-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_10/scaffold_10_17108142-17221967

-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 GeneMark_model.46161_t
Valid prediction for GeneMark_model.46155_t
Couldn't classify 61025, 61090
Sorry, prediction pasa_asmbl_5022.p1 fails validation.
(ACA)	 AG	61025-61090	GT	TGG
(GTG)	 AG	61294-61437	GT	ATG
(GAC)	 AG	61586-61746	GT	AGG
(GAG)	 AG	62067-62130	GT	CAG
(TAC)	 AG	62336-62394	GT	AGG
(GCA)	 AG	62535-62718	GT	AGG
(CAC)	 AG	63131-63230	GT	GAG
(CTT)	 AG	63757-63971	CA	AAC
-recovered pasa_asmbl_5022.p1, terminal, 63131, 63230
-recovered pasa_asmbl_5022.p1, terminal, 63757, 63971
-recovered pasa_asmbl_5022.p1, internal, 61025, 61090
-recovered pasa_asmbl_5022.p1, internal, 61294, 61437
-recovered pasa_asmbl_5022.p1, internal, 61586, 61746
-recovered pasa_asmbl_5022.p1, internal, 62067, 62130
-recovered pasa_asmbl_5022.p1, internal, 62336, 62394
-recovered pasa_asmbl_5022.p1, internal, 62535, 62718
-recovered pasa_asmbl_5022.p1, internal, 63131, 63230
Valid prediction for GeneMark_model.46153_t
Valid prediction for snap_scaffold_10-snap.3488-T1
Valid prediction for snap_scaffold_10-snap.3497-T1
Valid prediction for snap_scaffold_10-snap.3506-T1
Valid prediction for GlimmerHMM_glimmerT_26733-T1
Couldn't classify 68859, 68937
Couldn't classify 73721, 73778
Sorry, prediction pasa_asmbl_5023.p1 fails validation.
(AGA)	 TC	68859-68937	GT	AGG
(ACT)	 AG	69113-69334	GT	GGG
(ACC)	 AG	69571-69662	GT	AGG
(GAC)	 AG	69955-70085	GT	AGG
(GCA)	 AG	70359-70516	GT	AGG
(ATC)	 AG	72311-72384	GT	AGG
(AGC)	 AG	73450-73577	GT	AAG
(TGA)	 AG	73721-73778	AG	AGA
-recovered pasa_asmbl_5023.p1, internal, 69113, 69334
-recovered pasa_asmbl_5023.p1, internal, 69571, 69662
-recovered pasa_asmbl_5023.p1, internal, 69955, 70085
-recovered pasa_asmbl_5023.p1, internal, 70359, 70516
-recovered pasa_asmbl_5023.p1, internal, 72311, 72384
-recovered pasa_asmbl_5023.p1, internal, 73450, 73577
Valid prediction for Augustus_model.g17912.t1
Valid prediction for GeneMark_model.46148_t
Valid prediction for GeneMark_model.46164_t
Valid prediction for snap_scaffold_10-snap.3503-T1
Valid prediction for GlimmerHMM_glimmerT_26734-T1
Valid prediction for snap_scaffold_10-snap.3483-T1
Couldn't classify 80071, 80139
Sorry, prediction pasa_asmbl_5025.p1 fails validation.
(AGC)	 CC	80071-80139	GT	AGG
(GTG)	 AG	80217-80330	GT	TTG
(AAA)	 AG	81004-81027	GT	AGG
(AGC)	 AG	82182-82271	GT	AGG
(ATG)	 AG	82822-82992	GT	AGG
(GTG)	 AG	83308-83451	GT	AGG
(TGT)	 AG	85018-85184	GT	AGG
(GAG)	 AG	86063-86129	GT	CTG
(ATA)	 AG	86313-86395	GT	AGG
(GGA)	 AG	88828-89011	GT	AGG
(AAT)	 AG	89706-89808	GT	ATG
(TGT)	 AG	92050-92258	TG	GAT
-recovered pasa_asmbl_5025.p1, initial, 82822, 82992
-recovered pasa_asmbl_5025.p1, terminal, 92050, 92258
-recovered pasa_asmbl_5025.p1, internal, 80217, 80330
-recovered pasa_asmbl_5025.p1, internal, 81004, 81027
-recovered pasa_asmbl_5025.p1, internal, 82182, 82271
-recovered pasa_asmbl_5025.p1, internal, 82822, 82992
-recovered pasa_asmbl_5025.p1, internal, 83308, 83451
-recovered pasa_asmbl_5025.p1, internal, 85018, 85184
-recovered pasa_asmbl_5025.p1, internal, 86063, 86129
-recovered pasa_asmbl_5025.p1, internal, 86313, 86395
-recovered pasa_asmbl_5025.p1, internal, 88828, 89011
-recovered pasa_asmbl_5025.p1, internal, 89706, 89808
Couldn't classify 103140, 103583
Sorry, prediction pasa_asmbl_3946.p1 fails validation.
(CTT)	 AG	103140-103583	CA	GCC
Valid prediction for GeneMark_model.46145_t
Valid prediction for snap_scaffold_10-snap.3479-T1
Valid prediction for GeneMark_model.46157_t
Valid prediction for snap_scaffold_10-snap.3490-T1
Valid prediction for snap_scaffold_10-snap.3494-T1
Valid prediction for snap_scaffold_10-snap.3493-T1
Valid prediction for GeneMark_model.46134_t
Valid prediction for Augustus_model.g17913.t1
Valid prediction for GeneMark_model.46149_t
Valid prediction for GeneMark_model.46140_t
Valid prediction for snap_scaffold_10-snap.3485-T1
Valid prediction for Augustus_model.g17914.t1
Couldn't classify 8488, 8609
Sorry, prediction pasa_asmbl_5016.p1 fails validation.
(GGC)	 AG	8488-8609	GT	GGG
(GAA)	 AG	8932-9043	GT	GGG
(GAG)	 AG	9575-9738	GT	GTG
(GCT)	 AG	10348-10495	GT	AGG
(GAT)	 AG	11389-11619	AA	GAA
-recovered pasa_asmbl_5016.p1, terminal, 11389, 11619
-recovered pasa_asmbl_5016.p1, internal, 8488, 8609
-recovered pasa_asmbl_5016.p1, internal, 8932, 9043
-recovered pasa_asmbl_5016.p1, internal, 9575, 9738
-recovered pasa_asmbl_5016.p1, internal, 10348, 10495
Valid prediction for GeneMark_model.46151_t
Valid prediction for GeneMark_model.46159_t
Valid prediction for GlimmerHMM_glimmerT_26735-T1
Valid prediction for snap_scaffold_10-snap.3481-T1
Valid prediction for snap_scaffold_10-snap.3504-T1
Valid prediction for GeneMark_model.46138_t
Valid prediction for GeneMark_model.46135_t
Valid prediction for snap_scaffold_10-snap.3489-T1
Valid prediction for CodingQuarry_transcript_5673-T1
Valid prediction for snap_scaffold_10-snap.3498-T1
Sorry, intron length (3) is less than minimum required (10)

-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 GeneMark_model.46160_t
Valid prediction for GlimmerHMM_glimmerT_26731-T1
Valid prediction for HiQ_model.g17911.t1
Valid prediction for GeneMark_model.46136_t
Valid prediction for snap_scaffold_10-snap.3496-T1
Valid prediction for snap_scaffold_10-snap.3480-T1
Valid prediction for snap_scaffold_10-snap.3499-T1
Valid prediction for Augustus_model.g17909.t1
Valid prediction for GeneMark_model.46143_t
Valid prediction for GeneMark_model.46165_t
Valid prediction for CodingQuarry_transcript_5672-T1
Valid prediction for snap_scaffold_10-snap.3495-T1
Valid prediction for GeneMark_model.46150_t
Valid prediction for GeneMark_model.46141_t
Valid prediction for snap_scaffold_10-snap.3501-T1
Valid prediction for GeneMark_model.46154_t
Valid prediction for snap_scaffold_10-snap.3482-T1
Valid prediction for snap_scaffold_10-snap.3484-T1
Valid prediction for snap_scaffold_10-snap.3505-T1
Valid prediction for GlimmerHMM_glimmerT_26729-T1
Valid prediction for GeneMark_model.46142_t
Valid prediction for GlimmerHMM_glimmerT_26736-T1
Valid prediction for snap_scaffold_10-snap.3492-T1
Valid prediction for snap_scaffold_10-snap.3486-T1
Valid prediction for GlimmerHMM_glimmerT_26732-T1
Valid prediction for GeneMark_model.46162_t
Valid prediction for Augustus_model.g17910.t1
Valid prediction for GlimmerHMM_glimmerT_26727-T1
Valid prediction for HiQ_model.g17915.t1
Valid prediction for GlimmerHMM_glimmerT_26728-T1
Valid prediction for snap_scaffold_10-snap.3487-T1
Valid prediction for GeneMark_model.46139_t
Valid prediction for Augustus_model.g17916.t1
Valid prediction for GeneMark_model.46146_t
Valid prediction for GeneMark_model.46144_t
Valid prediction for pasa_asmbl_3938.p1
Valid prediction for snap_scaffold_10-snap.3502-T1
Valid prediction for GlimmerHMM_glimmerT_26730-T1
Valid prediction for snap_scaffold_10-snap.3500-T1
Valid prediction for GeneMark_model.46133_t
Valid prediction for pasa_asmbl_3937.p1
Valid prediction for GeneMark_model.46156_t
Valid prediction for GeneMark_model.46158_t
Valid prediction for GeneMark_model.46152_t
Valid prediction for GlimmerHMM_glimmerT_26737-T1
Valid prediction for snap_scaffold_10-snap.3491-T1
Valid prediction for GlimmerHMM_glimmerT_26726-T1
Valid prediction for GeneMark_model.46147_t
Valid prediction for GeneMark_model.46137_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9682, rend_intergenic: 8506  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11613, rend_intergenic: 10370  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17409, rend_intergenic: 14256  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23980, rend_intergenic: 17570  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35466, rend_intergenic: 28756  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51712, rend_intergenic: 47712  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60474, rend_intergenic: 55626  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92258, rend_intergenic: 64792  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103385, rend_intergenic: 99086  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109649, rend_intergenic: 103558  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112075, rend_intergenic: 109656  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 113826
-exon list size: 449


building trellis

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98.0    
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98.4    
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98.9    
99.1    
99.3    
99.6    
99.8    
-found 14 predictions from path traversal
Error with prediction: snap lend_intergenic: 9682, rend_intergenic: 8506  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11613, rend_intergenic: 10370  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17409, rend_intergenic: 14256  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23980, rend_intergenic: 17570  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35466, rend_intergenic: 28756  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51712, rend_intergenic: 47712  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60474, rend_intergenic: 55626  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92258, rend_intergenic: 64792  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103385, rend_intergenic: 99086  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109649, rend_intergenic: 103558  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112075, rend_intergenic: 109656  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 11 predictions persist after filtering for low support