-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_22/scaffold_22_1570923-1839041

-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 snap_scaffold_22-snap.291-T1
Valid prediction for GlimmerHMM_glimmerT_48967-T1
Valid prediction for snap_scaffold_22-snap.298-T1
Valid prediction for snap_scaffold_22-snap.306-T1
Valid prediction for pasa_asmbl_30536.p1
Valid prediction for snap_scaffold_22-snap.288-T1
Valid prediction for snap_scaffold_22-snap.305-T1
Valid prediction for GlimmerHMM_glimmerT_48963-T1
Valid prediction for pasa_asmbl_29925.p1
Valid prediction for HiQ_model.g32698.t1
Valid prediction for Augustus_model.g32704.t1
Valid prediction for snap_scaffold_22-snap.275-T1
Valid prediction for Augustus_model.g32705.t1
Valid prediction for snap_scaffold_22-snap.287-T1
Valid prediction for GlimmerHMM_glimmerT_48973-T1
Valid prediction for Augustus_model.g32692.t1
Valid prediction for Augustus_model.g32706.t1
Valid prediction for GlimmerHMM_glimmerT_48977-T1
Valid prediction for snap_scaffold_22-snap.290-T1
Valid prediction for Augustus_model.g32695.t1
Couldn't classify 128109, 128138
Sorry, prediction pasa_asmbl_29926.p1 fails validation.
(CTG)	 CA	128109-128138	GT	AGG
(ATG)	 AG	129028-129099	GT	AGG
(ATT)	 AG	129209-129311	GT	AGG
(TTC)	 AG	129676-129756	GT	AGG
(GAC)	 AG	129913-130041	GT	TGG
(GTG)	 AG	130227-130342	GT	CGG
(TCT)	 AG	130477-130737	GT	AGG
(GAC)	 AG	130856-130945	GT	AGG
(ACT)	 AG	131242-131419	GT	AGG
(ATG)	 AG	131950-132047	GT	AGG
(GCA)	 AG	132699-132947	GT	AGG
(TTT)	 AG	133281-133356	GT	AGG
(CTG)	 AG	133717-133790	CA	AGC
-recovered pasa_asmbl_29926.p1, initial, 129028, 129099
add_exon() Sorry, pasa_asmbl_29926.p1 131950-132047-initial-1 is invalid.
-recovered pasa_asmbl_29926.p1, initial, 131950, 132047
-recovered pasa_asmbl_29926.p1, terminal, 129209, 129311
-recovered pasa_asmbl_29926.p1, terminal, 133717, 133790
-recovered pasa_asmbl_29926.p1, internal, 129028, 129099
-recovered pasa_asmbl_29926.p1, internal, 129209, 129311
-recovered pasa_asmbl_29926.p1, internal, 129676, 129756
-recovered pasa_asmbl_29926.p1, internal, 129913, 130041
-recovered pasa_asmbl_29926.p1, internal, 130227, 130342
-recovered pasa_asmbl_29926.p1, internal, 130477, 130737
-recovered pasa_asmbl_29926.p1, internal, 130856, 130945
-recovered pasa_asmbl_29926.p1, internal, 131242, 131419
-recovered pasa_asmbl_29926.p1, internal, 131950, 132047
-recovered pasa_asmbl_29926.p1, internal, 132699, 132947
-recovered pasa_asmbl_29926.p1, internal, 133281, 133356
Valid prediction for snap_scaffold_22-snap.293-T1
Valid prediction for GlimmerHMM_glimmerT_48966-T1
Valid prediction for snap_scaffold_22-snap.308-T1
Valid prediction for snap_scaffold_22-snap.301-T1
Valid prediction for snap_scaffold_22-snap.278-T1
Valid prediction for CodingQuarry_transcript_34109-T1
Valid prediction for GlimmerHMM_glimmerT_48974-T1
Couldn't classify 218471, 218529
Couldn't classify 222151, 222282
Sorry, prediction pasa_asmbl_29934.p1 fails validation.
(GAC)	 CA	218471-218529	GT	AGG
(GAG)	 AG	219640-219757	GT	AGG
(GCT)	 AG	222151-222282	GA	GTG
-recovered pasa_asmbl_29934.p1, internal, 219640, 219757
Valid prediction for CodingQuarry_transcript_34111-T1
Valid prediction for Augustus_model.g32703.t1
Valid prediction for snap_scaffold_22-snap.300-T1
Couldn't classify 149203, 149258
Sorry, prediction pasa_asmbl_29929.p1 fails validation.
(GTG)	 CT	149203-149258	GT	AGG
(TGC)	 AG	149540-149604	GT	TGG
(GTG)	 AG	149732-149837	GT	AGG
(TTA)	 AG	149917-150005	GT	TGG
(TTT)	 AG	150193-150240	GT	AGG
(CGG)	 AG	150375-150517	GT	AGG
(CCC)	 AG	150728-150826	TG	GAT
-recovered pasa_asmbl_29929.p1, terminal, 150728, 150826
-recovered pasa_asmbl_29929.p1, internal, 149540, 149604
-recovered pasa_asmbl_29929.p1, internal, 149732, 149837
-recovered pasa_asmbl_29929.p1, internal, 149917, 150005
-recovered pasa_asmbl_29929.p1, internal, 150193, 150240
-recovered pasa_asmbl_29929.p1, internal, 150375, 150517
Valid prediction for GlimmerHMM_glimmerT_48978-T1
Valid prediction for GlimmerHMM_glimmerT_48976-T1
Valid prediction for GlimmerHMM_glimmerT_48968-T1
Valid prediction for Augustus_model.g32699.t1
Valid prediction for Augustus_model.g32693.t1
Valid prediction for GlimmerHMM_glimmerT_48972-T1
Valid prediction for snap_scaffold_22-snap.283-T1
Valid prediction for snap_scaffold_22-snap.310-T1
Valid prediction for snap_scaffold_22-snap.304-T1
Valid prediction for GlimmerHMM_glimmerT_48965-T1
Valid prediction for snap_scaffold_22-snap.289-T1
Couldn't classify 82909, 83008
Couldn't classify 83439, 83538
Sorry, prediction pasa_asmbl_29923.p1 fails validation.
(TAC)	 AC	82909-83008	GT	CAG
(ATG)	 AG	83154-83301	GT	AGG
(CTA)	 AG	83439-83538	AA	ACA
add_exon() Sorry, pasa_asmbl_29923.p1 83154-83301-initial-1 is invalid.
-recovered pasa_asmbl_29923.p1, initial, 83154, 83301
-recovered pasa_asmbl_29923.p1, internal, 83154, 83301
Valid prediction for snap_scaffold_22-snap.299-T1
Valid prediction for GlimmerHMM_glimmerT_48959-T1
Valid prediction for CodingQuarry_transcript_34110-T1
Couldn't classify 117788, 117883
Couldn't classify 119466, 119567
Sorry, prediction pasa_asmbl_30474.p1 fails validation.
(CTC)	 CA	117788-117883	GT	AGG
(GTC)	 AG	118612-118716	GT	AGG
(TTG)	 AG	119466-119567	GT	AGG
-recovered pasa_asmbl_30474.p1, internal, 118612, 118716
-recovered pasa_asmbl_30474.p1, internal, 119466, 119567
Valid prediction for Augustus_model.g32697.t1
Valid prediction for CodingQuarry_transcript_34108-T1
Valid prediction for snap_scaffold_22-snap.312-T1
Valid prediction for Augustus_model.g32702.t1
Valid prediction for HiQ_model.g32700.t1
Valid prediction for snap_scaffold_22-snap.276-T1
Valid prediction for GlimmerHMM_glimmerT_48970-T1
Valid prediction for snap_scaffold_22-snap.297-T1
Couldn't classify 168107, 168184
Sorry, prediction pasa_asmbl_29932.p1 fails validation.
(GTT)	 AG	168107-168184	GT	AGG
(GGC)	 AG	168895-168933	GT	AGG
(CCG)	 AG	171353-171415	GT	ACG
(GGG)	 AG	173842-173992	GT	ATG
(ATG)	 AG	175644-175771	GT	AGG
(ATT)	 AG	176931-176993	AG	GAA
-recovered pasa_asmbl_29932.p1, initial, 175644, 175771
-recovered pasa_asmbl_29932.p1, terminal, 176931, 176993
-recovered pasa_asmbl_29932.p1, internal, 168107, 168184
-recovered pasa_asmbl_29932.p1, internal, 168895, 168933
-recovered pasa_asmbl_29932.p1, internal, 171353, 171415
-recovered pasa_asmbl_29932.p1, internal, 173842, 173992
-recovered pasa_asmbl_29932.p1, internal, 175644, 175771

-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_22-snap.282-T1
Valid prediction for snap_scaffold_22-snap.295-T1
Valid prediction for snap_scaffold_22-snap.309-T1
Valid prediction for Augustus_model.g32690.t1
Valid prediction for Augustus_model.g32694.t1
Valid prediction for GlimmerHMM_glimmerT_48964-T1
Valid prediction for GlimmerHMM_glimmerT_48958-T1
Valid prediction for snap_scaffold_22-snap.286-T1
Valid prediction for GlimmerHMM_glimmerT_48975-T1
Valid prediction for snap_scaffold_22-snap.311-T1
Valid prediction for GlimmerHMM_glimmerT_48971-T1
Valid prediction for snap_scaffold_22-snap.294-T1
Valid prediction for snap_scaffold_22-snap.279-T1
Valid prediction for snap_scaffold_22-snap.307-T1
Valid prediction for GlimmerHMM_glimmerT_48969-T1
Valid prediction for snap_scaffold_22-snap.281-T1
Valid prediction for GlimmerHMM_glimmerT_48960-T1
Valid prediction for snap_scaffold_22-snap.285-T1
Valid prediction for Augustus_model.g32691.t1
Valid prediction for snap_scaffold_22-snap.292-T1
Valid prediction for GlimmerHMM_glimmerT_48962-T1
Valid prediction for snap_scaffold_22-snap.280-T1
Valid prediction for snap_scaffold_22-snap.313-T1
Valid prediction for snap_scaffold_22-snap.284-T1
Valid prediction for HiQ_model.g32696.t1
Valid prediction for GlimmerHMM_glimmerT_48961-T1
Valid prediction for snap_scaffold_22-snap.303-T1
Valid prediction for snap_scaffold_22-snap.296-T1
Valid prediction for pasa_asmbl_29147.p1
Couldn't classify 76398, 76587
Sorry, prediction pasa_asmbl_29152.p1 fails validation.
(GGA)	 AG	76398-76587	GT	GGG
(GCA)	 AG	77157-77329	GT	CTG
(GGC)	 AG	77790-77897	GT	AGG
(AGC)	 AG	78668-78718	CA	AAC
-recovered pasa_asmbl_29152.p1, terminal, 78668, 78718
-recovered pasa_asmbl_29152.p1, internal, 76398, 76587
-recovered pasa_asmbl_29152.p1, internal, 77157, 77329
-recovered pasa_asmbl_29152.p1, internal, 77790, 77897
Valid prediction for snap_scaffold_22-snap.302-T1
Valid prediction for HiQ_model.g32701.t1
Valid prediction for snap_scaffold_22-snap.277-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 234649, rend_intergenic: 230820  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 256865, rend_intergenic: 254639  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 263667, rend_intergenic: 262250  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 264978, rend_intergenic: 263696  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 268119
-exon list size: 329


building trellis

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98.2    
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99.1    
99.4    
99.7    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 234649, rend_intergenic: 230820  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 256865, rend_intergenic: 254639  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 263667, rend_intergenic: 262250  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 264978, rend_intergenic: 263696  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 16509
-exon list size: 1


building trellis

33.3    
66.7    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support