-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_2/scaffold_2_11737751-11945905

-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_2-snap.2313-T1
Valid prediction for GeneMark_model.7480_t
Valid prediction for GeneMark_model.7499_t
Valid prediction for snap_scaffold_2-snap.2295-T1
Valid prediction for GlimmerHMM_glimmerT_4688-T1
Valid prediction for snap_scaffold_2-snap.2291-T1
Valid prediction for GlimmerHMM_glimmerT_4693-T1
Valid prediction for GeneMark_model.7492_t
Valid prediction for GlimmerHMM_glimmerT_4670-T1
Valid prediction for snap_scaffold_2-snap.2284-T1
Valid prediction for GlimmerHMM_glimmerT_4681-T1
Valid prediction for snap_scaffold_2-snap.2306-T1
Valid prediction for GlimmerHMM_glimmerT_4684-T1
Valid prediction for GeneMark_model.7478_t
Valid prediction for snap_scaffold_2-snap.2301-T1
Valid prediction for GlimmerHMM_glimmerT_4687-T1
Valid prediction for snap_scaffold_2-snap.2302-T1
Couldn't classify 43827, 43956
Sorry, prediction pasa_asmbl_24805.p1 fails validation.
(GAT)	 AC	43827-43956	GT	CGG
(ACG)	 AG	44972-45072	GT	AGG
(CCC)	 AG	46094-46280	GT	GAG
(CAA)	 AG	46463-46547	GT	AAG
(TAT)	 AG	46773-46909	GT	CAG
(TTG)	 AG	47181-47317	AT	AGA
-recovered pasa_asmbl_24805.p1, terminal, 47181, 47317
-recovered pasa_asmbl_24805.p1, internal, 44972, 45072
-recovered pasa_asmbl_24805.p1, internal, 46094, 46280
-recovered pasa_asmbl_24805.p1, internal, 46463, 46547
-recovered pasa_asmbl_24805.p1, internal, 46773, 46909
Valid prediction for snap_scaffold_2-snap.2297-T1
Valid prediction for GeneMark_model.7512_t
Valid prediction for GeneMark_model.7490_t
Valid prediction for GeneMark_model.7491_t
Valid prediction for snap_scaffold_2-snap.2320-T1
Couldn't classify 166998, 167363
Sorry, prediction pasa_asmbl_24818.p1 fails validation.
(ATA)	 GC	166998-167363	GA	AGG
Valid prediction for snap_scaffold_2-snap.2289-T1
Valid prediction for GeneMark_model.7505_t
Couldn't classify 57414, 57578
Sorry, prediction pasa_asmbl_24808.p1 fails validation.
(CCA)	 GC	57414-57578	GT	ACG
(CGT)	 AG	57951-58118	GG	GAG
-recovered pasa_asmbl_24808.p1, terminal, 57951, 58118
Valid prediction for GlimmerHMM_glimmerT_4689-T1
Valid prediction for Augustus_model.g3142.t1
Valid prediction for GlimmerHMM_glimmerT_4671-T1
Valid prediction for GlimmerHMM_glimmerT_4695-T1
Valid prediction for GlimmerHMM_glimmerT_4685-T1
Valid prediction for snap_scaffold_2-snap.2285-T1
Valid prediction for snap_scaffold_2-snap.2309-T1
Valid prediction for GlimmerHMM_glimmerT_4673-T1
Valid prediction for snap_scaffold_2-snap.2307-T1
Valid prediction for GlimmerHMM_glimmerT_4674-T1
Valid prediction for Augustus_model.g3141.t1
Valid prediction for GlimmerHMM_glimmerT_4680-T1
Valid prediction for GeneMark_model.7501_t
Valid prediction for HiQ_model.g3157.t1
Valid prediction for snap_scaffold_2-snap.2288-T1
Valid prediction for GlimmerHMM_glimmerT_4679-T1
Valid prediction for HiQ_model.g3143.t1
Valid prediction for Augustus_model.g3146.t1
Valid prediction for GeneMark_model.7485_t
Valid prediction for Augustus_model.g3154.t1
Valid prediction for GeneMark_model.7497_t
Valid prediction for snap_scaffold_2-snap.2300-T1
Valid prediction for GeneMark_model.7509_t
Valid prediction for Augustus_model.g3159.t1
Valid prediction for GlimmerHMM_glimmerT_4668-T1
Valid prediction for snap_scaffold_2-snap.2310-T1
Valid prediction for Augustus_model.g3145.t1
Valid prediction for GeneMark_model.7479_t
Valid prediction for snap_scaffold_2-snap.2296-T1
Valid prediction for Augustus_model.g3161.t1
Valid prediction for Augustus_model.g3163.t1
Valid prediction for snap_scaffold_2-snap.2287-T1
Valid prediction for GeneMark_model.7481_t
Valid prediction for GeneMark_model.7486_t
Couldn't classify 55014, 55125
Couldn't classify 56964, 57016
Sorry, prediction pasa_asmbl_24807.p1 fails validation.
(GTG)	 AG	55014-55125	GT	AGG
(GCG)	 AG	55209-55469	GT	AGG
(GGA)	 AG	55721-55953	GT	AGG
(GTG)	 AG	56095-56271	GT	AGG
(GTG)	 AG	56452-56523	GT	GCG
(GTC)	 AG	56673-56772	GT	GGG
(GGA)	 AG	56964-57016	CC	CCC
-recovered pasa_asmbl_24807.p1, internal, 55014, 55125
-recovered pasa_asmbl_24807.p1, internal, 55209, 55469
-recovered pasa_asmbl_24807.p1, internal, 55721, 55953
-recovered pasa_asmbl_24807.p1, internal, 56095, 56271
-recovered pasa_asmbl_24807.p1, internal, 56452, 56523
-recovered pasa_asmbl_24807.p1, internal, 56673, 56772
Valid prediction for GlimmerHMM_glimmerT_4691-T1
Valid prediction for GeneMark_model.7494_t
Valid prediction for GeneMark_model.7507_t
Valid prediction for GeneMark_model.7483_t
Valid prediction for GeneMark_model.7488_t
Valid prediction for GeneMark_model.7503_t
Couldn't classify 52122, 52262
Couldn't classify 53646, 53719
Sorry, prediction pasa_asmbl_24806.p1 fails validation.
(AAC)	 GC	52122-52262	GT	AGG
(ATT)	 AG	52366-52430	GT	TTG
(TGC)	 AG	52595-52766	GT	CTG
(GTC)	 AG	53042-53205	GT	AGG
(GGG)	 AG	53451-53563	GT	AGG
(ATA)	 AG	53646-53719	AA	AGA
-recovered pasa_asmbl_24806.p1, internal, 52366, 52430
-recovered pasa_asmbl_24806.p1, internal, 52595, 52766
-recovered pasa_asmbl_24806.p1, internal, 53042, 53205
-recovered pasa_asmbl_24806.p1, internal, 53451, 53563
Valid prediction for snap_scaffold_2-snap.2319-T1
Valid prediction for snap_scaffold_2-snap.2314-T1
Couldn't classify 40184, 40237
Couldn't classify 41158, 41384
Sorry, prediction pasa_asmbl_24803.p1 fails validation.
(GAG)	 TG	40184-40237	GT	AGG
(GAA)	 AG	40324-40374	GT	AGG
(GTT)	 AG	40541-40720	GT	AGG
(GCT)	 AG	40913-41030	GT	AAG
(CCC)	 AG	41158-41384	AC	CCA
-recovered pasa_asmbl_24803.p1, internal, 40324, 40374
-recovered pasa_asmbl_24803.p1, internal, 40541, 40720
-recovered pasa_asmbl_24803.p1, internal, 40913, 41030
Valid prediction for snap_scaffold_2-snap.2298-T1
Valid prediction for GeneMark_model.7476_t
Couldn't classify 161391, 161709
Couldn't classify 162243, 162259
Sorry, prediction pasa_asmbl_24815.p1 fails validation.
(GGA)	 TG	161391-161709	GT	AGG
(ATT)	 AG	162243-162259	CC	ACC
Valid prediction for snap_scaffold_2-snap.2308-T1
Valid prediction for GlimmerHMM_glimmerT_4675-T1
Valid prediction for GeneMark_model.7504_t
Valid prediction for GeneMark_model.7496_t
Valid prediction for Augustus_model.g3158.t1
Valid prediction for Augustus_model.g3153.t1
Valid prediction for GlimmerHMM_glimmerT_4686-T1
Couldn't classify 162401, 162979
Couldn't classify 166466, 166549
Sorry, prediction pasa_asmbl_24816.p1 fails validation.
(GCC)	 GG	162401-162979	GT	GCG
(GGA)	 AG	163119-163178	GT	GGG
(CTG)	 AG	163358-163428	GT	TTG
(TCT)	 AG	163580-163649	GT	GTG
(GTT)	 AG	163764-163830	GT	AGG
(ATG)	 AG	163942-164039	GT	AGG
(CCC)	 AG	164166-164243	GT	AGG
(GGG)	 AG	164422-164522	GT	AAG
(GCA)	 AG	165252-165341	GT	AGG
(CCT)	 AG	165569-165614	GT	AGG
(GAC)	 AG	165837-165978	GT	GGG
(ACT)	 AG	166072-166214	GT	AGG
(TAC)	 AG	166466-166549	GC	AGG
add_exon() Sorry, pasa_asmbl_24816.p1 163942-164039-initial-1 is invalid.
-recovered pasa_asmbl_24816.p1, initial, 163942, 164039
-recovered pasa_asmbl_24816.p1, internal, 163119, 163178
-recovered pasa_asmbl_24816.p1, internal, 163358, 163428
-recovered pasa_asmbl_24816.p1, internal, 163580, 163649
-recovered pasa_asmbl_24816.p1, internal, 163764, 163830
-recovered pasa_asmbl_24816.p1, internal, 163942, 164039
-recovered pasa_asmbl_24816.p1, internal, 164166, 164243
-recovered pasa_asmbl_24816.p1, internal, 164422, 164522
-recovered pasa_asmbl_24816.p1, internal, 165252, 165341
-recovered pasa_asmbl_24816.p1, internal, 165569, 165614
-recovered pasa_asmbl_24816.p1, internal, 165837, 165978
-recovered pasa_asmbl_24816.p1, internal, 166072, 166214
-recovered pasa_asmbl_24816.p1, internal, 166466, 166549
Valid prediction for GlimmerHMM_glimmerT_4678-T1
Valid prediction for snap_scaffold_2-snap.2316-T1
Valid prediction for snap_scaffold_2-snap.2305-T1
Valid prediction for snap_scaffold_2-snap.2317-T1
Valid prediction for GlimmerHMM_glimmerT_4694-T1
Valid prediction for GlimmerHMM_glimmerT_4669-T1
Valid prediction for GeneMark_model.7493_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_2-snap.2315-T1
Valid prediction for GlimmerHMM_glimmerT_4672-T1
Valid prediction for GeneMark_model.7482_t
Valid prediction for snap_scaffold_2-snap.2311-T1
Couldn't classify 125826, 125895
Sorry, prediction pasa_asmbl_23475.p1 fails validation.
(GTC)	 AG	125826-125895	GT	AGG
(AGC)	 AG	126369-126539	GT	GGG
(GGC)	 AG	126754-126925	GT	CAG
(GCA)	 AG	127092-127392	GT	TGG
(GGC)	 AG	127529-127623	GT	AAG
(GTG)	 AG	127708-127849	GT	AGG
(TCT)	 AG	128015-128155	GT	AGG
(GAC)	 AG	128302-128429	GT	AGG
(GGT)	 AG	128514-128580	GT	AGG
(GCT)	 AG	128762-128875	GT	GGG
(ATC)	 AG	129137-129252	GT	AGG
(ACA)	 AG	129539-129656	GT	AGG
(GTG)	 AG	129955-130110	GT	CGG
(ACT)	 AG	130289-130558	GG	GAG
add_exon() Sorry, pasa_asmbl_23475.p1 128302-128429-terminal-2 is invalid.
-recovered pasa_asmbl_23475.p1, terminal, 128302, 128429
-recovered pasa_asmbl_23475.p1, terminal, 130289, 130558
-recovered pasa_asmbl_23475.p1, internal, 125826, 125895
-recovered pasa_asmbl_23475.p1, internal, 126369, 126539
-recovered pasa_asmbl_23475.p1, internal, 126754, 126925
-recovered pasa_asmbl_23475.p1, internal, 127092, 127392
-recovered pasa_asmbl_23475.p1, internal, 127529, 127623
-recovered pasa_asmbl_23475.p1, internal, 127708, 127849
-recovered pasa_asmbl_23475.p1, internal, 128015, 128155
-recovered pasa_asmbl_23475.p1, internal, 128302, 128429
-recovered pasa_asmbl_23475.p1, internal, 128514, 128580
-recovered pasa_asmbl_23475.p1, internal, 128762, 128875
-recovered pasa_asmbl_23475.p1, internal, 129137, 129252
-recovered pasa_asmbl_23475.p1, internal, 129539, 129656
-recovered pasa_asmbl_23475.p1, internal, 129955, 130110
Valid prediction for GeneMark_model.7508_t
Valid prediction for GeneMark_model.7502_t
Valid prediction for GlimmerHMM_glimmerT_4682-T1
Valid prediction for snap_scaffold_2-snap.2299-T1
Valid prediction for snap_scaffold_2-snap.2293-T1
Valid prediction for GlimmerHMM_glimmerT_4677-T1
Valid prediction for GeneMark_model.7489_t
Valid prediction for Augustus_model.g3150.t1
Valid prediction for Augustus_model.g3151.t1
Couldn't classify 87288, 87378
Sorry, prediction pasa_asmbl_23477.p1 fails validation.
(AGA)	 CC	87288-87378	GT	AGG
(GTG)	 AG	89420-89592	GT	AGG
(GGT)	 AG	91823-92035	GT	TTG
(GTG)	 AG	93943-94043	GT	AAG
(CAC)	 AG	96971-97074	GT	AGG
(TGA)	 AG	97373-97490	GT	AGG
(GGA)	 AG	97641-97820	GT	AGG
(GCC)	 AG	99078-99205	GT	CGG
(GCA)	 AG	100652-100780	GT	AGG
(AGT)	 AG	101659-102374	CG	AGC
add_exon() Sorry, pasa_asmbl_23477.p1 100652-100780-terminal-1 is invalid.
-recovered pasa_asmbl_23477.p1, terminal, 100652, 100780
-recovered pasa_asmbl_23477.p1, terminal, 101659, 102374
-recovered pasa_asmbl_23477.p1, internal, 89420, 89592
-recovered pasa_asmbl_23477.p1, internal, 91823, 92035
-recovered pasa_asmbl_23477.p1, internal, 93943, 94043
-recovered pasa_asmbl_23477.p1, internal, 96971, 97074
-recovered pasa_asmbl_23477.p1, internal, 97373, 97490
-recovered pasa_asmbl_23477.p1, internal, 97641, 97820
-recovered pasa_asmbl_23477.p1, internal, 99078, 99205
-recovered pasa_asmbl_23477.p1, internal, 100652, 100780
Valid prediction for GlimmerHMM_glimmerT_4692-T1
Valid prediction for Augustus_model.g3148.t1
Valid prediction for GlimmerHMM_glimmerT_4667-T1
Valid prediction for Augustus_model.g3162.t1
Valid prediction for GeneMark_model.7506_t
Valid prediction for HiQ_model.g3147.t1
Valid prediction for snap_scaffold_2-snap.2290-T1
Valid prediction for GeneMark_model.7500_t
Valid prediction for GeneMark_model.7498_t
Valid prediction for Augustus_model.g3160.t1
Valid prediction for Augustus_model.g3156.t1
Valid prediction for GlimmerHMM_glimmerT_4683-T1
Valid prediction for GeneMark_model.7495_t
Valid prediction for snap_scaffold_2-snap.2294-T1
Valid prediction for Augustus_model.g3152.t1
Valid prediction for snap_scaffold_2-snap.2286-T1
Valid prediction for GeneMark_model.7511_t
Valid prediction for snap_scaffold_2-snap.2318-T1
Valid prediction for Augustus_model.g3149.t1
Valid prediction for snap_scaffold_2-snap.2303-T1
Valid prediction for Augustus_model.g3155.t1
Valid prediction for GeneMark_model.7487_t
Valid prediction for snap_scaffold_2-snap.2304-T1
Valid prediction for GeneMark_model.7513_t
Valid prediction for snap_scaffold_2-snap.2292-T1
Valid prediction for GlimmerHMM_glimmerT_4676-T1
Valid prediction for GeneMark_model.7477_t
Valid prediction for GlimmerHMM_glimmerT_4690-T1
Valid prediction for Augustus_model.g3144.t1
Valid prediction for GeneMark_model.7484_t
Valid prediction for snap_scaffold_2-snap.2312-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 58118, rend_intergenic: 52613  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117523, rend_intergenic: 108887  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120373, rend_intergenic: 118048  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155178, rend_intergenic: 136081  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181588, rend_intergenic: 175996  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 208155
-exon list size: 678


building trellis

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56.2    
56.3    
56.5    
56.6    
56.8    
56.9    
57.1    
57.2    
57.4    
57.5    
57.6    
57.8    
57.9    
58.1    
58.2    
58.4    
58.5    
58.7    
58.8    
59.0    
59.1    
59.3    
59.4    
59.6    
59.7    
59.9    
60.0    
60.1    
60.3    
60.4    
60.6    
60.7    
60.9    
61.0    
61.2    
61.3    
61.5    
61.6    
61.8    
61.9    
62.1    
62.2    
62.4    
62.5    
62.6    
62.8    
62.9    
63.1    
63.2    
63.4    
63.5    
63.7    
63.8    
64.0    
64.1    
64.3    
64.4    
64.6    
64.7    
64.9    
65.0    
65.1    
65.3    
65.4    
65.6    
65.7    
65.9    
66.0    
66.2    
66.3    
66.5    
66.6    
66.8    
66.9    
67.1    
67.2    
67.4    
67.5    
67.6    
67.8    
67.9    
68.1    
68.2    
68.4    
68.5    
68.7    
68.8    
69.0    
69.1    
69.3    
69.4    
69.6    
69.7    
69.9    
70.0    
70.1    
70.3    
70.4    
70.6    
70.7    
70.9    
71.0    
71.2    
71.3    
71.5    
71.6    
71.8    
71.9    
72.1    
72.2    
72.4    
72.5    
72.6    
72.8    
72.9    
73.1    
73.2    
73.4    
73.5    
73.7    
73.8    
74.0    
74.1    
74.3    
74.4    
74.6    
74.7    
74.9    
75.0    
75.1    
75.3    
75.4    
75.6    
75.7    
75.9    
76.0    
76.2    
76.3    
76.5    
76.6    
76.8    
76.9    
77.1    
77.2    
77.4    
77.5    
77.6    
77.8    
77.9    
78.1    
78.2    
78.4    
78.5    
78.7    
78.8    
79.0    
79.1    
79.3    
79.4    
79.6    
79.7    
79.9    
80.0    
80.1    
80.3    
80.4    
80.6    
80.7    
80.9    
81.0    
81.2    
81.3    
81.5    
81.6    
81.8    
81.9    
82.1    
82.2    
82.4    
82.5    
82.6    
82.8    
82.9    
83.1    
83.2    
83.4    
83.5    
83.7    
83.8    
84.0    
84.1    
84.3    
84.4    
84.6    
84.7    
84.9    
85.0    
85.1    
85.3    
85.4    
85.6    
85.7    
85.9    
86.0    
86.2    
86.3    
86.5    
86.6    
86.8    
86.9    
87.1    
87.2    
87.4    
87.5    
87.6    
87.8    
87.9    
88.1    
88.2    
88.4    
88.5    
88.7    
88.8    
89.0    
89.1    
89.3    
89.4    
89.6    
89.7    
89.9    
90.0    
90.1    
90.3    
90.4    
90.6    
90.7    
90.9    
91.0    
91.2    
91.3    
91.5    
91.6    
91.8    
91.9    
92.1    
92.2    
92.4    
92.5    
92.6    
92.8    
92.9    
93.1    
93.2    
93.4    
93.5    
93.7    
93.8    
94.0    
94.1    
94.3    
94.4    
94.6    
94.7    
94.9    
95.0    
95.1    
95.3    
95.4    
95.6    
95.7    
95.9    
96.0    
96.2    
96.3    
96.5    
96.6    
96.8    
96.9    
97.1    
97.2    
97.4    
97.5    
97.6    
97.8    
97.9    
98.1    
98.2    
98.4    
98.5    
98.7    
98.8    
99.0    
99.1    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 58118, rend_intergenic: 52613  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117523, rend_intergenic: 108887  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120373, rend_intergenic: 118048  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155178, rend_intergenic: 136081  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181588, rend_intergenic: 175996  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support