-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_5154141-5420353

-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 Augustus_model.g4366.t1
Couldn't classify 83637, 83742
Couldn't classify 89245, 89335
Sorry, prediction pasa_asmbl_40024.p1 fails validation.
(ACA)	 GG	83637-83742	GT	CAG
(TTG)	 AG	83861-83959	GT	CGG
(ATG)	 AG	84630-84724	GT	CGG
(AAG)	 AG	85624-85830	GT	AGG
(GGC)	 AG	87319-87450	GT	GGG
(ATT)	 AG	88389-88516	GT	CAG
(AGC)	 AG	89245-89335	CA	GCC
add_exon() Sorry, pasa_asmbl_40024.p1 84630-84724-initial-1 is invalid.
-recovered pasa_asmbl_40024.p1, initial, 84630, 84724
-recovered pasa_asmbl_40024.p1, internal, 83861, 83959
-recovered pasa_asmbl_40024.p1, internal, 84630, 84724
-recovered pasa_asmbl_40024.p1, internal, 85624, 85830
-recovered pasa_asmbl_40024.p1, internal, 87319, 87450
-recovered pasa_asmbl_40024.p1, internal, 88389, 88516
Valid prediction for snap_scaffold_3-snap.1144-T1
Valid prediction for GlimmerHMM_glimmerT_6681-T1
Valid prediction for snap_scaffold_3-snap.1117-T1
Valid prediction for snap_scaffold_3-snap.1113-T1
Valid prediction for Augustus_model.g4363.t1
Valid prediction for GlimmerHMM_glimmerT_6686-T1
Valid prediction for GeneMark_model.11037_t
Valid prediction for GeneMark_model.11057_t
Valid prediction for snap_scaffold_3-snap.1146-T1
Valid prediction for GeneMark_model.11073_t
Valid prediction for snap_scaffold_3-snap.1131-T1
Valid prediction for GlimmerHMM_glimmerT_6689-T1
Valid prediction for snap_scaffold_3-snap.1136-T1
Valid prediction for GlimmerHMM_glimmerT_6680-T1
Valid prediction for GeneMark_model.11064_t
Valid prediction for GlimmerHMM_glimmerT_6675-T1
Valid prediction for GlimmerHMM_glimmerT_6685-T1
Valid prediction for GlimmerHMM_glimmerT_6671-T1
Valid prediction for snap_scaffold_3-snap.1124-T1
Valid prediction for GeneMark_model.11055_t
Couldn't classify 80451, 80479
Couldn't classify 82102, 82173
Sorry, prediction pasa_asmbl_40797.p1 fails validation.
(ATT)	 AC	80451-80479	GT	AGG
(CAT)	 AG	80696-80846	GT	CGG
(TGG)	 AG	81671-81790	GT	TGG
(GTG)	 AG	82102-82173	AA	ACA
-recovered pasa_asmbl_40797.p1, internal, 80696, 80846
-recovered pasa_asmbl_40797.p1, internal, 81671, 81790
Valid prediction for snap_scaffold_3-snap.1158-T1
Valid prediction for GlimmerHMM_glimmerT_6667-T1
Valid prediction for snap_scaffold_3-snap.1129-T1
Valid prediction for GeneMark_model.11070_t
Valid prediction for GeneMark_model.11049_t
Valid prediction for GeneMark_model.11059_t
Valid prediction for snap_scaffold_3-snap.1130-T1
Valid prediction for GeneMark_model.11042_t
Valid prediction for snap_scaffold_3-snap.1143-T1
Valid prediction for GlimmerHMM_glimmerT_6676-T1
Valid prediction for GlimmerHMM_glimmerT_6683-T1
Valid prediction for GeneMark_model.11061_t
Valid prediction for snap_scaffold_3-snap.1119-T1
Valid prediction for GlimmerHMM_glimmerT_6663-T1
Valid prediction for snap_scaffold_3-snap.1142-T1
Valid prediction for GlimmerHMM_glimmerT_6670-T1
Valid prediction for GlimmerHMM_glimmerT_6664-T1
Valid prediction for GeneMark_model.11051_t
Valid prediction for GeneMark_model.11041_t
Valid prediction for snap_scaffold_3-snap.1147-T1
Valid prediction for GeneMark_model.11065_t
Valid prediction for snap_scaffold_3-snap.1141-T1
Valid prediction for snap_scaffold_3-snap.1137-T1
Valid prediction for Augustus_model.g4367.t1
Valid prediction for Augustus_model.g4355.t1
Valid prediction for Augustus_model.g4360.t1
Valid prediction for GeneMark_model.11052_t
Valid prediction for GlimmerHMM_glimmerT_6660-T1
Valid prediction for Augustus_model.g4354.t1
Valid prediction for GeneMark_model.11038_t
Valid prediction for Augustus_model.g4368.t1
Valid prediction for snap_scaffold_3-snap.1127-T1
Valid prediction for GlimmerHMM_glimmerT_6669-T1
Valid prediction for snap_scaffold_3-snap.1122-T1
Valid prediction for GlimmerHMM_glimmerT_6677-T1
Valid prediction for Augustus_model.g4352.t1
Valid prediction for Augustus_model.g4364.t1
Couldn't classify 101283, 101376
Sorry, prediction pasa_asmbl_40026.p1 fails validation.
(ATG)	 GC	98292-98392	GT	AGG
(AAT)	 AG	98560-98644	GT	AGG
(GAG)	 AG	99201-99383	GT	AGG
(ATA)	 AG	99625-99785	GT	AGG
(TGC)	 AG	101283-101376	AG	ACA
-recovered pasa_asmbl_40026.p1, initial, 98292, 98392
-recovered pasa_asmbl_40026.p1, internal, 98560, 98644
-recovered pasa_asmbl_40026.p1, internal, 99201, 99383
-recovered pasa_asmbl_40026.p1, internal, 99625, 99785
Valid prediction for GeneMark_model.11048_t
Valid prediction for GlimmerHMM_glimmerT_6661-T1
Valid prediction for Augustus_model.g4362.t1
Valid prediction for GeneMark_model.11036_t
Valid prediction for Augustus_model.g4357.t1
Valid prediction for GlimmerHMM_glimmerT_6682-T1
Valid prediction for snap_scaffold_3-snap.1148-T1
Valid prediction for snap_scaffold_3-snap.1150-T1
Valid prediction for GeneMark_model.11063_t
Valid prediction for GlimmerHMM_glimmerT_6665-T1
Valid prediction for GeneMark_model.11039_t
Valid prediction for GeneMark_model.11067_t
Valid prediction for snap_scaffold_3-snap.1115-T1
Valid prediction for snap_scaffold_3-snap.1126-T1
Couldn't classify 201630, 201816
Sorry, prediction pasa_asmbl_40029.p2 fails validation.
(ACA)	 TC	201630-201816	GT	AGG
(AAA)	 AG	201999-202159	TC	AAT
-recovered pasa_asmbl_40029.p2, terminal, 201999, 202159
Valid prediction for snap_scaffold_3-snap.1118-T1
Valid prediction for snap_scaffold_3-snap.1123-T1
Valid prediction for GeneMark_model.11054_t
Valid prediction for GlimmerHMM_glimmerT_6684-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 GlimmerHMM_glimmerT_6673-T1
Valid prediction for GeneMark_model.11074_t
Valid prediction for GlimmerHMM_glimmerT_6662-T1
Valid prediction for snap_scaffold_3-snap.1134-T1
Valid prediction for snap_scaffold_3-snap.1139-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.11053_t
Valid prediction for snap_scaffold_3-snap.1153-T1
Valid prediction for GlimmerHMM_glimmerT_6688-T1
Valid prediction for GeneMark_model.11044_t
Valid prediction for snap_scaffold_3-snap.1155-T1
Valid prediction for GlimmerHMM_glimmerT_6674-T1
Valid prediction for GlimmerHMM_glimmerT_6666-T1
Valid prediction for GeneMark_model.11045_t
Valid prediction for snap_scaffold_3-snap.1120-T1
Valid prediction for Augustus_model.g4371.t1
Valid prediction for GeneMark_model.11068_t
Valid prediction for snap_scaffold_3-snap.1151-T1
Valid prediction for Augustus_model.g4365.t1
Valid prediction for GeneMark_model.11033_t
Valid prediction for Augustus_model.g4358.t1
Valid prediction for GeneMark_model.11046_t
Valid prediction for Augustus_model.g4372.t1
Valid prediction for Augustus_model.g4353.t1
Valid prediction for GeneMark_model.11047_t
Valid prediction for GlimmerHMM_glimmerT_6659-T1
Valid prediction for CodingQuarry_transcript_46050-T1
Valid prediction for GeneMark_model.11069_t
Valid prediction for snap_scaffold_3-snap.1116-T1
Valid prediction for snap_scaffold_3-snap.1121-T1
Valid prediction for GeneMark_model.11043_t
Valid prediction for GeneMark_model.11062_t
Valid prediction for GeneMark_model.11035_t
Valid prediction for CodingQuarry_transcript_46049-T1
Valid prediction for snap_scaffold_3-snap.1112-T1
Valid prediction for snap_scaffold_3-snap.1145-T1
Valid prediction for GeneMark_model.11066_t
Valid prediction for GeneMark_model.11071_t
Valid prediction for snap_scaffold_3-snap.1132-T1
Valid prediction for GeneMark_model.11034_t
Valid prediction for snap_scaffold_3-snap.1140-T1
Valid prediction for GlimmerHMM_glimmerT_6668-T1
Valid prediction for Augustus_model.g4359.t1
Valid prediction for Augustus_model.g4361.t1
Valid prediction for GeneMark_model.11060_t
Valid prediction for Augustus_model.g4369.t1
Valid prediction for snap_scaffold_3-snap.1133-T1
Valid prediction for Augustus_model.g4373.t1
Valid prediction for snap_scaffold_3-snap.1138-T1
Valid prediction for GeneMark_model.11050_t
Valid prediction for GeneMark_model.11040_t
Valid prediction for snap_scaffold_3-snap.1128-T1
Valid prediction for snap_scaffold_3-snap.1114-T1
Valid prediction for Augustus_model.g4370.t1
Valid prediction for GlimmerHMM_glimmerT_6672-T1
Couldn't classify 157363, 157536
Sorry, prediction pasa_asmbl_38798.p1 fails validation.
(AGC)	 GT	157363-157536	GT	AGG
(GAT)	 AG	157693-157813	GT	AGG
(CTG)	 AG	159661-159793	GT	AGG
(ATC)	 AG	160097-160245	GT	AGG
(AGA)	 AG	160413-160570	GC	GAG
-recovered pasa_asmbl_38798.p1, terminal, 160413, 160570
-recovered pasa_asmbl_38798.p1, internal, 157693, 157813
-recovered pasa_asmbl_38798.p1, internal, 159661, 159793
-recovered pasa_asmbl_38798.p1, internal, 160097, 160245
-recovered pasa_asmbl_38798.p1, internal, 160413, 160570
Valid prediction for GlimmerHMM_glimmerT_6679-T1
Valid prediction for GeneMark_model.11058_t
Valid prediction for snap_scaffold_3-snap.1152-T1
Valid prediction for GlimmerHMM_glimmerT_6687-T1
Valid prediction for GlimmerHMM_glimmerT_6658-T1
Valid prediction for snap_scaffold_3-snap.1156-T1
Couldn't classify 24158, 24538
Sorry, prediction pasa_asmbl_38803.p1 fails validation.
(GAA)	 CA	24158-24538	CG	ACC
Valid prediction for snap_scaffold_3-snap.1111-T1
Valid prediction for snap_scaffold_3-snap.1125-T1
Valid prediction for snap_scaffold_3-snap.1157-T1
Valid prediction for snap_scaffold_3-snap.1154-T1
Valid prediction for snap_scaffold_3-snap.1135-T1
Valid prediction for GeneMark_model.11075_t
Valid prediction for Augustus_model.g4356.t1
Valid prediction for snap_scaffold_3-snap.1149-T1
Valid prediction for GlimmerHMM_glimmerT_6678-T1
Valid prediction for GeneMark_model.11072_t
Valid prediction for GeneMark_model.11056_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13132, rend_intergenic: 7760  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89909, rend_intergenic: 87298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93650, rend_intergenic: 93066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97491, rend_intergenic: 94327  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 266213
-exon list size: 618


building trellis

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-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 13132, rend_intergenic: 7760  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89909, rend_intergenic: 87298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93650, rend_intergenic: 93066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97491, rend_intergenic: 94327  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 27 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 251277 - 266213
-exon list size: 9


building trellis

9.1    
18.2    
27.3    
36.4    
45.5    
54.5    
63.6    
72.7    
81.8    
90.9    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 251277 - 262062
-exon list size: 8


building trellis

10.0    
20.0    
30.0    
40.0    
50.0    
60.0    
70.0    
80.0    
90.0    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support