-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_10/scaffold_10_2632004-2847252

-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_24295-T1
Valid prediction for snap_scaffold_10-snap.571-T1
Valid prediction for snap_scaffold_10-snap.577-T1
Valid prediction for Augustus_model.g16193.t1
Valid prediction for HiQ_model.g16198.t1
Valid prediction for HiQ_model.g16196.t1
Valid prediction for CodingQuarry_transcript_5303-T1
Valid prediction for HiQ_model.g16177.t1
Valid prediction for HiQ_model.g16183.t1
Valid prediction for CodingQuarry_transcript_5312-T1
Valid prediction for HiQ_model.g16179.t1
Valid prediction for GlimmerHMM_glimmerT_24308-T1
Valid prediction for pasa_asmbl_3006.p1
Valid prediction for GlimmerHMM_glimmerT_24290-T1
Valid prediction for CodingQuarry_transcript_5298-T1
Valid prediction for snap_scaffold_10-snap.581-T1
Couldn't classify 116761, 116878
Sorry, prediction pasa_asmbl_3007.p1 fails validation.
(CTG)	 CT	116761-116878	GT	AAG
(GGG)	 AG	118069-118344	GT	TGG
(TTC)	 AG	118555-119131	GT	AGG
(TAA)	 AG	119259-119444	GT	AGG
(TGG)	 AG	119620-119704	GT	AGG
(GTG)	 AG	119847-120005	GG	GAG
-recovered pasa_asmbl_3007.p1, terminal, 119847, 120005
-recovered pasa_asmbl_3007.p1, internal, 118069, 118344
-recovered pasa_asmbl_3007.p1, internal, 118555, 119131
-recovered pasa_asmbl_3007.p1, internal, 119259, 119444
-recovered pasa_asmbl_3007.p1, internal, 119620, 119704
Valid prediction for GlimmerHMM_glimmerT_24297-T1
Valid prediction for pasa_asmbl_2986.p1
Valid prediction for snap_scaffold_10-snap.606-T1
Valid prediction for CodingQuarry_transcript_5299-T1
Valid prediction for CodingQuarry_transcript_5304-T1
Valid prediction for HiQ_model.g16182.t1
Valid prediction for GlimmerHMM_glimmerT_24314-T1
Valid prediction for snap_scaffold_10-snap.603-T1
Valid prediction for pasa_asmbl_3013.p1
Valid prediction for GlimmerHMM_glimmerT_24307-T1
Valid prediction for snap_scaffold_10-snap.566-T1
Valid prediction for pasa_asmbl_3014.p1
Valid prediction for snap_scaffold_10-snap.569-T1
Valid prediction for GlimmerHMM_glimmerT_24305-T1
Couldn't classify 87131, 87322
Sorry, prediction pasa_asmbl_2998.p1 fails validation.
(CAT)	 CA	87131-87322	GT	AGG
(ACT)	 AG	89487-89762	AG	AGA
-recovered pasa_asmbl_2998.p1, terminal, 89487, 89762
Valid prediction for snap_scaffold_10-snap.563-T1
Valid prediction for HiQ_model.g16181.t1
Valid prediction for snap_scaffold_10-snap.599-T1
Valid prediction for HiQ_model.g16189.t1
Valid prediction for snap_scaffold_10-snap.591-T1
Valid prediction for snap_scaffold_10-snap.602-T1
Valid prediction for snap_scaffold_10-snap.586-T1
Valid prediction for CodingQuarry_transcript_5300-T1
Valid prediction for CodingQuarry_transcript_5310-T1
Valid prediction for GlimmerHMM_glimmerT_24311-T1
Valid prediction for CodingQuarry_transcript_5296-T1
Valid prediction for snap_scaffold_10-snap.585-T1
Valid prediction for HiQ_model.g16190.t1
Couldn't classify 39669, 39711
Sorry, prediction pasa_asmbl_2990.p1 fails validation.
(GAG)	 TT	39669-39711	GT	AGG
(TAC)	 AG	40782-41003	GT	AGG
(GTG)	 AG	41091-41173	GT	AGG
(GGA)	 AG	41288-41509	GT	AGG
(GTG)	 AG	41672-42148	TG	AAT
-recovered pasa_asmbl_2990.p1, terminal, 41672, 42148
-recovered pasa_asmbl_2990.p1, internal, 40782, 41003
-recovered pasa_asmbl_2990.p1, internal, 41091, 41173
-recovered pasa_asmbl_2990.p1, internal, 41288, 41509
Valid prediction for snap_scaffold_10-snap.568-T1
Valid prediction for snap_scaffold_10-snap.580-T1
Valid prediction for CodingQuarry_transcript_5309-T1
Valid prediction for HiQ_model.g16192.t1
Valid prediction for pasa_asmbl_2995.p1
Valid prediction for snap_scaffold_10-snap.579-T1
Valid prediction for CodingQuarry_transcript_5302-T1
Valid prediction for snap_scaffold_10-snap.596-T1
Valid prediction for snap_scaffold_10-snap.598-T1
Valid prediction for GlimmerHMM_glimmerT_24317-T1
Valid prediction for snap_scaffold_10-snap.597-T1
Valid prediction for CodingQuarry_transcript_5301-T1
Valid prediction for GlimmerHMM_glimmerT_24298-T1
Valid prediction for GlimmerHMM_glimmerT_24316-T1
Valid prediction for CodingQuarry_transcript_5294-T1
Valid prediction for pasa_asmbl_3003.p1
Valid prediction for snap_scaffold_10-snap.570-T1
Valid prediction for pasa_asmbl_2983.p1
Valid prediction for pasa_asmbl_3010.p1
Valid prediction for GlimmerHMM_glimmerT_24320-T1
Valid prediction for GlimmerHMM_glimmerT_24293-T1
Valid prediction for pasa_asmbl_2991.p1
Valid prediction for snap_scaffold_10-snap.601-T1
Valid prediction for snap_scaffold_10-snap.582-T1
Valid prediction for CodingQuarry_transcript_5306-T1
Valid prediction for snap_scaffold_10-snap.583-T1
Valid prediction for GlimmerHMM_glimmerT_24312-T1
Valid prediction for Augustus_model.g16188.t1
Valid prediction for GlimmerHMM_glimmerT_24304-T1
Valid prediction for Augustus_model.g16187.t1
Valid prediction for snap_scaffold_10-snap.560-T1
Valid prediction for snap_scaffold_10-snap.592-T1
Valid prediction for GlimmerHMM_glimmerT_24309-T1
Valid prediction for snap_scaffold_10-snap.578-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 snap_scaffold_10-snap.589-T1
Valid prediction for snap_scaffold_10-snap.590-T1
Valid prediction for snap_scaffold_10-snap.562-T1
Valid prediction for snap_scaffold_10-snap.559-T1
Valid prediction for Augustus_model.g16202.t1
Valid prediction for snap_scaffold_10-snap.588-T1
Valid prediction for CodingQuarry_transcript_5307-T1
Valid prediction for snap_scaffold_10-snap.573-T1
Valid prediction for HiQ_model.g16184.t1
Valid prediction for CodingQuarry_transcript_5305-T1
Valid prediction for HiQ_model.g16197.t1
Valid prediction for snap_scaffold_10-snap.574-T1
Valid prediction for CodingQuarry_transcript_5311-T1
Valid prediction for Augustus_model.g16175.t1
Valid prediction for HiQ_model.g16195.t1
Valid prediction for GlimmerHMM_glimmerT_24310-T1
Valid prediction for pasa_asmbl_4131.p1
Valid prediction for GlimmerHMM_glimmerT_24321-T1
Valid prediction for snap_scaffold_10-snap.593-T1
Valid prediction for HiQ_model.g16199.t1
Valid prediction for GlimmerHMM_glimmerT_24313-T1
Valid prediction for GlimmerHMM_glimmerT_24294-T1
Valid prediction for CodingQuarry_transcript_5314-T1
Valid prediction for CodingQuarry_transcript_5313-T1
Valid prediction for snap_scaffold_10-snap.565-T1
Valid prediction for GlimmerHMM_glimmerT_24303-T1
Valid prediction for GlimmerHMM_glimmerT_24306-T1
Valid prediction for snap_scaffold_10-snap.567-T1
Valid prediction for GlimmerHMM_glimmerT_24291-T1
Valid prediction for GlimmerHMM_glimmerT_24287-T1
Couldn't classify 192650, 192763
Sorry, prediction pasa_asmbl_4110.p1 fails validation.
(GCT)	 CA	192650-192763	GT	GGG
(GTA)	 AG	193726-193898	GT	AGG
(ATT)	 AG	194207-194301	GT	AGG
(GCG)	 AG	195126-195159	GT	AAG
(GTT)	 AG	195278-195323	GT	AGG
(ATT)	 AG	195498-195678	GT	AAG
(GTG)	 AG	195904-196030	GT	AGG
(GAA)	 AG	196474-196643	GT	AGG
(GGA)	 AG	196818-196899	GT	AGG
(TTT)	 AG	197240-197348	GT	AGG
(CTT)	 AG	197458-197560	GT	TGG
(AGC)	 AG	197659-197727	GC	AGG
(GGG)	 AG	197881-198038	GA	GAG
-recovered pasa_asmbl_4110.p1, terminal, 197881, 198038
-recovered pasa_asmbl_4110.p1, internal, 193726, 193898
-recovered pasa_asmbl_4110.p1, internal, 194207, 194301
-recovered pasa_asmbl_4110.p1, internal, 195126, 195159
-recovered pasa_asmbl_4110.p1, internal, 195278, 195323
-recovered pasa_asmbl_4110.p1, internal, 195498, 195678
-recovered pasa_asmbl_4110.p1, internal, 195904, 196030
-recovered pasa_asmbl_4110.p1, internal, 196474, 196643
-recovered pasa_asmbl_4110.p1, internal, 196818, 196899
-recovered pasa_asmbl_4110.p1, internal, 197240, 197348
-recovered pasa_asmbl_4110.p1, internal, 197458, 197560
-recovered pasa_asmbl_4110.p1, internal, 197659, 197727
Valid prediction for CodingQuarry_transcript_5308-T1
Valid prediction for Augustus_model.g16194.t1
Valid prediction for snap_scaffold_10-snap.575-T1
Couldn't classify 189686, 189758
Couldn't classify 191631, 191663
Sorry, prediction pasa_asmbl_5078.p1 fails validation.
(TTG)	 AT	189686-189758	GT	AGG
(GCT)	 AG	190120-190189	GT	TGG
(TCC)	 AG	190374-190487	GT	CGG
(GCC)	 AG	190742-190820	GT	AGG
(GAC)	 AG	191631-191663	CA	ACC
-recovered pasa_asmbl_5078.p1, internal, 190120, 190189
-recovered pasa_asmbl_5078.p1, internal, 190374, 190487
-recovered pasa_asmbl_5078.p1, internal, 190742, 190820
Valid prediction for GlimmerHMM_glimmerT_24288-T1
Valid prediction for Augustus_model.g16186.t1
Valid prediction for snap_scaffold_10-snap.587-T1
Valid prediction for GlimmerHMM_glimmerT_24292-T1
Valid prediction for snap_scaffold_10-snap.595-T1
Valid prediction for snap_scaffold_10-snap.604-T1
Valid prediction for GlimmerHMM_glimmerT_24299-T1
Valid prediction for HiQ_model.g16174.t1
Valid prediction for CodingQuarry_transcript_5295-T1
Valid prediction for snap_scaffold_10-snap.561-T1
Valid prediction for Augustus_model.g16176.t1
Valid prediction for pasa_asmbl_4126.p1
Couldn't classify 160776, 160928
Sorry, prediction pasa_asmbl_4120.p2 fails validation.
(ATG)	 AT	159601-159624	GT	AGG
(CAG)	 AG	159783-159983	GT	AGG
(AAC)	 AG	160776-160928	AC	GGA
-recovered pasa_asmbl_4120.p2, initial, 159601, 159624
-recovered pasa_asmbl_4120.p2, internal, 159783, 159983
Valid prediction for pasa_asmbl_4116.p1
Valid prediction for snap_scaffold_10-snap.594-T1
Valid prediction for HiQ_model.g16180.t1
Valid prediction for snap_scaffold_10-snap.600-T1
Valid prediction for GlimmerHMM_glimmerT_24319-T1
Valid prediction for GlimmerHMM_glimmerT_24315-T1
Valid prediction for HiQ_model.g16200.t1
Valid prediction for GlimmerHMM_glimmerT_24301-T1
Valid prediction for GlimmerHMM_glimmerT_24318-T1
Valid prediction for CodingQuarry_transcript_5297-T1
Valid prediction for snap_scaffold_10-snap.584-T1
Valid prediction for snap_scaffold_10-snap.564-T1
Couldn't classify 161067, 161185
Sorry, prediction pasa_asmbl_4118.p1 fails validation.
(TTG)	 CC	161067-161185	GT	AGG
(ACA)	 AG	161398-161505	GT	GGG
(GCG)	 AG	162057-162243	GA	GAG
-recovered pasa_asmbl_4118.p1, terminal, 162057, 162243
-recovered pasa_asmbl_4118.p1, internal, 161398, 161505
Valid prediction for GlimmerHMM_glimmerT_24300-T1
Couldn't classify 40875, 40958
Couldn't classify 43153, 43191
Sorry, prediction pasa_asmbl_4139.p1 fails validation.
(GAG)	 AG	40875-40958	GT	GAG
(GGT)	 AG	41294-41347	GT	AGG
(GGA)	 AG	41502-41609	GT	TGG
(GGA)	 AG	41801-41854	GT	AGG
(GGT)	 AG	41955-42008	GT	AGG
(GGT)	 AG	42929-42985	GT	TCG
(GGT)	 AG	43153-43191	GA	GGG
-recovered pasa_asmbl_4139.p1, internal, 40875, 40958
-recovered pasa_asmbl_4139.p1, internal, 41294, 41347
-recovered pasa_asmbl_4139.p1, internal, 41502, 41609
-recovered pasa_asmbl_4139.p1, internal, 41801, 41854
-recovered pasa_asmbl_4139.p1, internal, 41955, 42008
-recovered pasa_asmbl_4139.p1, internal, 42929, 42985
Valid prediction for snap_scaffold_10-snap.576-T1
Valid prediction for GlimmerHMM_glimmerT_24296-T1
Valid prediction for GlimmerHMM_glimmerT_24302-T1
Couldn't classify 47674, 47727
Couldn't classify 48342, 48428
Sorry, prediction pasa_asmbl_5124.p1 fails validation.
(TGC)	 CC	47674-47727	GT	AGG
(TTG)	 AG	47992-48210	GT	GGG
(ATG)	 AG	48342-48428	CC	TGC
-recovered pasa_asmbl_5124.p1, internal, 47992, 48210
Valid prediction for pasa_asmbl_4128.p1
Valid prediction for GlimmerHMM_glimmerT_24289-T1
Valid prediction for pasa_asmbl_4123.p1
Valid prediction for HiQ_model.g16191.t1
Valid prediction for Augustus_model.g16185.t1
Valid prediction for snap_scaffold_10-snap.572-T1
Couldn't classify 175025, 175150
Sorry, prediction pasa_asmbl_4117.p1 fails validation.
(CTA)	 CC	175025-175150	GC	TGG
(ATA)	 AG	175308-175368	GT	AGG
(GAC)	 AG	175591-175718	GT	AGG
(GTA)	 AG	175809-175891	GT	GAG
(TCC)	 AG	176040-176231	GT	GGG
(GAT)	 AG	176442-176514	GT	AGG
(GTG)	 AG	176634-176796	GT	GGG
(CCA)	 AG	176958-177039	GT	TGG
(GTA)	 AG	177223-177289	AT	AAA
-recovered pasa_asmbl_4117.p1, terminal, 177223, 177289
-recovered pasa_asmbl_4117.p1, internal, 175308, 175368
-recovered pasa_asmbl_4117.p1, internal, 175591, 175718
-recovered pasa_asmbl_4117.p1, internal, 175809, 175891
-recovered pasa_asmbl_4117.p1, internal, 176040, 176231
-recovered pasa_asmbl_4117.p1, internal, 176442, 176514
-recovered pasa_asmbl_4117.p1, internal, 176634, 176796
-recovered pasa_asmbl_4117.p1, internal, 176958, 177039
Valid prediction for HiQ_model.g16178.t1
Valid prediction for Augustus_model.g16201.t1
Valid prediction for CodingQuarry_transcript_5293-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 181034, rend_intergenic: 166580  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196474, rend_intergenic: 182934  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204865, rend_intergenic: 200504  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 215249
-exon list size: 480


building trellis

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88.4    
88.6    
88.8    
89.0    
89.2    
89.4    
89.6    
89.8    
90.0    
90.2    
90.5    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
91.9    
92.1    
92.3    
92.5    
92.7    
92.9    
93.2    
93.4    
93.6    
93.8    
94.0    
94.2    
94.4    
94.6    
94.8    
95.0    
95.2    
95.4    
95.6    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 181034, rend_intergenic: 166580  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196474, rend_intergenic: 182934  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204865, rend_intergenic: 200504  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 30 predictions persist after filtering for low support