-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_4/scaffold_4_16486942-16668359

-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 CodingQuarry_transcript_49277-T1
Valid prediction for snap_scaffold_4-snap.3347-T1
Valid prediction for snap_scaffold_4-snap.3370-T1
Valid prediction for pasa_asmbl_41993.p1
Valid prediction for HiQ_model.g7137.t1
Valid prediction for Augustus_model.g7133.t1
Valid prediction for GlimmerHMM_glimmerT_10884-T1
Valid prediction for snap_scaffold_4-snap.3354-T1
Valid prediction for snap_scaffold_4-snap.3359-T1
Valid prediction for snap_scaffold_4-snap.3378-T1
Valid prediction for snap_scaffold_4-snap.3349-T1
Valid prediction for HiQ_model.g7126.t1
Valid prediction for snap_scaffold_4-snap.3384-T1
Valid prediction for GlimmerHMM_glimmerT_10892-T1
Valid prediction for Augustus_model.g7120.t1
Valid prediction for snap_scaffold_4-snap.3355-T1
Valid prediction for snap_scaffold_4-snap.3365-T1
Valid prediction for snap_scaffold_4-snap.3369-T1
Couldn't classify 142076, 142088
Couldn't classify 149579, 149720
Sorry, prediction pasa_asmbl_41984.p1 fails validation.
(AAA)	 CC	142076-142088	GT	AGG
(GTC)	 AG	142178-142299	GT	CTG
(AGC)	 AG	142554-142674	GT	AGG
(TGG)	 AG	142931-143103	GT	GTG
(GAG)	 AG	143834-144082	GT	CGG
(TGC)	 AG	144885-145088	GT	AGG
(CTG)	 AG	145378-145589	GT	AGG
(TGT)	 AG	145992-146123	GT	AGG
(AGA)	 AG	146583-146682	GT	ACG
(CCC)	 AG	146961-147152	GT	AGG
(GGC)	 AG	147563-147763	GT	AGG
(AAA)	 AG	148160-148297	GT	AGG
(TTC)	 AG	148899-149020	GT	AAG
(TAA)	 AG	149273-149446	GT	AAG
(GAA)	 AG	149579-149720	GT	TGG
-recovered pasa_asmbl_41984.p1, internal, 142178, 142299
-recovered pasa_asmbl_41984.p1, internal, 142554, 142674
-recovered pasa_asmbl_41984.p1, internal, 142931, 143103
-recovered pasa_asmbl_41984.p1, internal, 143834, 144082
-recovered pasa_asmbl_41984.p1, internal, 144885, 145088
-recovered pasa_asmbl_41984.p1, internal, 145378, 145589
-recovered pasa_asmbl_41984.p1, internal, 145992, 146123
-recovered pasa_asmbl_41984.p1, internal, 146583, 146682
-recovered pasa_asmbl_41984.p1, internal, 146961, 147152
-recovered pasa_asmbl_41984.p1, internal, 147563, 147763
-recovered pasa_asmbl_41984.p1, internal, 148160, 148297
-recovered pasa_asmbl_41984.p1, internal, 148899, 149020
-recovered pasa_asmbl_41984.p1, internal, 149273, 149446
-recovered pasa_asmbl_41984.p1, internal, 149579, 149720
Valid prediction for snap_scaffold_4-snap.3374-T1
Valid prediction for snap_scaffold_4-snap.3382-T1
Couldn't classify 150504, 150624
Sorry, prediction pasa_asmbl_41986.p1 fails validation.
(CAG)	 CT	150504-150624	GT	CGG
(CTC)	 AG	150735-150859	GT	AGG
(GCG)	 AG	151025-151259	GT	GGG
(GTG)	 AG	151523-151692	GT	AGG
(GAG)	 AG	151992-152169	GT	AGG
(ATT)	 AG	153429-153515	GT	AGG
(CTA)	 AG	153622-153713	GT	AGG
(GTG)	 AG	153822-153955	GT	AAG
(GGC)	 AG	154193-154337	GT	AGG
(GTG)	 AG	154438-154594	GT	AGG
(AGG)	 AG	155063-155160	GT	AGG
(ATC)	 AG	155471-155696	GT	AGG
(TGG)	 AG	155782-155838	GT	AGG
(AAC)	 AG	155976-156140	GT	AGG
(AAC)	 AG	156794-156902	GT	CAG
(ACA)	 AG	158746-158878	GT	AGG
(CTC)	 AG	159309-159504	GT	GGG
(TGC)	 AG	159784-159986	CC	GAC
-recovered pasa_asmbl_41986.p1, terminal, 159784, 159986
-recovered pasa_asmbl_41986.p1, internal, 150735, 150859
-recovered pasa_asmbl_41986.p1, internal, 151025, 151259
-recovered pasa_asmbl_41986.p1, internal, 151523, 151692
-recovered pasa_asmbl_41986.p1, internal, 151992, 152169
-recovered pasa_asmbl_41986.p1, internal, 153429, 153515
-recovered pasa_asmbl_41986.p1, internal, 153622, 153713
-recovered pasa_asmbl_41986.p1, internal, 153822, 153955
-recovered pasa_asmbl_41986.p1, internal, 154193, 154337
-recovered pasa_asmbl_41986.p1, internal, 154438, 154594
-recovered pasa_asmbl_41986.p1, internal, 155063, 155160
-recovered pasa_asmbl_41986.p1, internal, 155471, 155696
-recovered pasa_asmbl_41986.p1, internal, 155782, 155838
-recovered pasa_asmbl_41986.p1, internal, 155976, 156140
-recovered pasa_asmbl_41986.p1, internal, 156794, 156902
-recovered pasa_asmbl_41986.p1, internal, 158746, 158878
-recovered pasa_asmbl_41986.p1, internal, 159309, 159504
Valid prediction for snap_scaffold_4-snap.3362-T1
Valid prediction for GlimmerHMM_glimmerT_10876-T1
Valid prediction for snap_scaffold_4-snap.3364-T1
Valid prediction for GlimmerHMM_glimmerT_10877-T1
Valid prediction for HiQ_model.g7136.t1
Valid prediction for CodingQuarry_transcript_49284-T1
Valid prediction for snap_scaffold_4-snap.3385-T1
Valid prediction for CodingQuarry_transcript_49283-T1
Valid prediction for GlimmerHMM_glimmerT_10872-T1
Valid prediction for Augustus_model.g7128.t1
Valid prediction for HiQ_model.g7135.t1
Valid prediction for Augustus_model.g7121.t1
Valid prediction for snap_scaffold_4-snap.3348-T1
Valid prediction for pasa_asmbl_41975.p1
Valid prediction for snap_scaffold_4-snap.3357-T1
Valid prediction for GlimmerHMM_glimmerT_10890-T1
Couldn't classify 28022, 28181
Sorry, prediction pasa_asmbl_41973.p1 fails validation.
(TCG)	 CC	28022-28181	GT	AGG
(CCC)	 AG	28770-28901	GT	AGG
(CGG)	 AG	29111-29244	GT	AGG
(GAG)	 AG	29450-29539	GT	CGG
(GAT)	 AG	29707-29759	GT	AGG
(AGC)	 AG	29855-29934	GT	AGG
(GTG)	 AG	30097-30224	GT	CTG
(GTT)	 AG	30334-30429	GT	AGG
(TTG)	 AG	30727-30877	GT	TGG
(GGG)	 AG	31018-31135	GT	AGG
(TGC)	 AG	31381-31456	GT	CGG
(GCC)	 AG	31619-31759	GT	TGG
(GAG)	 AG	32157-32330	GA	GAG
-recovered pasa_asmbl_41973.p1, terminal, 32157, 32330
-recovered pasa_asmbl_41973.p1, internal, 28770, 28901
-recovered pasa_asmbl_41973.p1, internal, 29111, 29244
-recovered pasa_asmbl_41973.p1, internal, 29450, 29539
-recovered pasa_asmbl_41973.p1, internal, 29707, 29759
-recovered pasa_asmbl_41973.p1, internal, 29855, 29934
-recovered pasa_asmbl_41973.p1, internal, 30097, 30224
-recovered pasa_asmbl_41973.p1, internal, 30334, 30429
-recovered pasa_asmbl_41973.p1, internal, 30727, 30877
-recovered pasa_asmbl_41973.p1, internal, 31018, 31135
-recovered pasa_asmbl_41973.p1, internal, 31381, 31456
-recovered pasa_asmbl_41973.p1, internal, 31619, 31759
Valid prediction for GlimmerHMM_glimmerT_10879-T1
Couldn't classify 141878, 142021
Sorry, prediction pasa_asmbl_41983.p1 fails validation.
(ATG)	 AT	139697-139760	GT	TGG
(ACG)	 AG	140352-140464	GT	AGG
(GAG)	 AG	140644-140916	GT	AGG
(CCC)	 AG	141041-141156	GT	AGG
(GCC)	 AG	141254-141353	GT	AGG
(GGC)	 AG	141878-142021	CC	CCC
-recovered pasa_asmbl_41983.p1, initial, 139697, 139760
-recovered pasa_asmbl_41983.p1, internal, 140352, 140464
-recovered pasa_asmbl_41983.p1, internal, 140644, 140916
-recovered pasa_asmbl_41983.p1, internal, 141041, 141156
-recovered pasa_asmbl_41983.p1, internal, 141254, 141353
Valid prediction for snap_scaffold_4-snap.3380-T1
Valid prediction for CodingQuarry_transcript_49285-T1
Couldn't classify 95188, 95431
Sorry, prediction pasa_asmbl_41981.p1 fails validation.
(CGT)	 AG	95188-95431	GT	AGG
(TTT)	 AG	95636-96255	CA	GAC
-recovered pasa_asmbl_41981.p1, terminal, 95636, 96255
-recovered pasa_asmbl_41981.p1, internal, 95188, 95431
Valid prediction for GlimmerHMM_glimmerT_10893-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 pasa_asmbl_43201.p1
Valid prediction for pasa_asmbl_43189.p1
Valid prediction for CodingQuarry_transcript_49282-T1
Valid prediction for GlimmerHMM_glimmerT_10888-T1
Valid prediction for Augustus_model.g7129.t1
Valid prediction for Augustus_model.g7124.t1
Valid prediction for HiQ_model.g7131.t1
Valid prediction for pasa_asmbl_43183.p1
Valid prediction for GlimmerHMM_glimmerT_10887-T1
Valid prediction for snap_scaffold_4-snap.3356-T1
Couldn't classify 86543, 86845
Sorry, prediction pasa_asmbl_43526.p1 fails validation.
(AAG)	 TG	86543-86845	CT	AGC
Valid prediction for GlimmerHMM_glimmerT_10882-T1
Valid prediction for Augustus_model.g7122.t1
Valid prediction for snap_scaffold_4-snap.3381-T1
Valid prediction for HiQ_model.g7119.t1
Valid prediction for snap_scaffold_4-snap.3368-T1
Valid prediction for snap_scaffold_4-snap.3353-T1
Valid prediction for snap_scaffold_4-snap.3372-T1
Valid prediction for HiQ_model.g7125.t1
Valid prediction for GlimmerHMM_glimmerT_10881-T1
Valid prediction for snap_scaffold_4-snap.3366-T1
Valid prediction for CodingQuarry_transcript_49279-T1
Valid prediction for GlimmerHMM_glimmerT_10891-T1
Valid prediction for snap_scaffold_4-snap.3344-T1
Valid prediction for snap_scaffold_4-snap.3351-T1
Couldn't classify 136538, 136880
Sorry, prediction pasa_asmbl_43187.p1 fails validation.
(CTG)	 AA	136538-136880	GT	AGG
(GCA)	 AG	136981-137057	GT	AGG
(ACC)	 AG	137327-137419	TC	AGT
-recovered pasa_asmbl_43187.p1, terminal, 137327, 137419
-recovered pasa_asmbl_43187.p1, internal, 136981, 137057
Valid prediction for GlimmerHMM_glimmerT_10880-T1
Valid prediction for snap_scaffold_4-snap.3350-T1
Valid prediction for GlimmerHMM_glimmerT_10878-T1
Valid prediction for Augustus_model.g7130.t1
Valid prediction for snap_scaffold_4-snap.3375-T1
Valid prediction for GlimmerHMM_glimmerT_10874-T1
Valid prediction for snap_scaffold_4-snap.3367-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g7127.t1
Valid prediction for GlimmerHMM_glimmerT_10885-T1
Valid prediction for snap_scaffold_4-snap.3376-T1
Valid prediction for GlimmerHMM_glimmerT_10886-T1
Valid prediction for snap_scaffold_4-snap.3377-T1
Valid prediction for snap_scaffold_4-snap.3379-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_10889-T1
Valid prediction for CodingQuarry_transcript_49280-T1
Valid prediction for snap_scaffold_4-snap.3358-T1
Valid prediction for CodingQuarry_transcript_49278-T1
Valid prediction for snap_scaffold_4-snap.3383-T1
Valid prediction for GlimmerHMM_glimmerT_10875-T1
Valid prediction for snap_scaffold_4-snap.3361-T1
Valid prediction for Augustus_model.g7123.t1
Valid prediction for GlimmerHMM_glimmerT_10883-T1
Valid prediction for GlimmerHMM_glimmerT_10873-T1
Valid prediction for snap_scaffold_4-snap.3352-T1
Valid prediction for CodingQuarry_transcript_49281-T1
Valid prediction for pasa_asmbl_43196.p1
Valid prediction for Augustus_model.g7118.t1
Valid prediction for Augustus_model.g7134.t1
Valid prediction for snap_scaffold_4-snap.3363-T1
Valid prediction for snap_scaffold_4-snap.3371-T1
Valid prediction for snap_scaffold_4-snap.3346-T1
Valid prediction for snap_scaffold_4-snap.3343-T1
Valid prediction for Augustus_model.g7132.t1
Valid prediction for snap_scaffold_4-snap.3373-T1
Valid prediction for CodingQuarry_transcript_49276-T1
Valid prediction for snap_scaffold_4-snap.3345-T1
Valid prediction for snap_scaffold_4-snap.3360-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 25020, rend_intergenic: 17823  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41972, rend_intergenic: 27279  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55559, rend_intergenic: 49827  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65799, rend_intergenic: 61952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73987, rend_intergenic: 68245  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77680, rend_intergenic: 74426  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101844, rend_intergenic: 97749  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123220, rend_intergenic: 114556  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152762, rend_intergenic: 141230  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157483, rend_intergenic: 153875  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160866, rend_intergenic: 159060  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174368, rend_intergenic: 165931  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 181418
-exon list size: 483


building trellis

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92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
94.0    
94.2    
94.4    
94.6    
94.8    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.3    
97.5    
97.7    
97.9    
98.1    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 25020, rend_intergenic: 17823  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41972, rend_intergenic: 27279  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55559, rend_intergenic: 49827  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65799, rend_intergenic: 61952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73987, rend_intergenic: 68245  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77680, rend_intergenic: 74426  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101844, rend_intergenic: 97749  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123220, rend_intergenic: 114556  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152762, rend_intergenic: 141230  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157483, rend_intergenic: 153875  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160866, rend_intergenic: 159060  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174368, rend_intergenic: 165931  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 10619
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support