-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_2627956-3044280

-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 GlimmerHMM_glimmerT_49096-T1
Valid prediction for snap_scaffold_22-snap.493-T1
Valid prediction for snap_scaffold_22-snap.471-T1
Valid prediction for snap_scaffold_22-snap.456-T1
Valid prediction for GlimmerHMM_glimmerT_49072-T1
Valid prediction for GlimmerHMM_glimmerT_49094-T1
Valid prediction for Augustus_model.g32776.t1
Valid prediction for snap_scaffold_22-snap.460-T1
Valid prediction for snap_scaffold_22-snap.447-T1
Valid prediction for GlimmerHMM_glimmerT_49075-T1
Valid prediction for snap_scaffold_22-snap.463-T1
Valid prediction for snap_scaffold_22-snap.476-T1
Valid prediction for snap_scaffold_22-snap.455-T1
Valid prediction for snap_scaffold_22-snap.488-T1
Valid prediction for GlimmerHMM_glimmerT_49073-T1
Couldn't classify 405799, 405915
Sorry, prediction pasa_asmbl_29949.p1 fails validation.
(GTG)	 CA	405799-405915	GT	AGG
(AAT)	 AG	407152-407276	GT	AAG
(AGA)	 AG	409609-409797	GT	AAG
(CCT)	 AG	410559-410652	GT	AGG
(GCA)	 AG	411470-411586	GT	AGG
(ACT)	 AG	411830-412000	GT	GGG
(GTG)	 AG	412611-412707	GT	AGG
(GTT)	 AG	412868-413013	GT	AGG
(TGT)	 AG	413142-413280	GT	AGG
(CGT)	 AG	413605-413723	GT	AGG
(CTC)	 AG	413915-414094	GT	TGG
(CAC)	 AG	414208-414399	GT	TGG
(AAC)	 AG	414475-414564	GT	AGG
(CTC)	 AG	414990-415130	CT	AAC
-recovered pasa_asmbl_29949.p1, terminal, 414990, 415130
-recovered pasa_asmbl_29949.p1, internal, 407152, 407276
-recovered pasa_asmbl_29949.p1, internal, 409609, 409797
-recovered pasa_asmbl_29949.p1, internal, 410559, 410652
-recovered pasa_asmbl_29949.p1, internal, 411470, 411586
-recovered pasa_asmbl_29949.p1, internal, 411830, 412000
-recovered pasa_asmbl_29949.p1, internal, 412611, 412707
-recovered pasa_asmbl_29949.p1, internal, 412868, 413013
-recovered pasa_asmbl_29949.p1, internal, 413142, 413280
-recovered pasa_asmbl_29949.p1, internal, 413605, 413723
-recovered pasa_asmbl_29949.p1, internal, 413915, 414094
-recovered pasa_asmbl_29949.p1, internal, 414208, 414399
-recovered pasa_asmbl_29949.p1, internal, 414475, 414564
Valid prediction for snap_scaffold_22-snap.492-T1
Couldn't classify 200799, 201050
Couldn't classify 205506, 205550
Sorry, prediction pasa_asmbl_29946.p1 fails validation.
(ATC)	 TG	200799-201050	GT	AGG
(CGC)	 AG	202337-202515	GT	AGG
(GCA)	 AG	202645-202771	GT	GGG
(GAA)	 AG	202870-202995	GT	GGG
(GAC)	 AG	203900-204054	GT	AGG
(TGC)	 AG	204720-204855	GT	AGG
(GAT)	 AG	205506-205550	AG	GAA
add_exon() Sorry, pasa_asmbl_29946.p1 203900-204054-terminal-2 is invalid.
-recovered pasa_asmbl_29946.p1, terminal, 203900, 204054
-recovered pasa_asmbl_29946.p1, internal, 202337, 202515
-recovered pasa_asmbl_29946.p1, internal, 202645, 202771
-recovered pasa_asmbl_29946.p1, internal, 202870, 202995
-recovered pasa_asmbl_29946.p1, internal, 203900, 204054
-recovered pasa_asmbl_29946.p1, internal, 204720, 204855
Valid prediction for snap_scaffold_22-snap.466-T1
Valid prediction for GlimmerHMM_glimmerT_49065-T1
Valid prediction for GlimmerHMM_glimmerT_49090-T1
Valid prediction for snap_scaffold_22-snap.465-T1
Valid prediction for GlimmerHMM_glimmerT_49078-T1
Valid prediction for GlimmerHMM_glimmerT_49064-T1
Valid prediction for GlimmerHMM_glimmerT_49085-T1
Valid prediction for Augustus_model.g32761.t1
Valid prediction for HiQ_model.g32777.t1
Valid prediction for GlimmerHMM_glimmerT_49077-T1
Valid prediction for snap_scaffold_22-snap.458-T1
Valid prediction for GlimmerHMM_glimmerT_49083-T1
Valid prediction for snap_scaffold_22-snap.477-T1
Couldn't classify 174439, 174679
Couldn't classify 175113, 175183
Sorry, prediction pasa_asmbl_30426.p1 fails validation.
(TGG)	 GC	174439-174679	GT	AGG
(TGT)	 AG	175113-175183	AA	ACA
Valid prediction for Augustus_model.g32766.t1
Valid prediction for snap_scaffold_22-snap.475-T1
Couldn't classify 190305, 190428
Couldn't classify 195336, 195440
Sorry, prediction pasa_asmbl_29945.p1 fails validation.
(TCC)	 AG	190305-190428	GT	TGG
(GTA)	 AG	193078-193253	GT	GGG
(GTG)	 AG	195083-195202	GT	AAG
(AAT)	 AG	195336-195440	GT	GGG
-recovered pasa_asmbl_29945.p1, internal, 190305, 190428
-recovered pasa_asmbl_29945.p1, internal, 193078, 193253
-recovered pasa_asmbl_29945.p1, internal, 195083, 195202
-recovered pasa_asmbl_29945.p1, internal, 195336, 195440
Valid prediction for snap_scaffold_22-snap.457-T1
Valid prediction for snap_scaffold_22-snap.474-T1
Valid prediction for GlimmerHMM_glimmerT_49084-T1
Valid prediction for snap_scaffold_22-snap.467-T1
Valid prediction for snap_scaffold_22-snap.444-T1
Valid prediction for Augustus_model.g32765.t1
Valid prediction for GlimmerHMM_glimmerT_49062-T1
Valid prediction for snap_scaffold_22-snap.464-T1
Valid prediction for snap_scaffold_22-snap.470-T1
Valid prediction for snap_scaffold_22-snap.486-T1
Valid prediction for pasa_asmbl_29950.p1
Valid prediction for snap_scaffold_22-snap.495-T1
Valid prediction for snap_scaffold_22-snap.445-T1
Valid prediction for snap_scaffold_22-snap.494-T1
Valid prediction for Augustus_model.g32774.t1
Valid prediction for Augustus_model.g32764.t1
Valid prediction for Augustus_model.g32760.t1
Valid prediction for GlimmerHMM_glimmerT_49074-T1
Valid prediction for snap_scaffold_22-snap.448-T1
Valid prediction for snap_scaffold_22-snap.472-T1
Valid prediction for GlimmerHMM_glimmerT_49081-T1
Valid prediction for GlimmerHMM_glimmerT_49082-T1
Valid prediction for snap_scaffold_22-snap.473-T1
Valid prediction for snap_scaffold_22-snap.453-T1
Valid prediction for GlimmerHMM_glimmerT_49097-T1
Valid prediction for Augustus_model.g32763.t1
Valid prediction for GlimmerHMM_glimmerT_49079-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 HiQ_model.g32771.t1
Valid prediction for GlimmerHMM_glimmerT_49093-T1
Valid prediction for snap_scaffold_22-snap.484-T1
Valid prediction for GlimmerHMM_glimmerT_49071-T1
Valid prediction for GlimmerHMM_glimmerT_49076-T1
Valid prediction for Augustus_model.g32772.t1
Valid prediction for snap_scaffold_22-snap.454-T1
Couldn't classify 90208, 90278
Sorry, prediction pasa_asmbl_29157.p1 fails validation.
(GAC)	 CA	90208-90278	GT	AGG
(GAA)	 AG	90467-91277	TG	GAT
-recovered pasa_asmbl_29157.p1, terminal, 90467, 91277
Valid prediction for GlimmerHMM_glimmerT_49080-T1
Valid prediction for snap_scaffold_22-snap.481-T1
Valid prediction for snap_scaffold_22-snap.490-T1
Valid prediction for CodingQuarry_transcript_34118-T1
Valid prediction for Augustus_model.g32757.t1
Valid prediction for GlimmerHMM_glimmerT_49086-T1
Valid prediction for Augustus_model.g32773.t1
Valid prediction for GlimmerHMM_glimmerT_49063-T1
Valid prediction for GlimmerHMM_glimmerT_49089-T1
Valid prediction for GlimmerHMM_glimmerT_49066-T1
Valid prediction for GlimmerHMM_glimmerT_49088-T1
Valid prediction for Augustus_model.g32767.t1
Valid prediction for Augustus_model.g32768.t1
Valid prediction for GlimmerHMM_glimmerT_49095-T1
Valid prediction for Augustus_model.g32770.t1
Valid prediction for snap_scaffold_22-snap.459-T1
Valid prediction for Augustus_model.g32775.t1
Valid prediction for HiQ_model.g32769.t1
Valid prediction for snap_scaffold_22-snap.462-T1
Valid prediction for snap_scaffold_22-snap.491-T1
Valid prediction for snap_scaffold_22-snap.489-T1
Valid prediction for CodingQuarry_transcript_34119-T1
Valid prediction for snap_scaffold_22-snap.449-T1
Valid prediction for snap_scaffold_22-snap.443-T1
Valid prediction for Augustus_model.g32762.t1
Valid prediction for snap_scaffold_22-snap.483-T1
Valid prediction for snap_scaffold_22-snap.450-T1
Valid prediction for Augustus_model.g32759.t1
Valid prediction for snap_scaffold_22-snap.452-T1
Valid prediction for snap_scaffold_22-snap.478-T1
Valid prediction for snap_scaffold_22-snap.482-T1
Valid prediction for snap_scaffold_22-snap.469-T1
Valid prediction for Augustus_model.g32758.t1
Valid prediction for snap_scaffold_22-snap.440-T1
Valid prediction for snap_scaffold_22-snap.451-T1
Valid prediction for snap_scaffold_22-snap.479-T1
Valid prediction for GlimmerHMM_glimmerT_49067-T1
Valid prediction for snap_scaffold_22-snap.485-T1
Couldn't classify 28758, 28827
Sorry, prediction pasa_asmbl_29166.p1 fails validation.
(GCA)	 GA	28758-28827	GT	GCG
(GGC)	 AG	30478-34517	TT	GAT
-recovered pasa_asmbl_29166.p1, terminal, 30478, 34517
Valid prediction for GlimmerHMM_glimmerT_49070-T1
Valid prediction for GlimmerHMM_glimmerT_49061-T1
Valid prediction for Augustus_model.g32756.t1
Valid prediction for GlimmerHMM_glimmerT_49068-T1
Valid prediction for GlimmerHMM_glimmerT_49069-T1
Valid prediction for snap_scaffold_22-snap.480-T1
Couldn't classify 71819, 71902
Couldn't classify 84866, 84932
Sorry, prediction pasa_asmbl_29158.p1 fails validation.
(CAG)	 GC	71819-71902	GT	CGG
(AGT)	 AG	72003-72149	GT	GGG
(CTC)	 AG	74676-74825	GC	AGG
(ATT)	 AG	76901-77069	GT	AGG
(GGC)	 AG	78762-78914	GT	AGG
(TAA)	 AG	80492-80635	GT	CGG
(ACC)	 AG	83196-83988	GT	AGG
(GGA)	 AG	84866-84932	GG	ACG
-recovered pasa_asmbl_29158.p1, internal, 72003, 72149
-recovered pasa_asmbl_29158.p1, internal, 74676, 74825
-recovered pasa_asmbl_29158.p1, internal, 76901, 77069
-recovered pasa_asmbl_29158.p1, internal, 78762, 78914
-recovered pasa_asmbl_29158.p1, internal, 80492, 80635
-recovered pasa_asmbl_29158.p1, internal, 83196, 83988
Valid prediction for snap_scaffold_22-snap.441-T1
Valid prediction for CodingQuarry_transcript_34120-T1
Valid prediction for pasa_asmbl_29161.p1
Valid prediction for snap_scaffold_22-snap.468-T1
Valid prediction for GlimmerHMM_glimmerT_49091-T1
Valid prediction for snap_scaffold_22-snap.461-T1
Valid prediction for snap_scaffold_22-snap.442-T1
Valid prediction for snap_scaffold_22-snap.446-T1
Valid prediction for snap_scaffold_22-snap.487-T1
Valid prediction for GlimmerHMM_glimmerT_49092-T1
Valid prediction for GlimmerHMM_glimmerT_49087-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 38385, rend_intergenic: 36158  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84990, rend_intergenic: 83621  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93949, rend_intergenic: 90869  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99925, rend_intergenic: 96352  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 375827, rend_intergenic: 374283  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 416325
-exon list size: 399


building trellis

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-found 39 predictions from path traversal
Error with prediction: snap lend_intergenic: 38385, rend_intergenic: 36158  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84990, rend_intergenic: 83621  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93949, rend_intergenic: 90869  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99925, rend_intergenic: 96352  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 375827, rend_intergenic: 374283  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 - 15483
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support
	-no exons in range 2353 - 15483