-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_20/scaffold_20_4463529-4622473

-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.82085_t
Valid prediction for GlimmerHMM_glimmerT_46993-T1
Valid prediction for GeneMark_model.82063_t
Valid prediction for snap_scaffold_20-snap.970-T1
Valid prediction for HiQ_model.g31359.t1
Valid prediction for snap_scaffold_20-snap.984-T1
Valid prediction for snap_scaffold_20-snap.990-T1
Couldn't classify 98369, 98495
Sorry, prediction pasa_asmbl_25748.p1 fails validation.
(CAG)	 CC	98369-98495	GT	CGG
(CTC)	 AG	98712-98826	GT	ATG
(AGT)	 AG	98950-99033	GT	AGG
(GGT)	 AG	99269-99329	GA	GAG
-recovered pasa_asmbl_25748.p1, terminal, 99269, 99329
-recovered pasa_asmbl_25748.p1, internal, 98712, 98826
-recovered pasa_asmbl_25748.p1, internal, 98950, 99033
Valid prediction for Augustus_model.g31358.t1
Valid prediction for snap_scaffold_20-snap.976-T1
Valid prediction for Augustus_model.g31352.t1
Valid prediction for snap_scaffold_20-snap.1002-T1
Valid prediction for GeneMark_model.82069_t
Valid prediction for GeneMark_model.82067_t
Valid prediction for GeneMark_model.82078_t
Valid prediction for snap_scaffold_20-snap.973-T1
Valid prediction for snap_scaffold_20-snap.991-T1
Valid prediction for GeneMark_model.82082_t
Valid prediction for GeneMark_model.82101_t
Valid prediction for GeneMark_model.82094_t
Valid prediction for GlimmerHMM_glimmerT_46994-T1
Valid prediction for snap_scaffold_20-snap.996-T1
Valid prediction for GeneMark_model.82068_t
Valid prediction for GeneMark_model.82097_t
Valid prediction for snap_scaffold_20-snap.971-T1
Valid prediction for GeneMark_model.82083_t
Valid prediction for snap_scaffold_20-snap.977-T1
Valid prediction for GeneMark_model.82080_t
Valid prediction for GeneMark_model.82065_t
Valid prediction for snap_scaffold_20-snap.978-T1
Valid prediction for snap_scaffold_20-snap.979-T1
Valid prediction for GeneMark_model.82088_t
Valid prediction for GeneMark_model.82074_t
Valid prediction for snap_scaffold_20-snap.987-T1
Valid prediction for GeneMark_model.82061_t
Valid prediction for GeneMark_model.82099_t
Valid prediction for snap_scaffold_20-snap.999-T1
Valid prediction for GlimmerHMM_glimmerT_47010-T1
Valid prediction for GeneMark_model.82096_t
Valid prediction for GlimmerHMM_glimmerT_47012-T1
Valid prediction for GeneMark_model.82059_t
Valid prediction for GlimmerHMM_glimmerT_47005-T1
Valid prediction for snap_scaffold_20-snap.997-T1
Valid prediction for GeneMark_model.82093_t
Valid prediction for GlimmerHMM_glimmerT_47001-T1
Valid prediction for snap_scaffold_20-snap.993-T1
Valid prediction for GlimmerHMM_glimmerT_46992-T1
Valid prediction for snap_scaffold_20-snap.1000-T1
Valid prediction for GlimmerHMM_glimmerT_47000-T1
Valid prediction for CodingQuarry_transcript_30439-T1
Valid prediction for GlimmerHMM_glimmerT_47009-T1
Valid prediction for GeneMark_model.82077_t

-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_46991-T1
Valid prediction for snap_scaffold_20-snap.988-T1
Valid prediction for GeneMark_model.82060_t
Valid prediction for GlimmerHMM_glimmerT_46997-T1
Valid prediction for GlimmerHMM_glimmerT_46996-T1
Valid prediction for snap_scaffold_20-snap.989-T1
Valid prediction for GeneMark_model.82087_t
Valid prediction for snap_scaffold_20-snap.995-T1
Valid prediction for GeneMark_model.82072_t
Valid prediction for GeneMark_model.82100_t
Valid prediction for CodingQuarry_transcript_30438-T1
Valid prediction for GlimmerHMM_glimmerT_46999-T1
Valid prediction for HiQ_model.g31354.t1
Valid prediction for snap_scaffold_20-snap.986-T1
Couldn't classify 110835, 110864
Sorry, prediction pasa_asmbl_26665.p2 fails validation.
(CGT)	 TG	110835-110864	GT	AGG
(ATG)	 AG	111425-111555	GT	AAG
(GCT)	 AG	111781-111877	GT	AGG
(TTC)	 AG	112145-112216	GT	CAG
(AAC)	 AG	112349-112411	GT	AGG
(TTG)	 AG	112557-112688	TC	AAT
-recovered pasa_asmbl_26665.p2, initial, 111425, 111555
-recovered pasa_asmbl_26665.p2, terminal, 112557, 112688
-recovered pasa_asmbl_26665.p2, internal, 111425, 111555
-recovered pasa_asmbl_26665.p2, internal, 111781, 111877
-recovered pasa_asmbl_26665.p2, internal, 112145, 112216
-recovered pasa_asmbl_26665.p2, internal, 112349, 112411
Valid prediction for GlimmerHMM_glimmerT_47011-T1
Valid prediction for GlimmerHMM_glimmerT_47007-T1
Valid prediction for GeneMark_model.82071_t
Valid prediction for snap_scaffold_20-snap.998-T1
Valid prediction for snap_scaffold_20-snap.983-T1
Valid prediction for Augustus_model.g31356.t1
Valid prediction for GeneMark_model.82084_t
Valid prediction for Augustus_model.g31355.t1
Valid prediction for GeneMark_model.82064_t
Valid prediction for GlimmerHMM_glimmerT_46998-T1
Valid prediction for GlimmerHMM_glimmerT_47003-T1
Valid prediction for GlimmerHMM_glimmerT_46995-T1
Valid prediction for GeneMark_model.82070_t
Couldn't classify 125708, 125840
Couldn't classify 126729, 126902
Sorry, prediction pasa_asmbl_27219.p1 fails validation.
(GTG)	 GT	125708-125840	GT	CTG
(GCA)	 AG	126246-126346	GT	GGG
(TCT)	 AG	126729-126902	CC	TAC
-recovered pasa_asmbl_27219.p1, internal, 126246, 126346
Valid prediction for GeneMark_model.82098_t
Valid prediction for snap_scaffold_20-snap.974-T1
Valid prediction for GeneMark_model.82062_t
Valid prediction for snap_scaffold_20-snap.975-T1
Valid prediction for snap_scaffold_20-snap.969-T1
Valid prediction for GeneMark_model.82089_t
Valid prediction for GeneMark_model.82079_t
Couldn't classify 131652, 131802
Couldn't classify 134739, 134813
Sorry, prediction pasa_asmbl_27188.p1 fails validation.
(GGT)	 AA	131652-131802	GT	AGG
(GAC)	 AG	131923-131986	GT	AGG
(TAT)	 AG	132202-132370	GT	AGG
(CTG)	 AG	132672-132854	GT	TGG
(AGG)	 AG	133111-133229	GT	AGG
(AGG)	 AG	133709-133865	GT	AGG
(GCA)	 AG	134425-134541	GT	AGG
(GAC)	 AG	134739-134813	TG	AGT
-recovered pasa_asmbl_27188.p1, internal, 131923, 131986
-recovered pasa_asmbl_27188.p1, internal, 132202, 132370
-recovered pasa_asmbl_27188.p1, internal, 132672, 132854
-recovered pasa_asmbl_27188.p1, internal, 133111, 133229
-recovered pasa_asmbl_27188.p1, internal, 133709, 133865
-recovered pasa_asmbl_27188.p1, internal, 134425, 134541
Valid prediction for snap_scaffold_20-snap.994-T1
Valid prediction for GeneMark_model.82091_t
Valid prediction for Augustus_model.g31353.t1
Valid prediction for GeneMark_model.82081_t
Valid prediction for snap_scaffold_20-snap.1003-T1
Couldn't classify 138095, 138221
Sorry, prediction pasa_asmbl_26655.p1 fails validation.
(CCT)	 CC	138095-138221	GT	AGG
(GGT)	 AG	140690-140806	GC	AGG
(CGG)	 AG	142670-142818	GT	AGG
(GTC)	 AG	143161-143313	GT	ACG
(GAT)	 AG	143764-143880	GT	ACG
(ACG)	 AG	144099-144186	GT	CGG
(AGG)	 AG	144418-144581	GT	CGG
(GAT)	 AG	144698-144763	CA	GAC
-recovered pasa_asmbl_26655.p1, terminal, 144698, 144763
-recovered pasa_asmbl_26655.p1, internal, 140690, 140806
-recovered pasa_asmbl_26655.p1, internal, 142670, 142818
-recovered pasa_asmbl_26655.p1, internal, 143161, 143313
-recovered pasa_asmbl_26655.p1, internal, 143764, 143880
-recovered pasa_asmbl_26655.p1, internal, 144099, 144186
-recovered pasa_asmbl_26655.p1, internal, 144418, 144581
Valid prediction for snap_scaffold_20-snap.981-T1
Valid prediction for GlimmerHMM_glimmerT_47004-T1
Valid prediction for GeneMark_model.82086_t
Valid prediction for Augustus_model.g31357.t1
Valid prediction for GlimmerHMM_glimmerT_47008-T1
Valid prediction for snap_scaffold_20-snap.980-T1
Valid prediction for GeneMark_model.82095_t
Valid prediction for GeneMark_model.82066_t
Valid prediction for GeneMark_model.82073_t
Valid prediction for GlimmerHMM_glimmerT_47002-T1
Valid prediction for GeneMark_model.82090_t
Valid prediction for GeneMark_model.82092_t
Valid prediction for GeneMark_model.82076_t
Valid prediction for snap_scaffold_20-snap.992-T1
Valid prediction for snap_scaffold_20-snap.982-T1
Valid prediction for snap_scaffold_20-snap.1001-T1
Valid prediction for GlimmerHMM_glimmerT_47006-T1
Valid prediction for GeneMark_model.82075_t
Valid prediction for snap_scaffold_20-snap.985-T1
Valid prediction for snap_scaffold_20-snap.972-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17637, rend_intergenic: 13697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41331, rend_intergenic: 19553  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61568, rend_intergenic: 57857  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74370, rend_intergenic: 70811  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88232, rend_intergenic: 86265  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103947, rend_intergenic: 102286  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 158945
-exon list size: 489


building trellis

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-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 17637, rend_intergenic: 13697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41331, rend_intergenic: 19553  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61568, rend_intergenic: 57857  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74370, rend_intergenic: 70811  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88232, rend_intergenic: 86265  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103947, rend_intergenic: 102286  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 13 predictions persist after filtering for low support