-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_9/scaffold_9_6164341-6395799

-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_9-snap.1345-T1
Valid prediction for GeneMark_model.39136_t
Valid prediction for GeneMark_model.39138_t
Valid prediction for snap_scaffold_9-snap.1320-T1
Valid prediction for Augustus_model.g15245.t1
Valid prediction for GeneMark_model.39146_t
Valid prediction for Augustus_model.g15236.t1
Valid prediction for GlimmerHMM_glimmerT_22798-T1
Valid prediction for Augustus_model.g15232.t1
Valid prediction for GeneMark_model.39132_t
Valid prediction for snap_scaffold_9-snap.1341-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.39117_t
Valid prediction for CodingQuarry_transcript_62037-T1
Valid prediction for GeneMark_model.39140_t
Valid prediction for GeneMark_model.39128_t
Valid prediction for snap_scaffold_9-snap.1348-T1
Valid prediction for HiQ_model.g15241.t1
Valid prediction for GeneMark_model.39147_t
Valid prediction for GeneMark_model.39148_t
Valid prediction for snap_scaffold_9-snap.1332-T1
Valid prediction for Augustus_model.g15242.t1
Valid prediction for Augustus_model.g15246.t1
Valid prediction for snap_scaffold_9-snap.1342-T1
Valid prediction for GlimmerHMM_glimmerT_22799-T1
Valid prediction for Augustus_model.g15239.t1
Valid prediction for GeneMark_model.39114_t
Valid prediction for GeneMark_model.39123_t
Couldn't classify 130994, 131191
Sorry, prediction pasa_asmbl_54076.p1 fails validation.
(TGG)	 GC	130994-131191	GT	AGG
(AAC)	 AG	131609-131735	GT	AGG
(AAT)	 AG	131986-132069	GT	GGG
(ATG)	 AG	132229-132257	AA	GAA
-recovered pasa_asmbl_54076.p1, terminal, 132229, 132257
-recovered pasa_asmbl_54076.p1, internal, 131609, 131735
-recovered pasa_asmbl_54076.p1, internal, 131986, 132069
Valid prediction for GlimmerHMM_glimmerT_22774-T1
Valid prediction for snap_scaffold_9-snap.1335-T1
Valid prediction for snap_scaffold_9-snap.1330-T1
Valid prediction for GlimmerHMM_glimmerT_22777-T1
Valid prediction for CodingQuarry_transcript_62041-T1
Valid prediction for pasa_asmbl_54066.p1
Valid prediction for snap_scaffold_9-snap.1338-T1
Valid prediction for GeneMark_model.39160_t
Valid prediction for CodingQuarry_transcript_62035-T1
Valid prediction for HiQ_model.g15243.t1
Valid prediction for GeneMark_model.39143_t
Valid prediction for GlimmerHMM_glimmerT_22785-T1
Valid prediction for Augustus_model.g15248.t1
Valid prediction for pasa_asmbl_54072.p1
Valid prediction for GeneMark_model.39157_t
Valid prediction for GlimmerHMM_glimmerT_22796-T1
Valid prediction for GlimmerHMM_glimmerT_22790-T1
Valid prediction for snap_scaffold_9-snap.1323-T1
Valid prediction for GlimmerHMM_glimmerT_22797-T1
Valid prediction for GlimmerHMM_glimmerT_22783-T1
Valid prediction for CodingQuarry_transcript_62038-T1
Valid prediction for snap_scaffold_9-snap.1353-T1
Valid prediction for GeneMark_model.39127_t
Valid prediction for GeneMark_model.39130_t
Valid prediction for GlimmerHMM_glimmerT_22800-T1
Valid prediction for snap_scaffold_9-snap.1321-T1
Valid prediction for GeneMark_model.39120_t
Valid prediction for snap_scaffold_9-snap.1331-T1
Valid prediction for Augustus_model.g15234.t1
Valid prediction for GlimmerHMM_glimmerT_22787-T1
Valid prediction for Augustus_model.g15237.t1
Valid prediction for snap_scaffold_9-snap.1343-T1
Valid prediction for GlimmerHMM_glimmerT_22792-T1
Valid prediction for snap_scaffold_9-snap.1354-T1
Valid prediction for GlimmerHMM_glimmerT_22804-T1
Valid prediction for GeneMark_model.39112_t
Valid prediction for GeneMark_model.39149_t
Valid prediction for snap_scaffold_9-snap.1352-T1
Valid prediction for GeneMark_model.39159_t
Couldn't classify 129564, 129830
Sorry, prediction pasa_asmbl_54075.p1 fails validation.
(ATG)	 CC	127640-127835	GT	AGG
(CCA)	 AG	128041-128517	GT	AGG
(GCC)	 AG	128655-128894	GT	AGG
(ATG)	 AG	129023-129132	GT	AGG
(AAT)	 AG	129364-129450	GT	AGG
(GAC)	 AG	129564-129830	GG	AAG
-recovered pasa_asmbl_54075.p1, initial, 127640, 127835
add_exon() Sorry, pasa_asmbl_54075.p1 129023-129132-initial-1 is invalid.
-recovered pasa_asmbl_54075.p1, initial, 129023, 129132
-recovered pasa_asmbl_54075.p1, internal, 128041, 128517
-recovered pasa_asmbl_54075.p1, internal, 128655, 128894
-recovered pasa_asmbl_54075.p1, internal, 129023, 129132
-recovered pasa_asmbl_54075.p1, internal, 129364, 129450
Valid prediction for GeneMark_model.39110_t
Valid prediction for GlimmerHMM_glimmerT_22784-T1
Valid prediction for snap_scaffold_9-snap.1327-T1
Valid prediction for snap_scaffold_9-snap.1346-T1
Valid prediction for GeneMark_model.39155_t
Valid prediction for Augustus_model.g15235.t1
Valid prediction for GlimmerHMM_glimmerT_22801-T1
Valid prediction for snap_scaffold_9-snap.1334-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.39116_t
Valid prediction for GlimmerHMM_glimmerT_22793-T1
Valid prediction for GeneMark_model.39139_t
Valid prediction for GlimmerHMM_glimmerT_22788-T1
Valid prediction for GlimmerHMM_glimmerT_22789-T1
Valid prediction for GeneMark_model.39135_t
Valid prediction for GeneMark_model.39137_t
Valid prediction for GeneMark_model.39150_t
Valid prediction for GeneMark_model.39124_t
Valid prediction for GeneMark_model.39121_t
Valid prediction for GeneMark_model.39141_t
Valid prediction for GeneMark_model.39131_t
Valid prediction for snap_scaffold_9-snap.1337-T1
Valid prediction for snap_scaffold_9-snap.1325-T1
Valid prediction for Augustus_model.g15230.t1
Valid prediction for GeneMark_model.39125_t
Couldn't classify 150821, 151501
Sorry, prediction pasa_asmbl_55012.p1 fails validation.
(CTC)	 AC	150821-151501	GC	CGG
Valid prediction for GlimmerHMM_glimmerT_22803-T1
Couldn't classify 156118, 156225
Couldn't classify 156268, 156417
Sorry, prediction CodingQuarry_transcript_62036-T1 fails validation.
(ATG)	 GT	156118-156225	AT	TCA
(ATC)	 TC	156268-156417	CC	AAC
Valid prediction for GlimmerHMM_glimmerT_22794-T1
Valid prediction for GeneMark_model.39142_t
Valid prediction for GeneMark_model.39153_t
Valid prediction for HiQ_model.g15240.t1
Valid prediction for GeneMark_model.39134_t
Valid prediction for snap_scaffold_9-snap.1350-T1
Valid prediction for GeneMark_model.39133_t
Valid prediction for GeneMark_model.39115_t
Valid prediction for GlimmerHMM_glimmerT_22778-T1
Valid prediction for Augustus_model.g15244.t1
Valid prediction for Augustus_model.g15238.t1
Valid prediction for GeneMark_model.39129_t
Valid prediction for GlimmerHMM_glimmerT_22795-T1
Valid prediction for GeneMark_model.39156_t
Valid prediction for GlimmerHMM_glimmerT_22775-T1
Valid prediction for snap_scaffold_9-snap.1349-T1
Valid prediction for Augustus_model.g15247.t1
Valid prediction for snap_scaffold_9-snap.1329-T1
Valid prediction for snap_scaffold_9-snap.1326-T1
Valid prediction for snap_scaffold_9-snap.1339-T1
Valid prediction for pasa_asmbl_55013.p1
Valid prediction for CodingQuarry_transcript_62040-T1
Valid prediction for GeneMark_model.39113_t
Valid prediction for GlimmerHMM_glimmerT_22782-T1
Valid prediction for GeneMark_model.39152_t
Valid prediction for GeneMark_model.39145_t
Valid prediction for GeneMark_model.39118_t
Valid prediction for GeneMark_model.39111_t
Valid prediction for GeneMark_model.39109_t
Valid prediction for GlimmerHMM_glimmerT_22802-T1
Valid prediction for GeneMark_model.39126_t
Valid prediction for snap_scaffold_9-snap.1324-T1
Valid prediction for snap_scaffold_9-snap.1347-T1
Valid prediction for snap_scaffold_9-snap.1340-T1
Valid prediction for GeneMark_model.39119_t
Valid prediction for snap_scaffold_9-snap.1344-T1
Valid prediction for snap_scaffold_9-snap.1351-T1
Valid prediction for GlimmerHMM_glimmerT_22780-T1
Valid prediction for Augustus_model.g15233.t1
Valid prediction for GlimmerHMM_glimmerT_22779-T1
Valid prediction for GeneMark_model.39154_t
Valid prediction for GlimmerHMM_glimmerT_22786-T1
Valid prediction for GeneMark_model.39122_t
Valid prediction for GlimmerHMM_glimmerT_22791-T1
Valid prediction for Augustus_model.g15231.t1
Valid prediction for GeneMark_model.39144_t
Valid prediction for GeneMark_model.39158_t
Valid prediction for snap_scaffold_9-snap.1322-T1
Valid prediction for snap_scaffold_9-snap.1336-T1
Valid prediction for GlimmerHMM_glimmerT_22776-T1
Couldn't classify 107318, 107369
Couldn't classify 107454, 107534
Sorry, prediction CodingQuarry_transcript_62039-T1 fails validation.
(ATG)	 AA	106498-106500	GT	TGG
(TCA)	 AG	106914-107010	GT	GAG
(TGA)	 AG	107185-107234	GC	AGG
(GAC)	 AG	107318-107369	AT	ATA
(TCA)	 AT	107454-107534	GT	TGG
(GAT)	 AG	107681-107754	GT	AGG
(GTT)	 AG	107867-107938	GG	GAG
-recovered CodingQuarry_transcript_62039-T1, initial, 106498, 106500
add_exon() Sorry, CodingQuarry_transcript_62039-T1 106914-107010-terminal-3 is invalid.
-recovered CodingQuarry_transcript_62039-T1, terminal, 106914, 107010
-recovered CodingQuarry_transcript_62039-T1, terminal, 107867, 107938
-recovered CodingQuarry_transcript_62039-T1, internal, 106914, 107010
-recovered CodingQuarry_transcript_62039-T1, internal, 107185, 107234
-recovered CodingQuarry_transcript_62039-T1, internal, 107681, 107754
Valid prediction for snap_scaffold_9-snap.1328-T1
Valid prediction for GlimmerHMM_glimmerT_22781-T1
Valid prediction for snap_scaffold_9-snap.1333-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 32426, rend_intergenic: 18064  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57033, rend_intergenic: 35420  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61933, rend_intergenic: 57786  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69047, rend_intergenic: 65879  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73425, rend_intergenic: 69479  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78076, rend_intergenic: 75043  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96046, rend_intergenic: 91418  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102905, rend_intergenic: 96847  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113234, rend_intergenic: 110466  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132990, rend_intergenic: 129638  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 231459
-exon list size: 667


building trellis

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95.8    
96.0    
96.1    
96.3    
96.4    
96.6    
96.7    
96.9    
97.0    
97.2    
97.3    
97.5    
97.6    
97.8    
97.9    
98.1    
98.2    
98.4    
98.5    
98.7    
98.8    
99.0    
99.1    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 40 predictions from path traversal
Error with prediction: snap lend_intergenic: 32426, rend_intergenic: 18064  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57033, rend_intergenic: 35420  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61933, rend_intergenic: 57786  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69047, rend_intergenic: 65879  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73425, rend_intergenic: 69479  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78076, rend_intergenic: 75043  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96046, rend_intergenic: 91418  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102905, rend_intergenic: 96847  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113234, rend_intergenic: 110466  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132990, rend_intergenic: 129638  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support