-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_7/scaffold_7_724904-905137

-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_16811-T1
Valid prediction for snap_scaffold_7-snap.190-T1
Valid prediction for snap_scaffold_7-snap.197-T1
Valid prediction for snap_scaffold_7-snap.188-T1
Valid prediction for GlimmerHMM_glimmerT_16803-T1
Valid prediction for snap_scaffold_7-snap.205-T1
Sorry, intron length (8) is less than minimum required (10)
Couldn't classify 175359, 175433
Couldn't classify 177615, 177671
Sorry, prediction pasa_asmbl_49571.p1 fails validation.
(ATC)	 AC	175359-175433	GT	AGG
(GAG)	 AG	176881-176926	GT	AGG
(AGA)	 AG	177038-177128	GT	AGG
(GTT)	 AG	177341-177482	GT	AGG
(AGG)	 AG	177615-177671	GA	GCG
-recovered pasa_asmbl_49571.p1, internal, 176881, 176926
-recovered pasa_asmbl_49571.p1, internal, 177038, 177128
-recovered pasa_asmbl_49571.p1, internal, 177341, 177482
Valid prediction for snap_scaffold_7-snap.184-T1
Valid prediction for snap_scaffold_7-snap.196-T1
Valid prediction for GlimmerHMM_glimmerT_16815-T1
Valid prediction for GlimmerHMM_glimmerT_16807-T1
Valid prediction for GlimmerHMM_glimmerT_16784-T1
Valid prediction for Augustus_model.g11216.t1
Valid prediction for pasa_asmbl_49569.p1
Valid prediction for snap_scaffold_7-snap.202-T1
Valid prediction for snap_scaffold_7-snap.192-T1
Valid prediction for snap_scaffold_7-snap.203-T1
Valid prediction for GlimmerHMM_glimmerT_16812-T1
Valid prediction for snap_scaffold_7-snap.207-T1
Valid prediction for GlimmerHMM_glimmerT_16804-T1
Valid prediction for Augustus_model.g11211.t1
Valid prediction for snap_scaffold_7-snap.187-T1
Valid prediction for HiQ_model.g11213.t1
Valid prediction for snap_scaffold_7-snap.214-T1
Valid prediction for GlimmerHMM_glimmerT_16808-T1
Valid prediction for CodingQuarry_transcript_57431-T1
Valid prediction for Augustus_model.g11218.t1
Valid prediction for Augustus_model.g11227.t1
Valid prediction for Augustus_model.g11207.t1
Valid prediction for snap_scaffold_7-snap.209-T1
Valid prediction for snap_scaffold_7-snap.183-T1
Valid prediction for GlimmerHMM_glimmerT_16805-T1
Valid prediction for GlimmerHMM_glimmerT_16791-T1
Valid prediction for GlimmerHMM_glimmerT_16792-T1
Valid prediction for GlimmerHMM_glimmerT_16801-T1
Valid prediction for GlimmerHMM_glimmerT_16797-T1
Valid prediction for Augustus_model.g11220.t1
Valid prediction for snap_scaffold_7-snap.194-T1
Valid prediction for Augustus_model.g11219.t1
Valid prediction for HiQ_model.g11226.t1
Couldn't classify 80882, 81080
Sorry, prediction pasa_asmbl_49562.p1 fails validation.
(ACA)	 TG	80882-81080	GT	AGG
(GAG)	 AG	81452-81523	GT	AGG
(ATG)	 AG	81911-82464	GT	GGG
(GGT)	 AG	82697-82781	GT	AGG
(TGC)	 AG	84201-84424	GT	TGG
(ACG)	 AG	85549-85689	GT	AGG
(GAG)	 AG	86088-86181	GT	ACG
(CTA)	 AG	86269-86439	GT	AGG
(TCC)	 AG	87270-87446	GT	TAG
(TTG)	 AG	88016-88189	GT	TGG
(ATG)	 AG	88307-88434	GT	AGG
(TGT)	 AG	88616-88768	GT	AGG
(GTG)	 AG	89541-89759	GT	AGG
(GAC)	 AG	89987-90094	GT	GAG
(GAC)	 AG	90229-90388	GT	CGG
(AGA)	 AG	90466-90584	GT	AGG
(GCG)	 AG	91027-91261	GT	TGG
(GAG)	 AG	91757-91984	GT	GGG
(GCT)	 AG	92080-92351	GT	AGG
(GTG)	 AG	92669-92766	GT	AGG
(GGT)	 AG	92920-93059	GT	AGG
(ATA)	 AG	94623-94630	GG	GAG
add_exon() Sorry, pasa_asmbl_49562.p1 81911-82464-initial-1 is invalid.
-recovered pasa_asmbl_49562.p1, initial, 81911, 82464
-recovered pasa_asmbl_49562.p1, initial, 88307, 88434
-recovered pasa_asmbl_49562.p1, terminal, 94623, 94630
-recovered pasa_asmbl_49562.p1, internal, 81452, 81523
-recovered pasa_asmbl_49562.p1, internal, 81911, 82464
-recovered pasa_asmbl_49562.p1, internal, 82697, 82781
-recovered pasa_asmbl_49562.p1, internal, 84201, 84424
-recovered pasa_asmbl_49562.p1, internal, 85549, 85689
-recovered pasa_asmbl_49562.p1, internal, 86088, 86181
-recovered pasa_asmbl_49562.p1, internal, 86269, 86439
-recovered pasa_asmbl_49562.p1, internal, 87270, 87446
-recovered pasa_asmbl_49562.p1, internal, 88016, 88189
-recovered pasa_asmbl_49562.p1, internal, 88307, 88434
-recovered pasa_asmbl_49562.p1, internal, 88616, 88768
-recovered pasa_asmbl_49562.p1, internal, 89541, 89759
-recovered pasa_asmbl_49562.p1, internal, 89987, 90094
-recovered pasa_asmbl_49562.p1, internal, 90229, 90388
-recovered pasa_asmbl_49562.p1, internal, 90466, 90584
-recovered pasa_asmbl_49562.p1, internal, 91027, 91261
-recovered pasa_asmbl_49562.p1, internal, 91757, 91984
-recovered pasa_asmbl_49562.p1, internal, 92080, 92351
-recovered pasa_asmbl_49562.p1, internal, 92669, 92766
-recovered pasa_asmbl_49562.p1, internal, 92920, 93059
Valid prediction for snap_scaffold_7-snap.212-T1
Valid prediction for GlimmerHMM_glimmerT_16800-T1
Valid prediction for GlimmerHMM_glimmerT_16787-T1
Valid prediction for GlimmerHMM_glimmerT_16793-T1
Valid prediction for Augustus_model.g11212.t1
Valid prediction for Augustus_model.g11222.t1
Valid prediction for GlimmerHMM_glimmerT_16796-T1
Valid prediction for GlimmerHMM_glimmerT_16814-T1
Valid prediction for Augustus_model.g11209.t1
Valid prediction for GlimmerHMM_glimmerT_16789-T1
Valid prediction for snap_scaffold_7-snap.206-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_16798-T1
Valid prediction for GlimmerHMM_glimmerT_16788-T1
Valid prediction for snap_scaffold_7-snap.208-T1
Valid prediction for GlimmerHMM_glimmerT_16809-T1
Valid prediction for snap_scaffold_7-snap.200-T1
Valid prediction for snap_scaffold_7-snap.199-T1
Valid prediction for Augustus_model.g11208.t1
Valid prediction for Augustus_model.g11217.t1
Valid prediction for snap_scaffold_7-snap.185-T1
Valid prediction for snap_scaffold_7-snap.210-T1
Valid prediction for snap_scaffold_7-snap.213-T1
Valid prediction for snap_scaffold_7-snap.186-T1
Couldn't classify 165114, 165179
Couldn't classify 171392, 171445
Sorry, prediction pasa_asmbl_50704.p1 fails validation.
(AGG)	 GC	165114-165179	GT	TGG
(CAT)	 AG	165786-165860	GT	AGG
(ATC)	 AG	166323-166445	GT	TGG
(GGT)	 AG	166952-167044	GT	TGG
(ATG)	 AG	167344-167609	GT	AAG
(GAC)	 AG	167704-167890	GT	TGG
(ATC)	 AG	169532-169621	GT	AGG
(GTG)	 AG	170378-170442	GT	AGG
(GTG)	 AG	170595-170745	GT	AGG
(GTA)	 AG	171392-171445	TT	GTT
-recovered pasa_asmbl_50704.p1, initial, 167344, 167609
-recovered pasa_asmbl_50704.p1, internal, 165786, 165860
-recovered pasa_asmbl_50704.p1, internal, 166323, 166445
-recovered pasa_asmbl_50704.p1, internal, 166952, 167044
-recovered pasa_asmbl_50704.p1, internal, 167344, 167609
-recovered pasa_asmbl_50704.p1, internal, 167704, 167890
-recovered pasa_asmbl_50704.p1, internal, 169532, 169621
-recovered pasa_asmbl_50704.p1, internal, 170378, 170442
-recovered pasa_asmbl_50704.p1, internal, 170595, 170745
Valid prediction for Augustus_model.g11214.t1
Valid prediction for snap_scaffold_7-snap.211-T1
Valid prediction for snap_scaffold_7-snap.215-T1
Valid prediction for Augustus_model.g11215.t1
Valid prediction for GlimmerHMM_glimmerT_16799-T1
Couldn't classify 156787, 156901
Sorry, prediction pasa_asmbl_50707.p1 fails validation.
(ATG)	 AT	152020-152216	GT	ACG
(GTA)	 AG	154126-154266	GT	AAG
(GAA)	 AG	156787-156901	AA	CCA
-recovered pasa_asmbl_50707.p1, initial, 152020, 152216
-recovered pasa_asmbl_50707.p1, internal, 154126, 154266
Valid prediction for Augustus_model.g11223.t1
Valid prediction for Augustus_model.g11225.t1
Valid prediction for GlimmerHMM_glimmerT_16806-T1
Valid prediction for snap_scaffold_7-snap.191-T1
Valid prediction for GlimmerHMM_glimmerT_16790-T1
Valid prediction for snap_scaffold_7-snap.189-T1
Valid prediction for snap_scaffold_7-snap.198-T1
Valid prediction for Augustus_model.g11206.t1
Valid prediction for snap_scaffold_7-snap.195-T1
Valid prediction for CodingQuarry_transcript_57430-T1
Valid prediction for GlimmerHMM_glimmerT_16785-T1
Valid prediction for GlimmerHMM_glimmerT_16802-T1
Valid prediction for Augustus_model.g11224.t1
Valid prediction for snap_scaffold_7-snap.204-T1
Valid prediction for GlimmerHMM_glimmerT_16795-T1
Valid prediction for Augustus_model.g11221.t1
Couldn't classify 172184, 172253
Couldn't classify 176127, 176233
Sorry, prediction pasa_asmbl_50701.p1 fails validation.
(TGT)	 AG	172184-172253	GT	CAG
(ATG)	 AG	172756-172823	GT	AGG
(GTG)	 AG	173765-173980	GT	AGG
(GAC)	 AG	174539-174696	GT	AGG
(AGA)	 AG	174874-174969	GT	CTG
(AGT)	 AG	175646-175701	GT	TGG
(ATG)	 AG	176127-176233	CT	TCC
add_exon() Sorry, pasa_asmbl_50701.p1 172756-172823-initial-1 is invalid.
-recovered pasa_asmbl_50701.p1, initial, 172756, 172823
-recovered pasa_asmbl_50701.p1, internal, 172184, 172253
-recovered pasa_asmbl_50701.p1, internal, 172756, 172823
-recovered pasa_asmbl_50701.p1, internal, 173765, 173980
-recovered pasa_asmbl_50701.p1, internal, 174539, 174696
-recovered pasa_asmbl_50701.p1, internal, 174874, 174969
-recovered pasa_asmbl_50701.p1, internal, 175646, 175701
Valid prediction for CodingQuarry_transcript_57429-T1
Valid prediction for GlimmerHMM_glimmerT_16810-T1
Valid prediction for GlimmerHMM_glimmerT_16794-T1
Valid prediction for snap_scaffold_7-snap.201-T1
Valid prediction for GlimmerHMM_glimmerT_16786-T1
Valid prediction for snap_scaffold_7-snap.193-T1
Valid prediction for GlimmerHMM_glimmerT_16813-T1
Valid prediction for Augustus_model.g11210.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7984, rend_intergenic: 2935  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16217, rend_intergenic: 12346  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36598, rend_intergenic: 31664  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44859, rend_intergenic: 36839  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54960, rend_intergenic: 44860  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63739, rend_intergenic: 56099  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70570, rend_intergenic: 65429  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74603, rend_intergenic: 70717  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93697, rend_intergenic: 82006  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168106, rend_intergenic: 164181  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179755, rend_intergenic: 171164  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 180234
-exon list size: 394


building trellis

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30.6    
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37.6    
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38.4    
38.6    
38.9    
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40.4    
40.7    
40.9    
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44.9    
45.2    
45.5    
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46.0    
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48.2    
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97.5    
97.7    
98.0    
98.2    
98.5    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 7984, rend_intergenic: 2935  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16217, rend_intergenic: 12346  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36598, rend_intergenic: 31664  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44859, rend_intergenic: 36839  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54960, rend_intergenic: 44860  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63739, rend_intergenic: 56099  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70570, rend_intergenic: 65429  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74603, rend_intergenic: 70717  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93697, rend_intergenic: 82006  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168106, rend_intergenic: 164181  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179755, rend_intergenic: 171164  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 26 predictions persist after filtering for low support