-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_10/scaffold_10_3810724-3951569

-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_25014-T1
Valid prediction for snap_scaffold_10-snap.831-T1
Valid prediction for GeneMark_model.42760_t
Couldn't classify 134225, 134538
Sorry, prediction pasa_asmbl_4374.p1 fails validation.
(AAC)	 CC	134225-134538	GT	AGG
(CAA)	 AG	134734-134776	GG	GAG
-recovered pasa_asmbl_4374.p1, terminal, 134734, 134776
Valid prediction for snap_scaffold_10-snap.817-T1
Valid prediction for GeneMark_model.42782_t
Valid prediction for GlimmerHMM_glimmerT_25025-T1
Valid prediction for GeneMark_model.42776_t
Valid prediction for GeneMark_model.42774_t
Valid prediction for GlimmerHMM_glimmerT_25036-T1
Valid prediction for GeneMark_model.42752_t
Valid prediction for GeneMark_model.42764_t
Valid prediction for Augustus_model.g16768.t1
Valid prediction for snap_scaffold_10-snap.828-T1
Couldn't classify 59300, 59358
Couldn't classify 60729, 60758
Sorry, prediction pasa_asmbl_4360.p1 fails validation.
(GAC)	 CT	59300-59358	GT	AGG
(TGG)	 AG	59768-59856	GT	AGG
(ACT)	 AG	60240-60384	GT	ACG
(GTA)	 AG	60512-60560	GT	TGG
(AGC)	 AG	60729-60758	GT	GGG
-recovered pasa_asmbl_4360.p1, internal, 59768, 59856
-recovered pasa_asmbl_4360.p1, internal, 60240, 60384
-recovered pasa_asmbl_4360.p1, internal, 60512, 60560
-recovered pasa_asmbl_4360.p1, internal, 60729, 60758
Couldn't classify 8801, 8894
Couldn't classify 9943, 10065
Sorry, prediction pasa_asmbl_4357.p1 fails validation.
(GCC)	 TG	8801-8894	GT	AGG
(ACT)	 AG	9082-9209	GT	AGG
(GGT)	 AG	9311-9500	GT	AGG
(GTC)	 AG	9715-9839	GT	AGG
(GGC)	 AG	9943-10065	GA	AGG
-recovered pasa_asmbl_4357.p1, internal, 9082, 9209
-recovered pasa_asmbl_4357.p1, internal, 9311, 9500
-recovered pasa_asmbl_4357.p1, internal, 9715, 9839
Valid prediction for snap_scaffold_10-snap.819-T1
Valid prediction for snap_scaffold_10-snap.824-T1
Valid prediction for GlimmerHMM_glimmerT_25019-T1
Valid prediction for GeneMark_model.42758_t
Valid prediction for Augustus_model.g16774.t1
Valid prediction for GeneMark_model.42772_t
Couldn't classify 105506, 105624
Sorry, prediction pasa_asmbl_4370.p1 fails validation.
(TCT)	 CC	105506-105624	GT	GAG
(CTA)	 AG	107770-107988	GT	GGG
(AGG)	 AG	108237-108346	GT	ACG
(GGA)	 AG	108642-108828	GT	TGG
(GTA)	 AG	108992-109115	GT	AGG
(GGG)	 AG	109686-109793	GT	AGG
(GTG)	 AG	109929-110033	GT	TGG
(GAC)	 AG	110176-110282	GT	AGG
(GGC)	 AG	110358-110520	GT	AGG
(GTG)	 AG	110693-110830	GT	AGG
(TAT)	 AG	111015-111249	GT	AGG
(ACG)	 AG	111518-111669	GT	CTG
(AAC)	 AG	111824-111922	GT	AGG
(AGT)	 AG	112280-112426	GA	GAG
-recovered pasa_asmbl_4370.p1, terminal, 112280, 112426
-recovered pasa_asmbl_4370.p1, internal, 107770, 107988
-recovered pasa_asmbl_4370.p1, internal, 108237, 108346
-recovered pasa_asmbl_4370.p1, internal, 108642, 108828
-recovered pasa_asmbl_4370.p1, internal, 108992, 109115
-recovered pasa_asmbl_4370.p1, internal, 109686, 109793
-recovered pasa_asmbl_4370.p1, internal, 109929, 110033
-recovered pasa_asmbl_4370.p1, internal, 110176, 110282
-recovered pasa_asmbl_4370.p1, internal, 110358, 110520
-recovered pasa_asmbl_4370.p1, internal, 110693, 110830
-recovered pasa_asmbl_4370.p1, internal, 111015, 111249
-recovered pasa_asmbl_4370.p1, internal, 111518, 111669
-recovered pasa_asmbl_4370.p1, internal, 111824, 111922
Valid prediction for GlimmerHMM_glimmerT_25018-T1
Valid prediction for GlimmerHMM_glimmerT_25020-T1
Valid prediction for GeneMark_model.42754_t
Couldn't classify 65391, 65560
Sorry, prediction pasa_asmbl_4364.p1 fails validation.
(TGC)	 AT	65391-65560	GT	AGG
(GTA)	 AG	65655-65843	GT	TGG
(CCT)	 AG	65933-66242	CC	GAC
-recovered pasa_asmbl_4364.p1, terminal, 65933, 66242
-recovered pasa_asmbl_4364.p1, internal, 65655, 65843
Valid prediction for GeneMark_model.42756_t
Couldn't classify 6103, 6228
Couldn't classify 7912, 7974
Sorry, prediction pasa_asmbl_5082.p1 fails validation.
(GAT)	 TA	6103-6228	GT	TTG
(AAA)	 AG	6825-6959	GT	AGG
(TCG)	 AG	7086-7173	GT	GAG
(ACA)	 AG	7428-7555	GT	TGG
(GAG)	 AG	7912-7974	GA	AGG
-recovered pasa_asmbl_5082.p1, internal, 6825, 6959
-recovered pasa_asmbl_5082.p1, internal, 7086, 7173
-recovered pasa_asmbl_5082.p1, internal, 7428, 7555
Valid prediction for GeneMark_model.42748_t
Valid prediction for snap_scaffold_10-snap.816-T1
Valid prediction for GeneMark_model.42755_t
Valid prediction for snap_scaffold_10-snap.837-T1
Couldn't classify 62241, 62338
Couldn't classify 62839, 62955
Sorry, prediction pasa_asmbl_4361.p1 fails validation.
(TGT)	 AC	62241-62338	GT	GGG
(TCC)	 AG	62461-62599	GT	AGG
(GCT)	 AG	62839-62955	GT	TGG
-recovered pasa_asmbl_4361.p1, internal, 62461, 62599
-recovered pasa_asmbl_4361.p1, internal, 62839, 62955
Couldn't classify 26163, 26223
Couldn't classify 26399, 26703
Sorry, prediction pasa_asmbl_5126.p1 fails validation.
(GAT)	 CA	26163-26223	GT	AGG
(CAA)	 AG	26399-26703	GG	TGG
Valid prediction for GlimmerHMM_glimmerT_25031-T1
Valid prediction for Augustus_model.g16778.t1
Valid prediction for GeneMark_model.42767_t
Valid prediction for GlimmerHMM_glimmerT_25033-T1
Valid prediction for snap_scaffold_10-snap.833-T1
Valid prediction for GeneMark_model.42757_t
Couldn't classify 64790, 64934
Couldn't classify 65090, 65244
Sorry, prediction pasa_asmbl_4363.p2 fails validation.
(CTG)	 GG	64790-64934	GT	GGG
(TCC)	 AG	65090-65244	CC	GCC
Valid prediction for snap_scaffold_10-snap.821-T1
Valid prediction for GeneMark_model.42770_t
Couldn't classify 84287, 84351
Sorry, prediction pasa_asmbl_4367.p1 fails validation.
(GCA)	 GA	84287-84351	GT	TGG
(GCC)	 AG	84683-84775	GT	GAG
(GGC)	 AG	85083-85179	GT	GGG
(AGC)	 AG	85572-85679	GT	CGG
(GTC)	 AG	86354-86422	AG	GAA
-recovered pasa_asmbl_4367.p1, terminal, 86354, 86422
-recovered pasa_asmbl_4367.p1, internal, 84683, 84775
-recovered pasa_asmbl_4367.p1, internal, 85083, 85179
-recovered pasa_asmbl_4367.p1, internal, 85572, 85679
Valid prediction for GeneMark_model.42780_t
Valid prediction for CodingQuarry_transcript_5340-T1
Valid prediction for snap_scaffold_10-snap.839-T1
Couldn't classify 63728, 63799
Couldn't classify 64642, 64690
Sorry, prediction pasa_asmbl_4362.p1 fails validation.
(AAA)	 CC	63728-63799	GT	AGG
(AAC)	 AG	63963-64121	GT	AGG
(GAG)	 AG	64380-64516	GT	GGG
(GGC)	 AG	64642-64690	AT	ACA
-recovered pasa_asmbl_4362.p1, internal, 63963, 64121
-recovered pasa_asmbl_4362.p1, internal, 64380, 64516
Valid prediction for HiQ_model.g16782.t1
Valid prediction for GlimmerHMM_glimmerT_25021-T1
Valid prediction for snap_scaffold_10-snap.842-T1
Valid prediction for GeneMark_model.42763_t
Valid prediction for snap_scaffold_10-snap.818-T1
Valid prediction for GlimmerHMM_glimmerT_25030-T1
Valid prediction for snap_scaffold_10-snap.840-T1
Valid prediction for GeneMark_model.42750_t
Valid prediction for GeneMark_model.42778_t
Valid prediction for CodingQuarry_transcript_5342-T1
Valid prediction for snap_scaffold_10-snap.829-T1
Valid prediction for GeneMark_model.42766_t
Valid prediction for GlimmerHMM_glimmerT_25026-T1
Valid prediction for Augustus_model.g16776.t1
Valid prediction for GlimmerHMM_glimmerT_25023-T1
Valid prediction for snap_scaffold_10-snap.835-T1
Valid prediction for Augustus_model.g16770.t1
Valid prediction for Augustus_model.g16769.t1
Valid prediction for GlimmerHMM_glimmerT_25028-T1
Valid prediction for Augustus_model.g16772.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 Augustus_model.g16777.t1
Valid prediction for GlimmerHMM_glimmerT_25015-T1
Valid prediction for GeneMark_model.42775_t
Valid prediction for Augustus_model.g16779.t1
Valid prediction for GeneMark_model.42771_t
Valid prediction for GeneMark_model.42749_t
Valid prediction for GlimmerHMM_glimmerT_25034-T1
Valid prediction for snap_scaffold_10-snap.827-T1
Valid prediction for GeneMark_model.42769_t
Valid prediction for snap_scaffold_10-snap.813-T1
Valid prediction for GeneMark_model.42747_t
Valid prediction for snap_scaffold_10-snap.826-T1
Valid prediction for GlimmerHMM_glimmerT_25035-T1
Valid prediction for snap_scaffold_10-snap.822-T1
Valid prediction for Augustus_model.g16771.t1
Valid prediction for GlimmerHMM_glimmerT_25017-T1
Valid prediction for GlimmerHMM_glimmerT_25029-T1
Valid prediction for snap_scaffold_10-snap.836-T1
Valid prediction for GlimmerHMM_glimmerT_25022-T1
Couldn't classify 95919, 96257
Sorry, prediction pasa_asmbl_3148.p1 fails validation.
(GGA)	 CA	95919-96257	CT	ACC
Valid prediction for snap_scaffold_10-snap.815-T1
Valid prediction for snap_scaffold_10-snap.830-T1
Valid prediction for GeneMark_model.42759_t
Valid prediction for snap_scaffold_10-snap.825-T1
Valid prediction for GeneMark_model.42777_t
Valid prediction for GeneMark_model.42768_t
Valid prediction for GlimmerHMM_glimmerT_25024-T1
Valid prediction for snap_scaffold_10-snap.823-T1
Couldn't classify 12682, 13098
Couldn't classify 14470, 14619
Sorry, prediction pasa_asmbl_3162.p1 fails validation.
(TGC)	 AC	12682-13098	GT	AGG
(ATC)	 AG	14470-14619	CC	CCC
Valid prediction for GeneMark_model.42783_t
Couldn't classify 123433, 123566
Sorry, prediction pasa_asmbl_3147.p1 fails validation.
(CAG)	 TT	123433-123566	GT	GGG
(TGC)	 AG	124693-124802	GT	AGG
(GTG)	 AG	124901-125028	CG	AAC
-recovered pasa_asmbl_3147.p1, terminal, 124901, 125028
-recovered pasa_asmbl_3147.p1, internal, 124693, 124802
Valid prediction for pasa_asmbl_3151.p1
Valid prediction for GeneMark_model.42781_t
Valid prediction for GlimmerHMM_glimmerT_25037-T1
Valid prediction for HiQ_model.g16781.t1
Valid prediction for GeneMark_model.42762_t
Valid prediction for Augustus_model.g16783.t1
Valid prediction for snap_scaffold_10-snap.814-T1
Valid prediction for GlimmerHMM_glimmerT_25032-T1
Valid prediction for GlimmerHMM_glimmerT_25027-T1
Valid prediction for snap_scaffold_10-snap.832-T1
Valid prediction for HiQ_model.g16767.t1
Valid prediction for snap_scaffold_10-snap.834-T1
Valid prediction for Augustus_model.g16780.t1
Valid prediction for GeneMark_model.42773_t
Valid prediction for GeneMark_model.42779_t
Valid prediction for GeneMark_model.42761_t
Valid prediction for GeneMark_model.42753_t
Valid prediction for snap_scaffold_10-snap.841-T1
Valid prediction for pasa_asmbl_3154.p1
Valid prediction for Augustus_model.g16766.t1
Valid prediction for GlimmerHMM_glimmerT_25016-T1
Valid prediction for GeneMark_model.42765_t
Valid prediction for snap_scaffold_10-snap.820-T1
Valid prediction for GeneMark_model.42751_t
Couldn't classify 10872, 11040
Couldn't classify 12350, 12624
Sorry, prediction pasa_asmbl_3163.p1 fails validation.
(AGG)	 GC	10872-11040	GT	TGG
(GTT)	 AG	12350-12624	CC	TGC
Valid prediction for snap_scaffold_10-snap.838-T1
Valid prediction for Augustus_model.g16775.t1
Valid prediction for Augustus_model.g16773.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 22603, rend_intergenic: 17244  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53568, rend_intergenic: 52827  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67829, rend_intergenic: 53799  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79829, rend_intergenic: 72913  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82200, rend_intergenic: 79931  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95991, rend_intergenic: 89824  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104106, rend_intergenic: 102702  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112915, rend_intergenic: 107304  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131988, rend_intergenic: 125268  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140468, rend_intergenic: 132218  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 140846
-exon list size: 592


building trellis

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81.6    
81.8    
82.0    
82.2    
82.3    
82.5    
82.7    
82.8    
83.0    
83.2    
83.3    
83.5    
83.7    
83.8    
84.0    
84.2    
84.3    
84.5    
84.7    
84.8    
85.0    
85.2    
85.4    
85.5    
85.7    
85.9    
86.0    
86.2    
86.4    
86.5    
86.7    
86.9    
87.0    
87.2    
87.4    
87.5    
87.7    
87.9    
88.0    
88.2    
88.4    
88.6    
88.7    
88.9    
89.1    
89.2    
89.4    
89.6    
89.7    
89.9    
90.1    
90.2    
90.4    
90.6    
90.7    
90.9    
91.1    
91.2    
91.4    
91.6    
91.8    
91.9    
92.1    
92.3    
92.4    
92.6    
92.8    
92.9    
93.1    
93.3    
93.4    
93.6    
93.8    
93.9    
94.1    
94.3    
94.4    
94.6    
94.8    
94.9    
95.1    
95.3    
95.5    
95.6    
95.8    
96.0    
96.1    
96.3    
96.5    
96.6    
96.8    
97.0    
97.1    
97.3    
97.5    
97.6    
97.8    
98.0    
98.1    
98.3    
98.5    
98.7    
98.8    
99.0    
99.2    
99.3    
99.5    
99.7    
99.8    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 22603, rend_intergenic: 17244  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53568, rend_intergenic: 52827  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67829, rend_intergenic: 53799  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79829, rend_intergenic: 72913  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82200, rend_intergenic: 79931  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95991, rend_intergenic: 89824  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104106, rend_intergenic: 102702  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112915, rend_intergenic: 107304  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131988, rend_intergenic: 125268  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140468, rend_intergenic: 132218  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