Valid prediction for GeneMark_model.83030_t
Valid prediction for Augustus_model.g31716.t1
Valid prediction for snap_scaffold_20-snap.1800-T1
Valid prediction for GeneMark_model.83044_t
Valid prediction for Augustus_model.g31731.t1
Valid prediction for CodingQuarry_transcript_30512-T1
Valid prediction for Augustus_model.g31725.t1
Valid prediction for snap_scaffold_20-snap.1806-T1
Valid prediction for GeneMark_model.83036_t
Valid prediction for snap_scaffold_20-snap.1786-T1
Valid prediction for pasa_asmbl_26891.p1
Valid prediction for GeneMark_model.83045_t
Valid prediction for Augustus_model.g31715.t1
Valid prediction for GlimmerHMM_glimmerT_47567-T1
Valid prediction for GeneMark_model.83021_t
Valid prediction for Augustus_model.g31724.t1
Valid prediction for snap_scaffold_20-snap.1803-T1
Couldn't classify 88050, 88592
Sorry, prediction pasa_asmbl_26883.p1 fails validation.
(GTG)	 AG	88050-88592	GT	AGG
(GAA)	 AG	88774-89221	GT	AGG
(CTG)	 AG	89398-89579	GT	AGG
(GTT)	 AG	89812-89949	GT	AGG
(GCT)	 AG	90118-90186	GT	AGG
(GTG)	 AG	90306-90364	GT	CGG
(GCT)	 AG	92306-92370	GT	TGG
(TGC)	 AG	92486-93112	GT	AGG
(ATA)	 AG	93371-93472	GT	AGG
(TGA)	 AG	93756-93833	GT	TGG
(GTG)	 AG	94032-94105	GT	TGG
(GAC)	 AG	94260-94727	GC	GAG
-recovered pasa_asmbl_26883.p1, terminal, 94260, 94727
-recovered pasa_asmbl_26883.p1, internal, 88050, 88592
-recovered pasa_asmbl_26883.p1, internal, 88774, 89221
-recovered pasa_asmbl_26883.p1, internal, 89398, 89579
-recovered pasa_asmbl_26883.p1, internal, 89812, 89949
-recovered pasa_asmbl_26883.p1, internal, 90118, 90186
-recovered pasa_asmbl_26883.p1, internal, 90306, 90364
-recovered pasa_asmbl_26883.p1, internal, 92306, 92370
-recovered pasa_asmbl_26883.p1, internal, 92486, 93112
-recovered pasa_asmbl_26883.p1, internal, 93371, 93472
-recovered pasa_asmbl_26883.p1, internal, 93756, 93833
-recovered pasa_asmbl_26883.p1, internal, 94032, 94105
-recovered pasa_asmbl_26883.p1, internal, 94260, 94727
Valid prediction for GeneMark_model.83051_t
Valid prediction for snap_scaffold_20-snap.1798-T1
Valid prediction for GeneMark_model.83025_t
Valid prediction for GlimmerHMM_glimmerT_47565-T1
Valid prediction for GlimmerHMM_glimmerT_47555-T1
Valid prediction for pasa_asmbl_26895.p1
Valid prediction for GlimmerHMM_glimmerT_47569-T1
Valid prediction for GlimmerHMM_glimmerT_47559-T1
Valid prediction for GeneMark_model.83041_t
Valid prediction for Augustus_model.g31717.t1
Valid prediction for GeneMark_model.83038_t
Valid prediction for HiQ_model.g31722.t1
Valid prediction for snap_scaffold_20-snap.1809-T1
Valid prediction for GeneMark_model.83034_t
Valid prediction for GlimmerHMM_glimmerT_47566-T1
Valid prediction for GeneMark_model.83042_t
Valid prediction for GlimmerHMM_glimmerT_47574-T1
Valid prediction for snap_scaffold_20-snap.1805-T1
Valid prediction for GlimmerHMM_glimmerT_47562-T1
Valid prediction for snap_scaffold_20-snap.1811-T1
Valid prediction for GeneMark_model.83054_t
Valid prediction for GeneMark_model.83050_t
Valid prediction for GeneMark_model.83018_t
Valid prediction for snap_scaffold_20-snap.1799-T1
Valid prediction for snap_scaffold_20-snap.1795-T1
Valid prediction for GeneMark_model.83053_t
Valid prediction for GlimmerHMM_glimmerT_47568-T1
Valid prediction for HiQ_model.g31723.t1
Valid prediction for Augustus_model.g31720.t1
Valid prediction for snap_scaffold_20-snap.1789-T1
Valid prediction for snap_scaffold_20-snap.1804-T1
Valid prediction for CodingQuarry_transcript_30511-T1
Valid prediction for GeneMark_model.83032_t
Valid prediction for snap_scaffold_20-snap.1801-T1
Valid prediction for snap_scaffold_20-snap.1787-T1
Valid prediction for Augustus_model.g31726.t1
Couldn't classify 93563, 93833
Sorry, prediction pasa_asmbl_26884.p1 fails validation.
(CAA)	 TC	93563-93833	GT	TGG
(GTG)	 AG	94032-94105	GT	TGG
(GAC)	 AG	94260-94727	GC	GAG
-recovered pasa_asmbl_26884.p1, terminal, 94260, 94727
-recovered pasa_asmbl_26884.p1, internal, 94032, 94105
-recovered pasa_asmbl_26884.p1, internal, 94260, 94727
Valid prediction for GeneMark_model.83019_t
Valid prediction for pasa_asmbl_26887.p1
Valid prediction for GlimmerHMM_glimmerT_47573-T1
Valid prediction for CodingQuarry_transcript_30513-T1
Valid prediction for GeneMark_model.83040_t
Valid prediction for snap_scaffold_20-snap.1788-T1
Valid prediction for GlimmerHMM_glimmerT_47556-T1
Valid prediction for GeneMark_model.83056_t
Valid prediction for GeneMark_model.83048_t
Valid prediction for snap_scaffold_20-snap.1792-T1
Valid prediction for snap_scaffold_20-snap.1802-T1
Valid prediction for GlimmerHMM_glimmerT_47557-T1
Valid prediction for GeneMark_model.83058_t
Valid prediction for GeneMark_model.83016_t
Valid prediction for GeneMark_model.83046_t
Valid prediction for snap_scaffold_20-snap.1807-T1
Valid prediction for HiQ_model.g31729.t1
Valid prediction for GlimmerHMM_glimmerT_47571-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7630, rend_intergenic: 7238  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19387, rend_intergenic: 16449  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35509, rend_intergenic: 26575  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48733, rend_intergenic: 45974  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54655, rend_intergenic: 49725  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61407, rend_intergenic: 56674  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 168114
-exon list size: 596


building trellis

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98.2    
98.3    
98.5    
98.7    
98.8    
99.0    
99.2    
99.3    
99.5    
99.7    
99.8    
-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 7630, rend_intergenic: 7238  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19387, rend_intergenic: 16449  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35509, rend_intergenic: 26575  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48733, rend_intergenic: 45974  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54655, rend_intergenic: 49725  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61407, rend_intergenic: 56674  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support