-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_5/scaffold_5_11202640-11431575

-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.21828_t
Valid prediction for GeneMark_model.21870_t
Valid prediction for GlimmerHMM_glimmerT_12906-T1
Valid prediction for GlimmerHMM_glimmerT_12927-T1
Valid prediction for GeneMark_model.21826_t
Valid prediction for GeneMark_model.21841_t
Valid prediction for GeneMark_model.21837_t
Valid prediction for GlimmerHMM_glimmerT_12916-T1
Valid prediction for Augustus_model.g8606.t1
Valid prediction for GeneMark_model.21835_t
Valid prediction for Augustus_model.g8599.t1
Valid prediction for GeneMark_model.21819_t
Valid prediction for snap_scaffold_5-snap.2108-T1
Valid prediction for GeneMark_model.21877_t
Valid prediction for GeneMark_model.21869_t
Valid prediction for snap_scaffold_5-snap.2125-T1
Valid prediction for GlimmerHMM_glimmerT_12930-T1
Valid prediction for GlimmerHMM_glimmerT_12931-T1
Valid prediction for snap_scaffold_5-snap.2111-T1
Valid prediction for GeneMark_model.21818_t
Valid prediction for snap_scaffold_5-snap.2103-T1
Valid prediction for Augustus_model.g8614.t1
Valid prediction for snap_scaffold_5-snap.2106-T1
Valid prediction for snap_scaffold_5-snap.2120-T1
Valid prediction for GeneMark_model.21830_t
Valid prediction for Augustus_model.g8605.t1
Valid prediction for GeneMark_model.21847_t
Valid prediction for GlimmerHMM_glimmerT_12905-T1
Valid prediction for snap_scaffold_5-snap.2094-T1
Valid prediction for GlimmerHMM_glimmerT_12919-T1
Valid prediction for GeneMark_model.21832_t
Valid prediction for GeneMark_model.21821_t
Valid prediction for GeneMark_model.21861_t
Valid prediction for snap_scaffold_5-snap.2090-T1
Valid prediction for GeneMark_model.21822_t
Valid prediction for GlimmerHMM_glimmerT_12913-T1
Valid prediction for Augustus_model.g8615.t1
Valid prediction for GeneMark_model.21867_t
Valid prediction for GeneMark_model.21873_t
Valid prediction for Augustus_model.g8617.t1
Valid prediction for Augustus_model.g8602.t1
Valid prediction for GeneMark_model.21859_t
Valid prediction for snap_scaffold_5-snap.2092-T1
Valid prediction for GeneMark_model.21843_t
Valid prediction for GeneMark_model.21878_t
Valid prediction for GeneMark_model.21876_t
Valid prediction for GlimmerHMM_glimmerT_12920-T1
Valid prediction for GlimmerHMM_glimmerT_12925-T1
Valid prediction for Augustus_model.g8598.t1
add_exon() Sorry, Augustus_model.g8598.t1 13797-14014-terminal-1 is invalid.
Valid prediction for GeneMark_model.21874_t
Valid prediction for snap_scaffold_5-snap.2121-T1
Valid prediction for snap_scaffold_5-snap.2100-T1
Valid prediction for GeneMark_model.21823_t
Valid prediction for GlimmerHMM_glimmerT_12934-T1
Valid prediction for snap_scaffold_5-snap.2118-T1
Valid prediction for snap_scaffold_5-snap.2097-T1
Valid prediction for Augustus_model.g8610.t1
Valid prediction for GlimmerHMM_glimmerT_12912-T1
Valid prediction for snap_scaffold_5-snap.2115-T1
Valid prediction for snap_scaffold_5-snap.2105-T1
Valid prediction for Augustus_model.g8611.t1
Valid prediction for Augustus_model.g8603.t1
Valid prediction for GeneMark_model.21865_t
Valid prediction for snap_scaffold_5-snap.2109-T1
Valid prediction for snap_scaffold_5-snap.2093-T1
Valid prediction for Augustus_model.g8601.t1
Valid prediction for GeneMark_model.21853_t
Valid prediction for GeneMark_model.21855_t
Valid prediction for GlimmerHMM_glimmerT_12933-T1
Valid prediction for GlimmerHMM_glimmerT_12926-T1
Valid prediction for GlimmerHMM_glimmerT_12932-T1
Valid prediction for GlimmerHMM_glimmerT_12907-T1
Valid prediction for GeneMark_model.21872_t
Valid prediction for GeneMark_model.21824_t
Valid prediction for snap_scaffold_5-snap.2088-T1
Valid prediction for GeneMark_model.21851_t
Valid prediction for snap_scaffold_5-snap.2114-T1
Valid prediction for Augustus_model.g8608.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_5-snap.2099-T1
Valid prediction for GlimmerHMM_glimmerT_12918-T1
Valid prediction for snap_scaffold_5-snap.2104-T1
Valid prediction for snap_scaffold_5-snap.2117-T1
Valid prediction for GlimmerHMM_glimmerT_12914-T1
Valid prediction for GlimmerHMM_glimmerT_12908-T1
Valid prediction for Augustus_model.g8600.t1
Valid prediction for GlimmerHMM_glimmerT_12909-T1
Valid prediction for GeneMark_model.21871_t
Valid prediction for GeneMark_model.21854_t
Valid prediction for Augustus_model.g8616.t1
Couldn't classify 1062, 1299
Couldn't classify 1457, 1581
Sorry, prediction pasa_asmbl_45790.p1 fails validation.
(GCA)	 GG	1062-1299	GT	AGG
(GAA)	 AG	1457-1581	AC	GGA
Valid prediction for GlimmerHMM_glimmerT_12917-T1
Valid prediction for snap_scaffold_5-snap.2086-T1
Valid prediction for Augustus_model.g8604.t1
Valid prediction for GeneMark_model.21829_t
Couldn't classify 1708, 2257
Sorry, prediction pasa_asmbl_45789.p1 fails validation.
(AAC)	 GA	1708-2257	GT	AGG
(GGA)	 AG	3235-3389	GT	AGG
(GCT)	 AG	3548-3652	GT	AGG
(AAT)	 AG	3755-3904	GT	CGG
(GAG)	 AG	4124-4246	GT	TGG
(GAG)	 AG	4339-4428	GT	AGG
(AGG)	 AG	4647-4889	GT	TGG
(ATT)	 AG	5102-5237	GT	AGG
(TGC)	 AG	5810-5921	GT	AGG
(GGA)	 AG	6276-6445	GT	AGG
(GTA)	 AG	6520-6650	GT	AGG
(GAA)	 AG	6771-6896	GT	AGG
(TCT)	 AG	7053-7109	GT	AGG
(ATG)	 AG	7278-7397	GT	AGG
(GGC)	 AG	7500-7667	CA	AGC
-recovered pasa_asmbl_45789.p1, initial, 7278, 7397
add_exon() Sorry, pasa_asmbl_45789.p1 6276-6445-terminal-2 is invalid.
-recovered pasa_asmbl_45789.p1, terminal, 6276, 6445
-recovered pasa_asmbl_45789.p1, terminal, 7500, 7667
-recovered pasa_asmbl_45789.p1, internal, 3235, 3389
-recovered pasa_asmbl_45789.p1, internal, 3548, 3652
-recovered pasa_asmbl_45789.p1, internal, 3755, 3904
-recovered pasa_asmbl_45789.p1, internal, 4124, 4246
-recovered pasa_asmbl_45789.p1, internal, 4339, 4428
-recovered pasa_asmbl_45789.p1, internal, 4647, 4889
-recovered pasa_asmbl_45789.p1, internal, 5102, 5237
-recovered pasa_asmbl_45789.p1, internal, 5810, 5921
-recovered pasa_asmbl_45789.p1, internal, 6276, 6445
-recovered pasa_asmbl_45789.p1, internal, 6520, 6650
-recovered pasa_asmbl_45789.p1, internal, 6771, 6896
-recovered pasa_asmbl_45789.p1, internal, 7053, 7109
-recovered pasa_asmbl_45789.p1, internal, 7278, 7397
Valid prediction for GeneMark_model.21850_t
Valid prediction for GlimmerHMM_glimmerT_12915-T1
Valid prediction for snap_scaffold_5-snap.2095-T1
Valid prediction for snap_scaffold_5-snap.2089-T1
Valid prediction for snap_scaffold_5-snap.2087-T1
Valid prediction for snap_scaffold_5-snap.2124-T1
Valid prediction for GeneMark_model.21856_t
Valid prediction for GeneMark_model.21836_t
Valid prediction for GeneMark_model.21857_t
Valid prediction for GeneMark_model.21825_t
Valid prediction for GlimmerHMM_glimmerT_12904-T1
Valid prediction for GeneMark_model.21860_t
Valid prediction for GlimmerHMM_glimmerT_12928-T1
Valid prediction for snap_scaffold_5-snap.2122-T1
Valid prediction for GeneMark_model.21880_t
Valid prediction for GeneMark_model.21864_t
Valid prediction for GeneMark_model.21834_t
Valid prediction for GlimmerHMM_glimmerT_12921-T1
Valid prediction for GeneMark_model.21838_t
Valid prediction for snap_scaffold_5-snap.2098-T1
Valid prediction for GeneMark_model.21862_t
Valid prediction for GeneMark_model.21831_t
Valid prediction for GeneMark_model.21875_t
Valid prediction for GlimmerHMM_glimmerT_12911-T1
Valid prediction for GlimmerHMM_glimmerT_12936-T1
Valid prediction for snap_scaffold_5-snap.2116-T1
Valid prediction for GeneMark_model.21820_t
Valid prediction for GlimmerHMM_glimmerT_12935-T1
Valid prediction for Augustus_model.g8612.t1
Valid prediction for snap_scaffold_5-snap.2112-T1
Valid prediction for GeneMark_model.21852_t
Valid prediction for GeneMark_model.21827_t
Valid prediction for snap_scaffold_5-snap.2126-T1
Valid prediction for GeneMark_model.21846_t
Valid prediction for snap_scaffold_5-snap.2096-T1
Valid prediction for GeneMark_model.21849_t
Valid prediction for GeneMark_model.21839_t
Valid prediction for GeneMark_model.21833_t
Valid prediction for snap_scaffold_5-snap.2113-T1
Valid prediction for snap_scaffold_5-snap.2102-T1
Valid prediction for snap_scaffold_5-snap.2101-T1
Valid prediction for Augustus_model.g8609.t1
Valid prediction for snap_scaffold_5-snap.2119-T1
Valid prediction for GeneMark_model.21840_t
Valid prediction for GeneMark_model.21845_t
Valid prediction for HiQ_model.g8618.t1
Valid prediction for snap_scaffold_5-snap.2107-T1
Valid prediction for snap_scaffold_5-snap.2123-T1
Valid prediction for GlimmerHMM_glimmerT_12924-T1
Valid prediction for GeneMark_model.21866_t
Valid prediction for Augustus_model.g8607.t1
Valid prediction for GeneMark_model.21848_t
Valid prediction for GlimmerHMM_glimmerT_12923-T1
Valid prediction for GeneMark_model.21844_t
Valid prediction for GlimmerHMM_glimmerT_12922-T1
Valid prediction for GlimmerHMM_glimmerT_12910-T1
Valid prediction for Augustus_model.g8613.t1
Valid prediction for snap_scaffold_5-snap.2110-T1
Valid prediction for GeneMark_model.21863_t
Valid prediction for GeneMark_model.21868_t
Valid prediction for snap_scaffold_5-snap.2091-T1
Valid prediction for GeneMark_model.21842_t
Valid prediction for snap_scaffold_5-snap.2127-T1
Valid prediction for GeneMark_model.21858_t
Valid prediction for GlimmerHMM_glimmerT_12929-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 48907, rend_intergenic: 44480  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51822, rend_intergenic: 49181  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65112, rend_intergenic: 52338  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71285, rend_intergenic: 66628  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72789, rend_intergenic: 71340  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89866, rend_intergenic: 75499  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98643, rend_intergenic: 95299  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106350, rend_intergenic: 99127  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124493, rend_intergenic: 113350  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132112, rend_intergenic: 126790  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141191, rend_intergenic: 136677  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161020, rend_intergenic: 147091  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167185, rend_intergenic: 161033  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187092, rend_intergenic: 186947  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198742, rend_intergenic: 187150  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 208532, rend_intergenic: 199918  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 224251, rend_intergenic: 221270  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 228936
-exon list size: 765


building trellis

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75.6    
75.7    
75.9    
76.0    
76.1    
76.3    
76.4    
76.5    
76.7    
76.8    
76.9    
77.1    
77.2    
77.3    
77.4    
77.6    
77.7    
77.8    
78.0    
78.1    
78.2    
78.4    
78.5    
78.6    
78.7    
78.9    
79.0    
79.1    
79.3    
79.4    
79.5    
79.7    
79.8    
79.9    
80.1    
80.2    
80.3    
80.4    
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    
82.7    
82.8    
82.9    
83.1    
83.2    
83.3    
83.4    
83.6    
83.7    
83.8    
84.0    
84.1    
84.2    
84.4    
84.5    
84.6    
84.7    
84.9    
85.0    
85.1    
85.3    
85.4    
85.5    
85.7    
85.8    
85.9    
86.0    
86.2    
86.3    
86.4    
86.6    
86.7    
86.8    
87.0    
87.1    
87.2    
87.4    
87.5    
87.6    
87.7    
87.9    
88.0    
88.1    
88.3    
88.4    
88.5    
88.7    
88.8    
88.9    
89.0    
89.2    
89.3    
89.4    
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    
91.7    
91.8    
91.9    
92.0    
92.2    
92.3    
92.4    
92.6    
92.7    
92.8    
93.0    
93.1    
93.2    
93.4    
93.5    
93.6    
93.7    
93.9    
94.0    
94.1    
94.3    
94.4    
94.5    
94.7    
94.8    
94.9    
95.0    
95.2    
95.3    
95.4    
95.6    
95.7    
95.8    
96.0    
96.1    
96.2    
96.3    
96.5    
96.6    
96.7    
96.9    
97.0    
97.1    
97.3    
97.4    
97.5    
97.7    
97.8    
97.9    
98.0    
98.2    
98.3    
98.4    
98.6    
98.7    
98.8    
99.0    
99.1    
99.2    
99.3    
99.5    
99.6    
99.7    
99.9    
-found 45 predictions from path traversal
Error with prediction: snap lend_intergenic: 48907, rend_intergenic: 44480  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51822, rend_intergenic: 49181  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65112, rend_intergenic: 52338  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71285, rend_intergenic: 66628  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72789, rend_intergenic: 71340  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89866, rend_intergenic: 75499  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98643, rend_intergenic: 95299  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106350, rend_intergenic: 99127  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124493, rend_intergenic: 113350  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132112, rend_intergenic: 126790  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141191, rend_intergenic: 136677  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161020, rend_intergenic: 147091  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167185, rend_intergenic: 161033  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187092, rend_intergenic: 186947  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198742, rend_intergenic: 187150  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 208532, rend_intergenic: 199918  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 224251, rend_intergenic: 221270  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support