-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_17/scaffold_17_13739478-13909520

-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 100594, 101049
Sorry, prediction pasa_asmbl_18475.p1 fails validation.
(AGC)	 CA	100594-101049	GT	AGG
(GCC)	 AG	101483-101875	GT	AGG
(GTG)	 AG	102247-102482	GT	AGG
(TCC)	 AG	103428-104097	TG	GAT
-recovered pasa_asmbl_18475.p1, terminal, 103428, 104097
-recovered pasa_asmbl_18475.p1, internal, 101483, 101875
-recovered pasa_asmbl_18475.p1, internal, 102247, 102482
Valid prediction for snap_scaffold_17-snap.2872-T1
Valid prediction for GeneMark_model.73249_t
Valid prediction for snap_scaffold_17-snap.2882-T1
Valid prediction for pasa_asmbl_18473.p1
Valid prediction for GlimmerHMM_glimmerT_42367-T1
Valid prediction for Augustus_model.g28373.t1
Valid prediction for GeneMark_model.73240_t
Valid prediction for Augustus_model.g28374.t1
Valid prediction for GeneMark_model.73253_t
Valid prediction for GlimmerHMM_glimmerT_42356-T1
Valid prediction for GlimmerHMM_glimmerT_42354-T1
Valid prediction for GeneMark_model.73248_t
Valid prediction for GeneMark_model.73251_t
Valid prediction for GeneMark_model.73254_t
Valid prediction for GlimmerHMM_glimmerT_42368-T1
Valid prediction for snap_scaffold_17-snap.2856-T1
Valid prediction for GlimmerHMM_glimmerT_42351-T1
Valid prediction for GlimmerHMM_glimmerT_42374-T1
Valid prediction for GeneMark_model.73245_t
Valid prediction for GlimmerHMM_glimmerT_42348-T1
Valid prediction for GlimmerHMM_glimmerT_42371-T1
Valid prediction for GlimmerHMM_glimmerT_42361-T1
Valid prediction for GlimmerHMM_glimmerT_42365-T1
Valid prediction for GeneMark_model.73238_t
Valid prediction for GeneMark_model.73266_t
Valid prediction for snap_scaffold_17-snap.2858-T1
Valid prediction for snap_scaffold_17-snap.2868-T1
Valid prediction for snap_scaffold_17-snap.2866-T1
Valid prediction for Augustus_model.g28372.t1
Valid prediction for GeneMark_model.73259_t
Valid prediction for GeneMark_model.73246_t
Valid prediction for GlimmerHMM_glimmerT_42349-T1
Valid prediction for snap_scaffold_17-snap.2881-T1
Valid prediction for GlimmerHMM_glimmerT_42353-T1
Valid prediction for GeneMark_model.73268_t
Valid prediction for snap_scaffold_17-snap.2862-T1
Valid prediction for Augustus_model.g28375.t1
Valid prediction for Augustus_model.g28362.t1
Valid prediction for snap_scaffold_17-snap.2879-T1
Valid prediction for GeneMark_model.73267_t
Valid prediction for GlimmerHMM_glimmerT_42372-T1
Valid prediction for snap_scaffold_17-snap.2855-T1
Valid prediction for snap_scaffold_17-snap.2852-T1
Valid prediction for snap_scaffold_17-snap.2877-T1
Valid prediction for Augustus_model.g28377.t1
Couldn't classify 67265, 67425
Couldn't classify 67802, 67993
Sorry, prediction pasa_asmbl_18643.p1 fails validation.
(GCG)	 CA	67265-67425	GT	AGG
(GCC)	 AG	67602-67692	GT	CTG
(GTG)	 AG	67802-67993	CA	ACC
-recovered pasa_asmbl_18643.p1, internal, 67602, 67692
Valid prediction for GlimmerHMM_glimmerT_42347-T1
Valid prediction for GeneMark_model.73256_t
Valid prediction for GeneMark_model.73270_t
Valid prediction for HiQ_model.g28364.t1
Valid prediction for GeneMark_model.73239_t
Valid prediction for snap_scaffold_17-snap.2874-T1
Valid prediction for snap_scaffold_17-snap.2869-T1
Valid prediction for GeneMark_model.73242_t
Valid prediction for HiQ_model.g28368.t1
Valid prediction for GeneMark_model.73258_t
Valid prediction for GlimmerHMM_glimmerT_42362-T1
Valid prediction for GlimmerHMM_glimmerT_42358-T1
Valid prediction for Augustus_model.g28367.t1
Valid prediction for GeneMark_model.73264_t
Valid prediction for HiQ_model.g28359.t1
Valid prediction for GeneMark_model.73262_t
Couldn't classify 128397, 128612
Sorry, prediction pasa_asmbl_18477.p1 fails validation.
(TTT)	 GC	128397-128612	GT	AGG
(GAT)	 AG	128802-128900	GT	CTG
(GCC)	 AG	129022-129139	GT	GGG
(TGG)	 AG	129313-129411	GT	TGG
(GCT)	 AG	129700-130293	GT	AGG
(GAG)	 AG	130415-130594	GT	AGG
(CTT)	 AG	130909-131763	GT	AGG
(ATA)	 AG	132109-132714	GT	AGG
(CAA)	 AG	132825-133046	GT	AGG
(GAG)	 AG	133512-133683	GT	GGG
(GTC)	 AG	134123-134213	AA	AGA
-recovered pasa_asmbl_18477.p1, terminal, 134123, 134213
-recovered pasa_asmbl_18477.p1, internal, 128802, 128900
-recovered pasa_asmbl_18477.p1, internal, 129022, 129139
-recovered pasa_asmbl_18477.p1, internal, 129313, 129411
-recovered pasa_asmbl_18477.p1, internal, 129700, 130293
-recovered pasa_asmbl_18477.p1, internal, 130415, 130594
-recovered pasa_asmbl_18477.p1, internal, 130909, 131763
-recovered pasa_asmbl_18477.p1, internal, 132109, 132714
-recovered pasa_asmbl_18477.p1, internal, 132825, 133046
-recovered pasa_asmbl_18477.p1, internal, 133512, 133683
Valid prediction for snap_scaffold_17-snap.2851-T1
Valid prediction for snap_scaffold_17-snap.2888-T1
Valid prediction for snap_scaffold_17-snap.2884-T1
Valid prediction for Augustus_model.g28361.t1
Valid prediction for GlimmerHMM_glimmerT_42373-T1
Valid prediction for snap_scaffold_17-snap.2889-T1
Valid prediction for snap_scaffold_17-snap.2864-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_17-snap.2857-T1
Valid prediction for GeneMark_model.73260_t
Valid prediction for GlimmerHMM_glimmerT_42366-T1
Valid prediction for CodingQuarry_transcript_22198-T1
Valid prediction for GlimmerHMM_glimmerT_42350-T1
Valid prediction for Augustus_model.g28358.t1
Valid prediction for GlimmerHMM_glimmerT_42363-T1
Valid prediction for CodingQuarry_transcript_22199-T1
Valid prediction for snap_scaffold_17-snap.2873-T1
Valid prediction for GlimmerHMM_glimmerT_42344-T1
Valid prediction for GeneMark_model.73261_t
Valid prediction for HiQ_model.g28376.t1
Valid prediction for snap_scaffold_17-snap.2853-T1
Valid prediction for snap_scaffold_17-snap.2887-T1
Valid prediction for snap_scaffold_17-snap.2876-T1
Valid prediction for GlimmerHMM_glimmerT_42357-T1
Valid prediction for pasa_asmbl_19426.p1
Valid prediction for GeneMark_model.73255_t
Valid prediction for HiQ_model.g28369.t1
Valid prediction for Augustus_model.g28366.t1
Valid prediction for Augustus_model.g28365.t1
Valid prediction for CodingQuarry_transcript_22196-T1
Valid prediction for CodingQuarry_transcript_22197-T1
Couldn't classify 63934, 63967
Sorry, prediction pasa_asmbl_19427.p1 fails validation.
(TCT)	 GT	63934-63967	GT	AGG
(CTG)	 AG	64676-64744	GT	TGG
(GTT)	 AG	64922-65088	GT	AGG
(GAT)	 AG	65175-65252	GC	GAG
-recovered pasa_asmbl_19427.p1, terminal, 65175, 65252
-recovered pasa_asmbl_19427.p1, internal, 64676, 64744
-recovered pasa_asmbl_19427.p1, internal, 64922, 65088
-recovered pasa_asmbl_19427.p1, internal, 65175, 65252
Valid prediction for GeneMark_model.73265_t
Valid prediction for CodingQuarry_transcript_22200-T1
Valid prediction for snap_scaffold_17-snap.2880-T1
Valid prediction for GeneMark_model.73244_t
Couldn't classify 84610, 84801
Sorry, prediction pasa_asmbl_19425.p1 fails validation.
(TGT)	 GT	84610-84801	GT	CAG
(GAA)	 AG	85017-85143	GT	AGG
(ATA)	 AG	85340-85416	AA	GAA
-recovered pasa_asmbl_19425.p1, terminal, 85340, 85416
-recovered pasa_asmbl_19425.p1, internal, 85017, 85143
Valid prediction for GlimmerHMM_glimmerT_42359-T1
Valid prediction for snap_scaffold_17-snap.2878-T1
Valid prediction for GeneMark_model.73257_t
Valid prediction for snap_scaffold_17-snap.2886-T1
Valid prediction for GlimmerHMM_glimmerT_42369-T1
Valid prediction for snap_scaffold_17-snap.2860-T1
Valid prediction for snap_scaffold_17-snap.2867-T1
Valid prediction for GlimmerHMM_glimmerT_42345-T1
Valid prediction for GlimmerHMM_glimmerT_42352-T1
Valid prediction for GlimmerHMM_glimmerT_42376-T1
Valid prediction for snap_scaffold_17-snap.2863-T1
Valid prediction for pasa_asmbl_19432.p1
Valid prediction for GlimmerHMM_glimmerT_42360-T1
Valid prediction for GlimmerHMM_glimmerT_42370-T1
Valid prediction for HiQ_model.g28363.t1
Valid prediction for GeneMark_model.73252_t
Valid prediction for GeneMark_model.73250_t
Valid prediction for snap_scaffold_17-snap.2871-T1
Valid prediction for GlimmerHMM_glimmerT_42364-T1
Valid prediction for pasa_asmbl_19430.p1
Valid prediction for snap_scaffold_17-snap.2870-T1
Valid prediction for GeneMark_model.73243_t
Valid prediction for GlimmerHMM_glimmerT_42346-T1
Valid prediction for GlimmerHMM_glimmerT_42375-T1
Valid prediction for GeneMark_model.73241_t
Valid prediction for snap_scaffold_17-snap.2865-T1
Valid prediction for GlimmerHMM_glimmerT_42355-T1
Valid prediction for snap_scaffold_17-snap.2849-T1
Valid prediction for GeneMark_model.73247_t
Valid prediction for snap_scaffold_17-snap.2861-T1
Valid prediction for snap_scaffold_17-snap.2875-T1
Valid prediction for snap_scaffold_17-snap.2885-T1
Valid prediction for GeneMark_model.73263_t
Valid prediction for snap_scaffold_17-snap.2850-T1
Valid prediction for HiQ_model.g28371.t1
Valid prediction for snap_scaffold_17-snap.2859-T1
Valid prediction for snap_scaffold_17-snap.2883-T1
Valid prediction for snap_scaffold_17-snap.2854-T1
Valid prediction for Augustus_model.g28360.t1
Valid prediction for GeneMark_model.73269_t
Valid prediction for HiQ_model.g28370.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7578, rend_intergenic: 4305  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 9121, rend_intergenic: 7958  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12200, rend_intergenic: 10432  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27401, rend_intergenic: 22699  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70951, rend_intergenic: 66407  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91040, rend_intergenic: 87710  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97278, rend_intergenic: 96709  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99526, rend_intergenic: 97892  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117887, rend_intergenic: 112821  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134213, rend_intergenic: 129692  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140870, rend_intergenic: 136971  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157575, rend_intergenic: 156644  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 170043
-exon list size: 571


building trellis

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99.8    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 7578, rend_intergenic: 4305  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 9121, rend_intergenic: 7958  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12200, rend_intergenic: 10432  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27401, rend_intergenic: 22699  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70951, rend_intergenic: 66407  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91040, rend_intergenic: 87710  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97278, rend_intergenic: 96709  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99526, rend_intergenic: 97892  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117887, rend_intergenic: 112821  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134213, rend_intergenic: 129692  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140870, rend_intergenic: 136971  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157575, rend_intergenic: 156644  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support