-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_20/scaffold_20_5109647-5338509

-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_20-snap.1119-T1
Valid prediction for snap_scaffold_20-snap.1131-T1
Valid prediction for GeneMark_model.82246_t
Valid prediction for GeneMark_model.82302_t
Valid prediction for GlimmerHMM_glimmerT_47079-T1
Valid prediction for GeneMark_model.82272_t
Valid prediction for GeneMark_model.82263_t
Valid prediction for GeneMark_model.82256_t
Valid prediction for GlimmerHMM_glimmerT_47088-T1
Valid prediction for snap_scaffold_20-snap.1153-T1
Valid prediction for GeneMark_model.82247_t
Valid prediction for GeneMark_model.82280_t
Valid prediction for GeneMark_model.82260_t
Valid prediction for GlimmerHMM_glimmerT_47078-T1
Valid prediction for GeneMark_model.82290_t
Valid prediction for GeneMark_model.82293_t
Valid prediction for GeneMark_model.82284_t
Valid prediction for Augustus_model.g31400.t1
Couldn't classify 79174, 79304
Sorry, prediction pasa_asmbl_25764.p1 fails validation.
(GAG)	 GG	79174-79304	GT	AAG
(CTT)	 AG	79427-79597	GT	AAG
(CCT)	 AG	79701-79874	GT	AGG
(GCT)	 AG	79998-80171	GT	CTG
(ACT)	 AG	80391-80564	GT	GAG
(CAT)	 AG	80648-80765	TT	AAT
-recovered pasa_asmbl_25764.p1, terminal, 80648, 80765
-recovered pasa_asmbl_25764.p1, internal, 79427, 79597
-recovered pasa_asmbl_25764.p1, internal, 79701, 79874
-recovered pasa_asmbl_25764.p1, internal, 79998, 80171
-recovered pasa_asmbl_25764.p1, internal, 80391, 80564
Valid prediction for snap_scaffold_20-snap.1139-T1
Valid prediction for GlimmerHMM_glimmerT_47072-T1
Valid prediction for GeneMark_model.82261_t
Valid prediction for GeneMark_model.82274_t
Valid prediction for GeneMark_model.82297_t
Valid prediction for GeneMark_model.82258_t
Valid prediction for GlimmerHMM_glimmerT_47076-T1
Couldn't classify 7036, 7129
Couldn't classify 9848, 9945
Sorry, prediction pasa_asmbl_25757.p1 fails validation.
(CAG)	 AG	7036-7129	GT	AGG
(TGG)	 AG	7482-7572	GT	ATG
(CGT)	 AG	7864-8099	GT	AGG
(ATG)	 AG	9848-9945	GT	AGG
add_exon() Sorry, pasa_asmbl_25757.p1 9848-9945-initial-1 is invalid.
-recovered pasa_asmbl_25757.p1, initial, 9848, 9945
-recovered pasa_asmbl_25757.p1, internal, 7036, 7129
-recovered pasa_asmbl_25757.p1, internal, 7482, 7572
-recovered pasa_asmbl_25757.p1, internal, 7864, 8099
-recovered pasa_asmbl_25757.p1, internal, 9848, 9945
Valid prediction for GeneMark_model.82239_t
Valid prediction for snap_scaffold_20-snap.1136-T1
Valid prediction for snap_scaffold_20-snap.1150-T1
Valid prediction for GeneMark_model.82235_t
Valid prediction for GlimmerHMM_glimmerT_47097-T1
Valid prediction for snap_scaffold_20-snap.1163-T1
Valid prediction for CodingQuarry_transcript_30442-T1
Valid prediction for snap_scaffold_20-snap.1142-T1
Valid prediction for GeneMark_model.82278_t
Valid prediction for snap_scaffold_20-snap.1130-T1
Valid prediction for GeneMark_model.82243_t
Couldn't classify 77029, 77763
Sorry, prediction pasa_asmbl_25763.p1 fails validation.
(CCT)	 TC	77029-77763	TA	AGT
Valid prediction for Augustus_model.g31404.t1
Valid prediction for snap_scaffold_20-snap.1134-T1
Valid prediction for GeneMark_model.82300_t
Valid prediction for Augustus_model.g31402.t1
Valid prediction for snap_scaffold_20-snap.1166-T1
Valid prediction for GlimmerHMM_glimmerT_47068-T1
Valid prediction for snap_scaffold_20-snap.1159-T1
Valid prediction for snap_scaffold_20-snap.1129-T1
Valid prediction for GlimmerHMM_glimmerT_47069-T1
Couldn't classify 66758, 67669
Couldn't classify 67730, 67855
Sorry, prediction pasa_asmbl_25759.p1 fails validation.
(ATG)	 GT	66758-67669	AT	AGA
(AGT)	 AC	67730-67855	CT	TCC
Valid prediction for GeneMark_model.82286_t
Valid prediction for GlimmerHMM_glimmerT_47066-T1
Valid prediction for pasa_asmbl_25761.p1
Valid prediction for snap_scaffold_20-snap.1161-T1
Valid prediction for GeneMark_model.82266_t
Valid prediction for snap_scaffold_20-snap.1125-T1
Valid prediction for GlimmerHMM_glimmerT_47087-T1
Valid prediction for snap_scaffold_20-snap.1123-T1
Valid prediction for GeneMark_model.82282_t
Valid prediction for GeneMark_model.82241_t
Valid prediction for GlimmerHMM_glimmerT_47082-T1
Valid prediction for GeneMark_model.82262_t
Valid prediction for GlimmerHMM_glimmerT_47074-T1
Valid prediction for snap_scaffold_20-snap.1137-T1
Valid prediction for snap_scaffold_20-snap.1157-T1
Valid prediction for Augustus_model.g31401.t1
Valid prediction for snap_scaffold_20-snap.1160-T1
Valid prediction for GeneMark_model.82252_t
Valid prediction for GeneMark_model.82295_t
Valid prediction for GlimmerHMM_glimmerT_47094-T1
Valid prediction for GeneMark_model.82277_t
Valid prediction for GlimmerHMM_glimmerT_47077-T1
Valid prediction for snap_scaffold_20-snap.1115-T1
Valid prediction for Augustus_model.g31399.t1
Valid prediction for GeneMark_model.82292_t
Valid prediction for snap_scaffold_20-snap.1147-T1
Valid prediction for GeneMark_model.82268_t
Valid prediction for GeneMark_model.82304_t
Valid prediction for GeneMark_model.82265_t
Valid prediction for GeneMark_model.82237_t
Valid prediction for GeneMark_model.82249_t
Valid prediction for Augustus_model.g31403.t1
Valid prediction for GeneMark_model.82270_t
Valid prediction for snap_scaffold_20-snap.1122-T1
Valid prediction for snap_scaffold_20-snap.1132-T1
Valid prediction for GeneMark_model.82253_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 snap_scaffold_20-snap.1162-T1
Valid prediction for GeneMark_model.82257_t
Valid prediction for GlimmerHMM_glimmerT_47091-T1
Valid prediction for snap_scaffold_20-snap.1128-T1
Valid prediction for GeneMark_model.82271_t
Valid prediction for GeneMark_model.82285_t
Valid prediction for snap_scaffold_20-snap.1151-T1
Valid prediction for GeneMark_model.82287_t
Valid prediction for GlimmerHMM_glimmerT_47096-T1
Valid prediction for snap_scaffold_20-snap.1165-T1
Valid prediction for snap_scaffold_20-snap.1121-T1
Valid prediction for GeneMark_model.82279_t
Valid prediction for GeneMark_model.82294_t
Valid prediction for snap_scaffold_20-snap.1146-T1
Valid prediction for GeneMark_model.82275_t
Valid prediction for snap_scaffold_20-snap.1116-T1
Valid prediction for GeneMark_model.82276_t
Valid prediction for GlimmerHMM_glimmerT_47071-T1
Valid prediction for snap_scaffold_20-snap.1164-T1
Valid prediction for GeneMark_model.82269_t
Valid prediction for GlimmerHMM_glimmerT_47070-T1
Valid prediction for Augustus_model.g31407.t1
Valid prediction for GeneMark_model.82273_t
Valid prediction for GeneMark_model.82298_t
Valid prediction for snap_scaffold_20-snap.1155-T1
Valid prediction for GeneMark_model.82289_t
Valid prediction for GlimmerHMM_glimmerT_47090-T1
Valid prediction for Augustus_model.g31412.t1
Valid prediction for snap_scaffold_20-snap.1140-T1
Valid prediction for snap_scaffold_20-snap.1126-T1
Valid prediction for GlimmerHMM_glimmerT_47081-T1
Valid prediction for GlimmerHMM_glimmerT_47092-T1
Valid prediction for Augustus_model.g31414.t1
Valid prediction for snap_scaffold_20-snap.1149-T1
Valid prediction for GlimmerHMM_glimmerT_47089-T1
Valid prediction for GlimmerHMM_glimmerT_47084-T1
Valid prediction for GeneMark_model.82259_t
Valid prediction for GeneMark_model.82301_t
Valid prediction for Augustus_model.g31416.t1
Valid prediction for snap_scaffold_20-snap.1135-T1
Valid prediction for GeneMark_model.82242_t
Valid prediction for Augustus_model.g31409.t1
Valid prediction for snap_scaffold_20-snap.1124-T1
Valid prediction for GlimmerHMM_glimmerT_47085-T1
Valid prediction for GeneMark_model.82236_t
Valid prediction for Augustus_model.g31413.t1
Valid prediction for snap_scaffold_20-snap.1127-T1
Valid prediction for snap_scaffold_20-snap.1144-T1
Valid prediction for GeneMark_model.82251_t
Valid prediction for GlimmerHMM_glimmerT_47083-T1
Valid prediction for GeneMark_model.82250_t
Valid prediction for snap_scaffold_20-snap.1138-T1
Valid prediction for GeneMark_model.82244_t
Valid prediction for GlimmerHMM_glimmerT_47098-T1
Valid prediction for snap_scaffold_20-snap.1156-T1
Valid prediction for snap_scaffold_20-snap.1148-T1
Valid prediction for GlimmerHMM_glimmerT_47086-T1
Valid prediction for GlimmerHMM_glimmerT_47080-T1
Valid prediction for GeneMark_model.82248_t
Valid prediction for GeneMark_model.82305_t
Valid prediction for GlimmerHMM_glimmerT_47067-T1
Valid prediction for snap_scaffold_20-snap.1118-T1
Valid prediction for GlimmerHMM_glimmerT_47095-T1
Valid prediction for GeneMark_model.82283_t
Valid prediction for GlimmerHMM_glimmerT_47093-T1
Valid prediction for snap_scaffold_20-snap.1120-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_20-snap.1152-T1
Valid prediction for GeneMark_model.82303_t
Valid prediction for snap_scaffold_20-snap.1143-T1
Valid prediction for GeneMark_model.82296_t
Valid prediction for GeneMark_model.82299_t
Valid prediction for GeneMark_model.82245_t
Valid prediction for Augustus_model.g31406.t1
Valid prediction for snap_scaffold_20-snap.1167-T1
Valid prediction for GeneMark_model.82238_t
Valid prediction for Augustus_model.g31410.t1
Valid prediction for Augustus_model.g31405.t1
Valid prediction for GeneMark_model.82291_t
Valid prediction for Augustus_model.g31408.t1
Valid prediction for GeneMark_model.82267_t
Valid prediction for Augustus_model.g31415.t1
Valid prediction for GlimmerHMM_glimmerT_47075-T1
Valid prediction for GeneMark_model.82281_t
Valid prediction for GeneMark_model.82255_t
Valid prediction for GeneMark_model.82306_t
Valid prediction for snap_scaffold_20-snap.1145-T1
Valid prediction for snap_scaffold_20-snap.1158-T1
Valid prediction for snap_scaffold_20-snap.1154-T1
Valid prediction for snap_scaffold_20-snap.1117-T1
Valid prediction for GeneMark_model.82264_t
Valid prediction for snap_scaffold_20-snap.1141-T1
Valid prediction for GeneMark_model.82254_t
Valid prediction for GlimmerHMM_glimmerT_47073-T1
Valid prediction for Augustus_model.g31411.t1
Valid prediction for GeneMark_model.82240_t
Valid prediction for snap_scaffold_20-snap.1133-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 16884, rend_intergenic: 8398  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26385, rend_intergenic: 21299  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40486, rend_intergenic: 29710  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45622, rend_intergenic: 41198  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70508, rend_intergenic: 52407  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74137, rend_intergenic: 71279  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92130, rend_intergenic: 87808  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99728, rend_intergenic: 97321  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107776, rend_intergenic: 102647  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115276, rend_intergenic: 113588  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137594, rend_intergenic: 134711  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163333, rend_intergenic: 160886  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177936, rend_intergenic: 177493  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181884, rend_intergenic: 178207  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196861, rend_intergenic: 184459  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 208101, rend_intergenic: 203687  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 224011, rend_intergenic: 218713  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 228863
-exon list size: 966


building trellis

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56.5    
56.6    
56.7    
56.8    
56.9    
57.0    
57.1    
57.2    
57.3    
57.4    
57.5    
57.6    
57.7    
57.9    
58.0    
58.1    
58.2    
58.3    
58.4    
58.5    
58.6    
58.7    
58.8    
58.9    
59.0    
59.1    
59.2    
59.3    
59.4    
59.5    
59.6    
59.7    
59.8    
59.9    
60.0    
60.1    
60.2    
60.3    
60.4    
60.5    
60.6    
60.7    
60.8    
61.0    
61.1    
61.2    
61.3    
61.4    
61.5    
61.6    
61.7    
61.8    
61.9    
62.0    
62.1    
62.2    
62.3    
62.4    
62.5    
62.6    
62.7    
62.8    
62.9    
63.0    
63.1    
63.2    
63.3    
63.4    
63.5    
63.6    
63.7    
63.8    
63.9    
64.0    
64.2    
64.3    
64.4    
64.5    
64.6    
64.7    
64.8    
64.9    
65.0    
65.1    
65.2    
65.3    
65.4    
65.5    
65.6    
65.7    
65.8    
65.9    
66.0    
66.1    
66.2    
66.3    
66.4    
66.5    
66.6    
66.7    
66.8    
66.9    
67.0    
67.1    
67.3    
67.4    
67.5    
67.6    
67.7    
67.8    
67.9    
68.0    
68.1    
68.2    
68.3    
68.4    
68.5    
68.6    
68.7    
68.8    
68.9    
69.0    
69.1    
69.2    
69.3    
69.4    
69.5    
69.6    
69.7    
69.8    
69.9    
70.0    
70.1    
70.2    
70.4    
70.5    
70.6    
70.7    
70.8    
70.9    
71.0    
71.1    
71.2    
71.3    
71.4    
71.5    
71.6    
71.7    
71.8    
71.9    
72.0    
72.1    
72.2    
72.3    
72.4    
72.5    
72.6    
72.7    
72.8    
72.9    
73.0    
73.1    
73.2    
73.3    
73.5    
73.6    
73.7    
73.8    
73.9    
74.0    
74.1    
74.2    
74.3    
74.4    
74.5    
74.6    
74.7    
74.8    
74.9    
75.0    
75.1    
75.2    
75.3    
75.4    
75.5    
75.6    
75.7    
75.8    
75.9    
76.0    
76.1    
76.2    
76.3    
76.4    
76.5    
76.7    
76.8    
76.9    
77.0    
77.1    
77.2    
77.3    
77.4    
77.5    
77.6    
77.7    
77.8    
77.9    
78.0    
78.1    
78.2    
78.3    
78.4    
78.5    
78.6    
78.7    
78.8    
78.9    
79.0    
79.1    
79.2    
79.3    
79.4    
79.5    
79.6    
79.8    
79.9    
80.0    
80.1    
80.2    
80.3    
80.4    
80.5    
80.6    
80.7    
80.8    
80.9    
81.0    
81.1    
81.2    
81.3    
81.4    
81.5    
81.6    
81.7    
81.8    
81.9    
82.0    
82.1    
82.2    
82.3    
82.4    
82.5    
82.6    
82.7    
82.9    
83.0    
83.1    
83.2    
83.3    
83.4    
83.5    
83.6    
83.7    
83.8    
83.9    
84.0    
84.1    
84.2    
84.3    
84.4    
84.5    
84.6    
84.7    
84.8    
84.9    
85.0    
85.1    
85.2    
85.3    
85.4    
85.5    
85.6    
85.7    
85.8    
86.0    
86.1    
86.2    
86.3    
86.4    
86.5    
86.6    
86.7    
86.8    
86.9    
87.0    
87.1    
87.2    
87.3    
87.4    
87.5    
87.6    
87.7    
87.8    
87.9    
88.0    
88.1    
88.2    
88.3    
88.4    
88.5    
88.6    
88.7    
88.8    
88.9    
89.0    
89.2    
89.3    
89.4    
89.5    
89.6    
89.7    
89.8    
89.9    
90.0    
90.1    
90.2    
90.3    
90.4    
90.5    
90.6    
90.7    
90.8    
90.9    
91.0    
91.1    
91.2    
91.3    
91.4    
91.5    
91.6    
91.7    
91.8    
91.9    
92.0    
92.1    
92.3    
92.4    
92.5    
92.6    
92.7    
92.8    
92.9    
93.0    
93.1    
93.2    
93.3    
93.4    
93.5    
93.6    
93.7    
93.8    
93.9    
94.0    
94.1    
94.2    
94.3    
94.4    
94.5    
94.6    
94.7    
94.8    
94.9    
95.0    
95.1    
95.2    
95.4    
95.5    
95.6    
95.7    
95.8    
95.9    
96.0    
96.1    
96.2    
96.3    
96.4    
96.5    
96.6    
96.7    
96.8    
96.9    
97.0    
97.1    
97.2    
97.3    
97.4    
97.5    
97.6    
97.7    
97.8    
97.9    
98.0    
98.1    
98.2    
98.3    
98.5    
98.6    
98.7    
98.8    
98.9    
99.0    
99.1    
99.2    
99.3    
99.4    
99.5    
99.6    
99.7    
99.8    
99.9    
-found 41 predictions from path traversal
Error with prediction: snap lend_intergenic: 16884, rend_intergenic: 8398  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26385, rend_intergenic: 21299  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40486, rend_intergenic: 29710  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45622, rend_intergenic: 41198  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70508, rend_intergenic: 52407  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74137, rend_intergenic: 71279  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92130, rend_intergenic: 87808  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99728, rend_intergenic: 97321  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107776, rend_intergenic: 102647  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115276, rend_intergenic: 113588  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137594, rend_intergenic: 134711  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163333, rend_intergenic: 160886  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177936, rend_intergenic: 177493  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181884, rend_intergenic: 178207  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196861, rend_intergenic: 184459  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 208101, rend_intergenic: 203687  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 224011, rend_intergenic: 218713  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support