-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_18/scaffold_18_768782-949615

-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 129253, 129429
Sorry, prediction pasa_asmbl_20333.p1 fails validation.
(ATC)	 AA	129253-129429	GT	GGG
(AGC)	 AG	129548-129733	GT	CTG
(GCG)	 AG	129952-130091	GT	AGG
(GTC)	 AG	130163-130335	GT	ATG
(CCT)	 AG	130431-130547	GT	CGG
(TGG)	 AG	130630-130743	GT	AGG
(GTG)	 AG	130823-131021	GT	AGG
(GGT)	 AG	131120-131292	GT	AGG
(GTC)	 AG	131405-131516	GT	AGG
(GGG)	 AG	131644-131800	AA	AAA
add_exon() Sorry, pasa_asmbl_20333.p1 131120-131292-terminal-2 is invalid.
-recovered pasa_asmbl_20333.p1, terminal, 131120, 131292
-recovered pasa_asmbl_20333.p1, terminal, 131644, 131800
-recovered pasa_asmbl_20333.p1, internal, 129548, 129733
-recovered pasa_asmbl_20333.p1, internal, 129952, 130091
-recovered pasa_asmbl_20333.p1, internal, 130163, 130335
-recovered pasa_asmbl_20333.p1, internal, 130431, 130547
-recovered pasa_asmbl_20333.p1, internal, 130630, 130743
-recovered pasa_asmbl_20333.p1, internal, 130823, 131021
-recovered pasa_asmbl_20333.p1, internal, 131120, 131292
-recovered pasa_asmbl_20333.p1, internal, 131405, 131516
Valid prediction for GlimmerHMM_glimmerT_41682-T1
Valid prediction for Augustus_model.g27751.t1
Valid prediction for GlimmerHMM_glimmerT_41683-T1
Valid prediction for snap_scaffold_18-snap.138-T1
Valid prediction for GlimmerHMM_glimmerT_41685-T1
Valid prediction for GlimmerHMM_glimmerT_41684-T1
Valid prediction for snap_scaffold_18-snap.145-T1
Valid prediction for snap_scaffold_18-snap.176-T1
Valid prediction for GlimmerHMM_glimmerT_41703-T1
Valid prediction for HiQ_model.g27753.t1
Valid prediction for CodingQuarry_transcript_23650-T1
Valid prediction for snap_scaffold_18-snap.156-T1
Valid prediction for snap_scaffold_18-snap.148-T1
Valid prediction for snap_scaffold_18-snap.164-T1
Valid prediction for GlimmerHMM_glimmerT_41688-T1
Valid prediction for snap_scaffold_18-snap.158-T1
Valid prediction for GlimmerHMM_glimmerT_41702-T1
Valid prediction for GlimmerHMM_glimmerT_41697-T1
Valid prediction for CodingQuarry_transcript_23648-T1
Valid prediction for snap_scaffold_18-snap.142-T1
Valid prediction for snap_scaffold_18-snap.163-T1
Valid prediction for snap_scaffold_18-snap.141-T1
Couldn't classify 46060, 46144
Sorry, prediction pasa_asmbl_20323.p1 fails validation.
(GTG)	 GT	46060-46144	GT	AGG
(CTG)	 AG	46520-46596	GT	GGG
(AAC)	 AG	46677-46775	GT	AGG
(ATT)	 AG	47252-47324	GT	AGG
(CTG)	 AG	48128-48231	GC	GAG
-recovered pasa_asmbl_20323.p1, terminal, 48128, 48231
-recovered pasa_asmbl_20323.p1, internal, 46520, 46596
-recovered pasa_asmbl_20323.p1, internal, 46677, 46775
-recovered pasa_asmbl_20323.p1, internal, 47252, 47324
-recovered pasa_asmbl_20323.p1, internal, 48128, 48231
Valid prediction for snap_scaffold_18-snap.154-T1
Valid prediction for GlimmerHMM_glimmerT_41700-T1
Valid prediction for GlimmerHMM_glimmerT_41687-T1
Valid prediction for CodingQuarry_transcript_23649-T1
Valid prediction for snap_scaffold_18-snap.146-T1
Valid prediction for GlimmerHMM_glimmerT_41686-T1
Valid prediction for snap_scaffold_18-snap.144-T1
Valid prediction for GlimmerHMM_glimmerT_41701-T1
Valid prediction for HiQ_model.g27762.t1
Valid prediction for pasa_asmbl_20334.p1
Valid prediction for GlimmerHMM_glimmerT_41694-T1
Valid prediction for HiQ_model.g27754.t1
Valid prediction for snap_scaffold_18-snap.175-T1
Valid prediction for snap_scaffold_18-snap.171-T1
Valid prediction for snap_scaffold_18-snap.151-T1
Valid prediction for pasa_asmbl_20327.p1
Valid prediction for Augustus_model.g27757.t1
Valid prediction for snap_scaffold_18-snap.140-T1
Valid prediction for Augustus_model.g27760.t1
Valid prediction for CodingQuarry_transcript_23651-T1
Valid prediction for snap_scaffold_18-snap.160-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for pasa_asmbl_20320.p1
Valid prediction for snap_scaffold_18-snap.173-T1
Valid prediction for snap_scaffold_18-snap.167-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 GlimmerHMM_glimmerT_41698-T1
Couldn't classify 63804, 63870
Sorry, prediction pasa_asmbl_19608.p1 fails validation.
(CCC)	 CT	63804-63870	GT	AGG
(GTC)	 AG	63960-64013	GT	CGG
(CGG)	 AG	64798-64914	GT	TGG
(GTG)	 AG	65251-65628	GT	GGG
(GTC)	 AG	65739-66007	AG	GAA
-recovered pasa_asmbl_19608.p1, terminal, 65739, 66007
-recovered pasa_asmbl_19608.p1, internal, 63960, 64013
-recovered pasa_asmbl_19608.p1, internal, 64798, 64914
-recovered pasa_asmbl_19608.p1, internal, 65251, 65628
Valid prediction for GlimmerHMM_glimmerT_41693-T1
Valid prediction for Augustus_model.g27752.t1
Valid prediction for GlimmerHMM_glimmerT_41704-T1
Valid prediction for snap_scaffold_18-snap.162-T1
Valid prediction for GlimmerHMM_glimmerT_41691-T1
Valid prediction for GlimmerHMM_glimmerT_41695-T1
Valid prediction for GlimmerHMM_glimmerT_41696-T1
Valid prediction for snap_scaffold_18-snap.153-T1
Valid prediction for GlimmerHMM_glimmerT_41690-T1
Valid prediction for snap_scaffold_18-snap.165-T1
Valid prediction for GlimmerHMM_glimmerT_41699-T1
Valid prediction for snap_scaffold_18-snap.152-T1
Couldn't classify 56078, 56197
Sorry, prediction pasa_asmbl_19610.p1 fails validation.
(GTC)	 AT	56078-56197	GT	TAG
(GCT)	 AG	56299-56343	GT	AGG
(GAG)	 AG	56727-56890	GT	ATG
(GAT)	 AG	57394-57504	GT	AGG
(TTC)	 AG	58727-59013	GT	AGG
(GAA)	 AG	59169-59338	GT	AGG
(GTT)	 AG	59856-59972	GA	GAG
-recovered pasa_asmbl_19610.p1, terminal, 59856, 59972
-recovered pasa_asmbl_19610.p1, internal, 56299, 56343
-recovered pasa_asmbl_19610.p1, internal, 56727, 56890
-recovered pasa_asmbl_19610.p1, internal, 57394, 57504
-recovered pasa_asmbl_19610.p1, internal, 58727, 59013
-recovered pasa_asmbl_19610.p1, internal, 59169, 59338
Valid prediction for pasa_asmbl_19603.p1
Valid prediction for snap_scaffold_18-snap.147-T1
Valid prediction for snap_scaffold_18-snap.170-T1
Couldn't classify 112799, 113055
Sorry, prediction pasa_asmbl_19598.p1 fails validation.
(TCA)	 TC	112799-113055	GT	AGG
(AGA)	 AG	113243-113381	GT	AGG
(ATT)	 AG	113609-113797	GT	AGG
(TTG)	 AG	113960-114088	GT	TGG
(AAA)	 AG	114191-114349	TC	GAT
-recovered pasa_asmbl_19598.p1, terminal, 114191, 114349
-recovered pasa_asmbl_19598.p1, internal, 113243, 113381
-recovered pasa_asmbl_19598.p1, internal, 113609, 113797
-recovered pasa_asmbl_19598.p1, internal, 113960, 114088
Valid prediction for snap_scaffold_18-snap.172-T1
Couldn't classify 86686, 86705
Sorry, prediction pasa_asmbl_19607.p1 fails validation.
(ATG)	 GG	81897-81987	GT	AGG
(ATT)	 AG	82772-82860	GT	ACG
(GTG)	 AG	84219-84459	GT	AGG
(ATA)	 AG	86686-86705	GG	AAG
-recovered pasa_asmbl_19607.p1, initial, 81897, 81987
-recovered pasa_asmbl_19607.p1, internal, 82772, 82860
-recovered pasa_asmbl_19607.p1, internal, 84219, 84459
Valid prediction for snap_scaffold_18-snap.159-T1
Valid prediction for GlimmerHMM_glimmerT_41680-T1
Valid prediction for GlimmerHMM_glimmerT_41689-T1
Valid prediction for GlimmerHMM_glimmerT_41692-T1
Valid prediction for snap_scaffold_18-snap.143-T1
Valid prediction for GlimmerHMM_glimmerT_41681-T1
Valid prediction for snap_scaffold_18-snap.139-T1
Valid prediction for GlimmerHMM_glimmerT_41705-T1
Valid prediction for Augustus_model.g27763.t1
Valid prediction for HiQ_model.g27761.t1
Valid prediction for HiQ_model.g27759.t1
Valid prediction for snap_scaffold_18-snap.166-T1
Valid prediction for snap_scaffold_18-snap.169-T1
Valid prediction for HiQ_model.g27755.t1
Valid prediction for HiQ_model.g27756.t1
Valid prediction for CodingQuarry_transcript_23652-T1
Valid prediction for Augustus_model.g27758.t1
Valid prediction for snap_scaffold_18-snap.157-T1
Valid prediction for snap_scaffold_18-snap.174-T1
Valid prediction for snap_scaffold_18-snap.155-T1
Valid prediction for GlimmerHMM_glimmerT_41706-T1
Couldn't classify 61341, 61428
Couldn't classify 63176, 63452
Sorry, prediction pasa_asmbl_19609.p1 fails validation.
(GTG)	 AG	61341-61428	GT	AGG
(GCA)	 AG	61650-61959	GT	GGG
(GTT)	 AG	63176-63452	GT	GGG
-recovered pasa_asmbl_19609.p1, internal, 61341, 61428
-recovered pasa_asmbl_19609.p1, internal, 61650, 61959
-recovered pasa_asmbl_19609.p1, internal, 63176, 63452
Valid prediction for snap_scaffold_18-snap.168-T1
Valid prediction for pasa_asmbl_19606.p1
Couldn't classify 45713, 45943
Sorry, prediction pasa_asmbl_19612.p1 fails validation.
(ACG)	 AC	45713-45943	GT	AGG
(AAT)	 AG	46111-46205	GT	GAG
(GGA)	 AG	46321-46364	GT	TGG
(GTA)	 AG	46449-46571	GT	AGG
(GGT)	 AG	46675-46859	GT	AGG
(GAG)	 AG	47042-47090	GC	AGG
(TTG)	 AG	47222-47279	GT	AGG
(TGC)	 AG	47400-47520	GT	AGG
(ATG)	 AG	47661-47780	GT	AGG
(GAG)	 AG	47868-47967	GT	AGG
(GTA)	 AG	48107-48207	GT	CGG
(GGT)	 AG	48382-48444	CC	GAC
-recovered pasa_asmbl_19612.p1, initial, 47661, 47780
-recovered pasa_asmbl_19612.p1, terminal, 48382, 48444
-recovered pasa_asmbl_19612.p1, internal, 46111, 46205
-recovered pasa_asmbl_19612.p1, internal, 46321, 46364
-recovered pasa_asmbl_19612.p1, internal, 46449, 46571
-recovered pasa_asmbl_19612.p1, internal, 46675, 46859
-recovered pasa_asmbl_19612.p1, internal, 47042, 47090
-recovered pasa_asmbl_19612.p1, internal, 47222, 47279
-recovered pasa_asmbl_19612.p1, internal, 47400, 47520
-recovered pasa_asmbl_19612.p1, internal, 47661, 47780
-recovered pasa_asmbl_19612.p1, internal, 47868, 47967
-recovered pasa_asmbl_19612.p1, internal, 48107, 48207
Valid prediction for snap_scaffold_18-snap.161-T1
Valid prediction for snap_scaffold_18-snap.149-T1
Valid prediction for snap_scaffold_18-snap.150-T1
Valid prediction for Augustus_model.g27764.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 31142, rend_intergenic: 26855  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36226, rend_intergenic: 32362  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56080, rend_intergenic: 53242  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64654, rend_intergenic: 58695  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72077, rend_intergenic: 68866  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74386, rend_intergenic: 73182  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86024, rend_intergenic: 82887  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91248, rend_intergenic: 88794  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98749, rend_intergenic: 92474  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114171, rend_intergenic: 107689  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119112, rend_intergenic: 115859  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124135, rend_intergenic: 122331  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131800, rend_intergenic: 129316  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147449, rend_intergenic: 138833  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149448, rend_intergenic: 147454  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154929, rend_intergenic: 149876  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155187, rend_intergenic: 155034  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164938, rend_intergenic: 159286  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 180834
-exon list size: 393


building trellis

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-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 31142, rend_intergenic: 26855  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36226, rend_intergenic: 32362  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56080, rend_intergenic: 53242  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64654, rend_intergenic: 58695  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72077, rend_intergenic: 68866  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74386, rend_intergenic: 73182  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86024, rend_intergenic: 82887  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91248, rend_intergenic: 88794  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98749, rend_intergenic: 92474  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114171, rend_intergenic: 107689  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119112, rend_intergenic: 115859  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124135, rend_intergenic: 122331  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131800, rend_intergenic: 129316  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147449, rend_intergenic: 138833  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149448, rend_intergenic: 147454  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154929, rend_intergenic: 149876  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155187, rend_intergenic: 155034  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164938, rend_intergenic: 159286  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 168682 - 180834
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-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

-building DP trellis

-building trellis in range 168853 - 180834
-exon list size: 1


building trellis

33.3    
66.7    
-found 1 predictions from path traversal

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