-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_2548118-2736096

-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_6336-T1
Valid prediction for snap_scaffold_3-snap.607-T1
Valid prediction for GlimmerHMM_glimmerT_6324-T1
Valid prediction for snap_scaffold_3-snap.619-T1
Valid prediction for snap_scaffold_3-snap.591-T1
Valid prediction for snap_scaffold_3-snap.617-T1
Valid prediction for GlimmerHMM_glimmerT_6330-T1
Valid prediction for GlimmerHMM_glimmerT_6314-T1
Valid prediction for GeneMark_model.10372_t
Valid prediction for GlimmerHMM_glimmerT_6320-T1
Valid prediction for snap_scaffold_3-snap.584-T1
Valid prediction for GlimmerHMM_glimmerT_6319-T1
Valid prediction for snap_scaffold_3-snap.581-T1
Valid prediction for GeneMark_model.10378_t
Valid prediction for GlimmerHMM_glimmerT_6311-T1
Valid prediction for GeneMark_model.10394_t
Valid prediction for GeneMark_model.10399_t
Valid prediction for GlimmerHMM_glimmerT_6316-T1
Valid prediction for GeneMark_model.10385_t
Valid prediction for GlimmerHMM_glimmerT_6323-T1
Valid prediction for GeneMark_model.10351_t
Valid prediction for GeneMark_model.10368_t
Valid prediction for GeneMark_model.10375_t
Valid prediction for snap_scaffold_3-snap.594-T1
Couldn't classify 98475, 99374
Sorry, prediction pasa_asmbl_39865.p1 fails validation.
(GAC)	 TA	98475-99374	TT	AGT
Valid prediction for Augustus_model.g4139.t1
Valid prediction for GeneMark_model.10397_t
Valid prediction for Augustus_model.g4149.t1
Valid prediction for GeneMark_model.10400_t
Valid prediction for snap_scaffold_3-snap.612-T1
Valid prediction for GeneMark_model.10376_t
Valid prediction for GeneMark_model.10363_t
Valid prediction for snap_scaffold_3-snap.613-T1
Valid prediction for Augustus_model.g4145.t1
Valid prediction for GeneMark_model.10393_t
Valid prediction for GlimmerHMM_glimmerT_6335-T1
Valid prediction for snap_scaffold_3-snap.609-T1
Valid prediction for Augustus_model.g4142.t1
Couldn't classify 106645, 106827
Couldn't classify 107192, 107314
Sorry, prediction pasa_asmbl_40739.p1 fails validation.
(GGT)	 CA	106645-106827	GT	AGG
(AGA)	 AG	107192-107314	CC	CCC
Valid prediction for GeneMark_model.10388_t
Couldn't classify 75389, 75412
Couldn't classify 83657, 83763
Sorry, prediction pasa_asmbl_39864.p1 fails validation.
(GAC)	 AC	75389-75412	GT	AAG
(GTG)	 AG	75666-75788	GT	AGG
(GGC)	 AG	76836-76900	GT	AGG
(TGC)	 AG	78818-78901	GT	AGG
(GTA)	 AG	79307-79419	GT	AGG
(GCT)	 AG	79719-79779	GT	TAG
(CAA)	 AG	82663-82738	GT	TGG
(CTC)	 AG	83135-83264	GT	AGG
(ATG)	 AG	83471-83536	GT	CGG
(GGA)	 AG	83657-83763	CC	ACC
-recovered pasa_asmbl_39864.p1, initial, 83471, 83536
-recovered pasa_asmbl_39864.p1, internal, 75666, 75788
-recovered pasa_asmbl_39864.p1, internal, 76836, 76900
-recovered pasa_asmbl_39864.p1, internal, 78818, 78901
-recovered pasa_asmbl_39864.p1, internal, 79307, 79419
-recovered pasa_asmbl_39864.p1, internal, 79719, 79779
-recovered pasa_asmbl_39864.p1, internal, 82663, 82738
-recovered pasa_asmbl_39864.p1, internal, 83135, 83264
-recovered pasa_asmbl_39864.p1, internal, 83471, 83536
Valid prediction for GlimmerHMM_glimmerT_6325-T1
Valid prediction for GlimmerHMM_glimmerT_6327-T1
Valid prediction for GlimmerHMM_glimmerT_6338-T1
Valid prediction for GlimmerHMM_glimmerT_6332-T1
Valid prediction for GeneMark_model.10354_t
Valid prediction for GeneMark_model.10353_t
Valid prediction for GeneMark_model.10356_t
Valid prediction for snap_scaffold_3-snap.604-T1
Valid prediction for GeneMark_model.10383_t
Valid prediction for Augustus_model.g4144.t1
Valid prediction for pasa_asmbl_39869.p1
Valid prediction for Augustus_model.g4141.t1
Valid prediction for snap_scaffold_3-snap.585-T1
Valid prediction for snap_scaffold_3-snap.596-T1
Valid prediction for GlimmerHMM_glimmerT_6321-T1
Valid prediction for GeneMark_model.10391_t
Valid prediction for GeneMark_model.10387_t
Valid prediction for GeneMark_model.10380_t
Valid prediction for snap_scaffold_3-snap.620-T1
Valid prediction for GeneMark_model.10396_t
Valid prediction for GlimmerHMM_glimmerT_6339-T1
Valid prediction for GeneMark_model.10358_t
Valid prediction for snap_scaffold_3-snap.601-T1
Valid prediction for GeneMark_model.10370_t
Valid prediction for snap_scaffold_3-snap.589-T1
Valid prediction for snap_scaffold_3-snap.587-T1
Valid prediction for GlimmerHMM_glimmerT_6329-T1
Valid prediction for GeneMark_model.10364_t
Valid prediction for GeneMark_model.10360_t
Valid prediction for GeneMark_model.10373_t
Valid prediction for GlimmerHMM_glimmerT_6341-T1
Valid prediction for GeneMark_model.10366_t
Valid prediction for snap_scaffold_3-snap.592-T1
Valid prediction for GeneMark_model.10390_t
Valid prediction for snap_scaffold_3-snap.578-T1
Valid prediction for GlimmerHMM_glimmerT_6337-T1
Valid prediction for snap_scaffold_3-snap.582-T1
Valid prediction for snap_scaffold_3-snap.598-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.10395_t
Valid prediction for GeneMark_model.10379_t
Valid prediction for Augustus_model.g4148.t1
Valid prediction for GlimmerHMM_glimmerT_6317-T1
Valid prediction for GeneMark_model.10369_t
Valid prediction for GlimmerHMM_glimmerT_6328-T1
Valid prediction for GeneMark_model.10381_t
Valid prediction for snap_scaffold_3-snap.600-T1
Valid prediction for GeneMark_model.10367_t
Valid prediction for GeneMark_model.10357_t
Valid prediction for GlimmerHMM_glimmerT_6313-T1
Valid prediction for Augustus_model.g4147.t1
Valid prediction for snap_scaffold_3-snap.593-T1
Valid prediction for GlimmerHMM_glimmerT_6310-T1
Valid prediction for snap_scaffold_3-snap.590-T1
Valid prediction for GlimmerHMM_glimmerT_6309-T1
Valid prediction for snap_scaffold_3-snap.608-T1
Valid prediction for GeneMark_model.10365_t
Valid prediction for GeneMark_model.10384_t
Valid prediction for snap_scaffold_3-snap.618-T1
Valid prediction for GeneMark_model.10359_t
Valid prediction for snap_scaffold_3-snap.595-T1
Valid prediction for Augustus_model.g4140.t1
Valid prediction for GeneMark_model.10362_t
Valid prediction for GeneMark_model.10382_t
Valid prediction for snap_scaffold_3-snap.610-T1
Valid prediction for snap_scaffold_3-snap.621-T1
Valid prediction for snap_scaffold_3-snap.586-T1
Valid prediction for GlimmerHMM_glimmerT_6333-T1
Valid prediction for GlimmerHMM_glimmerT_6312-T1
Valid prediction for GlimmerHMM_glimmerT_6334-T1
Valid prediction for snap_scaffold_3-snap.579-T1
Valid prediction for snap_scaffold_3-snap.614-T1
Valid prediction for GeneMark_model.10352_t
Valid prediction for snap_scaffold_3-snap.605-T1
Valid prediction for Augustus_model.g4151.t1
Valid prediction for GlimmerHMM_glimmerT_6340-T1
Valid prediction for snap_scaffold_3-snap.588-T1
Valid prediction for snap_scaffold_3-snap.583-T1
Valid prediction for snap_scaffold_3-snap.615-T1
Valid prediction for GlimmerHMM_glimmerT_6331-T1
Valid prediction for GlimmerHMM_glimmerT_6318-T1
Valid prediction for snap_scaffold_3-snap.603-T1
Valid prediction for snap_scaffold_3-snap.599-T1
Valid prediction for GeneMark_model.10386_t
Valid prediction for GeneMark_model.10374_t
Valid prediction for snap_scaffold_3-snap.611-T1
Valid prediction for GeneMark_model.10392_t
Valid prediction for GeneMark_model.10361_t
Valid prediction for GeneMark_model.10377_t
Valid prediction for GeneMark_model.10398_t
Valid prediction for Augustus_model.g4150.t1
Valid prediction for GeneMark_model.10389_t
Valid prediction for Augustus_model.g4146.t1
Valid prediction for GeneMark_model.10355_t
Valid prediction for Augustus_model.g4143.t1
Valid prediction for snap_scaffold_3-snap.577-T1
Valid prediction for snap_scaffold_3-snap.616-T1
Valid prediction for GlimmerHMM_glimmerT_6326-T1
Valid prediction for GlimmerHMM_glimmerT_6322-T1
Valid prediction for GeneMark_model.10371_t
Valid prediction for GlimmerHMM_glimmerT_6315-T1
Valid prediction for snap_scaffold_3-snap.580-T1
Valid prediction for snap_scaffold_3-snap.602-T1
Valid prediction for snap_scaffold_3-snap.606-T1
Valid prediction for snap_scaffold_3-snap.597-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 19301, rend_intergenic: 13949  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24997, rend_intergenic: 19330  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26561, rend_intergenic: 25007  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34657, rend_intergenic: 32540  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43991, rend_intergenic: 41262  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46689, rend_intergenic: 46212  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50519, rend_intergenic: 47093  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60887, rend_intergenic: 53673  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68154, rend_intergenic: 60995  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71123, rend_intergenic: 70107  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80031, rend_intergenic: 75651  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83226, rend_intergenic: 80077  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91539, rend_intergenic: 83604  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94197, rend_intergenic: 91589  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104060, rend_intergenic: 94313  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122591, rend_intergenic: 111796  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136720, rend_intergenic: 133034  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171051, rend_intergenic: 169501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 187979
-exon list size: 730


building trellis

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89.5    
89.6    
89.8    
89.9    
90.0    
90.2    
90.3    
90.4    
90.6    
90.7    
90.8    
91.0    
91.1    
91.3    
91.4    
91.5    
91.7    
91.8    
91.9    
92.1    
92.2    
92.3    
92.5    
92.6    
92.8    
92.9    
93.0    
93.2    
93.3    
93.4    
93.6    
93.7    
93.9    
94.0    
94.1    
94.3    
94.4    
94.5    
94.7    
94.8    
94.9    
95.1    
95.2    
95.4    
95.5    
95.6    
95.8    
95.9    
96.0    
96.2    
96.3    
96.4    
96.6    
96.7    
96.9    
97.0    
97.1    
97.3    
97.4    
97.5    
97.7    
97.8    
98.0    
98.1    
98.2    
98.4    
98.5    
98.6    
98.8    
98.9    
99.0    
99.2    
99.3    
99.5    
99.6    
99.7    
99.9    
-found 40 predictions from path traversal
Error with prediction: snap lend_intergenic: 19301, rend_intergenic: 13949  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24997, rend_intergenic: 19330  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26561, rend_intergenic: 25007  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34657, rend_intergenic: 32540  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43991, rend_intergenic: 41262  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46689, rend_intergenic: 46212  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50519, rend_intergenic: 47093  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60887, rend_intergenic: 53673  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68154, rend_intergenic: 60995  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71123, rend_intergenic: 70107  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80031, rend_intergenic: 75651  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83226, rend_intergenic: 80077  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91539, rend_intergenic: 83604  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94197, rend_intergenic: 91589  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104060, rend_intergenic: 94313  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122591, rend_intergenic: 111796  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136720, rend_intergenic: 133034  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171051, rend_intergenic: 169501  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