-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_3/scaffold_3_5180618-5427688

-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: +)Couldn't classify 175153, 175339
Sorry, prediction pasa_asmbl_40068.p2 fails validation.
(ACA)	 TC	175153-175339	GT	AGG
(AAA)	 AG	175522-175682	TC	AAT
-recovered pasa_asmbl_40068.p2, terminal, 175522, 175682
Valid prediction for Augustus_model.g4249.t1
Valid prediction for snap_scaffold_3-snap.1127-T1
Valid prediction for snap_scaffold_3-snap.1161-T1
Valid prediction for GlimmerHMM_glimmerT_6549-T1
Valid prediction for GlimmerHMM_glimmerT_6546-T1
Valid prediction for snap_scaffold_3-snap.1152-T1
Valid prediction for GlimmerHMM_glimmerT_6548-T1
Valid prediction for Augustus_model.g4250.t1
Valid prediction for Augustus_model.g4238.t1
Valid prediction for snap_scaffold_3-snap.1142-T1
Valid prediction for Augustus_model.g4241.t1
Valid prediction for GlimmerHMM_glimmerT_6539-T1
Valid prediction for snap_scaffold_3-snap.1131-T1
Valid prediction for GlimmerHMM_glimmerT_6554-T1
Valid prediction for GlimmerHMM_glimmerT_6533-T1
Valid prediction for snap_scaffold_3-snap.1119-T1
Valid prediction for GlimmerHMM_glimmerT_6540-T1
Couldn't classify 57160, 57265
Couldn't classify 62768, 62858
Sorry, prediction pasa_asmbl_40063.p1 fails validation.
(ACA)	 GG	57160-57265	GT	CAG
(TTG)	 AG	57384-57482	GT	CGG
(ATG)	 AG	58153-58247	GT	CGG
(AAG)	 AG	59147-59353	GT	AGG
(GGC)	 AG	60842-60973	GT	GGG
(ATT)	 AG	61912-62039	GT	CAG
(AGC)	 AG	62768-62858	CA	GCC
add_exon() Sorry, pasa_asmbl_40063.p1 58153-58247-initial-1 is invalid.
-recovered pasa_asmbl_40063.p1, initial, 58153, 58247
-recovered pasa_asmbl_40063.p1, internal, 57384, 57482
-recovered pasa_asmbl_40063.p1, internal, 58153, 58247
-recovered pasa_asmbl_40063.p1, internal, 59147, 59353
-recovered pasa_asmbl_40063.p1, internal, 60842, 60973
-recovered pasa_asmbl_40063.p1, internal, 61912, 62039
Valid prediction for snap_scaffold_3-snap.1150-T1
Valid prediction for snap_scaffold_3-snap.1135-T1
Valid prediction for Augustus_model.g4252.t1
Valid prediction for GlimmerHMM_glimmerT_6555-T1
Valid prediction for snap_scaffold_3-snap.1118-T1
Valid prediction for GlimmerHMM_glimmerT_6535-T1
Valid prediction for GlimmerHMM_glimmerT_6536-T1
Valid prediction for snap_scaffold_3-snap.1123-T1
Valid prediction for GlimmerHMM_glimmerT_6547-T1
Valid prediction for GlimmerHMM_glimmerT_6553-T1
Valid prediction for snap_scaffold_3-snap.1149-T1
Valid prediction for GlimmerHMM_glimmerT_6558-T1
Valid prediction for snap_scaffold_3-snap.1130-T1
Valid prediction for snap_scaffold_3-snap.1128-T1
Valid prediction for snap_scaffold_3-snap.1144-T1
Couldn't classify 74806, 74899
Sorry, prediction pasa_asmbl_40065.p1 fails validation.
(ATG)	 GC	71815-71915	GT	AGG
(AAT)	 AG	72083-72167	GT	AGG
(GAG)	 AG	72724-72906	GT	AGG
(ATA)	 AG	73148-73308	GT	AGG
(TGC)	 AG	74806-74899	AG	ACA
-recovered pasa_asmbl_40065.p1, initial, 71815, 71915
-recovered pasa_asmbl_40065.p1, internal, 72083, 72167
-recovered pasa_asmbl_40065.p1, internal, 72724, 72906
-recovered pasa_asmbl_40065.p1, internal, 73148, 73308
Valid prediction for Augustus_model.g4242.t1
Valid prediction for GlimmerHMM_glimmerT_6531-T1
Valid prediction for snap_scaffold_3-snap.1136-T1
Valid prediction for snap_scaffold_3-snap.1126-T1
Valid prediction for Augustus_model.g4248.t1
Valid prediction for snap_scaffold_3-snap.1148-T1
Valid prediction for GlimmerHMM_glimmerT_6559-T1
Valid prediction for Augustus_model.g4247.t1
Valid prediction for snap_scaffold_3-snap.1124-T1
Valid prediction for snap_scaffold_3-snap.1145-T1
Valid prediction for snap_scaffold_3-snap.1138-T1
Valid prediction for Augustus_model.g4251.t1
Valid prediction for Augustus_model.g4245.t1
Valid prediction for snap_scaffold_3-snap.1120-T1
Valid prediction for GlimmerHMM_glimmerT_6530-T1
Valid prediction for GlimmerHMM_glimmerT_6541-T1
Valid prediction for GlimmerHMM_glimmerT_6538-T1
Couldn't classify 53974, 54002
Couldn't classify 55625, 55696
Sorry, prediction pasa_asmbl_40888.p1 fails validation.
(ATT)	 AC	53974-54002	GT	AGG
(CAT)	 AG	54219-54369	GT	CGG
(TGG)	 AG	55194-55313	GT	TGG
(GTG)	 AG	55625-55696	AA	ACA
-recovered pasa_asmbl_40888.p1, internal, 54219, 54369
-recovered pasa_asmbl_40888.p1, internal, 55194, 55313
Valid prediction for GlimmerHMM_glimmerT_6551-T1
Valid prediction for Augustus_model.g4239.t1
Valid prediction for GlimmerHMM_glimmerT_6550-T1
Valid prediction for snap_scaffold_3-snap.1143-T1
Valid prediction for snap_scaffold_3-snap.1137-T1
Valid prediction for GlimmerHMM_glimmerT_6552-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_6534-T1
Valid prediction for Augustus_model.g4256.t1
Valid prediction for Augustus_model.g4246.t1
Valid prediction for snap_scaffold_3-snap.1117-T1
Valid prediction for snap_scaffold_3-snap.1146-T1
Valid prediction for GlimmerHMM_glimmerT_6543-T1
Valid prediction for Augustus_model.g4243.t1
Valid prediction for snap_scaffold_3-snap.1132-T1
Valid prediction for snap_scaffold_3-snap.1156-T1
Valid prediction for snap_scaffold_3-snap.1157-T1
Valid prediction for snap_scaffold_3-snap.1159-T1
Valid prediction for GlimmerHMM_glimmerT_6560-T1
Valid prediction for GlimmerHMM_glimmerT_6557-T1
Valid prediction for snap_scaffold_3-snap.1129-T1
Valid prediction for Augustus_model.g4257.t1
Valid prediction for snap_scaffold_3-snap.1141-T1
Valid prediction for snap_scaffold_3-snap.1116-T1
Valid prediction for CodingQuarry_transcript_46162-T1
Valid prediction for GlimmerHMM_glimmerT_6537-T1
Valid prediction for Augustus_model.g4240.t1
Valid prediction for snap_scaffold_3-snap.1160-T1
Valid prediction for snap_scaffold_3-snap.1139-T1
Valid prediction for snap_scaffold_3-snap.1121-T1
Valid prediction for Augustus_model.g4253.t1
Valid prediction for snap_scaffold_3-snap.1125-T1
Valid prediction for Augustus_model.g4258.t1
Valid prediction for snap_scaffold_3-snap.1140-T1
Valid prediction for GlimmerHMM_glimmerT_6532-T1
Valid prediction for GlimmerHMM_glimmerT_6544-T1
Valid prediction for snap_scaffold_3-snap.1153-T1
Valid prediction for CodingQuarry_transcript_46163-T1
Valid prediction for snap_scaffold_3-snap.1147-T1
Valid prediction for snap_scaffold_3-snap.1154-T1
Valid prediction for GlimmerHMM_glimmerT_6542-T1
Valid prediction for snap_scaffold_3-snap.1122-T1
Valid prediction for snap_scaffold_3-snap.1155-T1
Valid prediction for GlimmerHMM_glimmerT_6529-T1
Valid prediction for Augustus_model.g4244.t1
Couldn't classify 31493, 31873
Sorry, prediction pasa_asmbl_38847.p1 fails validation.
(GAA)	 CA	31493-31873	CG	ACC
Valid prediction for snap_scaffold_3-snap.1133-T1
Valid prediction for GlimmerHMM_glimmerT_6556-T1
Valid prediction for GlimmerHMM_glimmerT_6545-T1
Valid prediction for snap_scaffold_3-snap.1151-T1
Valid prediction for Augustus_model.g4237.t1
Couldn't classify 164698, 164871
Sorry, prediction pasa_asmbl_38842.p1 fails validation.
(AGC)	 GT	164698-164871	GT	AGG
(GAT)	 AG	165028-165148	GT	AGG
(CTG)	 AG	166996-167128	GT	AGG
(ATC)	 AG	167432-167580	GT	AGG
(AGA)	 AG	167748-167905	GC	GAG
-recovered pasa_asmbl_38842.p1, terminal, 167748, 167905
-recovered pasa_asmbl_38842.p1, internal, 165028, 165148
-recovered pasa_asmbl_38842.p1, internal, 166996, 167128
-recovered pasa_asmbl_38842.p1, internal, 167432, 167580
-recovered pasa_asmbl_38842.p1, internal, 167748, 167905
Valid prediction for snap_scaffold_3-snap.1134-T1
Valid prediction for Augustus_model.g4255.t1
Valid prediction for Augustus_model.g4254.t1
Valid prediction for snap_scaffold_3-snap.1158-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 240582, rend_intergenic: 240579  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63432, rend_intergenic: 60821  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71034, rend_intergenic: 68220  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 247071
-exon list size: 393


building trellis

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-found 36 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 240582, rend_intergenic: 240579  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63432, rend_intergenic: 60821  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71034, rend_intergenic: 68220  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 30 predictions persist after filtering for low support