-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_9/scaffold_9_5560301-5739135

-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.1194-T1
Valid prediction for snap_scaffold_9-snap.1211-T1
Valid prediction for snap_scaffold_9-snap.1202-T1
Valid prediction for snap_scaffold_9-snap.1197-T1
Valid prediction for snap_scaffold_9-snap.1196-T1
Valid prediction for GeneMark_model.38977_t
Valid prediction for snap_scaffold_9-snap.1207-T1
Valid prediction for GlimmerHMM_glimmerT_22677-T1
Valid prediction for HiQ_model.g15164.t1
Valid prediction for snap_scaffold_9-snap.1192-T1
Valid prediction for GlimmerHMM_glimmerT_22666-T1
Valid prediction for GlimmerHMM_glimmerT_22658-T1
Valid prediction for snap_scaffold_9-snap.1187-T1
Valid prediction for snap_scaffold_9-snap.1209-T1
Valid prediction for snap_scaffold_9-snap.1180-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_9-snap.1182-T1
Valid prediction for GeneMark_model.38981_t
Valid prediction for HiQ_model.g15163.t1
Valid prediction for snap_scaffold_9-snap.1200-T1
Valid prediction for GlimmerHMM_glimmerT_22655-T1
Valid prediction for pasa_asmbl_54052.p1
Valid prediction for GeneMark_model.38959_t
Valid prediction for snap_scaffold_9-snap.1185-T1
Valid prediction for GlimmerHMM_glimmerT_22661-T1
Valid prediction for GlimmerHMM_glimmerT_22669-T1
Valid prediction for Augustus_model.g15166.t1
Valid prediction for pasa_asmbl_54046.p1
Valid prediction for Augustus_model.g15159.t1
Valid prediction for GeneMark_model.38973_t
Valid prediction for GeneMark_model.38940_t
Valid prediction for GeneMark_model.38951_t
Valid prediction for snap_scaffold_9-snap.1188-T1
Couldn't classify 28702, 28823
Couldn't classify 30089, 30153
Sorry, prediction pasa_asmbl_54710.p2 fails validation.
(CAC)	 CC	28702-28823	GT	AGG
(GTT)	 AG	29715-29878	GT	AGG
(ACA)	 AG	30089-30153	GC	GGG
-recovered pasa_asmbl_54710.p2, internal, 29715, 29878
-recovered pasa_asmbl_54710.p2, internal, 30089, 30153
Valid prediction for GeneMark_model.38942_t
Valid prediction for pasa_asmbl_54049.p1
Valid prediction for GeneMark_model.38948_t
Valid prediction for GlimmerHMM_glimmerT_22659-T1
Valid prediction for GeneMark_model.38958_t
Valid prediction for GeneMark_model.38983_t
Valid prediction for GeneMark_model.38984_t
Valid prediction for HiQ_model.g15162.t1
Valid prediction for GeneMark_model.38943_t
Valid prediction for GeneMark_model.38941_t
Valid prediction for GeneMark_model.38961_t
Valid prediction for snap_scaffold_9-snap.1205-T1
Valid prediction for GlimmerHMM_glimmerT_22675-T1
Valid prediction for snap_scaffold_9-snap.1190-T1
Valid prediction for GeneMark_model.38967_t
Valid prediction for GlimmerHMM_glimmerT_22660-T1
Valid prediction for GeneMark_model.38956_t
Valid prediction for Augustus_model.g15157.t1
Valid prediction for snap_scaffold_9-snap.1183-T1
Valid prediction for GlimmerHMM_glimmerT_22671-T1
Valid prediction for GeneMark_model.38965_t
Valid prediction for Augustus_model.g15155.t1
Valid prediction for GeneMark_model.38945_t
Valid prediction for GlimmerHMM_glimmerT_22670-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_22684-T1
Valid prediction for GlimmerHMM_glimmerT_22667-T1
Valid prediction for snap_scaffold_9-snap.1186-T1
Valid prediction for snap_scaffold_9-snap.1201-T1
Valid prediction for GeneMark_model.38953_t
Valid prediction for GeneMark_model.38963_t
Valid prediction for snap_scaffold_9-snap.1204-T1
Valid prediction for snap_scaffold_9-snap.1199-T1
Valid prediction for GeneMark_model.38971_t
Valid prediction for CodingQuarry_transcript_62027-T1
Valid prediction for GeneMark_model.38969_t
Valid prediction for Augustus_model.g15152.t1
Valid prediction for snap_scaffold_9-snap.1210-T1
Valid prediction for GlimmerHMM_glimmerT_22664-T1
Valid prediction for GlimmerHMM_glimmerT_22676-T1
Valid prediction for Augustus_model.g15168.t1
Valid prediction for GeneMark_model.38975_t
Valid prediction for GeneMark_model.38955_t
Valid prediction for GlimmerHMM_glimmerT_22657-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_9-snap.1215-T1
Valid prediction for GlimmerHMM_glimmerT_22683-T1
Valid prediction for Augustus_model.g15153.t1
Valid prediction for Augustus_model.g15167.t1
Valid prediction for Augustus_model.g15169.t1
Valid prediction for GlimmerHMM_glimmerT_22685-T1
Valid prediction for GlimmerHMM_glimmerT_22654-T1
Valid prediction for Augustus_model.g15173.t1
Valid prediction for GlimmerHMM_glimmerT_22668-T1
Valid prediction for GeneMark_model.38978_t
Couldn't classify 48467, 48577
Sorry, prediction pasa_asmbl_54982.p1 fails validation.
(ATG)	 AC	42955-43504	GT	AGG
(GCT)	 AG	44850-45013	GT	AGG
(GAG)	 AG	45779-45832	GT	AGG
(GTC)	 AG	45957-46053	GT	GGG
(GCG)	 AG	46734-46882	GT	CGG
(CCT)	 AG	48467-48577	GT	AGG
-recovered pasa_asmbl_54982.p1, initial, 42955, 43504
-recovered pasa_asmbl_54982.p1, internal, 44850, 45013
-recovered pasa_asmbl_54982.p1, internal, 45779, 45832
-recovered pasa_asmbl_54982.p1, internal, 45957, 46053
-recovered pasa_asmbl_54982.p1, internal, 46734, 46882
-recovered pasa_asmbl_54982.p1, internal, 48467, 48577
Valid prediction for Augustus_model.g15172.t1
Valid prediction for Augustus_model.g15154.t1
Valid prediction for GeneMark_model.38962_t
Couldn't classify 38023, 38478
Sorry, prediction pasa_asmbl_54985.p1 fails validation.
(GGG)	 GC	38023-38478	GG	CAG
Valid prediction for snap_scaffold_9-snap.1193-T1
Valid prediction for snap_scaffold_9-snap.1206-T1
Valid prediction for GeneMark_model.38950_t
Valid prediction for GeneMark_model.38970_t
Valid prediction for GeneMark_model.38980_t
Valid prediction for snap_scaffold_9-snap.1198-T1
Valid prediction for snap_scaffold_9-snap.1216-T1
Valid prediction for GeneMark_model.38944_t
Valid prediction for Augustus_model.g15151.t1
Valid prediction for snap_scaffold_9-snap.1189-T1
Valid prediction for GlimmerHMM_glimmerT_22673-T1
Valid prediction for GlimmerHMM_glimmerT_22663-T1
Valid prediction for GeneMark_model.38974_t
Valid prediction for Augustus_model.g15161.t1
Valid prediction for GlimmerHMM_glimmerT_22656-T1
Valid prediction for snap_scaffold_9-snap.1191-T1
Valid prediction for Augustus_model.g15165.t1
Valid prediction for GeneMark_model.38972_t
Couldn't classify 172841, 172909
Sorry, prediction pasa_asmbl_54978.p2 fails validation.
(GTG)	 AG	172841-172909	GT	AGG
(CAA)	 AG	173336-173487	GT	AAG
(GTG)	 AG	173908-174074	GT	AGG
(GGA)	 AG	174241-174437	CG	GAC
-recovered pasa_asmbl_54978.p2, terminal, 174241, 174437
-recovered pasa_asmbl_54978.p2, internal, 172841, 172909
-recovered pasa_asmbl_54978.p2, internal, 173336, 173487
-recovered pasa_asmbl_54978.p2, internal, 173908, 174074
Valid prediction for Augustus_model.g15171.t1
Valid prediction for GeneMark_model.38949_t
Valid prediction for GeneMark_model.38947_t
Valid prediction for GeneMark_model.38946_t
Valid prediction for GeneMark_model.38966_t
Valid prediction for GlimmerHMM_glimmerT_22678-T1
Valid prediction for snap_scaffold_9-snap.1181-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_22679-T1
Valid prediction for GeneMark_model.38939_t
Valid prediction for GlimmerHMM_glimmerT_22681-T1
Valid prediction for GlimmerHMM_glimmerT_22680-T1
Valid prediction for snap_scaffold_9-snap.1208-T1
Valid prediction for GeneMark_model.38957_t
Couldn't classify 26594, 26636
Couldn't classify 30207, 30472
Sorry, prediction pasa_asmbl_54987.p1 fails validation.
(AGT)	 GC	26594-26636	GT	AGG
(GCA)	 AG	27844-27986	GT	AGG
(GGT)	 AG	28555-28682	GT	CAG
(GAA)	 AG	28955-29060	GT	AGG
(ACA)	 AG	29486-29597	GT	AGG
(ACT)	 AG	30207-30472	CC	CCC
-recovered pasa_asmbl_54987.p1, internal, 27844, 27986
-recovered pasa_asmbl_54987.p1, internal, 28555, 28682
-recovered pasa_asmbl_54987.p1, internal, 28955, 29060
-recovered pasa_asmbl_54987.p1, internal, 29486, 29597
Valid prediction for snap_scaffold_9-snap.1213-T1
Valid prediction for GeneMark_model.38964_t
Valid prediction for GeneMark_model.38976_t
Valid prediction for GeneMark_model.38960_t
Valid prediction for snap_scaffold_9-snap.1184-T1
Valid prediction for GlimmerHMM_glimmerT_22682-T1
Valid prediction for GeneMark_model.38952_t
Valid prediction for Augustus_model.g15170.t1
Valid prediction for Augustus_model.g15158.t1
Valid prediction for GlimmerHMM_glimmerT_22672-T1
Couldn't classify 33010, 33019
Couldn't classify 37514, 37968
Sorry, prediction pasa_asmbl_54986.p1 fails validation.
(CTC)	 GT	33010-33019	GT	AGG
(AGA)	 AG	33231-33427	GT	AGG
(AGT)	 AG	34251-34463	GT	AGG
(GGG)	 AG	34549-34691	GT	AGG
(CTC)	 AG	35642-35760	GT	AGG
(ATT)	 AG	36494-36556	GT	AGG
(GGG)	 AG	37514-37968	TT	ACT
-recovered pasa_asmbl_54986.p1, terminal, 36494, 36556
-recovered pasa_asmbl_54986.p1, internal, 33231, 33427
-recovered pasa_asmbl_54986.p1, internal, 34251, 34463
-recovered pasa_asmbl_54986.p1, internal, 34549, 34691
-recovered pasa_asmbl_54986.p1, internal, 35642, 35760
-recovered pasa_asmbl_54986.p1, internal, 36494, 36556
Valid prediction for Augustus_model.g15160.t1
Valid prediction for GeneMark_model.38968_t
Valid prediction for snap_scaffold_9-snap.1212-T1
Valid prediction for snap_scaffold_9-snap.1214-T1
Valid prediction for snap_scaffold_9-snap.1195-T1
Valid prediction for GlimmerHMM_glimmerT_22674-T1
Valid prediction for GlimmerHMM_glimmerT_22662-T1
Valid prediction for GeneMark_model.38985_t
Valid prediction for GlimmerHMM_glimmerT_22665-T1
Valid prediction for GeneMark_model.38954_t
Valid prediction for GeneMark_model.38982_t
Valid prediction for Augustus_model.g15156.t1
Valid prediction for snap_scaffold_9-snap.1203-T1
Valid prediction for GeneMark_model.38979_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9017, rend_intergenic: 4399  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12534, rend_intergenic: 9156  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15608, rend_intergenic: 12639  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48445, rend_intergenic: 47004  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57607, rend_intergenic: 55165  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60597, rend_intergenic: 59486  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73863, rend_intergenic: 70918  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88636, rend_intergenic: 81792  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109408, rend_intergenic: 108929  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115346, rend_intergenic: 109481  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135881, rend_intergenic: 129021  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152675, rend_intergenic: 141496  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 178835
-exon list size: 702


building trellis

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83.1    
83.2    
83.4    
83.5    
83.7    
83.8    
83.9    
84.1    
84.2    
84.4    
84.5    
84.7    
84.8    
84.9    
85.1    
85.2    
85.4    
85.5    
85.7    
85.8    
85.9    
86.1    
86.2    
86.4    
86.5    
86.6    
86.8    
86.9    
87.1    
87.2    
87.4    
87.5    
87.6    
87.8    
87.9    
88.1    
88.2    
88.4    
88.5    
88.6    
88.8    
88.9    
89.1    
89.2    
89.3    
89.5    
89.6    
89.8    
89.9    
90.1    
90.2    
90.3    
90.5    
90.6    
90.8    
90.9    
91.1    
91.2    
91.3    
91.5    
91.6    
91.8    
91.9    
92.0    
92.2    
92.3    
92.5    
92.6    
92.8    
92.9    
93.0    
93.2    
93.3    
93.5    
93.6    
93.8    
93.9    
94.0    
94.2    
94.3    
94.5    
94.6    
94.7    
94.9    
95.0    
95.2    
95.3    
95.5    
95.6    
95.7    
95.9    
96.0    
96.2    
96.3    
96.4    
96.6    
96.7    
96.9    
97.0    
97.2    
97.3    
97.4    
97.6    
97.7    
97.9    
98.0    
98.2    
98.3    
98.4    
98.6    
98.7    
98.9    
99.0    
99.1    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 9017, rend_intergenic: 4399  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12534, rend_intergenic: 9156  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15608, rend_intergenic: 12639  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48445, rend_intergenic: 47004  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57607, rend_intergenic: 55165  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60597, rend_intergenic: 59486  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73863, rend_intergenic: 70918  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88636, rend_intergenic: 81792  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109408, rend_intergenic: 108929  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115346, rend_intergenic: 109481  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135881, rend_intergenic: 129021  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152675, rend_intergenic: 141496  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