-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_14/scaffold_14_6803354-6965491

-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_34847-T1
Valid prediction for GeneMark_model.59649_t
Valid prediction for GeneMark_model.59679_t
Valid prediction for snap_scaffold_14-snap.1425-T1
Valid prediction for snap_scaffold_14-snap.1439-T1
Valid prediction for GlimmerHMM_glimmerT_34846-T1
Valid prediction for GeneMark_model.59678_t
Valid prediction for snap_scaffold_14-snap.1434-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_14-snap.1409-T1
Valid prediction for pasa_asmbl_12084.p1
Valid prediction for GeneMark_model.59664_t
Valid prediction for snap_scaffold_14-snap.1410-T1
Valid prediction for GeneMark_model.59667_t
Valid prediction for GlimmerHMM_glimmerT_34855-T1
Valid prediction for snap_scaffold_14-snap.1438-T1
Valid prediction for snap_scaffold_14-snap.1417-T1
Valid prediction for HiQ_model.g23418.t1
Valid prediction for snap_scaffold_14-snap.1443-T1
Valid prediction for CodingQuarry_transcript_15639-T1
Valid prediction for GeneMark_model.59646_t
Valid prediction for GlimmerHMM_glimmerT_34860-T1
Valid prediction for CodingQuarry_transcript_15640-T1
Valid prediction for snap_scaffold_14-snap.1415-T1
Valid prediction for GeneMark_model.59672_t
Valid prediction for Augustus_model.g23414.t1
Valid prediction for GeneMark_model.59674_t
Valid prediction for GlimmerHMM_glimmerT_34851-T1
Valid prediction for HiQ_model.g23430.t1
Valid prediction for snap_scaffold_14-snap.1437-T1
Valid prediction for GlimmerHMM_glimmerT_34842-T1
Valid prediction for HiQ_model.g23426.t1
Valid prediction for CodingQuarry_transcript_15643-T1
Valid prediction for GlimmerHMM_glimmerT_34856-T1
Valid prediction for CodingQuarry_transcript_15642-T1
Valid prediction for GlimmerHMM_glimmerT_34853-T1
Valid prediction for GeneMark_model.59647_t
Valid prediction for snap_scaffold_14-snap.1412-T1
Valid prediction for GlimmerHMM_glimmerT_34854-T1
Valid prediction for GeneMark_model.59661_t
Valid prediction for GlimmerHMM_glimmerT_34833-T1
Valid prediction for GeneMark_model.59676_t
Valid prediction for snap_scaffold_14-snap.1430-T1
Valid prediction for GlimmerHMM_glimmerT_34832-T1
Valid prediction for GeneMark_model.59658_t
Valid prediction for HiQ_model.g23431.t1
Valid prediction for GeneMark_model.59644_t
Valid prediction for snap_scaffold_14-snap.1421-T1
Valid prediction for GeneMark_model.59642_t
Valid prediction for GeneMark_model.59670_t
Valid prediction for HiQ_model.g23422.t1
Valid prediction for Augustus_model.g23432.t1
Valid prediction for GlimmerHMM_glimmerT_34838-T1
Valid prediction for GlimmerHMM_glimmerT_34831-T1
Valid prediction for pasa_asmbl_12085.p1
Couldn't classify 98088, 98195
Couldn't classify 106187, 106347
Sorry, prediction pasa_asmbl_12091.p1 fails validation.
(CAG)	 CA	98088-98195	GT	ACG
(TCC)	 AG	98571-98603	GT	AGG
(AAA)	 AG	99084-99160	GT	GGG
(GAA)	 AG	99694-99805	GT	AGG
(GTG)	 AG	100099-100175	GT	AGG
(ATG)	 AG	100543-100660	GT	AGG
(GAC)	 AG	100914-100982	GT	TGG
(CTC)	 AG	101178-101259	GT	AGG
(ACT)	 AG	102036-102163	GT	AGG
(GGT)	 AG	103030-103141	GT	TGG
(GAG)	 AG	103245-103326	GT	AAG
(TGT)	 AG	103436-103516	GT	AGG
(GTA)	 AG	103933-104046	GT	GGG
(CAC)	 AG	104152-104243	GT	AGG
(ACG)	 AG	104359-104515	GT	AGG
(CAA)	 AG	105925-106076	GT	AGG
(GTA)	 AG	106187-106347	AG	CCA
add_exon() Sorry, pasa_asmbl_12091.p1 100543-100660-initial-1 is invalid.
-recovered pasa_asmbl_12091.p1, initial, 100543, 100660
-recovered pasa_asmbl_12091.p1, internal, 98571, 98603
-recovered pasa_asmbl_12091.p1, internal, 99084, 99160
-recovered pasa_asmbl_12091.p1, internal, 99694, 99805
-recovered pasa_asmbl_12091.p1, internal, 100099, 100175
-recovered pasa_asmbl_12091.p1, internal, 100543, 100660
-recovered pasa_asmbl_12091.p1, internal, 100914, 100982
-recovered pasa_asmbl_12091.p1, internal, 101178, 101259
-recovered pasa_asmbl_12091.p1, internal, 102036, 102163
-recovered pasa_asmbl_12091.p1, internal, 103030, 103141
-recovered pasa_asmbl_12091.p1, internal, 103245, 103326
-recovered pasa_asmbl_12091.p1, internal, 103436, 103516
-recovered pasa_asmbl_12091.p1, internal, 103933, 104046
-recovered pasa_asmbl_12091.p1, internal, 104152, 104243
-recovered pasa_asmbl_12091.p1, internal, 104359, 104515
-recovered pasa_asmbl_12091.p1, internal, 105925, 106076
Valid prediction for GeneMark_model.59652_t
Valid prediction for snap_scaffold_14-snap.1418-T1
Valid prediction for snap_scaffold_14-snap.1435-T1
Valid prediction for snap_scaffold_14-snap.1413-T1
Valid prediction for Augustus_model.g23415.t1
Valid prediction for GeneMark_model.59668_t
Valid prediction for snap_scaffold_14-snap.1414-T1
Valid prediction for pasa_asmbl_12097.p1
Valid prediction for GeneMark_model.59682_t
Valid prediction for pasa_asmbl_12101.p1

-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.59656_t
Valid prediction for GlimmerHMM_glimmerT_34858-T1
Valid prediction for GeneMark_model.59677_t
Valid prediction for snap_scaffold_14-snap.1420-T1
Valid prediction for GeneMark_model.59662_t
Valid prediction for GeneMark_model.59681_t
Valid prediction for snap_scaffold_14-snap.1429-T1
Valid prediction for GeneMark_model.59660_t
Valid prediction for GlimmerHMM_glimmerT_34844-T1
Valid prediction for Augustus_model.g23420.t1
Valid prediction for snap_scaffold_14-snap.1436-T1
Valid prediction for snap_scaffold_14-snap.1427-T1
Valid prediction for GlimmerHMM_glimmerT_34848-T1
Valid prediction for GeneMark_model.59650_t
Valid prediction for pasa_asmbl_13149.p1
Valid prediction for snap_scaffold_14-snap.1411-T1
Valid prediction for Augustus_model.g23419.t1
Valid prediction for Augustus_model.g23423.t1
Valid prediction for GlimmerHMM_glimmerT_34859-T1
Valid prediction for snap_scaffold_14-snap.1432-T1
Valid prediction for GlimmerHMM_glimmerT_34852-T1
Valid prediction for snap_scaffold_14-snap.1442-T1
Valid prediction for GlimmerHMM_glimmerT_34850-T1
Valid prediction for GlimmerHMM_glimmerT_34840-T1
Valid prediction for GeneMark_model.59648_t
Valid prediction for snap_scaffold_14-snap.1419-T1
Valid prediction for pasa_asmbl_13147.p1
Valid prediction for Augustus_model.g23417.t1
Couldn't classify 14746, 14786
Couldn't classify 15628, 15735
Sorry, prediction pasa_asmbl_13151.p1 fails validation.
(ACA)	 AC	14746-14786	GT	AGG
(GTC)	 AG	14956-15031	GT	AGG
(GCA)	 AG	15386-15538	GT	CGG
(GGA)	 AG	15628-15735	TT	AGT
-recovered pasa_asmbl_13151.p1, internal, 14956, 15031
-recovered pasa_asmbl_13151.p1, internal, 15386, 15538
Valid prediction for GlimmerHMM_glimmerT_34835-T1
Valid prediction for GeneMark_model.59653_t
Valid prediction for GeneMark_model.59671_t
Valid prediction for Augustus_model.g23416.t1
Valid prediction for GlimmerHMM_glimmerT_34843-T1
Valid prediction for Augustus_model.g23413.t1
Valid prediction for Augustus_model.g23427.t1
Valid prediction for GlimmerHMM_glimmerT_34839-T1
Valid prediction for HiQ_model.g23424.t1
Valid prediction for GlimmerHMM_glimmerT_34834-T1
Valid prediction for snap_scaffold_14-snap.1428-T1
Valid prediction for Augustus_model.g23428.t1
Valid prediction for snap_scaffold_14-snap.1423-T1
Valid prediction for snap_scaffold_14-snap.1416-T1
Valid prediction for GeneMark_model.59666_t
Valid prediction for Augustus_model.g23434.t1
Valid prediction for snap_scaffold_14-snap.1424-T1
Valid prediction for GeneMark_model.59657_t
Valid prediction for Augustus_model.g23429.t1
Valid prediction for GlimmerHMM_glimmerT_34837-T1
Valid prediction for GlimmerHMM_glimmerT_34836-T1
Valid prediction for GeneMark_model.59673_t
Valid prediction for GeneMark_model.59669_t
Valid prediction for snap_scaffold_14-snap.1431-T1
Valid prediction for GeneMark_model.59654_t
Valid prediction for HiQ_model.g23433.t1
Valid prediction for Augustus_model.g23425.t1
Valid prediction for snap_scaffold_14-snap.1426-T1
Valid prediction for GeneMark_model.59655_t
Valid prediction for GeneMark_model.59651_t
Valid prediction for GeneMark_model.59659_t
Valid prediction for GeneMark_model.59665_t
Valid prediction for snap_scaffold_14-snap.1441-T1
Valid prediction for GlimmerHMM_glimmerT_34830-T1
Valid prediction for snap_scaffold_14-snap.1433-T1
Valid prediction for GeneMark_model.59663_t
Valid prediction for GlimmerHMM_glimmerT_34857-T1
Valid prediction for snap_scaffold_14-snap.1422-T1
Valid prediction for GeneMark_model.59645_t
Valid prediction for GeneMark_model.59675_t
Valid prediction for GeneMark_model.59643_t
Valid prediction for GlimmerHMM_glimmerT_34841-T1
Valid prediction for HiQ_model.g23421.t1
Valid prediction for snap_scaffold_14-snap.1440-T1
Valid prediction for CodingQuarry_transcript_15641-T1
Valid prediction for snap_scaffold_14-snap.1408-T1
Valid prediction for GlimmerHMM_glimmerT_34849-T1
Valid prediction for GeneMark_model.59680_t
Valid prediction for GlimmerHMM_glimmerT_34845-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13870, rend_intergenic: 5694  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40444, rend_intergenic: 22673  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57484, rend_intergenic: 41283  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66139, rend_intergenic: 62743  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111497, rend_intergenic: 98039  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132564, rend_intergenic: 118355  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 162138
-exon list size: 624


building trellis

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98.4    
98.6    
98.7    
98.9    
99.0    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 13870, rend_intergenic: 5694  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40444, rend_intergenic: 22673  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57484, rend_intergenic: 41283  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66139, rend_intergenic: 62743  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111497, rend_intergenic: 98039  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132564, rend_intergenic: 118355  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support