-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_7/scaffold_7_10656328-10856193

-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: +)Couldn't classify 194288, 194599
Sorry, prediction pasa_asmbl_51026.p1 fails validation.
(ATG)	 AC	186687-186737	GT	AGG
(TCA)	 AG	186849-186983	GT	GGG
(AAA)	 AG	187243-187378	GT	AGG
(GAG)	 AG	188841-188992	GT	AGG
(GTC)	 AG	189165-189290	GT	AGG
(GGT)	 AG	189419-189550	GT	ATG
(GAG)	 AG	189917-189984	GT	AAG
(ATG)	 AG	190094-190182	GT	AGG
(ATG)	 AG	190313-190410	GT	CTG
(GGA)	 AG	192591-192678	GT	CTG
(GGG)	 AG	192781-192879	GT	TGG
(GGG)	 AG	193985-194115	GT	AGG
(GCC)	 AG	194288-194599	GA	CCG
-recovered pasa_asmbl_51026.p1, initial, 186687, 186737
-recovered pasa_asmbl_51026.p1, initial, 190094, 190182
-recovered pasa_asmbl_51026.p1, initial, 190313, 190410
add_exon() Sorry, pasa_asmbl_51026.p1 190094-190182-terminal-2 is invalid.
-recovered pasa_asmbl_51026.p1, terminal, 190094, 190182
-recovered pasa_asmbl_51026.p1, internal, 186849, 186983
-recovered pasa_asmbl_51026.p1, internal, 187243, 187378
-recovered pasa_asmbl_51026.p1, internal, 188841, 188992
-recovered pasa_asmbl_51026.p1, internal, 189165, 189290
-recovered pasa_asmbl_51026.p1, internal, 189419, 189550
-recovered pasa_asmbl_51026.p1, internal, 189917, 189984
-recovered pasa_asmbl_51026.p1, internal, 190094, 190182
-recovered pasa_asmbl_51026.p1, internal, 190313, 190410
-recovered pasa_asmbl_51026.p1, internal, 192591, 192678
-recovered pasa_asmbl_51026.p1, internal, 192781, 192879
-recovered pasa_asmbl_51026.p1, internal, 193985, 194115
Valid prediction for GlimmerHMM_glimmerT_18453-T1
Valid prediction for GeneMark_model.30938_t
Valid prediction for CodingQuarry_transcript_57472-T1
Valid prediction for GlimmerHMM_glimmerT_18464-T1
Valid prediction for snap_scaffold_7-snap.2055-T1
Valid prediction for GeneMark_model.30979_t
Valid prediction for GeneMark_model.30951_t
Valid prediction for GlimmerHMM_glimmerT_18476-T1
Valid prediction for CodingQuarry_transcript_57470-T1
Valid prediction for GlimmerHMM_glimmerT_18466-T1
Couldn't classify 7278, 7503
Couldn't classify 9148, 9266
Sorry, prediction pasa_asmbl_51462.p1 fails validation.
(CAG)	 CT	7278-7503	GT	GGG
(AAC)	 AG	9148-9266	GT	GGG
-recovered pasa_asmbl_51462.p1, internal, 9148, 9266
Valid prediction for GeneMark_model.30974_t
Valid prediction for snap_scaffold_7-snap.2073-T1
Valid prediction for GeneMark_model.30991_t
Valid prediction for snap_scaffold_7-snap.2075-T1
Valid prediction for snap_scaffold_7-snap.2077-T1
Valid prediction for Augustus_model.g12458.t1
Valid prediction for GlimmerHMM_glimmerT_18478-T1
Valid prediction for GeneMark_model.30949_t
Valid prediction for GlimmerHMM_glimmerT_18473-T1
Valid prediction for snap_scaffold_7-snap.2057-T1
Valid prediction for GeneMark_model.30990_t
Valid prediction for GeneMark_model.30943_t
Valid prediction for GeneMark_model.30946_t
Valid prediction for GeneMark_model.30986_t
Valid prediction for Augustus_model.g12451.t1
Couldn't classify 12115, 12414
Sorry, prediction pasa_asmbl_51015.p1 fails validation.
(TGG)	 GC	12115-12414	CG	AGC
Valid prediction for GeneMark_model.30954_t
Valid prediction for snap_scaffold_7-snap.2063-T1
Valid prediction for GeneMark_model.30976_t
Valid prediction for GeneMark_model.30977_t
Valid prediction for Augustus_model.g12448.t1
Valid prediction for Augustus_model.g12450.t1
Valid prediction for pasa_asmbl_51023.p1
Valid prediction for GlimmerHMM_glimmerT_18455-T1
Valid prediction for GeneMark_model.30983_t
Valid prediction for GeneMark_model.30960_t
Valid prediction for Augustus_model.g12461.t1
Valid prediction for GeneMark_model.30958_t
Valid prediction for GlimmerHMM_glimmerT_18474-T1
Valid prediction for HiQ_model.g12453.t1
Valid prediction for GeneMark_model.30981_t
Valid prediction for GlimmerHMM_glimmerT_18471-T1
Valid prediction for GeneMark_model.30970_t
Valid prediction for snap_scaffold_7-snap.2067-T1
Couldn't classify 26604, 26666
Sorry, prediction pasa_asmbl_51018.p1 fails validation.
(GCT)	 CA	26604-26666	GT	AGG
(TAT)	 AG	27791-27940	GT	GGG
(TTT)	 AG	30598-30684	GT	AGG
(GGC)	 AG	31267-31384	GT	CGG
(GTG)	 AG	31552-31661	CT	GAC
-recovered pasa_asmbl_51018.p1, terminal, 31552, 31661
-recovered pasa_asmbl_51018.p1, internal, 27791, 27940
-recovered pasa_asmbl_51018.p1, internal, 30598, 30684
-recovered pasa_asmbl_51018.p1, internal, 31267, 31384
Valid prediction for CodingQuarry_transcript_57471-T1
Valid prediction for GlimmerHMM_glimmerT_18477-T1
Valid prediction for Augustus_model.g12449.t1
Valid prediction for snap_scaffold_7-snap.2071-T1
Valid prediction for GeneMark_model.30963_t
Valid prediction for GlimmerHMM_glimmerT_18467-T1
Valid prediction for snap_scaffold_7-snap.2053-T1
Valid prediction for GlimmerHMM_glimmerT_18469-T1
Valid prediction for GeneMark_model.30966_t
Couldn't classify 181576, 181718
Couldn't classify 184256, 184310
Sorry, prediction pasa_asmbl_51025.p1 fails validation.
(AGG)	 CT	181576-181718	GT	AAG
(ACA)	 AG	181818-181843	GT	AGG
(CCA)	 AG	182238-182273	GT	AGG
(AGG)	 AG	183919-184042	GT	GTG
(ATA)	 AG	184256-184310	GA	GGG
-recovered pasa_asmbl_51025.p1, internal, 181818, 181843
-recovered pasa_asmbl_51025.p1, internal, 182238, 182273
-recovered pasa_asmbl_51025.p1, internal, 183919, 184042
Valid prediction for GlimmerHMM_glimmerT_18454-T1
Valid prediction for GeneMark_model.30984_t
Valid prediction for GeneMark_model.30961_t
Valid prediction for GeneMark_model.30941_t
Valid prediction for Augustus_model.g12452.t1
Valid prediction for snap_scaffold_7-snap.2056-T1
Valid prediction for GeneMark_model.30953_t
Valid prediction for GeneMark_model.30965_t
Valid prediction for snap_scaffold_7-snap.2070-T1
Valid prediction for GlimmerHMM_glimmerT_18461-T1
Valid prediction for GlimmerHMM_glimmerT_18452-T1
Valid prediction for GlimmerHMM_glimmerT_18451-T1
Valid prediction for GeneMark_model.30962_t
Valid prediction for GeneMark_model.30988_t
Couldn't classify 39405, 39500
Couldn't classify 43606, 43704
Sorry, prediction pasa_asmbl_51020.p1 fails validation.
(GAT)	 TA	39405-39500	GT	TGG
(AAA)	 AG	42091-42350	GT	AGG
(GGA)	 AG	42884-42962	GT	GGG
(ATG)	 AG	43606-43704	GC	ACG
-recovered pasa_asmbl_51020.p1, initial, 43606, 43704
-recovered pasa_asmbl_51020.p1, internal, 42091, 42350
-recovered pasa_asmbl_51020.p1, internal, 42884, 42962
-recovered pasa_asmbl_51020.p1, internal, 43606, 43704
Valid prediction for snap_scaffold_7-snap.2050-T1
Valid prediction for snap_scaffold_7-snap.2062-T1
Valid prediction for GeneMark_model.30948_t
Valid prediction for GeneMark_model.30956_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 GeneMark_model.30959_t
Valid prediction for Augustus_model.g12454.t1
Valid prediction for GeneMark_model.30978_t
Valid prediction for Augustus_model.g12455.t1
Valid prediction for snap_scaffold_7-snap.2061-T1
Valid prediction for snap_scaffold_7-snap.2064-T1
Valid prediction for snap_scaffold_7-snap.2051-T1
Valid prediction for GlimmerHMM_glimmerT_18462-T1
Valid prediction for snap_scaffold_7-snap.2076-T1
Valid prediction for snap_scaffold_7-snap.2068-T1
Valid prediction for snap_scaffold_7-snap.2074-T1
Valid prediction for snap_scaffold_7-snap.2078-T1
Valid prediction for snap_scaffold_7-snap.2059-T1
Valid prediction for GeneMark_model.30972_t
Valid prediction for GeneMark_model.30952_t
Valid prediction for snap_scaffold_7-snap.2058-T1
Valid prediction for GeneMark_model.30950_t
Valid prediction for CodingQuarry_transcript_57473-T1
Valid prediction for snap_scaffold_7-snap.2066-T1
Valid prediction for HiQ_model.g12462.t1
Valid prediction for GlimmerHMM_glimmerT_18475-T1
Valid prediction for GeneMark_model.30968_t
Valid prediction for GeneMark_model.30944_t
Valid prediction for GlimmerHMM_glimmerT_18479-T1
Valid prediction for GlimmerHMM_glimmerT_18468-T1
Valid prediction for snap_scaffold_7-snap.2081-T1
Valid prediction for GeneMark_model.30987_t
Valid prediction for GeneMark_model.30945_t
Valid prediction for snap_scaffold_7-snap.2080-T1
Valid prediction for GeneMark_model.30964_t
Valid prediction for GlimmerHMM_glimmerT_18463-T1
Valid prediction for Augustus_model.g12460.t1
Valid prediction for GeneMark_model.30940_t
Valid prediction for GlimmerHMM_glimmerT_18472-T1
Valid prediction for GlimmerHMM_glimmerT_18456-T1
Valid prediction for GlimmerHMM_glimmerT_18457-T1
Valid prediction for GeneMark_model.30969_t
Valid prediction for snap_scaffold_7-snap.2052-T1
Valid prediction for GeneMark_model.30942_t
Valid prediction for GeneMark_model.30973_t
Valid prediction for snap_scaffold_7-snap.2060-T1
Valid prediction for snap_scaffold_7-snap.2054-T1
Valid prediction for snap_scaffold_7-snap.2065-T1
Valid prediction for GeneMark_model.30971_t
Valid prediction for GlimmerHMM_glimmerT_18460-T1
Valid prediction for GeneMark_model.30975_t
Valid prediction for snap_scaffold_7-snap.2069-T1
Valid prediction for GeneMark_model.30947_t
Valid prediction for GeneMark_model.30985_t
Valid prediction for GlimmerHMM_glimmerT_18465-T1
Valid prediction for snap_scaffold_7-snap.2072-T1
Valid prediction for GeneMark_model.30989_t
Valid prediction for GeneMark_model.30957_t
Valid prediction for GlimmerHMM_glimmerT_18458-T1
Valid prediction for Augustus_model.g12457.t1
Valid prediction for Augustus_model.g12456.t1
Valid prediction for Augustus_model.g12459.t1
Valid prediction for GeneMark_model.30955_t
Valid prediction for GeneMark_model.30967_t
Valid prediction for GeneMark_model.30980_t
Valid prediction for GeneMark_model.30982_t
Valid prediction for GlimmerHMM_glimmerT_18470-T1
Valid prediction for GlimmerHMM_glimmerT_18459-T1
Valid prediction for GeneMark_model.30939_t
Valid prediction for snap_scaffold_7-snap.2079-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 78398, rend_intergenic: 78395  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15594, rend_intergenic: 4311  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28074, rend_intergenic: 27830  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31525, rend_intergenic: 28536  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62668, rend_intergenic: 42106  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86183, rend_intergenic: 68340  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98493, rend_intergenic: 87499  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120815, rend_intergenic: 114929  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127280, rend_intergenic: 122146  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146860, rend_intergenic: 142715  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162495, rend_intergenic: 151018  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165122, rend_intergenic: 163453  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194797, rend_intergenic: 165468  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 199866
-exon list size: 780


building trellis

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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    
77.7    
77.9    
78.0    
78.1    
78.3    
78.4    
78.5    
78.6    
78.8    
78.9    
79.0    
79.2    
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    
80.9    
81.1    
81.2    
81.3    
81.5    
81.6    
81.7    
81.8    
82.0    
82.1    
82.2    
82.4    
82.5    
82.6    
82.7    
82.9    
83.0    
83.1    
83.2    
83.4    
83.5    
83.6    
83.8    
83.9    
84.0    
84.1    
84.3    
84.4    
84.5    
84.7    
84.8    
84.9    
85.0    
85.2    
85.3    
85.4    
85.5    
85.7    
85.8    
85.9    
86.1    
86.2    
86.3    
86.4    
86.6    
86.7    
86.8    
87.0    
87.1    
87.2    
87.3    
87.5    
87.6    
87.7    
87.9    
88.0    
88.1    
88.2    
88.4    
88.5    
88.6    
88.7    
88.9    
89.0    
89.1    
89.3    
89.4    
89.5    
89.6    
89.8    
89.9    
90.0    
90.2    
90.3    
90.4    
90.5    
90.7    
90.8    
90.9    
91.0    
91.2    
91.3    
91.4    
91.6    
91.7    
91.8    
91.9    
92.1    
92.2    
92.3    
92.5    
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    
94.2    
94.4    
94.5    
94.6    
94.8    
94.9    
95.0    
95.1    
95.3    
95.4    
95.5    
95.7    
95.8    
95.9    
96.0    
96.2    
96.3    
96.4    
96.5    
96.7    
96.8    
96.9    
97.1    
97.2    
97.3    
97.4    
97.6    
97.7    
97.8    
98.0    
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 31 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 78398, rend_intergenic: 78395  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15594, rend_intergenic: 4311  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28074, rend_intergenic: 27830  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31525, rend_intergenic: 28536  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62668, rend_intergenic: 42106  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86183, rend_intergenic: 68340  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98493, rend_intergenic: 87499  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120815, rend_intergenic: 114929  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127280, rend_intergenic: 122146  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146860, rend_intergenic: 142715  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162495, rend_intergenic: 151018  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165122, rend_intergenic: 163453  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194797, rend_intergenic: 165468  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