-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_9/scaffold_9_1131748-1393032

-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_21596-T1
Valid prediction for GlimmerHMM_glimmerT_21579-T1
Valid prediction for snap_scaffold_9-snap.261-T1
Valid prediction for Augustus_model.g14368.t1
Couldn't classify 153948, 154045
Sorry, prediction pasa_asmbl_53812.p1 fails validation.
(AAT)	 AG	153948-154045	GT	AAG
(GTT)	 AG	154290-154362	GT	AGG
(GAG)	 AG	154482-155192	AT	GAA
-recovered pasa_asmbl_53812.p1, terminal, 154482, 155192
-recovered pasa_asmbl_53812.p1, internal, 153948, 154045
-recovered pasa_asmbl_53812.p1, internal, 154290, 154362
Valid prediction for Augustus_model.g14366.t1
Valid prediction for snap_scaffold_9-snap.284-T1
Valid prediction for Augustus_model.g14354.t1
Valid prediction for snap_scaffold_9-snap.288-T1
Valid prediction for snap_scaffold_9-snap.267-T1
Valid prediction for snap_scaffold_9-snap.293-T1
Valid prediction for snap_scaffold_9-snap.273-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_9-snap.285-T1
Valid prediction for snap_scaffold_9-snap.292-T1
Couldn't classify 112098, 112193
Sorry, prediction pasa_asmbl_53808.p1 fails validation.
(ATG)	 TA	108278-108313	GT	ATG
(TTG)	 AG	108428-108531	GT	GAG
(GTG)	 AG	109613-109671	GT	AGG
(TCT)	 AG	109914-110033	GT	CGG
(GAA)	 AG	110253-110386	GT	ATG
(TTA)	 AG	111040-111105	GT	AGG
(GCT)	 AG	112098-112193	GT	AGG
-recovered pasa_asmbl_53808.p1, initial, 108278, 108313
add_exon() Sorry, pasa_asmbl_53808.p1 109613-109671-terminal-2 is invalid.
-recovered pasa_asmbl_53808.p1, terminal, 109613, 109671
-recovered pasa_asmbl_53808.p1, internal, 108428, 108531
-recovered pasa_asmbl_53808.p1, internal, 109613, 109671
-recovered pasa_asmbl_53808.p1, internal, 109914, 110033
-recovered pasa_asmbl_53808.p1, internal, 110253, 110386
-recovered pasa_asmbl_53808.p1, internal, 111040, 111105
-recovered pasa_asmbl_53808.p1, internal, 112098, 112193
Valid prediction for snap_scaffold_9-snap.270-T1
Valid prediction for snap_scaffold_9-snap.276-T1
Couldn't classify 93431, 93545
Couldn't classify 95549, 95712
Sorry, prediction pasa_asmbl_53803.p1 fails validation.
(AAG)	 CC	93431-93545	GT	CGG
(ATG)	 AG	95283-95318	GT	AGG
(CTT)	 AG	95549-95712	CT	GTC
-recovered pasa_asmbl_53803.p1, initial, 95283, 95318
-recovered pasa_asmbl_53803.p1, internal, 95283, 95318
Valid prediction for GlimmerHMM_glimmerT_21601-T1
Valid prediction for snap_scaffold_9-snap.251-T1
Valid prediction for snap_scaffold_9-snap.254-T1
Valid prediction for snap_scaffold_9-snap.290-T1
Valid prediction for GlimmerHMM_glimmerT_21600-T1
Valid prediction for Augustus_model.g14353.t1
Valid prediction for GlimmerHMM_glimmerT_21583-T1
Valid prediction for Augustus_model.g14356.t1
Valid prediction for snap_scaffold_9-snap.253-T1
Valid prediction for Augustus_model.g14347.t1
Valid prediction for snap_scaffold_9-snap.279-T1
Valid prediction for CodingQuarry_transcript_62105-T1
Valid prediction for GlimmerHMM_glimmerT_21586-T1
Valid prediction for snap_scaffold_9-snap.289-T1
Valid prediction for GlimmerHMM_glimmerT_21597-T1
Valid prediction for Augustus_model.g14365.t1
Valid prediction for snap_scaffold_9-snap.265-T1
Valid prediction for GlimmerHMM_glimmerT_21577-T1
Valid prediction for snap_scaffold_9-snap.281-T1
Valid prediction for snap_scaffold_9-snap.255-T1
Valid prediction for snap_scaffold_9-snap.257-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_9-snap.287-T1
Valid prediction for HiQ_model.g14362.t1
Valid prediction for Augustus_model.g14367.t1
Valid prediction for GlimmerHMM_glimmerT_21593-T1
Valid prediction for snap_scaffold_9-snap.264-T1
Valid prediction for snap_scaffold_9-snap.294-T1
Valid prediction for GlimmerHMM_glimmerT_21588-T1
Valid prediction for snap_scaffold_9-snap.295-T1
Valid prediction for snap_scaffold_9-snap.291-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_21604-T1
Valid prediction for snap_scaffold_9-snap.250-T1
Couldn't classify 103907, 104041
Couldn't classify 105476, 105592
Sorry, prediction pasa_asmbl_53806.p1 fails validation.
(GCA)	 AG	103907-104041	GT	ACG
(GCC)	 AG	104476-104577	GT	GAG
(GAG)	 AG	104735-104871	GT	AGG
(GGA)	 AG	105071-105164	GT	AGG
(GCC)	 AG	105476-105592	AG	AGA
-recovered pasa_asmbl_53806.p1, internal, 103907, 104041
-recovered pasa_asmbl_53806.p1, internal, 104476, 104577
-recovered pasa_asmbl_53806.p1, internal, 104735, 104871
-recovered pasa_asmbl_53806.p1, internal, 105071, 105164
Valid prediction for GlimmerHMM_glimmerT_21603-T1
Valid prediction for GlimmerHMM_glimmerT_21599-T1
Couldn't classify 100271, 100352
Couldn't classify 100785, 100903
Sorry, prediction pasa_asmbl_53805.p2 fails validation.
(GGT)	 CA	100271-100352	GT	GAG
(GTC)	 AG	100463-100558	GT	TGG
(GTG)	 AG	100785-100903	GT	ATG
-recovered pasa_asmbl_53805.p2, internal, 100463, 100558
-recovered pasa_asmbl_53805.p2, internal, 100785, 100903
Valid prediction for Augustus_model.g14358.t1
Valid prediction for GlimmerHMM_glimmerT_21590-T1
Valid prediction for GlimmerHMM_glimmerT_21578-T1
Valid prediction for GlimmerHMM_glimmerT_21587-T1
Valid prediction for Augustus_model.g14348.t1
Valid prediction for snap_scaffold_9-snap.278-T1
Valid prediction for Augustus_model.g14361.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 Augustus_model.g14357.t1
Valid prediction for snap_scaffold_9-snap.260-T1
Valid prediction for GlimmerHMM_glimmerT_21602-T1
Valid prediction for GlimmerHMM_glimmerT_21572-T1
Valid prediction for snap_scaffold_9-snap.280-T1
Valid prediction for GlimmerHMM_glimmerT_21582-T1
Valid prediction for GlimmerHMM_glimmerT_21575-T1
Couldn't classify 223868, 223973
Couldn't classify 229760, 229886
Sorry, prediction pasa_asmbl_54819.p1 fails validation.
(GAT)	 CT	223868-223973	GT	TGG
(GTC)	 AG	224935-225016	GT	AGG
(GTA)	 AG	225893-226033	GT	AAG
(GTA)	 AG	226163-226268	GT	AGG
(GAA)	 AG	227993-228080	GT	AGG
(ATC)	 AG	228493-228548	GT	CAG
(GTG)	 AG	229026-229090	GT	AGG
(CAT)	 AG	229760-229886	GA	GGG
-recovered pasa_asmbl_54819.p1, internal, 224935, 225016
-recovered pasa_asmbl_54819.p1, internal, 225893, 226033
-recovered pasa_asmbl_54819.p1, internal, 226163, 226268
-recovered pasa_asmbl_54819.p1, internal, 227993, 228080
-recovered pasa_asmbl_54819.p1, internal, 228493, 228548
-recovered pasa_asmbl_54819.p1, internal, 229026, 229090
Valid prediction for Augustus_model.g14349.t1
Valid prediction for Augustus_model.g14360.t1
Valid prediction for GlimmerHMM_glimmerT_21595-T1
Valid prediction for GlimmerHMM_glimmerT_21573-T1
Valid prediction for snap_scaffold_9-snap.286-T1
Valid prediction for snap_scaffold_9-snap.274-T1
Valid prediction for Augustus_model.g14359.t1
Valid prediction for snap_scaffold_9-snap.296-T1
Valid prediction for snap_scaffold_9-snap.275-T1
Valid prediction for Augustus_model.g14351.t1
Valid prediction for GlimmerHMM_glimmerT_21591-T1
Valid prediction for GlimmerHMM_glimmerT_21594-T1
Valid prediction for snap_scaffold_9-snap.277-T1
Valid prediction for Augustus_model.g14350.t1
Valid prediction for GlimmerHMM_glimmerT_21592-T1
Valid prediction for GlimmerHMM_glimmerT_21576-T1
Valid prediction for GlimmerHMM_glimmerT_21584-T1
Valid prediction for snap_scaffold_9-snap.272-T1
Valid prediction for snap_scaffold_9-snap.269-T1
Valid prediction for Augustus_model.g14352.t1
Valid prediction for snap_scaffold_9-snap.259-T1
Valid prediction for snap_scaffold_9-snap.249-T1
Valid prediction for snap_scaffold_9-snap.258-T1
Valid prediction for snap_scaffold_9-snap.252-T1
Valid prediction for snap_scaffold_9-snap.266-T1
Valid prediction for GlimmerHMM_glimmerT_21598-T1
Valid prediction for snap_scaffold_9-snap.263-T1
Valid prediction for snap_scaffold_9-snap.283-T1
Valid prediction for Augustus_model.g14364.t1
Valid prediction for GlimmerHMM_glimmerT_21574-T1
Valid prediction for snap_scaffold_9-snap.268-T1
Valid prediction for snap_scaffold_9-snap.271-T1
Valid prediction for GlimmerHMM_glimmerT_21605-T1
Valid prediction for Augustus_model.g14363.t1
Valid prediction for Augustus_model.g14369.t1
Valid prediction for snap_scaffold_9-snap.262-T1
Valid prediction for Augustus_model.g14355.t1
Valid prediction for GlimmerHMM_glimmerT_21585-T1
Valid prediction for GlimmerHMM_glimmerT_21581-T1
Valid prediction for GlimmerHMM_glimmerT_21580-T1
Valid prediction for snap_scaffold_9-snap.282-T1
Valid prediction for snap_scaffold_9-snap.256-T1
Valid prediction for GlimmerHMM_glimmerT_21589-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 18081, rend_intergenic: 12131  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22833, rend_intergenic: 18492  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28120, rend_intergenic: 22876  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38149, rend_intergenic: 28846  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44387, rend_intergenic: 38225  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58211, rend_intergenic: 44421  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77665, rend_intergenic: 65092  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86958, rend_intergenic: 77792  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113068, rend_intergenic: 87833  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123748, rend_intergenic: 113316  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154374, rend_intergenic: 152997  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165247, rend_intergenic: 154535  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185639, rend_intergenic: 175898  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190433, rend_intergenic: 186498  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 215957, rend_intergenic: 211167  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 261285
-exon list size: 550


building trellis

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-found 38 predictions from path traversal
Error with prediction: snap lend_intergenic: 18081, rend_intergenic: 12131  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22833, rend_intergenic: 18492  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28120, rend_intergenic: 22876  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38149, rend_intergenic: 28846  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44387, rend_intergenic: 38225  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58211, rend_intergenic: 44421  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77665, rend_intergenic: 65092  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86958, rend_intergenic: 77792  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113068, rend_intergenic: 87833  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123748, rend_intergenic: 113316  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154374, rend_intergenic: 152997  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165247, rend_intergenic: 154535  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185639, rend_intergenic: 175898  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190433, rend_intergenic: 186498  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 215957, rend_intergenic: 211167  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 31 predictions persist after filtering for low support