-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_16/scaffold_16_10922223-11122845

-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 GlimmerHMM_glimmerT_39872-T1
Valid prediction for GeneMark_model.68330_t
Valid prediction for Augustus_model.g26793.t1
Valid prediction for GeneMark_model.68292_t
Valid prediction for GeneMark_model.68341_t
Valid prediction for Augustus_model.g26789.t1
Valid prediction for GlimmerHMM_glimmerT_39858-T1
Valid prediction for GlimmerHMM_glimmerT_39866-T1
Valid prediction for snap_scaffold_16-snap.2035-T1
Valid prediction for snap_scaffold_16-snap.2060-T1
Valid prediction for snap_scaffold_16-snap.2047-T1
Valid prediction for GlimmerHMM_glimmerT_39870-T1
Valid prediction for GeneMark_model.68317_t
Valid prediction for GlimmerHMM_glimmerT_39876-T1
Valid prediction for snap_scaffold_16-snap.2057-T1
Valid prediction for GlimmerHMM_glimmerT_39877-T1
Valid prediction for snap_scaffold_16-snap.2074-T1
Valid prediction for GeneMark_model.68344_t
Valid prediction for GeneMark_model.68294_t
Valid prediction for snap_scaffold_16-snap.2048-T1
Valid prediction for GeneMark_model.68349_t
Valid prediction for Augustus_model.g26785.t1
Valid prediction for GeneMark_model.68346_t
Valid prediction for GlimmerHMM_glimmerT_39860-T1
Valid prediction for GeneMark_model.68326_t
Valid prediction for Augustus_model.g26795.t1
Valid prediction for snap_scaffold_16-snap.2072-T1
Valid prediction for GeneMark_model.68322_t
Valid prediction for GeneMark_model.68299_t
Valid prediction for Augustus_model.g26786.t1
Valid prediction for GlimmerHMM_glimmerT_39868-T1
Valid prediction for snap_scaffold_16-snap.2071-T1
Valid prediction for snap_scaffold_16-snap.2037-T1
Valid prediction for Augustus_model.g26805.t1
Valid prediction for GeneMark_model.68336_t
Valid prediction for GeneMark_model.68352_t
Valid prediction for GlimmerHMM_glimmerT_39878-T1
Valid prediction for snap_scaffold_16-snap.2059-T1
Valid prediction for Augustus_model.g26802.t1
Valid prediction for Augustus_model.g26788.t1
Valid prediction for GeneMark_model.68350_t
Valid prediction for GlimmerHMM_glimmerT_39873-T1
Valid prediction for Augustus_model.g26804.t1
Valid prediction for GeneMark_model.68324_t
Valid prediction for GeneMark_model.68316_t
Valid prediction for snap_scaffold_16-snap.2067-T1
Valid prediction for GlimmerHMM_glimmerT_39884-T1
Valid prediction for GlimmerHMM_glimmerT_39856-T1
Valid prediction for snap_scaffold_16-snap.2038-T1
Valid prediction for GlimmerHMM_glimmerT_39864-T1
Valid prediction for GeneMark_model.68296_t
Valid prediction for snap_scaffold_16-snap.2065-T1
Valid prediction for Augustus_model.g26799.t1
Valid prediction for GeneMark_model.68314_t
Valid prediction for GeneMark_model.68301_t
Valid prediction for GeneMark_model.68309_t
Valid prediction for snap_scaffold_16-snap.2064-T1
Valid prediction for GeneMark_model.68334_t
Valid prediction for GlimmerHMM_glimmerT_39857-T1
Valid prediction for snap_scaffold_16-snap.2055-T1
Valid prediction for GeneMark_model.68307_t
Valid prediction for GlimmerHMM_glimmerT_39861-T1
Valid prediction for snap_scaffold_16-snap.2070-T1
Valid prediction for GeneMark_model.68320_t
Valid prediction for GeneMark_model.68312_t
Valid prediction for GeneMark_model.68348_t
Valid prediction for GeneMark_model.68338_t
Valid prediction for GlimmerHMM_glimmerT_39875-T1
Valid prediction for snap_scaffold_16-snap.2041-T1
Valid prediction for snap_scaffold_16-snap.2063-T1
Valid prediction for GeneMark_model.68339_t
Valid prediction for Augustus_model.g26790.t1
Valid prediction for GeneMark_model.68305_t
Valid prediction for GeneMark_model.68303_t
Valid prediction for snap_scaffold_16-snap.2045-T1
Valid prediction for snap_scaffold_16-snap.2050-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.68337_t
Valid prediction for GlimmerHMM_glimmerT_39883-T1
Valid prediction for GeneMark_model.68329_t
Valid prediction for GeneMark_model.68335_t
Valid prediction for Augustus_model.g26806.t1
Valid prediction for GeneMark_model.68327_t
Couldn't classify 151060, 151746
Sorry, prediction pasa_asmbl_16497.p1 fails validation.
(GGG)	 CT	151060-151746	GA	GAG
Valid prediction for HiQ_model.g26791.t1
Valid prediction for GlimmerHMM_glimmerT_39869-T1
Valid prediction for snap_scaffold_16-snap.2058-T1
Valid prediction for Augustus_model.g26787.t1
Valid prediction for GlimmerHMM_glimmerT_39881-T1
Valid prediction for GlimmerHMM_glimmerT_39865-T1
Valid prediction for snap_scaffold_16-snap.2039-T1
Valid prediction for snap_scaffold_16-snap.2068-T1
Valid prediction for GeneMark_model.68300_t
Valid prediction for snap_scaffold_16-snap.2036-T1
Valid prediction for snap_scaffold_16-snap.2061-T1
Valid prediction for GeneMark_model.68319_t
Valid prediction for GlimmerHMM_glimmerT_39879-T1
Valid prediction for snap_scaffold_16-snap.2043-T1
Valid prediction for GeneMark_model.68347_t
Valid prediction for Augustus_model.g26801.t1
Valid prediction for GeneMark_model.68331_t
Valid prediction for GeneMark_model.68333_t
Valid prediction for snap_scaffold_16-snap.2046-T1
Couldn't classify 127531, 127762
Couldn't classify 130782, 130825
Sorry, prediction pasa_asmbl_16503.p1 fails validation.
(GGA)	 CA	127531-127762	GT	GGG
(GCT)	 AG	128996-129235	GT	AGG
(GGT)	 AG	130782-130825	CC	TCC
-recovered pasa_asmbl_16503.p1, internal, 128996, 129235
Valid prediction for GlimmerHMM_glimmerT_39863-T1
Valid prediction for GeneMark_model.68295_t
Valid prediction for Augustus_model.g26794.t1
Valid prediction for snap_scaffold_16-snap.2069-T1
Couldn't classify 136517, 136576
Sorry, prediction pasa_asmbl_16499.p1 fails validation.
(AAC)	 CC	136517-136576	GT	AGG
(GTT)	 AG	136997-137172	GT	GTG
(GAA)	 AG	137531-137659	GT	AGG
(ATT)	 AG	138044-138100	GT	GGG
(TAA)	 AG	140487-140616	GT	AGG
(AAG)	 AG	143570-143795	GT	ACG
(GCT)	 AG	144459-144705	GT	AAG
(ATG)	 AG	144924-145020	GT	AAG
(ATC)	 AG	145270-145364	GT	AGG
(CTA)	 AG	145631-145702	GT	AAG
(GGA)	 AG	146599-146765	GT	CCG
(TGG)	 AG	146992-147134	GT	AGG
(CTG)	 AG	147293-147416	GT	AGG
(GAG)	 AG	149173-149206	GT	AGG
(CCC)	 AG	150794-150824	GC	AAG
add_exon() Sorry, pasa_asmbl_16499.p1 144924-145020-initial-1 is invalid.
-recovered pasa_asmbl_16499.p1, initial, 144924, 145020
add_exon() Sorry, pasa_asmbl_16499.p1 145631-145702-terminal-1 is invalid.
-recovered pasa_asmbl_16499.p1, terminal, 145631, 145702
-recovered pasa_asmbl_16499.p1, terminal, 150794, 150824
-recovered pasa_asmbl_16499.p1, internal, 136997, 137172
-recovered pasa_asmbl_16499.p1, internal, 137531, 137659
-recovered pasa_asmbl_16499.p1, internal, 138044, 138100
-recovered pasa_asmbl_16499.p1, internal, 140487, 140616
-recovered pasa_asmbl_16499.p1, internal, 143570, 143795
-recovered pasa_asmbl_16499.p1, internal, 144459, 144705
-recovered pasa_asmbl_16499.p1, internal, 144924, 145020
-recovered pasa_asmbl_16499.p1, internal, 145270, 145364
-recovered pasa_asmbl_16499.p1, internal, 145631, 145702
-recovered pasa_asmbl_16499.p1, internal, 146599, 146765
-recovered pasa_asmbl_16499.p1, internal, 146992, 147134
-recovered pasa_asmbl_16499.p1, internal, 147293, 147416
-recovered pasa_asmbl_16499.p1, internal, 149173, 149206
-recovered pasa_asmbl_16499.p1, internal, 150794, 150824
Valid prediction for GlimmerHMM_glimmerT_39862-T1
Valid prediction for GeneMark_model.68313_t
Valid prediction for GlimmerHMM_glimmerT_39871-T1
Valid prediction for snap_scaffold_16-snap.2040-T1
Valid prediction for GlimmerHMM_glimmerT_39886-T1
Valid prediction for GlimmerHMM_glimmerT_39867-T1
Valid prediction for snap_scaffold_16-snap.2056-T1
Valid prediction for GeneMark_model.68306_t
Valid prediction for GeneMark_model.68302_t
Valid prediction for GeneMark_model.68343_t
Valid prediction for GlimmerHMM_glimmerT_39882-T1
Valid prediction for snap_scaffold_16-snap.2042-T1
Valid prediction for GeneMark_model.68308_t
Valid prediction for GeneMark_model.68342_t
Valid prediction for snap_scaffold_16-snap.2052-T1
Valid prediction for GeneMark_model.68298_t
Valid prediction for snap_scaffold_16-snap.2044-T1
Valid prediction for Augustus_model.g26800.t1
Valid prediction for snap_scaffold_16-snap.2053-T1
Valid prediction for GlimmerHMM_glimmerT_39885-T1
Valid prediction for snap_scaffold_16-snap.2073-T1
Valid prediction for snap_scaffold_16-snap.2054-T1
Valid prediction for GeneMark_model.68351_t
Valid prediction for snap_scaffold_16-snap.2049-T1
Valid prediction for Augustus_model.g26798.t1
Valid prediction for GeneMark_model.68297_t
Valid prediction for GeneMark_model.68310_t
Valid prediction for GeneMark_model.68340_t
Valid prediction for snap_scaffold_16-snap.2062-T1
Couldn't classify 53949, 53991
Sorry, prediction pasa_asmbl_16505.p1 fails validation.
(TCA)	 AA	53949-53991	GT	AAG
(AGG)	 AG	54102-54598	GT	AGG
(GAT)	 AG	56761-56857	GT	GTG
(GTA)	 AG	58683-58724	GT	AGG
(GCC)	 AG	59807-59814	TG	AGT
-recovered pasa_asmbl_16505.p1, terminal, 59807, 59814
-recovered pasa_asmbl_16505.p1, internal, 54102, 54598
-recovered pasa_asmbl_16505.p1, internal, 56761, 56857
-recovered pasa_asmbl_16505.p1, internal, 58683, 58724
Valid prediction for GeneMark_model.68332_t
Valid prediction for GeneMark_model.68304_t
Valid prediction for GeneMark_model.68328_t
Valid prediction for GeneMark_model.68318_t
Valid prediction for Augustus_model.g26796.t1
Valid prediction for Augustus_model.g26792.t1
Valid prediction for GeneMark_model.68323_t
Valid prediction for snap_scaffold_16-snap.2066-T1
Valid prediction for GeneMark_model.68321_t
Valid prediction for GeneMark_model.68315_t
Valid prediction for GeneMark_model.68293_t
Valid prediction for GeneMark_model.68345_t
Valid prediction for Augustus_model.g26803.t1
Valid prediction for GeneMark_model.68325_t
Valid prediction for GeneMark_model.68311_t
Valid prediction for Augustus_model.g26797.t1
Valid prediction for Augustus_model.g26807.t1
Valid prediction for GlimmerHMM_glimmerT_39859-T1
Valid prediction for GlimmerHMM_glimmerT_39874-T1
Valid prediction for snap_scaffold_16-snap.2051-T1
Valid prediction for GlimmerHMM_glimmerT_39880-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11784, rend_intergenic: 7125  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23298, rend_intergenic: 16363  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28181, rend_intergenic: 25023  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45610, rend_intergenic: 28430  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63164, rend_intergenic: 56395  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74360, rend_intergenic: 67924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76602, rend_intergenic: 74617  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81130, rend_intergenic: 79456  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96798, rend_intergenic: 81971  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112283, rend_intergenic: 109235  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114728, rend_intergenic: 113105  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122507, rend_intergenic: 117425  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127832, rend_intergenic: 125954  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160119, rend_intergenic: 156000  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179169, rend_intergenic: 165447  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195732, rend_intergenic: 181125  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 200623
-exon list size: 864


building trellis

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62.4    
62.5    
62.6    
62.7    
62.8    
62.9    
63.0    
63.2    
63.3    
63.4    
63.5    
63.6    
63.7    
63.9    
64.0    
64.1    
64.2    
64.3    
64.4    
64.5    
64.7    
64.8    
64.9    
65.0    
65.1    
65.2    
65.4    
65.5    
65.6    
65.7    
65.8    
65.9    
66.1    
66.2    
66.3    
66.4    
66.5    
66.6    
66.7    
66.9    
67.0    
67.1    
67.2    
67.3    
67.4    
67.6    
67.7    
67.8    
67.9    
68.0    
68.1    
68.2    
68.4    
68.5    
68.6    
68.7    
68.8    
68.9    
69.1    
69.2    
69.3    
69.4    
69.5    
69.6    
69.7    
69.9    
70.0    
70.1    
70.2    
70.3    
70.4    
70.6    
70.7    
70.8    
70.9    
71.0    
71.1    
71.2    
71.4    
71.5    
71.6    
71.7    
71.8    
71.9    
72.1    
72.2    
72.3    
72.4    
72.5    
72.6    
72.7    
72.9    
73.0    
73.1    
73.2    
73.3    
73.4    
73.6    
73.7    
73.8    
73.9    
74.0    
74.1    
74.2    
74.4    
74.5    
74.6    
74.7    
74.8    
74.9    
75.1    
75.2    
75.3    
75.4    
75.5    
75.6    
75.8    
75.9    
76.0    
76.1    
76.2    
76.3    
76.4    
76.6    
76.7    
76.8    
76.9    
77.0    
77.1    
77.3    
77.4    
77.5    
77.6    
77.7    
77.8    
77.9    
78.1    
78.2    
78.3    
78.4    
78.5    
78.6    
78.8    
78.9    
79.0    
79.1    
79.2    
79.3    
79.4    
79.6    
79.7    
79.8    
79.9    
80.0    
80.1    
80.3    
80.4    
80.5    
80.6    
80.7    
80.8    
80.9    
81.1    
81.2    
81.3    
81.4    
81.5    
81.6    
81.8    
81.9    
82.0    
82.1    
82.2    
82.3    
82.4    
82.6    
82.7    
82.8    
82.9    
83.0    
83.1    
83.3    
83.4    
83.5    
83.6    
83.7    
83.8    
83.9    
84.1    
84.2    
84.3    
84.4    
84.5    
84.6    
84.8    
84.9    
85.0    
85.1    
85.2    
85.3    
85.5    
85.6    
85.7    
85.8    
85.9    
86.0    
86.1    
86.3    
86.4    
86.5    
86.6    
86.7    
86.8    
87.0    
87.1    
87.2    
87.3    
87.4    
87.5    
87.6    
87.8    
87.9    
88.0    
88.1    
88.2    
88.3    
88.5    
88.6    
88.7    
88.8    
88.9    
89.0    
89.1    
89.3    
89.4    
89.5    
89.6    
89.7    
89.8    
90.0    
90.1    
90.2    
90.3    
90.4    
90.5    
90.6    
90.8    
90.9    
91.0    
91.1    
91.2    
91.3    
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    
93.0    
93.1    
93.2    
93.3    
93.4    
93.5    
93.6    
93.8    
93.9    
94.0    
94.1    
94.2    
94.3    
94.5    
94.6    
94.7    
94.8    
94.9    
95.0    
95.2    
95.3    
95.4    
95.5    
95.6    
95.7    
95.8    
96.0    
96.1    
96.2    
96.3    
96.4    
96.5    
96.7    
96.8    
96.9    
97.0    
97.1    
97.2    
97.3    
97.5    
97.6    
97.7    
97.8    
97.9    
98.0    
98.2    
98.3    
98.4    
98.5    
98.6    
98.7    
98.8    
99.0    
99.1    
99.2    
99.3    
99.4    
99.5    
99.7    
99.8    
99.9    
-found 37 predictions from path traversal
Error with prediction: snap lend_intergenic: 11784, rend_intergenic: 7125  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23298, rend_intergenic: 16363  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28181, rend_intergenic: 25023  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45610, rend_intergenic: 28430  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63164, rend_intergenic: 56395  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74360, rend_intergenic: 67924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76602, rend_intergenic: 74617  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81130, rend_intergenic: 79456  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96798, rend_intergenic: 81971  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112283, rend_intergenic: 109235  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114728, rend_intergenic: 113105  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122507, rend_intergenic: 117425  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127832, rend_intergenic: 125954  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160119, rend_intergenic: 156000  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179169, rend_intergenic: 165447  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195732, rend_intergenic: 181125  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support