-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_4417624-4628452

-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_1-snap.688-T1
Valid prediction for CodingQuarry_transcript_2588-T1
Valid prediction for GeneMark_model.618_t
Valid prediction for GeneMark_model.614_t
Valid prediction for GeneMark_model.656_t
Valid prediction for Augustus_model.g411.t1
Valid prediction for GlimmerHMM_glimmerT_532-T1
Valid prediction for snap_scaffold_1-snap.661-T1
Valid prediction for snap_scaffold_1-snap.659-T1
Valid prediction for snap_scaffold_1-snap.696-T1
Valid prediction for GeneMark_model.660_t
Valid prediction for HiQ_model.g426.t1
Valid prediction for GeneMark_model.645_t
Valid prediction for pasa_asmbl_1672.p1
Valid prediction for snap_scaffold_1-snap.670-T1
Valid prediction for GlimmerHMM_glimmerT_551-T1
Valid prediction for snap_scaffold_1-snap.665-T1
Valid prediction for Augustus_model.g406.t1
Valid prediction for snap_scaffold_1-snap.673-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_1-snap.694-T1
Valid prediction for GeneMark_model.641_t
Valid prediction for GeneMark_model.633_t
Valid prediction for GeneMark_model.646_t
Valid prediction for snap_scaffold_1-snap.671-T1
Valid prediction for GeneMark_model.657_t
Couldn't classify 192742, 192866
Couldn't classify 193476, 194547
Sorry, prediction pasa_asmbl_1680.p1 fails validation.
(GAG)	 CC	192742-192866	GT	AGG
(GTT)	 AG	193476-194547	GG	ATG
Valid prediction for snap_scaffold_1-snap.683-T1
Valid prediction for GlimmerHMM_glimmerT_545-T1
Valid prediction for CodingQuarry_transcript_2583-T1
Valid prediction for GlimmerHMM_glimmerT_544-T1
Valid prediction for snap_scaffold_1-snap.664-T1
Valid prediction for CodingQuarry_transcript_2592-T1
Valid prediction for pasa_asmbl_1678.p1
Valid prediction for GeneMark_model.609_t
Valid prediction for GeneMark_model.616_t
Valid prediction for GlimmerHMM_glimmerT_523-T1
Valid prediction for GeneMark_model.620_t
Valid prediction for GlimmerHMM_glimmerT_525-T1
Valid prediction for Augustus_model.g412.t1
Valid prediction for GlimmerHMM_glimmerT_527-T1
Valid prediction for HiQ_model.g427.t1
Valid prediction for GlimmerHMM_glimmerT_534-T1
Valid prediction for GlimmerHMM_glimmerT_537-T1
Valid prediction for GlimmerHMM_glimmerT_543-T1
Valid prediction for Augustus_model.g422.t1
Couldn't classify 102975, 103130
Sorry, prediction pasa_asmbl_1669.p3 fails validation.
(CTC)	 AG	102975-103130	GT	AGG
(ATC)	 AG	103755-103850	GT	AAG
(GAG)	 AG	104288-104413	GT	GGG
(CTG)	 AG	104990-105010	TG	GAT
-recovered pasa_asmbl_1669.p3, terminal, 104990, 105010
-recovered pasa_asmbl_1669.p3, internal, 102975, 103130
-recovered pasa_asmbl_1669.p3, internal, 103755, 103850
-recovered pasa_asmbl_1669.p3, internal, 104288, 104413
Valid prediction for GeneMark_model.638_t
Valid prediction for snap_scaffold_1-snap.680-T1
Valid prediction for GlimmerHMM_glimmerT_550-T1
Valid prediction for snap_scaffold_1-snap.697-T1
Valid prediction for GeneMark_model.659_t
Valid prediction for CodingQuarry_transcript_2591-T1
Valid prediction for GlimmerHMM_glimmerT_526-T1
Valid prediction for Augustus_model.g417.t1
Valid prediction for snap_scaffold_1-snap.681-T1
Valid prediction for GlimmerHMM_glimmerT_549-T1
Valid prediction for GeneMark_model.639_t
Valid prediction for HiQ_model.g428.t1
Valid prediction for GlimmerHMM_glimmerT_517-T1
Valid prediction for snap_scaffold_1-snap.663-T1
Valid prediction for snap_scaffold_1-snap.657-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_548-T1
Valid prediction for GeneMark_model.651_t
Valid prediction for GlimmerHMM_glimmerT_546-T1
Valid prediction for GeneMark_model.649_t
Valid prediction for snap_scaffold_1-snap.689-T1
Valid prediction for snap_scaffold_1-snap.674-T1
Valid prediction for snap_scaffold_1-snap.679-T1
Valid prediction for GlimmerHMM_glimmerT_538-T1
Valid prediction for GeneMark_model.629_t
Valid prediction for GlimmerHMM_glimmerT_530-T1
Valid prediction for GeneMark_model.613_t
Valid prediction for GeneMark_model.637_t
Valid prediction for Augustus_model.g416.t1
Couldn't classify 195080, 195259
Sorry, prediction pasa_asmbl_1682.p1 fails validation.
(TTT)	 AG	195080-195259	GT	AGG
(ACA)	 AG	195484-195590	GT	AGG
(GTA)	 AG	195887-196125	GT	AGG
(GAA)	 AG	196251-196382	GT	GGG
(GGA)	 AG	196576-196724	GT	AGG
(ATC)	 AG	196872-197015	GT	CGG
(GGG)	 AG	197329-197443	GT	AGG
(ACA)	 AG	197661-197893	GT	AGG
(ATT)	 AG	198199-198338	GT	CGG
(GTT)	 AG	198727-199027	GT	AGG
(CTC)	 AG	200772-200882	GT	AGG
(CAC)	 AG	201045-201140	GT	AGG
(GGC)	 AG	201290-203731	AT	AAA
-recovered pasa_asmbl_1682.p1, terminal, 201290, 203731
-recovered pasa_asmbl_1682.p1, internal, 195080, 195259
-recovered pasa_asmbl_1682.p1, internal, 195484, 195590
-recovered pasa_asmbl_1682.p1, internal, 195887, 196125
-recovered pasa_asmbl_1682.p1, internal, 196251, 196382
-recovered pasa_asmbl_1682.p1, internal, 196576, 196724
-recovered pasa_asmbl_1682.p1, internal, 196872, 197015
-recovered pasa_asmbl_1682.p1, internal, 197329, 197443
-recovered pasa_asmbl_1682.p1, internal, 197661, 197893
-recovered pasa_asmbl_1682.p1, internal, 198199, 198338
-recovered pasa_asmbl_1682.p1, internal, 198727, 199027
-recovered pasa_asmbl_1682.p1, internal, 200772, 200882
-recovered pasa_asmbl_1682.p1, internal, 201045, 201140
Valid prediction for snap_scaffold_1-snap.690-T1
Valid prediction for pasa_asmbl_1676.p1
Valid prediction for GeneMark_model.611_t
Valid prediction for GeneMark_model.631_t
Valid prediction for GlimmerHMM_glimmerT_552-T1
Valid prediction for GeneMark_model.642_t
Valid prediction for GlimmerHMM_glimmerT_536-T1
Valid prediction for GeneMark_model.654_t
Valid prediction for snap_scaffold_1-snap.669-T1
Valid prediction for GlimmerHMM_glimmerT_531-T1
Valid prediction for GeneMark_model.635_t
Valid prediction for GeneMark_model.658_t
Valid prediction for snap_scaffold_1-snap.695-T1
Couldn't classify 188194, 188256
Sorry, prediction pasa_asmbl_1679.p1 fails validation.
(ATC)	 TC	188194-188256	GT	AGG
(GTG)	 AG	188714-188855	GT	AGG
(CCC)	 AG	189422-189575	GT	AGG
(GCG)	 AG	189692-189773	GT	CGG
(GTC)	 AG	190183-190360	GT	AGG
(ATG)	 AG	190523-190629	GT	AGG
(ATC)	 AG	190748-190844	GT	CAG
(TGA)	 AG	190948-191039	GT	CCG
(GCA)	 AG	191244-191364	GT	AGG
(CGA)	 AG	191468-191564	GT	GGG
(ACC)	 AG	191687-191761	GT	AAG
(ATT)	 AG	192128-192143	GC	AAG
add_exon() Sorry, pasa_asmbl_1679.p1 190523-190629-initial-1 is invalid.
-recovered pasa_asmbl_1679.p1, initial, 190523, 190629
-recovered pasa_asmbl_1679.p1, terminal, 192128, 192143
-recovered pasa_asmbl_1679.p1, internal, 188714, 188855
-recovered pasa_asmbl_1679.p1, internal, 189422, 189575
-recovered pasa_asmbl_1679.p1, internal, 189692, 189773
-recovered pasa_asmbl_1679.p1, internal, 190183, 190360
-recovered pasa_asmbl_1679.p1, internal, 190523, 190629
-recovered pasa_asmbl_1679.p1, internal, 190748, 190844
-recovered pasa_asmbl_1679.p1, internal, 190948, 191039
-recovered pasa_asmbl_1679.p1, internal, 191244, 191364
-recovered pasa_asmbl_1679.p1, internal, 191468, 191564
-recovered pasa_asmbl_1679.p1, internal, 191687, 191761
-recovered pasa_asmbl_1679.p1, internal, 192128, 192143
Valid prediction for GeneMark_model.627_t
Valid prediction for Augustus_model.g413.t1
Valid prediction for HiQ_model.g423.t1
Valid prediction for snap_scaffold_1-snap.653-T1
Valid prediction for GeneMark_model.625_t
Valid prediction for GeneMark_model.622_t

-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 HiQ_model.g421.t1
Valid prediction for snap_scaffold_1-snap.662-T1
Valid prediction for GlimmerHMM_glimmerT_522-T1
Valid prediction for snap_scaffold_1-snap.682-T1
Valid prediction for snap_scaffold_1-snap.656-T1
Valid prediction for snap_scaffold_1-snap.686-T1
Valid prediction for Augustus_model.g407.t1
Valid prediction for Augustus_model.g401.t1
Valid prediction for pasa_asmbl_201.p1
Valid prediction for snap_scaffold_1-snap.654-T1
Valid prediction for GlimmerHMM_glimmerT_520-T1
Valid prediction for GeneMark_model.607_t
Valid prediction for snap_scaffold_1-snap.655-T1
Valid prediction for GeneMark_model.648_t
Valid prediction for snap_scaffold_1-snap.668-T1
Valid prediction for GlimmerHMM_glimmerT_533-T1
Valid prediction for snap_scaffold_1-snap.677-T1
Valid prediction for snap_scaffold_1-snap.693-T1
Valid prediction for snap_scaffold_1-snap.666-T1
Valid prediction for Augustus_model.g415.t1
Valid prediction for GlimmerHMM_glimmerT_518-T1
Valid prediction for GeneMark_model.632_t
Valid prediction for GlimmerHMM_glimmerT_535-T1
Valid prediction for CodingQuarry_transcript_2586-T1
Valid prediction for pasa_asmbl_216.p1
Valid prediction for GeneMark_model.650_t
Valid prediction for CodingQuarry_transcript_2587-T1
Valid prediction for GeneMark_model.644_t
Valid prediction for GlimmerHMM_glimmerT_519-T1
Valid prediction for snap_scaffold_1-snap.685-T1
Valid prediction for CodingQuarry_transcript_2589-T1
Valid prediction for snap_scaffold_1-snap.684-T1
Valid prediction for snap_scaffold_1-snap.667-T1
Valid prediction for GeneMark_model.615_t
Valid prediction for Augustus_model.g408.t1
Valid prediction for CodingQuarry_transcript_2584-T1
Valid prediction for GeneMark_model.634_t
Valid prediction for GeneMark_model.619_t
Valid prediction for HiQ_model.g420.t1
Valid prediction for GlimmerHMM_glimmerT_547-T1
Valid prediction for Augustus_model.g414.t1
Valid prediction for GlimmerHMM_glimmerT_528-T1
Valid prediction for Augustus_model.g425.t1
Valid prediction for GlimmerHMM_glimmerT_521-T1
Valid prediction for GeneMark_model.621_t
Valid prediction for GeneMark_model.636_t
Valid prediction for Augustus_model.g402.t1
Valid prediction for GeneMark_model.630_t
Valid prediction for Augustus_model.g404.t1
Valid prediction for Augustus_model.g418.t1
Valid prediction for GlimmerHMM_glimmerT_524-T1
Valid prediction for GlimmerHMM_glimmerT_541-T1
Valid prediction for GeneMark_model.623_t
Valid prediction for snap_scaffold_1-snap.692-T1
Valid prediction for CodingQuarry_transcript_2585-T1
Valid prediction for GeneMark_model.655_t
Valid prediction for GlimmerHMM_glimmerT_540-T1
Valid prediction for GeneMark_model.652_t
Valid prediction for GeneMark_model.610_t
Valid prediction for Augustus_model.g419.t1
Valid prediction for Augustus_model.g424.t1
Valid prediction for snap_scaffold_1-snap.676-T1
Valid prediction for pasa_asmbl_199.p1
Valid prediction for GeneMark_model.643_t
Valid prediction for GlimmerHMM_glimmerT_542-T1
Valid prediction for snap_scaffold_1-snap.672-T1
Valid prediction for snap_scaffold_1-snap.675-T1
Valid prediction for Augustus_model.g405.t1
Valid prediction for GeneMark_model.628_t
Valid prediction for GeneMark_model.608_t
Valid prediction for GlimmerHMM_glimmerT_539-T1
Valid prediction for snap_scaffold_1-snap.687-T1
Valid prediction for snap_scaffold_1-snap.658-T1
Valid prediction for snap_scaffold_1-snap.678-T1
Valid prediction for Augustus_model.g403.t1
Valid prediction for GeneMark_model.612_t
Valid prediction for Augustus_model.g410.t1
Valid prediction for GeneMark_model.647_t
Valid prediction for snap_scaffold_1-snap.660-T1
Valid prediction for GeneMark_model.617_t
Valid prediction for GlimmerHMM_glimmerT_529-T1
Valid prediction for GeneMark_model.624_t
Valid prediction for snap_scaffold_1-snap.691-T1
Valid prediction for Augustus_model.g409.t1
Valid prediction for pasa_asmbl_204.p1
Valid prediction for GeneMark_model.626_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7832, rend_intergenic: 4003  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17100, rend_intergenic: 13255  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26782, rend_intergenic: 17397  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30740, rend_intergenic: 27333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36843, rend_intergenic: 34720  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43947, rend_intergenic: 38002  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57565, rend_intergenic: 44790  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61952, rend_intergenic: 58282  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105010, rend_intergenic: 98893  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127581, rend_intergenic: 127297  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130886, rend_intergenic: 127944  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 210829
-exon list size: 776


building trellis

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62.2    
62.3    
62.5    
62.6    
62.7    
62.9    
63.0    
63.1    
63.2    
63.4    
63.5    
63.6    
63.8    
63.9    
64.0    
64.1    
64.3    
64.4    
64.5    
64.7    
64.8    
64.9    
65.0    
65.2    
65.3    
65.4    
65.6    
65.7    
65.8    
65.9    
66.1    
66.2    
66.3    
66.5    
66.6    
66.7    
66.8    
67.0    
67.1    
67.2    
67.4    
67.5    
67.6    
67.7    
67.9    
68.0    
68.1    
68.3    
68.4    
68.5    
68.6    
68.8    
68.9    
69.0    
69.2    
69.3    
69.4    
69.5    
69.7    
69.8    
69.9    
70.1    
70.2    
70.3    
70.4    
70.6    
70.7    
70.8    
71.0    
71.1    
71.2    
71.3    
71.5    
71.6    
71.7    
71.9    
72.0    
72.1    
72.2    
72.4    
72.5    
72.6    
72.8    
72.9    
73.0    
73.1    
73.3    
73.4    
73.5    
73.7    
73.8    
73.9    
74.0    
74.2    
74.3    
74.4    
74.6    
74.7    
74.8    
74.9    
75.1    
75.2    
75.3    
75.4    
75.6    
75.7    
75.8    
76.0    
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    
78.1    
78.3    
78.4    
78.5    
78.7    
78.8    
78.9    
79.0    
79.2    
79.3    
79.4    
79.6    
79.7    
79.8    
79.9    
80.1    
80.2    
80.3    
80.5    
80.6    
80.7    
80.8    
81.0    
81.1    
81.2    
81.4    
81.5    
81.6    
81.7    
81.9    
82.0    
82.1    
82.3    
82.4    
82.5    
82.6    
82.8    
82.9    
83.0    
83.2    
83.3    
83.4    
83.5    
83.7    
83.8    
83.9    
84.1    
84.2    
84.3    
84.4    
84.6    
84.7    
84.8    
85.0    
85.1    
85.2    
85.3    
85.5    
85.6    
85.7    
85.9    
86.0    
86.1    
86.2    
86.4    
86.5    
86.6    
86.8    
86.9    
87.0    
87.1    
87.3    
87.4    
87.5    
87.7    
87.8    
87.9    
88.0    
88.2    
88.3    
88.4    
88.6    
88.7    
88.8    
88.9    
89.1    
89.2    
89.3    
89.5    
89.6    
89.7    
89.8    
90.0    
90.1    
90.2    
90.4    
90.5    
90.6    
90.7    
90.9    
91.0    
91.1    
91.3    
91.4    
91.5    
91.6    
91.8    
91.9    
92.0    
92.2    
92.3    
92.4    
92.5    
92.7    
92.8    
92.9    
93.1    
93.2    
93.3    
93.4    
93.6    
93.7    
93.8    
94.0    
94.1    
94.2    
94.3    
94.5    
94.6    
94.7    
94.9    
95.0    
95.1    
95.2    
95.4    
95.5    
95.6    
95.8    
95.9    
96.0    
96.1    
96.3    
96.4    
96.5    
96.7    
96.8    
96.9    
97.0    
97.2    
97.3    
97.4    
97.6    
97.7    
97.8    
97.9    
98.1    
98.2    
98.3    
98.5    
98.6    
98.7    
98.8    
99.0    
99.1    
99.2    
99.4    
99.5    
99.6    
99.7    
99.9    
-found 39 predictions from path traversal
Error with prediction: snap lend_intergenic: 7832, rend_intergenic: 4003  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17100, rend_intergenic: 13255  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26782, rend_intergenic: 17397  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30740, rend_intergenic: 27333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36843, rend_intergenic: 34720  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43947, rend_intergenic: 38002  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57565, rend_intergenic: 44790  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61952, rend_intergenic: 58282  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105010, rend_intergenic: 98893  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127581, rend_intergenic: 127297  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130886, rend_intergenic: 127944  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 32 predictions persist after filtering for low support