-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_11/scaffold_11_1952844-2130069

-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_11-snap.491-T1
Valid prediction for Augustus_model.g17629.t1
Valid prediction for GlimmerHMM_glimmerT_26620-T1
Valid prediction for GlimmerHMM_glimmerT_26613-T1
Valid prediction for Augustus_model.g17631.t1
Valid prediction for pasa_asmbl_5357.p1
Valid prediction for snap_scaffold_11-snap.527-T1
Valid prediction for snap_scaffold_11-snap.510-T1
Valid prediction for HiQ_model.g17626.t1
Valid prediction for snap_scaffold_11-snap.524-T1
Valid prediction for pasa_asmbl_5356.p1
Valid prediction for Augustus_model.g17622.t1
Valid prediction for GlimmerHMM_glimmerT_26602-T1
Valid prediction for snap_scaffold_11-snap.517-T1
Valid prediction for GlimmerHMM_glimmerT_26628-T1
Valid prediction for GlimmerHMM_glimmerT_26604-T1
Valid prediction for GlimmerHMM_glimmerT_26625-T1
Valid prediction for GlimmerHMM_glimmerT_26624-T1
Valid prediction for GlimmerHMM_glimmerT_26614-T1
Valid prediction for snap_scaffold_11-snap.515-T1
Valid prediction for pasa_asmbl_5361.p1
Valid prediction for pasa_asmbl_5349.p1
Valid prediction for snap_scaffold_11-snap.522-T1
Valid prediction for snap_scaffold_11-snap.499-T1
Valid prediction for GlimmerHMM_glimmerT_26622-T1
Valid prediction for Augustus_model.g17617.t1
Valid prediction for snap_scaffold_11-snap.503-T1
Valid prediction for snap_scaffold_11-snap.509-T1
Valid prediction for CodingQuarry_transcript_7983-T1
Valid prediction for HiQ_model.g17615.t1
Valid prediction for snap_scaffold_11-snap.494-T1
Valid prediction for snap_scaffold_11-snap.520-T1
Valid prediction for HiQ_model.g17624.t1
Valid prediction for Augustus_model.g17633.t1
Valid prediction for GlimmerHMM_glimmerT_26610-T1
Valid prediction for GlimmerHMM_glimmerT_26621-T1
Valid prediction for GlimmerHMM_glimmerT_26616-T1
Valid prediction for snap_scaffold_11-snap.495-T1
Valid prediction for HiQ_model.g17628.t1
Valid prediction for CodingQuarry_transcript_7985-T1
Valid prediction for GlimmerHMM_glimmerT_26618-T1
Valid prediction for GlimmerHMM_glimmerT_26608-T1
Valid prediction for snap_scaffold_11-snap.498-T1
Valid prediction for snap_scaffold_11-snap.492-T1
Valid prediction for Augustus_model.g17620.t1
Valid prediction for GlimmerHMM_glimmerT_26619-T1
Valid prediction for snap_scaffold_11-snap.519-T1
Valid prediction for Augustus_model.g17627.t1
Couldn't classify 152674, 152796
Sorry, prediction CodingQuarry_transcript_7989-T1 fails validation.
(ATG)	 TC	149199-149237	GT	GGG
(ACA)	 AG	149744-149785	GT	TGG
(CCT)	 AG	149902-149976	GT	CTG
(GCC)	 AG	150784-150945	GT	TTG
(AAA)	 AG	151245-151323	GT	GCG
(AGG)	 AG	151778-152079	GT	ATG
(GCT)	 CA	152674-152796	GT	TGG
(GGA)	 AG	153154-153343	GT	AGG
(GGG)	 AG	154095-154276	GT	CCG
(CCC)	 AG	154433-154612	GT	AGG
(ATC)	 AG	155576-155674	GT	AAG
(GGT)	 AG	156144-156248	AC	AGA
-recovered CodingQuarry_transcript_7989-T1, initial, 149199, 149237
-recovered CodingQuarry_transcript_7989-T1, terminal, 156144, 156248
-recovered CodingQuarry_transcript_7989-T1, internal, 149744, 149785
-recovered CodingQuarry_transcript_7989-T1, internal, 149902, 149976
-recovered CodingQuarry_transcript_7989-T1, internal, 150784, 150945
-recovered CodingQuarry_transcript_7989-T1, internal, 151245, 151323
-recovered CodingQuarry_transcript_7989-T1, internal, 151778, 152079
-recovered CodingQuarry_transcript_7989-T1, internal, 153154, 153343
-recovered CodingQuarry_transcript_7989-T1, internal, 154095, 154276
-recovered CodingQuarry_transcript_7989-T1, internal, 154433, 154612
-recovered CodingQuarry_transcript_7989-T1, internal, 155576, 155674

-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_11-snap.518-T1
Valid prediction for Augustus_model.g17618.t1
Valid prediction for CodingQuarry_transcript_7986-T1
Valid prediction for snap_scaffold_11-snap.523-T1
Valid prediction for GlimmerHMM_glimmerT_26606-T1
Couldn't classify 144923, 146003
Sorry, prediction pasa_asmbl_6465.p1 fails validation.
(GAG)	 AA	144923-146003	GT	AGG
(GGA)	 AG	146401-146480	GT	TGG
(GTT)	 AG	146586-146813	CG	AGC
-recovered pasa_asmbl_6465.p1, terminal, 146586, 146813
-recovered pasa_asmbl_6465.p1, internal, 146401, 146480
Valid prediction for pasa_asmbl_6473.p1
Couldn't classify 131425, 131466
Sorry, prediction pasa_asmbl_6470.p1 fails validation.
(ATG)	 AA	129457-129648	GT	AGG
(GAC)	 AG	129967-130144	GT	TGG
(GGG)	 AG	130254-130309	GT	AGG
(GTT)	 AG	130498-130568	GT	AGG
(GGA)	 AG	130693-130798	GT	CGG
(TGT)	 AG	130882-131013	GT	CGG
(AAT)	 AG	131211-131321	GT	AGG
(GAT)	 AG	131425-131466	CC	AGC
-recovered pasa_asmbl_6470.p1, initial, 129457, 129648
-recovered pasa_asmbl_6470.p1, internal, 129967, 130144
-recovered pasa_asmbl_6470.p1, internal, 130254, 130309
-recovered pasa_asmbl_6470.p1, internal, 130498, 130568
-recovered pasa_asmbl_6470.p1, internal, 130693, 130798
-recovered pasa_asmbl_6470.p1, internal, 130882, 131013
-recovered pasa_asmbl_6470.p1, internal, 131211, 131321
Valid prediction for GlimmerHMM_glimmerT_26607-T1
Valid prediction for snap_scaffold_11-snap.525-T1
Valid prediction for snap_scaffold_11-snap.493-T1
Valid prediction for Augustus_model.g17614.t1
Valid prediction for snap_scaffold_11-snap.521-T1
Valid prediction for CodingQuarry_transcript_7988-T1
Valid prediction for Augustus_model.g17621.t1
Valid prediction for snap_scaffold_11-snap.505-T1
Valid prediction for GlimmerHMM_glimmerT_26603-T1
Valid prediction for snap_scaffold_11-snap.500-T1
Valid prediction for GlimmerHMM_glimmerT_26609-T1
Valid prediction for snap_scaffold_11-snap.528-T1
Valid prediction for CodingQuarry_transcript_7987-T1
Valid prediction for snap_scaffold_11-snap.513-T1
Valid prediction for pasa_asmbl_6467.p1
Valid prediction for snap_scaffold_11-snap.502-T1
Valid prediction for Augustus_model.g17623.t1
Valid prediction for Augustus_model.g17619.t1
Valid prediction for GlimmerHMM_glimmerT_26617-T1
Valid prediction for snap_scaffold_11-snap.506-T1
Valid prediction for Augustus_model.g17632.t1
Valid prediction for GlimmerHMM_glimmerT_26623-T1
Valid prediction for snap_scaffold_11-snap.514-T1
Valid prediction for snap_scaffold_11-snap.488-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g17616.t1
Valid prediction for GlimmerHMM_glimmerT_26601-T1
Valid prediction for Augustus_model.g17630.t1
Valid prediction for GlimmerHMM_glimmerT_26615-T1
Couldn't classify 158859, 159086
Sorry, prediction pasa_asmbl_7369.p1 fails validation.
(CCC)	 CC	158859-159086	GT	AGG
(TGG)	 AG	159413-159517	GT	GGG
(GAA)	 AG	159918-160103	TG	GAT
-recovered pasa_asmbl_7369.p1, terminal, 159918, 160103
-recovered pasa_asmbl_7369.p1, internal, 159413, 159517
Valid prediction for pasa_asmbl_6472.p1
Valid prediction for snap_scaffold_11-snap.497-T1
Valid prediction for Augustus_model.g17625.t1
Couldn't classify 134289, 134319
Sorry, prediction pasa_asmbl_6468.p1 fails validation.
(CCT)	 CT	134289-134319	GT	CGG
(AGC)	 AG	134417-134578	GT	GGG
(ATA)	 AG	134737-134904	GT	GGG
(AGA)	 AG	135025-135081	GT	CAG
(GTC)	 AG	135593-135774	GT	AGG
(GAG)	 AG	135877-136038	GT	CGG
(ACC)	 AG	136129-136233	GT	AGG
(CTT)	 AG	136343-136396	GT	AGG
(TTC)	 AG	136481-136660	AG	GAA
-recovered pasa_asmbl_6468.p1, terminal, 136481, 136660
-recovered pasa_asmbl_6468.p1, internal, 134417, 134578
-recovered pasa_asmbl_6468.p1, internal, 134737, 134904
-recovered pasa_asmbl_6468.p1, internal, 135025, 135081
-recovered pasa_asmbl_6468.p1, internal, 135593, 135774
-recovered pasa_asmbl_6468.p1, internal, 135877, 136038
-recovered pasa_asmbl_6468.p1, internal, 136129, 136233
-recovered pasa_asmbl_6468.p1, internal, 136343, 136396
Valid prediction for CodingQuarry_transcript_7984-T1
Couldn't classify 15911, 15955
Sorry, prediction pasa_asmbl_6477.p1 fails validation.
(AAG)	 AC	15911-15955	GT	AGG
(GTC)	 AG	16162-16232	GT	GTG
(GCA)	 AG	16825-16969	GT	AGG
(GAA)	 AG	19366-19461	GT	GGG
(AAT)	 AG	20210-20257	GA	GAG
-recovered pasa_asmbl_6477.p1, terminal, 20210, 20257
-recovered pasa_asmbl_6477.p1, internal, 16162, 16232
-recovered pasa_asmbl_6477.p1, internal, 16825, 16969
-recovered pasa_asmbl_6477.p1, internal, 19366, 19461
Valid prediction for GlimmerHMM_glimmerT_26626-T1
Couldn't classify 132004, 132069
Sorry, prediction pasa_asmbl_6469.p1 fails validation.
(CAT)	 AG	132004-132069	GT	CTG
(AAC)	 AG	132347-132491	GT	CGG
(ACG)	 AG	132635-132835	GT	TGG
(GGC)	 AG	133024-133070	GT	AAG
(GTG)	 AG	133463-133648	CA	AAC
-recovered pasa_asmbl_6469.p1, terminal, 133463, 133648
-recovered pasa_asmbl_6469.p1, internal, 132004, 132069
-recovered pasa_asmbl_6469.p1, internal, 132347, 132491
-recovered pasa_asmbl_6469.p1, internal, 132635, 132835
-recovered pasa_asmbl_6469.p1, internal, 133024, 133070
Valid prediction for snap_scaffold_11-snap.490-T1
Valid prediction for snap_scaffold_11-snap.526-T1
Valid prediction for GlimmerHMM_glimmerT_26627-T1
Valid prediction for Augustus_model.g17612.t1
Valid prediction for snap_scaffold_11-snap.516-T1
Valid prediction for snap_scaffold_11-snap.496-T1
Valid prediction for snap_scaffold_11-snap.504-T1
Valid prediction for GlimmerHMM_glimmerT_26605-T1
Valid prediction for snap_scaffold_11-snap.501-T1
Valid prediction for snap_scaffold_11-snap.511-T1
Valid prediction for GlimmerHMM_glimmerT_26611-T1
Valid prediction for snap_scaffold_11-snap.508-T1
Valid prediction for HiQ_model.g17613.t1
Valid prediction for GlimmerHMM_glimmerT_26612-T1
Valid prediction for snap_scaffold_11-snap.489-T1
Valid prediction for snap_scaffold_11-snap.507-T1
Valid prediction for CodingQuarry_transcript_7982-T1
Valid prediction for snap_scaffold_11-snap.512-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14537, rend_intergenic: 9664  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20545, rend_intergenic: 17124  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44558, rend_intergenic: 40567  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60138, rend_intergenic: 57707  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83272, rend_intergenic: 61873  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87673, rend_intergenic: 84196  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104406, rend_intergenic: 88461  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133368, rend_intergenic: 122614  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152462, rend_intergenic: 151233  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154718, rend_intergenic: 152543  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177062, rend_intergenic: 170620  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 177226
-exon list size: 516


building trellis

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88.0    
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89.8    
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90.7    
90.9    
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91.7    
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93.8    
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98.1    
98.3    
98.5    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 14537, rend_intergenic: 9664  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20545, rend_intergenic: 17124  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44558, rend_intergenic: 40567  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60138, rend_intergenic: 57707  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83272, rend_intergenic: 61873  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87673, rend_intergenic: 84196  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104406, rend_intergenic: 88461  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133368, rend_intergenic: 122614  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152462, rend_intergenic: 151233  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154718, rend_intergenic: 152543  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177062, rend_intergenic: 170620  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 27 predictions persist after filtering for low support