-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_5/scaffold_5_17129395-17341869

-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_13478-T1
Valid prediction for Augustus_model.g8973.t1
Valid prediction for CodingQuarry_transcript_52432-T1
Valid prediction for GlimmerHMM_glimmerT_13491-T1
Couldn't classify 204988, 205152
Sorry, prediction pasa_asmbl_46172.p1 fails validation.
(ATG)	 TC	202953-203089	GT	AAG
(GGA)	 AG	204096-204240	GT	AGG
(GGG)	 AG	204428-204571	GT	AGG
(CTG)	 AG	204988-205152	AA	ACA
-recovered pasa_asmbl_46172.p1, initial, 202953, 203089
-recovered pasa_asmbl_46172.p1, internal, 204096, 204240
-recovered pasa_asmbl_46172.p1, internal, 204428, 204571
Valid prediction for Augustus_model.g8958.t1
Valid prediction for GlimmerHMM_glimmerT_13470-T1
Valid prediction for pasa_asmbl_46159.p1
Couldn't classify 202233, 202348
Sorry, prediction pasa_asmbl_46170.p1 fails validation.
(ATG)	 CA	198077-198109	GT	AGG
(GTC)	 AG	198389-198413	GT	TGG
(ATA)	 AG	200044-200140	GT	AGG
(CGA)	 AG	200532-200655	GT	AGG
(AAC)	 AG	200793-200851	GT	AGG
(GGA)	 AG	201145-201264	GT	GAG
(ATT)	 AG	201390-201486	GC	AGG
(GAC)	 AG	201594-201679	GT	TGG
(GTG)	 AG	201880-201995	GT	CGG
(GCA)	 AG	202233-202348	AG	GGA
-recovered pasa_asmbl_46170.p1, initial, 198077, 198109
-recovered pasa_asmbl_46170.p1, internal, 198389, 198413
-recovered pasa_asmbl_46170.p1, internal, 200044, 200140
-recovered pasa_asmbl_46170.p1, internal, 200532, 200655
-recovered pasa_asmbl_46170.p1, internal, 200793, 200851
-recovered pasa_asmbl_46170.p1, internal, 201145, 201264
-recovered pasa_asmbl_46170.p1, internal, 201390, 201486
-recovered pasa_asmbl_46170.p1, internal, 201594, 201679
-recovered pasa_asmbl_46170.p1, internal, 201880, 201995
Valid prediction for snap_scaffold_5-snap.3210-T1
Valid prediction for GlimmerHMM_glimmerT_13476-T1
Valid prediction for snap_scaffold_5-snap.3202-T1
Valid prediction for GlimmerHMM_glimmerT_13497-T1
Valid prediction for Augustus_model.g8960.t1
Valid prediction for snap_scaffold_5-snap.3205-T1
Valid prediction for GlimmerHMM_glimmerT_13492-T1
Valid prediction for snap_scaffold_5-snap.3174-T1
Valid prediction for snap_scaffold_5-snap.3181-T1
Valid prediction for snap_scaffold_5-snap.3214-T1
Valid prediction for GlimmerHMM_glimmerT_13487-T1
Couldn't classify 62857, 62988
Sorry, prediction pasa_asmbl_46141.p2 fails validation.
(ATG)	 CC	61967-61978	GT	AGG
(GGA)	 AG	62335-62437	GT	CGG
(GAG)	 AG	62645-62745	GT	TGG
(GGA)	 AG	62857-62988	CT	TCC
-recovered pasa_asmbl_46141.p2, initial, 61967, 61978
-recovered pasa_asmbl_46141.p2, internal, 62335, 62437
-recovered pasa_asmbl_46141.p2, internal, 62645, 62745
Valid prediction for GlimmerHMM_glimmerT_13480-T1
Valid prediction for pasa_asmbl_46147.p1
Valid prediction for Augustus_model.g8955.t1
Valid prediction for snap_scaffold_5-snap.3204-T1
Valid prediction for snap_scaffold_5-snap.3196-T1
Valid prediction for snap_scaffold_5-snap.3190-T1
Valid prediction for GlimmerHMM_glimmerT_13486-T1
Valid prediction for Augustus_model.g8975.t1
Valid prediction for GlimmerHMM_glimmerT_13471-T1
Valid prediction for snap_scaffold_5-snap.3188-T1
Valid prediction for GlimmerHMM_glimmerT_13469-T1
Valid prediction for GlimmerHMM_glimmerT_13466-T1
Couldn't classify 118019, 118304
Sorry, prediction pasa_asmbl_46155.p1 fails validation.
(CAG)	 AG	118019-118304	GT	AGG
(AGG)	 AG	118766-118832	GT	GAG
(ACC)	 AG	119480-119552	GT	AGG
(GTC)	 AG	120275-120435	GT	GGG
(AGT)	 AG	120584-120699	GT	GGG
(GAC)	 AG	121868-121938	GT	AGG
(CAT)	 AG	122443-122595	GT	CGG
(TGG)	 AG	122708-122808	GT	CGG
(GGA)	 AG	122926-123034	GT	AGG
(GAA)	 AG	123135-123226	GT	ATG
(GAT)	 AG	123584-123699	GT	AGG
(ACC)	 AG	123939-124078	GT	AGG
(GAA)	 AG	124395-124487	GT	ATG
(GTC)	 AG	124623-124727	GT	AGG
(GTG)	 AG	124931-125068	GT	AGG
(GAC)	 AG	126520-126699	GA	AAG
-recovered pasa_asmbl_46155.p1, terminal, 126520, 126699
-recovered pasa_asmbl_46155.p1, internal, 118019, 118304
-recovered pasa_asmbl_46155.p1, internal, 118766, 118832
-recovered pasa_asmbl_46155.p1, internal, 119480, 119552
-recovered pasa_asmbl_46155.p1, internal, 120275, 120435
-recovered pasa_asmbl_46155.p1, internal, 120584, 120699
-recovered pasa_asmbl_46155.p1, internal, 121868, 121938
-recovered pasa_asmbl_46155.p1, internal, 122443, 122595
-recovered pasa_asmbl_46155.p1, internal, 122708, 122808
-recovered pasa_asmbl_46155.p1, internal, 122926, 123034
-recovered pasa_asmbl_46155.p1, internal, 123135, 123226
-recovered pasa_asmbl_46155.p1, internal, 123584, 123699
-recovered pasa_asmbl_46155.p1, internal, 123939, 124078
-recovered pasa_asmbl_46155.p1, internal, 124395, 124487
-recovered pasa_asmbl_46155.p1, internal, 124623, 124727
-recovered pasa_asmbl_46155.p1, internal, 124931, 125068
Valid prediction for Augustus_model.g8966.t1
Valid prediction for snap_scaffold_5-snap.3176-T1
Valid prediction for snap_scaffold_5-snap.3211-T1
Valid prediction for CodingQuarry_transcript_52431-T1
Valid prediction for GlimmerHMM_glimmerT_13481-T1
Valid prediction for snap_scaffold_5-snap.3194-T1
Valid prediction for HiQ_model.g8972.t1
Valid prediction for snap_scaffold_5-snap.3193-T1
Couldn't classify 191303, 192949
Sorry, prediction pasa_asmbl_46164.p1 fails validation.
(ATA)	 AG	191303-192949	AT	CCA
Valid prediction for GlimmerHMM_glimmerT_13494-T1
Valid prediction for GlimmerHMM_glimmerT_13485-T1
Valid prediction for GlimmerHMM_glimmerT_13479-T1
Couldn't classify 62335, 62437
Couldn't classify 65440, 65571
Sorry, prediction pasa_asmbl_46143.p2 fails validation.
(GGA)	 AG	62335-62437	GT	CGG
(GAG)	 AG	62645-62745	GT	TGG
(GGA)	 AG	65440-65571	CT	TCC
-recovered pasa_asmbl_46143.p2, internal, 62335, 62437
-recovered pasa_asmbl_46143.p2, internal, 62645, 62745
Valid prediction for snap_scaffold_5-snap.3209-T1
Valid prediction for Augustus_model.g8961.t1
Valid prediction for snap_scaffold_5-snap.3213-T1
Couldn't classify 190331, 190528
Couldn't classify 191054, 191293
Sorry, prediction pasa_asmbl_46163.p1 fails validation.
(CAA)	 AA	190331-190528	GT	AGG
(CAA)	 AG	190671-190901	GT	AGG
(ATG)	 AG	191054-191293	CA	CCC
-recovered pasa_asmbl_46163.p1, internal, 190671, 190901
Valid prediction for snap_scaffold_5-snap.3180-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for Augustus_model.g8965.t1
Couldn't classify 206020, 206134
Sorry, prediction pasa_asmbl_46173.p1 fails validation.
(ACG)	 AG	206020-206134	GT	CTG
(CGG)	 AG	206501-206628	GT	AGG
(ATA)	 AG	206866-206960	GT	AAG
(GGC)	 AG	207368-207517	GT	TGG
(GTG)	 AG	208814-208916	AT	AAA
-recovered pasa_asmbl_46173.p1, terminal, 208814, 208916
-recovered pasa_asmbl_46173.p1, internal, 206020, 206134
-recovered pasa_asmbl_46173.p1, internal, 206501, 206628
-recovered pasa_asmbl_46173.p1, internal, 206866, 206960
-recovered pasa_asmbl_46173.p1, internal, 207368, 207517
Valid prediction for snap_scaffold_5-snap.3198-T1
Valid prediction for snap_scaffold_5-snap.3207-T1
Valid prediction for GlimmerHMM_glimmerT_13495-T1
Couldn't classify 192953, 193952
Sorry, prediction pasa_asmbl_46165.p1 fails validation.
(CTA)	 TC	192953-193952	GT	AGG
(CTC)	 AG	194148-194204	GT	TGG
(ACG)	 AG	194327-194354	GT	GGG
(ATG)	 AG	195596-195637	GT	AGG
(GGT)	 AG	195918-196051	GT	AGG
(AAA)	 AG	197088-197134	GC	AGG
-recovered pasa_asmbl_46165.p1, initial, 195596, 195637
-recovered pasa_asmbl_46165.p1, terminal, 197088, 197134
-recovered pasa_asmbl_46165.p1, internal, 194148, 194204
-recovered pasa_asmbl_46165.p1, internal, 194327, 194354
-recovered pasa_asmbl_46165.p1, internal, 195596, 195637
-recovered pasa_asmbl_46165.p1, internal, 195918, 196051
-recovered pasa_asmbl_46165.p1, internal, 197088, 197134
Valid prediction for CodingQuarry_transcript_52433-T1
Valid prediction for HiQ_model.g8967.t1
Valid prediction for snap_scaffold_5-snap.3192-T1
Valid prediction for GlimmerHMM_glimmerT_13498-T1
Valid prediction for snap_scaffold_5-snap.3197-T1
Valid prediction for Augustus_model.g8971.t1
Valid prediction for GlimmerHMM_glimmerT_13496-T1
Valid prediction for GlimmerHMM_glimmerT_13474-T1
Valid prediction for snap_scaffold_5-snap.3200-T1
Valid prediction for snap_scaffold_5-snap.3184-T1
Couldn't classify 185913, 185944
Sorry, prediction pasa_asmbl_46162.p1 fails validation.
(ATG)	 AG	185435-185726	GT	GGG
(ACT)	 AG	185913-185944	TG	CGT
-recovered pasa_asmbl_46162.p1, initial, 185435, 185726
-recovered pasa_asmbl_46162.p1, internal, 185435, 185726
Valid prediction for snap_scaffold_5-snap.3177-T1
Couldn't classify 43967, 44142
Couldn't classify 45564, 45629
Sorry, prediction pasa_asmbl_46139.p1 fails validation.
(GCA)	 TG	43967-44142	GT	AGG
(GGT)	 AG	44851-45036	GT	AGG
(GTA)	 AG	45377-45467	GT	AGG
(GCT)	 AG	45564-45629	AC	GGA
-recovered pasa_asmbl_46139.p1, internal, 44851, 45036
-recovered pasa_asmbl_46139.p1, internal, 45377, 45467
Valid prediction for GlimmerHMM_glimmerT_13484-T1
Valid prediction for Augustus_model.g8974.t1
Valid prediction for snap_scaffold_5-snap.3189-T1
Valid prediction for HiQ_model.g8964.t1
Valid prediction for snap_scaffold_5-snap.3195-T1
Valid prediction for Augustus_model.g8956.t1
Valid prediction for GlimmerHMM_glimmerT_13468-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 snap_scaffold_5-snap.3212-T1
Valid prediction for Augustus_model.g8970.t1
Valid prediction for GlimmerHMM_glimmerT_13483-T1
Valid prediction for snap_scaffold_5-snap.3182-T1
Valid prediction for snap_scaffold_5-snap.3187-T1
Valid prediction for GlimmerHMM_glimmerT_13475-T1
Valid prediction for snap_scaffold_5-snap.3186-T1
Valid prediction for GlimmerHMM_glimmerT_13467-T1
Valid prediction for GlimmerHMM_glimmerT_13482-T1
Valid prediction for GlimmerHMM_glimmerT_13472-T1
Valid prediction for CodingQuarry_transcript_52429-T1
Valid prediction for snap_scaffold_5-snap.3208-T1
Valid prediction for GlimmerHMM_glimmerT_13489-T1
Valid prediction for GlimmerHMM_glimmerT_13488-T1
Valid prediction for snap_scaffold_5-snap.3185-T1
Valid prediction for snap_scaffold_5-snap.3206-T1
Couldn't classify 130214, 130603
Sorry, prediction pasa_asmbl_44798.p1 fails validation.
(AAT)	 AG	130214-130603	GT	ACG
(ATT)	 AG	130918-130972	GT	AGG
(TAT)	 AG	131254-131435	TA	AGT
-recovered pasa_asmbl_44798.p1, terminal, 131254, 131435
-recovered pasa_asmbl_44798.p1, internal, 130214, 130603
-recovered pasa_asmbl_44798.p1, internal, 130918, 130972
Valid prediction for Augustus_model.g8962.t1
Valid prediction for HiQ_model.g8963.t1
Valid prediction for Augustus_model.g8957.t1
Valid prediction for Augustus_model.g8969.t1
Valid prediction for GlimmerHMM_glimmerT_13473-T1
Valid prediction for snap_scaffold_5-snap.3191-T1
Valid prediction for snap_scaffold_5-snap.3179-T1
Valid prediction for GlimmerHMM_glimmerT_13493-T1
Valid prediction for GlimmerHMM_glimmerT_13490-T1
Valid prediction for snap_scaffold_5-snap.3173-T1
Valid prediction for snap_scaffold_5-snap.3203-T1
Valid prediction for snap_scaffold_5-snap.3175-T1
Valid prediction for Augustus_model.g8954.t1
Valid prediction for GlimmerHMM_glimmerT_13477-T1
Valid prediction for snap_scaffold_5-snap.3183-T1
Valid prediction for snap_scaffold_5-snap.3178-T1
Valid prediction for Augustus_model.g8959.t1
Valid prediction for pasa_asmbl_44795.p1
Valid prediction for snap_scaffold_5-snap.3215-T1
Valid prediction for Augustus_model.g8968.t1
Valid prediction for CodingQuarry_transcript_52430-T1
Valid prediction for snap_scaffold_5-snap.3199-T1
Valid prediction for snap_scaffold_5-snap.3201-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 5705, rend_intergenic: 2909  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44950, rend_intergenic: 39807  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55600, rend_intergenic: 51551  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63743, rend_intergenic: 60031  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66197, rend_intergenic: 65118  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88485, rend_intergenic: 82952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96392, rend_intergenic: 94191  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138577, rend_intergenic: 134086  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141172, rend_intergenic: 139311  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146697, rend_intergenic: 141650  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161624, rend_intergenic: 155895  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194358, rend_intergenic: 187041  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 208916, rend_intergenic: 201141  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 212475
-exon list size: 485


building trellis

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78.4    
78.6    
78.9    
79.1    
79.3    
79.5    
79.7    
79.9    
80.1    
80.3    
80.5    
80.7    
80.9    
81.1    
81.3    
81.5    
81.7    
81.9    
82.1    
82.3    
82.5    
82.8    
83.0    
83.2    
83.4    
83.6    
83.8    
84.0    
84.2    
84.4    
84.6    
84.8    
85.0    
85.2    
85.4    
85.6    
85.8    
86.0    
86.2    
86.4    
86.7    
86.9    
87.1    
87.3    
87.5    
87.7    
87.9    
88.1    
88.3    
88.5    
88.7    
88.9    
89.1    
89.3    
89.5    
89.7    
89.9    
90.1    
90.3    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.8    
92.0    
92.2    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
94.0    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.3    
97.5    
97.7    
97.9    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 5705, rend_intergenic: 2909  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44950, rend_intergenic: 39807  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55600, rend_intergenic: 51551  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63743, rend_intergenic: 60031  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66197, rend_intergenic: 65118  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88485, rend_intergenic: 82952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96392, rend_intergenic: 94191  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138577, rend_intergenic: 134086  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141172, rend_intergenic: 139311  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146697, rend_intergenic: 141650  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161624, rend_intergenic: 155895  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194358, rend_intergenic: 187041  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 208916, rend_intergenic: 201141  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 26 predictions persist after filtering for low support