-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_12/scaffold_12_1246373-1475842

-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 GeneMark_model.50880_t
Valid prediction for snap_scaffold_12-snap.312-T1
Valid prediction for Augustus_model.g19608.t1
Valid prediction for GlimmerHMM_glimmerT_29466-T1
Valid prediction for GeneMark_model.50883_t
Valid prediction for GlimmerHMM_glimmerT_29450-T1
Valid prediction for GeneMark_model.50839_t
Valid prediction for GeneMark_model.50872_t
Valid prediction for GeneMark_model.50863_t
Valid prediction for GlimmerHMM_glimmerT_29476-T1
Valid prediction for GlimmerHMM_glimmerT_29452-T1
Valid prediction for GeneMark_model.50852_t
Valid prediction for GeneMark_model.50878_t
Valid prediction for snap_scaffold_12-snap.321-T1
Valid prediction for snap_scaffold_12-snap.328-T1
Valid prediction for GlimmerHMM_glimmerT_29458-T1
Valid prediction for GeneMark_model.50871_t
Valid prediction for snap_scaffold_12-snap.298-T1
Valid prediction for GlimmerHMM_glimmerT_29465-T1
Valid prediction for GeneMark_model.50869_t
Valid prediction for GeneMark_model.50864_t
Valid prediction for GeneMark_model.50856_t
Valid prediction for GeneMark_model.50841_t
Valid prediction for snap_scaffold_12-snap.317-T1
Valid prediction for snap_scaffold_12-snap.324-T1
Valid prediction for snap_scaffold_12-snap.295-T1
Valid prediction for GeneMark_model.50848_t
Valid prediction for Augustus_model.g19609.t1
Valid prediction for GlimmerHMM_glimmerT_29473-T1
Valid prediction for GlimmerHMM_glimmerT_29460-T1
Valid prediction for GlimmerHMM_glimmerT_29474-T1
Valid prediction for GlimmerHMM_glimmerT_29453-T1
Couldn't classify 91537, 91692
Sorry, prediction pasa_asmbl_8432.p1 fails validation.
(ACT)	 GT	91537-91692	GT	AGG
(GTC)	 AG	91786-91879	GT	AGG
(AGA)	 AG	92956-92981	GT	AGG
(GAG)	 AG	94914-95006	GT	AGG
(GAA)	 AG	95406-95588	GT	TGG
(ACG)	 AG	96198-96289	GT	GGG
(TTC)	 AG	96466-96696	GT	AGG
(GTG)	 AG	96985-97089	GT	AGG
(GTC)	 AG	97369-97477	GT	AGG
(TGT)	 AG	98245-98347	GT	CTG
(CTG)	 AG	98624-98649	CC	GAC
-recovered pasa_asmbl_8432.p1, terminal, 98624, 98649
-recovered pasa_asmbl_8432.p1, internal, 91786, 91879
-recovered pasa_asmbl_8432.p1, internal, 92956, 92981
-recovered pasa_asmbl_8432.p1, internal, 94914, 95006
-recovered pasa_asmbl_8432.p1, internal, 95406, 95588
-recovered pasa_asmbl_8432.p1, internal, 96198, 96289
-recovered pasa_asmbl_8432.p1, internal, 96466, 96696
-recovered pasa_asmbl_8432.p1, internal, 96985, 97089
-recovered pasa_asmbl_8432.p1, internal, 97369, 97477
-recovered pasa_asmbl_8432.p1, internal, 98245, 98347
Valid prediction for GeneMark_model.50874_t
Valid prediction for snap_scaffold_12-snap.326-T1
Valid prediction for HiQ_model.g19612.t1
Valid prediction for GeneMark_model.50860_t
Valid prediction for CodingQuarry_transcript_10103-T1
Valid prediction for GeneMark_model.50843_t
Valid prediction for snap_scaffold_12-snap.300-T1
Valid prediction for GeneMark_model.50858_t
Valid prediction for pasa_asmbl_8437.p1
Valid prediction for GlimmerHMM_glimmerT_29457-T1
Valid prediction for snap_scaffold_12-snap.319-T1
Valid prediction for GeneMark_model.50837_t
Valid prediction for CodingQuarry_transcript_10102-T1
Valid prediction for GeneMark_model.50867_t
Valid prediction for snap_scaffold_12-snap.331-T1
Valid prediction for pasa_asmbl_8435.p1
Valid prediction for GlimmerHMM_glimmerT_29471-T1
Valid prediction for GlimmerHMM_glimmerT_29455-T1
Valid prediction for GeneMark_model.50835_t
Valid prediction for snap_scaffold_12-snap.330-T1
Valid prediction for snap_scaffold_12-snap.292-T1
Valid prediction for snap_scaffold_12-snap.304-T1
Valid prediction for GeneMark_model.50832_t
Valid prediction for Augustus_model.g19616.t1
Valid prediction for GeneMark_model.50851_t
Valid prediction for HiQ_model.g19615.t1
Valid prediction for snap_scaffold_12-snap.288-T1
Valid prediction for snap_scaffold_12-snap.323-T1
Valid prediction for Augustus_model.g19607.t1
Valid prediction for GeneMark_model.50870_t
Valid prediction for snap_scaffold_12-snap.296-T1
Valid prediction for GeneMark_model.50854_t
Valid prediction for Augustus_model.g19610.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_12-snap.309-T1
Valid prediction for GeneMark_model.50862_t
Valid prediction for GlimmerHMM_glimmerT_29459-T1
Couldn't classify 81146, 81161
Couldn't classify 84473, 84497
Sorry, prediction pasa_asmbl_7434.p1 fails validation.
(ATC)	 TC	81146-81161	GT	AGG
(GGA)	 AG	83198-83376	GT	AGG
(ATA)	 AG	83662-83762	GT	AGG
(GTT)	 AG	83932-84078	GT	AGG
(TTG)	 AG	84473-84497	GG	GGG
-recovered pasa_asmbl_7434.p1, internal, 83198, 83376
-recovered pasa_asmbl_7434.p1, internal, 83662, 83762
-recovered pasa_asmbl_7434.p1, internal, 83932, 84078
Valid prediction for GlimmerHMM_glimmerT_29462-T1
Valid prediction for snap_scaffold_12-snap.313-T1
Valid prediction for GeneMark_model.50855_t
Valid prediction for GeneMark_model.50831_t
Valid prediction for snap_scaffold_12-snap.320-T1
Valid prediction for snap_scaffold_12-snap.306-T1
Valid prediction for GeneMark_model.50842_t
Valid prediction for Augustus_model.g19613.t1
Valid prediction for GeneMark_model.50868_t
Valid prediction for snap_scaffold_12-snap.311-T1
Valid prediction for GlimmerHMM_glimmerT_29448-T1
Valid prediction for snap_scaffold_12-snap.293-T1
Valid prediction for GlimmerHMM_glimmerT_29447-T1
Valid prediction for GlimmerHMM_glimmerT_29461-T1
Valid prediction for GeneMark_model.50873_t
Valid prediction for snap_scaffold_12-snap.315-T1
Valid prediction for Augustus_model.g19606.t1
Valid prediction for GlimmerHMM_glimmerT_29470-T1
Valid prediction for GeneMark_model.50882_t
Couldn't classify 169276, 169310
Sorry, prediction GeneMark_model.50847_t fails validation.
(ATG)	 GC	167034-167040	GT	AAG
(AAC)	 AG	167365-167665	GT	GAG
(GGA)	 AG	169072-169116	GT	AAG
(GTG)	 AG	169183-169254	GT	GGG
(AGG)	 AG	169276-169310	GT	TGG
-recovered GeneMark_model.50847_t, initial, 167034, 167040
-recovered GeneMark_model.50847_t, internal, 167365, 167665
-recovered GeneMark_model.50847_t, internal, 169072, 169116
-recovered GeneMark_model.50847_t, internal, 169183, 169254
-recovered GeneMark_model.50847_t, internal, 169276, 169310
Valid prediction for snap_scaffold_12-snap.302-T1
Valid prediction for GeneMark_model.50833_t
Valid prediction for GlimmerHMM_glimmerT_29468-T1
Valid prediction for GlimmerHMM_glimmerT_29469-T1
Valid prediction for snap_scaffold_12-snap.289-T1
Valid prediction for snap_scaffold_12-snap.327-T1
Couldn't classify 177099, 177110
Sorry, prediction GeneMark_model.50846_t fails validation.
(GGA)	 AG	177099-177110	GT	AGG
(GAT)	 AG	177134-177151	GT	GGG
(TGG)	 AG	177177-177209	GT	GGG
(GCT)	 AG	177231-177266	GT	GGG
(AGA)	 AG	177397-177435	GT	GGG
(GAG)	 AG	177590-177698	CA	AGC
-recovered GeneMark_model.50846_t, terminal, 177590, 177698
-recovered GeneMark_model.50846_t, internal, 177099, 177110
-recovered GeneMark_model.50846_t, internal, 177134, 177151
-recovered GeneMark_model.50846_t, internal, 177177, 177209
-recovered GeneMark_model.50846_t, internal, 177231, 177266
-recovered GeneMark_model.50846_t, internal, 177397, 177435
Valid prediction for GeneMark_model.50876_t
Valid prediction for GlimmerHMM_glimmerT_29451-T1
Valid prediction for snap_scaffold_12-snap.303-T1
Valid prediction for GeneMark_model.50875_t
Valid prediction for GeneMark_model.50840_t
Valid prediction for GeneMark_model.50859_t
Valid prediction for GlimmerHMM_glimmerT_29472-T1
Valid prediction for GeneMark_model.50849_t
Valid prediction for GeneMark_model.50850_t
Valid prediction for snap_scaffold_12-snap.301-T1
Valid prediction for snap_scaffold_12-snap.314-T1
Valid prediction for GlimmerHMM_glimmerT_29463-T1
Valid prediction for snap_scaffold_12-snap.322-T1
Valid prediction for snap_scaffold_12-snap.318-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_29475-T1
Valid prediction for GlimmerHMM_glimmerT_29467-T1
Valid prediction for Augustus_model.g19617.t1
Valid prediction for GlimmerHMM_glimmerT_29454-T1
Valid prediction for GeneMark_model.50865_t
Valid prediction for Augustus_model.g19614.t1
Valid prediction for snap_scaffold_12-snap.299-T1
Valid prediction for snap_scaffold_12-snap.325-T1
Valid prediction for GeneMark_model.50879_t
Valid prediction for GeneMark_model.50853_t
Valid prediction for GlimmerHMM_glimmerT_29445-T1
Valid prediction for snap_scaffold_12-snap.291-T1
Valid prediction for Augustus_model.g19611.t1
Valid prediction for GeneMark_model.50877_t
Valid prediction for GeneMark_model.50845_t
Valid prediction for snap_scaffold_12-snap.308-T1
Valid prediction for GeneMark_model.50881_t
Valid prediction for GeneMark_model.50866_t
Valid prediction for GlimmerHMM_glimmerT_29464-T1
Valid prediction for GlimmerHMM_glimmerT_29456-T1
Valid prediction for snap_scaffold_12-snap.329-T1
Valid prediction for snap_scaffold_12-snap.316-T1
Valid prediction for snap_scaffold_12-snap.305-T1
Valid prediction for snap_scaffold_12-snap.294-T1
Valid prediction for snap_scaffold_12-snap.307-T1
Valid prediction for snap_scaffold_12-snap.310-T1
Valid prediction for GlimmerHMM_glimmerT_29449-T1
Valid prediction for GeneMark_model.50836_t
Valid prediction for GlimmerHMM_glimmerT_29446-T1
Valid prediction for GeneMark_model.50844_t
Valid prediction for GeneMark_model.50861_t
Valid prediction for GeneMark_model.50838_t
Valid prediction for snap_scaffold_12-snap.297-T1
Valid prediction for GeneMark_model.50834_t
Valid prediction for snap_scaffold_12-snap.290-T1
Valid prediction for GeneMark_model.50857_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 16976, rend_intergenic: 5029  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17689, rend_intergenic: 17134  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23577, rend_intergenic: 17997  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27603, rend_intergenic: 25283  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29473, rend_intergenic: 28564  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38783, rend_intergenic: 29715  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62193, rend_intergenic: 41002  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72771, rend_intergenic: 63382  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99241, rend_intergenic: 72977  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123706, rend_intergenic: 112211  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147744, rend_intergenic: 144888  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148385, rend_intergenic: 147744  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155054, rend_intergenic: 150681  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156034, rend_intergenic: 155409  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176602, rend_intergenic: 174402  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181329, rend_intergenic: 178973  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185243, rend_intergenic: 183299  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 229470
-exon list size: 754


building trellis

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73.0    
73.1    
73.3    
73.4    
73.5    
73.7    
73.8    
73.9    
74.1    
74.2    
74.3    
74.5    
74.6    
74.7    
74.9    
75.0    
75.1    
75.3    
75.4    
75.5    
75.7    
75.8    
75.9    
76.1    
76.2    
76.3    
76.5    
76.6    
76.7    
76.9    
77.0    
77.1    
77.2    
77.4    
77.5    
77.6    
77.8    
77.9    
78.0    
78.2    
78.3    
78.4    
78.6    
78.7    
78.8    
79.0    
79.1    
79.2    
79.4    
79.5    
79.6    
79.8    
79.9    
80.0    
80.2    
80.3    
80.4    
80.6    
80.7    
80.8    
81.0    
81.1    
81.2    
81.3    
81.5    
81.6    
81.7    
81.9    
82.0    
82.1    
82.3    
82.4    
82.5    
82.7    
82.8    
82.9    
83.1    
83.2    
83.3    
83.5    
83.6    
83.7    
83.9    
84.0    
84.1    
84.3    
84.4    
84.5    
84.7    
84.8    
84.9    
85.1    
85.2    
85.3    
85.4    
85.6    
85.7    
85.8    
86.0    
86.1    
86.2    
86.4    
86.5    
86.6    
86.8    
86.9    
87.0    
87.2    
87.3    
87.4    
87.6    
87.7    
87.8    
88.0    
88.1    
88.2    
88.4    
88.5    
88.6    
88.8    
88.9    
89.0    
89.2    
89.3    
89.4    
89.6    
89.7    
89.8    
89.9    
90.1    
90.2    
90.3    
90.5    
90.6    
90.7    
90.9    
91.0    
91.1    
91.3    
91.4    
91.5    
91.7    
91.8    
91.9    
92.1    
92.2    
92.3    
92.5    
92.6    
92.7    
92.9    
93.0    
93.1    
93.3    
93.4    
93.5    
93.7    
93.8    
93.9    
94.0    
94.2    
94.3    
94.4    
94.6    
94.7    
94.8    
95.0    
95.1    
95.2    
95.4    
95.5    
95.6    
95.8    
95.9    
96.0    
96.2    
96.3    
96.4    
96.6    
96.7    
96.8    
97.0    
97.1    
97.2    
97.4    
97.5    
97.6    
97.8    
97.9    
98.0    
98.1    
98.3    
98.4    
98.5    
98.7    
98.8    
98.9    
99.1    
99.2    
99.3    
99.5    
99.6    
99.7    
99.9    
-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 16976, rend_intergenic: 5029  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17689, rend_intergenic: 17134  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23577, rend_intergenic: 17997  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27603, rend_intergenic: 25283  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29473, rend_intergenic: 28564  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38783, rend_intergenic: 29715  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62193, rend_intergenic: 41002  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72771, rend_intergenic: 63382  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99241, rend_intergenic: 72977  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123706, rend_intergenic: 112211  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147744, rend_intergenic: 144888  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148385, rend_intergenic: 147744  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155054, rend_intergenic: 150681  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156034, rend_intergenic: 155409  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176602, rend_intergenic: 174402  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181329, rend_intergenic: 178973  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185243, rend_intergenic: 183299  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support