-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_11/scaffold_11_13506453-13764266

-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.2892-T1
Valid prediction for GeneMark_model.49688_t
Valid prediction for snap_scaffold_11-snap.2912-T1
Valid prediction for GeneMark_model.49710_t
Valid prediction for snap_scaffold_11-snap.2927-T1
Couldn't classify 171022, 171088
Sorry, prediction pasa_asmbl_6047.p1 fails validation.
(ATG)	 AA	168870-168935	GT	AGG
(TGG)	 AG	169308-169353	GT	TGG
(ACA)	 AG	169466-169564	GT	TGG
(GTA)	 AG	169764-169841	GT	TGG
(TCA)	 AG	170386-170423	GT	AGG
(CTG)	 AG	170623-170759	GT	AGG
(TTC)	 AG	171022-171088	TG	TGT
-recovered pasa_asmbl_6047.p1, initial, 168870, 168935
-recovered pasa_asmbl_6047.p1, internal, 169308, 169353
-recovered pasa_asmbl_6047.p1, internal, 169466, 169564
-recovered pasa_asmbl_6047.p1, internal, 169764, 169841
-recovered pasa_asmbl_6047.p1, internal, 170386, 170423
-recovered pasa_asmbl_6047.p1, internal, 170623, 170759
Valid prediction for snap_scaffold_11-snap.2896-T1
Valid prediction for snap_scaffold_11-snap.2921-T1
Couldn't classify 129036, 129299
Couldn't classify 133724, 133761
Sorry, prediction pasa_asmbl_6044.p1 fails validation.
(CAG)	 CG	129036-129299	GT	CGG
(ACG)	 AG	129489-129633	GT	CGG
(GTG)	 AG	129913-130051	GT	CGG
(GGA)	 AG	130155-130246	GT	CAG
(CGG)	 AG	130438-130597	GT	CAG
(ATT)	 AG	130829-130892	GT	AGG
(TCG)	 AG	131560-131648	GT	AGG
(AAC)	 AG	132023-132071	GT	AGG
(GTT)	 AG	133276-133411	GC	AGG
(TAA)	 AG	133724-133761	AG	GAA
-recovered pasa_asmbl_6044.p1, internal, 129489, 129633
-recovered pasa_asmbl_6044.p1, internal, 129913, 130051
-recovered pasa_asmbl_6044.p1, internal, 130155, 130246
-recovered pasa_asmbl_6044.p1, internal, 130438, 130597
-recovered pasa_asmbl_6044.p1, internal, 130829, 130892
-recovered pasa_asmbl_6044.p1, internal, 131560, 131648
-recovered pasa_asmbl_6044.p1, internal, 132023, 132071
-recovered pasa_asmbl_6044.p1, internal, 133276, 133411
Valid prediction for Augustus_model.g19224.t1
Valid prediction for CodingQuarry_transcript_8264-T1
Valid prediction for GlimmerHMM_glimmerT_28800-T1
Valid prediction for Augustus_model.g19237.t1
Valid prediction for GlimmerHMM_glimmerT_28793-T1
Valid prediction for GeneMark_model.49700_t
Valid prediction for Augustus_model.g19214.t1
Valid prediction for snap_scaffold_11-snap.2887-T1
Valid prediction for GeneMark_model.49709_t
Valid prediction for snap_scaffold_11-snap.2906-T1
Valid prediction for CodingQuarry_transcript_8268-T1
Valid prediction for GlimmerHMM_glimmerT_28781-T1
Couldn't classify 205373, 205464
Couldn't classify 208345, 208428
Sorry, prediction pasa_asmbl_6053.p1 fails validation.
(CGT)	 TC	205373-205464	GT	TGG
(GCG)	 AG	206380-206583	GT	AGG
(AGA)	 AG	206747-206893	GT	TGG
(GGT)	 AG	207172-207304	GT	CGG
(GAA)	 AG	207432-207542	GT	AGG
(TGG)	 AG	207714-207878	GT	AGG
(ATA)	 AG	207991-208125	GT	AGG
(GCC)	 AG	208345-208428	GA	CCG
-recovered pasa_asmbl_6053.p1, internal, 206380, 206583
-recovered pasa_asmbl_6053.p1, internal, 206747, 206893
-recovered pasa_asmbl_6053.p1, internal, 207172, 207304
-recovered pasa_asmbl_6053.p1, internal, 207432, 207542
-recovered pasa_asmbl_6053.p1, internal, 207714, 207878
-recovered pasa_asmbl_6053.p1, internal, 207991, 208125
Valid prediction for Augustus_model.g19229.t1
Valid prediction for Augustus_model.g19213.t1
Valid prediction for snap_scaffold_11-snap.2900-T1
Couldn't classify 34722, 34818
Sorry, prediction pasa_asmbl_6037.p2 fails validation.
(GAC)	 TT	34722-34818	GT	TGG
(GCT)	 AG	34927-35103	GT	GGG
(GGG)	 AG	35202-35374	AA	AGA
-recovered pasa_asmbl_6037.p2, terminal, 35202, 35374
-recovered pasa_asmbl_6037.p2, internal, 34927, 35103
Valid prediction for pasa_asmbl_6045.p1
Valid prediction for snap_scaffold_11-snap.2883-T1
Valid prediction for snap_scaffold_11-snap.2918-T1
Valid prediction for GlimmerHMM_glimmerT_28788-T1
Valid prediction for pasa_asmbl_6337.p1
Valid prediction for GeneMark_model.49702_t
Valid prediction for snap_scaffold_11-snap.2885-T1
Valid prediction for Augustus_model.g19236.t1
Valid prediction for HiQ_model.g19230.t1
Valid prediction for GeneMark_model.49690_t
Valid prediction for snap_scaffold_11-snap.2915-T1
Valid prediction for GeneMark_model.49719_t
Valid prediction for snap_scaffold_11-snap.2904-T1
Valid prediction for Augustus_model.g19217.t1
Valid prediction for snap_scaffold_11-snap.2920-T1
Valid prediction for GeneMark_model.49707_t
Valid prediction for CodingQuarry_transcript_8263-T1
Valid prediction for snap_scaffold_11-snap.2893-T1
Valid prediction for snap_scaffold_11-snap.2903-T1
Valid prediction for pasa_asmbl_6051.p1
Valid prediction for GeneMark_model.49717_t
Valid prediction for snap_scaffold_11-snap.2907-T1
Valid prediction for Augustus_model.g19223.t1
Valid prediction for snap_scaffold_11-snap.2924-T1
Valid prediction for snap_scaffold_11-snap.2917-T1
Valid prediction for Augustus_model.g19233.t1
Valid prediction for GlimmerHMM_glimmerT_28776-T1
Valid prediction for GeneMark_model.49698_t
Couldn't classify 208879, 209108
Sorry, prediction pasa_asmbl_6054.p1 fails validation.
(CGT)	 TC	208879-209108	GT	GGG
(GGC)	 AG	209242-209392	CA	GAC
-recovered pasa_asmbl_6054.p1, terminal, 209242, 209392
Valid prediction for GeneMark_model.49708_t
Valid prediction for GlimmerHMM_glimmerT_28775-T1
Valid prediction for snap_scaffold_11-snap.2901-T1
Valid prediction for GlimmerHMM_glimmerT_28792-T1
Valid prediction for GlimmerHMM_glimmerT_28794-T1
Couldn't classify 212065, 212667
Sorry, prediction pasa_asmbl_6055.p1 fails validation.
(GCT)	 CT	212065-212667	AC	AAA
Couldn't classify 173765, 173882
Sorry, prediction pasa_asmbl_6048.p1 fails validation.
(CCA)	 GA	173765-173882	GT	GGG
(GTC)	 AG	175240-175319	GT	AGG
(GTG)	 AG	175418-175516	GT	AGG
(GCA)	 AG	175761-175853	GT	AGG
(ATT)	 AG	176004-176180	GT	AGG
(GCG)	 AG	176340-176644	GT	AAG
(GGC)	 AG	177064-177166	GT	AGG
(TCT)	 AG	177525-177680	GT	GAG
-recovered pasa_asmbl_6048.p1, terminal, 177525, 177680
-recovered pasa_asmbl_6048.p1, internal, 175240, 175319
-recovered pasa_asmbl_6048.p1, internal, 175418, 175516
-recovered pasa_asmbl_6048.p1, internal, 175761, 175853
-recovered pasa_asmbl_6048.p1, internal, 176004, 176180
-recovered pasa_asmbl_6048.p1, internal, 176340, 176644
-recovered pasa_asmbl_6048.p1, internal, 177064, 177166
-recovered pasa_asmbl_6048.p1, internal, 177525, 177680
Valid prediction for GeneMark_model.49722_t
Valid prediction for snap_scaffold_11-snap.2913-T1
Valid prediction for GlimmerHMM_glimmerT_28787-T1
Valid prediction for GeneMark_model.49704_t
Valid prediction for snap_scaffold_11-snap.2895-T1
Valid prediction for snap_scaffold_11-snap.2882-T1
Valid prediction for snap_scaffold_11-snap.2886-T1
Valid prediction for GlimmerHMM_glimmerT_28797-T1
Valid prediction for snap_scaffold_11-snap.2916-T1
Valid prediction for GlimmerHMM_glimmerT_28789-T1
Valid prediction for snap_scaffold_11-snap.2911-T1
Valid prediction for GlimmerHMM_glimmerT_28778-T1
Valid prediction for Augustus_model.g19232.t1
Valid prediction for Augustus_model.g19231.t1
Valid prediction for Augustus_model.g19234.t1
Valid prediction for Augustus_model.g19225.t1
Valid prediction for snap_scaffold_11-snap.2919-T1
Couldn't classify 109820, 111025
Sorry, prediction pasa_asmbl_6041.p1 fails validation.
(CCC)	 CC	109820-111025	GG	GAG
Valid prediction for HiQ_model.g19218.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 GeneMark_model.49703_t
Valid prediction for Augustus_model.g19228.t1
Valid prediction for snap_scaffold_11-snap.2909-T1
Valid prediction for Augustus_model.g19212.t1
Valid prediction for snap_scaffold_11-snap.2910-T1
Couldn't classify 196661, 197059
Sorry, prediction pasa_asmbl_7118.p1 fails validation.
(TGC)	 TG	196661-197059	AG	AGA
Valid prediction for GlimmerHMM_glimmerT_28783-T1
Valid prediction for GlimmerHMM_glimmerT_28785-T1
Valid prediction for Augustus_model.g19219.t1
Valid prediction for GlimmerHMM_glimmerT_28780-T1
Valid prediction for Augustus_model.g19221.t1
Valid prediction for GeneMark_model.49697_t
Valid prediction for GeneMark_model.49716_t
Valid prediction for Augustus_model.g19227.t1
Valid prediction for GlimmerHMM_glimmerT_28799-T1
Valid prediction for GeneMark_model.49696_t
Valid prediction for snap_scaffold_11-snap.2926-T1
Valid prediction for snap_scaffold_11-snap.2890-T1
Valid prediction for GeneMark_model.49714_t
Valid prediction for GeneMark_model.49692_t
Valid prediction for GeneMark_model.49689_t
Valid prediction for GlimmerHMM_glimmerT_28798-T1
Valid prediction for snap_scaffold_11-snap.2889-T1
Couldn't classify 209259, 209383
Sorry, prediction pasa_asmbl_7115.p1 fails validation.
(ATC)	 AC	209259-209383	GT	ATG
(TGT)	 AG	209733-209772	GT	TGG
(CCA)	 AG	209921-210101	GC	AGG
(GAG)	 AG	210256-210525	GT	AGG
(ACA)	 AG	210733-210821	GT	AGG
(TGG)	 AG	210928-211338	GT	AGG
(GTT)	 AG	211488-211704	GT	AGG
(GCA)	 AG	211884-212086	GT	TGG
(CAT)	 AG	212316-212498	GT	AGG
(ATT)	 AG	212650-212759	GT	AGG
(GTT)	 AG	213077-213322	GT	AGG
(ATA)	 AG	213435-213690	CA	GAC
add_exon() Sorry, pasa_asmbl_7115.p1 211488-211704-terminal-3 is invalid.
-recovered pasa_asmbl_7115.p1, terminal, 211488, 211704
-recovered pasa_asmbl_7115.p1, terminal, 213435, 213690
-recovered pasa_asmbl_7115.p1, internal, 209733, 209772
-recovered pasa_asmbl_7115.p1, internal, 209921, 210101
-recovered pasa_asmbl_7115.p1, internal, 210256, 210525
-recovered pasa_asmbl_7115.p1, internal, 210733, 210821
-recovered pasa_asmbl_7115.p1, internal, 210928, 211338
-recovered pasa_asmbl_7115.p1, internal, 211488, 211704
-recovered pasa_asmbl_7115.p1, internal, 211884, 212086
-recovered pasa_asmbl_7115.p1, internal, 212316, 212498
-recovered pasa_asmbl_7115.p1, internal, 212650, 212759
-recovered pasa_asmbl_7115.p1, internal, 213077, 213322
Valid prediction for CodingQuarry_transcript_8265-T1
Valid prediction for snap_scaffold_11-snap.2902-T1
Valid prediction for snap_scaffold_11-snap.2894-T1
Valid prediction for GeneMark_model.49718_t
Valid prediction for GeneMark_model.49706_t
Valid prediction for snap_scaffold_11-snap.2899-T1
Valid prediction for snap_scaffold_11-snap.2888-T1
Valid prediction for snap_scaffold_11-snap.2891-T1
Valid prediction for CodingQuarry_transcript_8267-T1
Valid prediction for GlimmerHMM_glimmerT_28796-T1
Valid prediction for snap_scaffold_11-snap.2897-T1
Valid prediction for snap_scaffold_11-snap.2898-T1
Valid prediction for Augustus_model.g19222.t1
Valid prediction for GlimmerHMM_glimmerT_28790-T1
Valid prediction for Augustus_model.g19220.t1
Valid prediction for GlimmerHMM_glimmerT_28784-T1
Valid prediction for GlimmerHMM_glimmerT_28777-T1
Valid prediction for GlimmerHMM_glimmerT_28786-T1
Valid prediction for snap_scaffold_11-snap.2905-T1
Valid prediction for GlimmerHMM_glimmerT_28791-T1
Valid prediction for snap_scaffold_11-snap.2925-T1
Valid prediction for GeneMark_model.49691_t
Valid prediction for Augustus_model.g19235.t1
Valid prediction for HiQ_model.g19216.t1
Valid prediction for GeneMark_model.49699_t
Valid prediction for snap_scaffold_11-snap.2923-T1
Valid prediction for Augustus_model.g19215.t1
Valid prediction for snap_scaffold_11-snap.2914-T1
Valid prediction for GlimmerHMM_glimmerT_28782-T1
Valid prediction for snap_scaffold_11-snap.2908-T1
Valid prediction for Augustus_model.g19226.t1
Valid prediction for pasa_asmbl_7131.p1
Valid prediction for pasa_asmbl_7114.p2
Valid prediction for Augustus_model.g19211.t1
Couldn't classify 183127, 183204
Sorry, prediction pasa_asmbl_7120.p1 fails validation.
(CAG)	 GA	183127-183204	GT	AGG
(GAA)	 AG	184143-184316	GT	AGG
(CTG)	 AG	184436-184567	GT	AGG
(GCA)	 AG	185090-185125	GT	AGG
(CTG)	 AG	187826-187981	AC	GAA
-recovered pasa_asmbl_7120.p1, terminal, 187826, 187981
-recovered pasa_asmbl_7120.p1, internal, 184143, 184316
-recovered pasa_asmbl_7120.p1, internal, 184436, 184567
-recovered pasa_asmbl_7120.p1, internal, 185090, 185125
Valid prediction for CodingQuarry_transcript_8266-T1
Couldn't classify 247182, 247282
Sorry, prediction pasa_asmbl_7111.p1 fails validation.
(ATG)	 TT	245968-246016	GT	AGG
(GGC)	 AG	246432-246542	GT	CAG
(TGG)	 AG	246931-247044	GT	TAG
(ATA)	 AG	247182-247282	AC	GCA
-recovered pasa_asmbl_7111.p1, initial, 245968, 246016
-recovered pasa_asmbl_7111.p1, internal, 246432, 246542
-recovered pasa_asmbl_7111.p1, internal, 246931, 247044
Valid prediction for GeneMark_model.49713_t
Valid prediction for GlimmerHMM_glimmerT_28795-T1
Valid prediction for GeneMark_model.49721_t
Valid prediction for GlimmerHMM_glimmerT_28779-T1
Valid prediction for snap_scaffold_11-snap.2884-T1
Valid prediction for pasa_asmbl_7129.p1
Valid prediction for GeneMark_model.49720_t
Valid prediction for GeneMark_model.49701_t
Valid prediction for snap_scaffold_11-snap.2922-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9595, rend_intergenic: 7978  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20586, rend_intergenic: 10845  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132113, rend_intergenic: 131982  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135195, rend_intergenic: 133711  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 254210, rend_intergenic: 247252  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 257814
-exon list size: 581


building trellis

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65.2    
65.4    
65.5    
65.7    
65.9    
66.0    
66.2    
66.4    
66.6    
66.7    
66.9    
67.1    
67.2    
67.4    
67.6    
67.8    
67.9    
68.1    
68.3    
68.4    
68.6    
68.8    
69.0    
69.1    
69.3    
69.5    
69.6    
69.8    
70.0    
70.2    
70.3    
70.5    
70.7    
70.8    
71.0    
71.2    
71.4    
71.5    
71.7    
71.9    
72.0    
72.2    
72.4    
72.6    
72.7    
72.9    
73.1    
73.2    
73.4    
73.6    
73.8    
73.9    
74.1    
74.3    
74.4    
74.6    
74.8    
75.0    
75.1    
75.3    
75.5    
75.6    
75.8    
76.0    
76.2    
76.3    
76.5    
76.7    
76.8    
77.0    
77.2    
77.4    
77.5    
77.7    
77.9    
78.0    
78.2    
78.4    
78.6    
78.7    
78.9    
79.1    
79.2    
79.4    
79.6    
79.8    
79.9    
80.1    
80.3    
80.4    
80.6    
80.8    
81.0    
81.1    
81.3    
81.5    
81.6    
81.8    
82.0    
82.2    
82.3    
82.5    
82.7    
82.8    
83.0    
83.2    
83.4    
83.5    
83.7    
83.9    
84.0    
84.2    
84.4    
84.6    
84.7    
84.9    
85.1    
85.2    
85.4    
85.6    
85.8    
85.9    
86.1    
86.3    
86.4    
86.6    
86.8    
87.0    
87.1    
87.3    
87.5    
87.7    
87.8    
88.0    
88.2    
88.3    
88.5    
88.7    
88.9    
89.0    
89.2    
89.4    
89.5    
89.7    
89.9    
90.1    
90.2    
90.4    
90.6    
90.7    
90.9    
91.1    
91.3    
91.4    
91.6    
91.8    
91.9    
92.1    
92.3    
92.5    
92.6    
92.8    
93.0    
93.1    
93.3    
93.5    
93.7    
93.8    
94.0    
94.2    
94.3    
94.5    
94.7    
94.9    
95.0    
95.2    
95.4    
95.5    
95.7    
95.9    
96.1    
96.2    
96.4    
96.6    
96.7    
96.9    
97.1    
97.3    
97.4    
97.6    
97.8    
97.9    
98.1    
98.3    
98.5    
98.6    
98.8    
99.0    
99.1    
99.3    
99.5    
99.7    
99.8    
-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 9595, rend_intergenic: 7978  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20586, rend_intergenic: 10845  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132113, rend_intergenic: 131982  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135195, rend_intergenic: 133711  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 254210, rend_intergenic: 247252  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 33 predictions persist after filtering for low support