-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_5/scaffold_5_12274017-12489578

-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_13063-T1
Valid prediction for GeneMark_model.22062_t
Valid prediction for GeneMark_model.22070_t
Valid prediction for GeneMark_model.22053_t
Valid prediction for pasa_asmbl_44464.p1
Valid prediction for GlimmerHMM_glimmerT_13070-T1
Valid prediction for GeneMark_model.22045_t
Valid prediction for GeneMark_model.22058_t
Valid prediction for GeneMark_model.22046_t
Valid prediction for HiQ_model.g8708.t1
Couldn't classify 79634, 80146
Sorry, prediction pasa_asmbl_44467.p1 fails validation.
(TTA)	 AG	79634-80146	AC	AGA
Valid prediction for snap_scaffold_5-snap.2281-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GeneMark_model.22044_t
Valid prediction for snap_scaffold_5-snap.2307-T1
Valid prediction for Augustus_model.g8718.t1
Valid prediction for GlimmerHMM_glimmerT_13085-T1
Valid prediction for GlimmerHMM_glimmerT_13064-T1
Valid prediction for Augustus_model.g8707.t1
Valid prediction for Augustus_model.g8714.t1
Valid prediction for Augustus_model.g8723.t1
Valid prediction for snap_scaffold_5-snap.2286-T1
Valid prediction for pasa_asmbl_44465.p1
Valid prediction for snap_scaffold_5-snap.2320-T1
Valid prediction for snap_scaffold_5-snap.2289-T1
Valid prediction for snap_scaffold_5-snap.2280-T1
Valid prediction for snap_scaffold_5-snap.2299-T1
Valid prediction for CodingQuarry_transcript_52158-T1
Valid prediction for CodingQuarry_transcript_52155-T1
Valid prediction for snap_scaffold_5-snap.2291-T1
Couldn't classify 89291, 89422
Couldn't classify 96591, 96658
Sorry, prediction pasa_asmbl_44469.p1 fails validation.
(AGG)	 CC	89291-89422	GT	AGG
(GAT)	 AG	90143-90320	GT	AGG
(ATC)	 AG	90402-90510	GT	GCG
(GTG)	 AG	92572-92671	GT	AGG
(AAT)	 AG	93963-94061	GT	AGG
(GGA)	 AG	95548-95637	GT	CAG
(CTG)	 AG	95751-95844	GT	AGG
(TGG)	 AG	96591-96658	CA	GTC
-recovered pasa_asmbl_44469.p1, internal, 90143, 90320
-recovered pasa_asmbl_44469.p1, internal, 90402, 90510
-recovered pasa_asmbl_44469.p1, internal, 92572, 92671
-recovered pasa_asmbl_44469.p1, internal, 93963, 94061
-recovered pasa_asmbl_44469.p1, internal, 95548, 95637
-recovered pasa_asmbl_44469.p1, internal, 95751, 95844
Valid prediction for GlimmerHMM_glimmerT_13072-T1
Valid prediction for snap_scaffold_5-snap.2282-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_5-snap.2297-T1
Valid prediction for GeneMark_model.22052_t
Valid prediction for snap_scaffold_5-snap.2310-T1
Valid prediction for CodingQuarry_transcript_52157-T1
Valid prediction for Augustus_model.g8711.t1
Valid prediction for pasa_asmbl_44990.p1
Valid prediction for snap_scaffold_5-snap.2305-T1
Couldn't classify 80267, 80572
Couldn't classify 85854, 85955
Sorry, prediction pasa_asmbl_44468.p1 fails validation.
(GCG)	 GC	80267-80572	GT	TTG
(CTG)	 AG	82188-82364	GT	AGG
(CTG)	 AG	85132-85263	GT	ATG
(CTG)	 AG	85854-85955	TG	GGT
-recovered pasa_asmbl_44468.p1, internal, 82188, 82364
-recovered pasa_asmbl_44468.p1, internal, 85132, 85263
Couldn't classify 206923, 206990
Sorry, prediction pasa_asmbl_44476.p1 fails validation.
(CAG)	 TC	206923-206990	GT	ATG
(GTG)	 AG	207130-207187	GT	TGG
(TCA)	 AG	207437-207487	GT	AGG
(ACC)	 AG	207625-207717	GT	AGG
(GAT)	 AG	208620-208748	GT	AGG
(GCT)	 AG	208995-209101	GT	TGG
(GGT)	 AG	209212-209368	GT	AGG
(GTG)	 AG	209468-209605	AC	GAA
-recovered pasa_asmbl_44476.p1, terminal, 209468, 209605
-recovered pasa_asmbl_44476.p1, internal, 207130, 207187
-recovered pasa_asmbl_44476.p1, internal, 207437, 207487
-recovered pasa_asmbl_44476.p1, internal, 207625, 207717
-recovered pasa_asmbl_44476.p1, internal, 208620, 208748
-recovered pasa_asmbl_44476.p1, internal, 208995, 209101
-recovered pasa_asmbl_44476.p1, internal, 209212, 209368
Valid prediction for snap_scaffold_5-snap.2287-T1
Valid prediction for GeneMark_model.22037_t
Valid prediction for CodingQuarry_transcript_52156-T1
Valid prediction for GlimmerHMM_glimmerT_13074-T1
Valid prediction for GlimmerHMM_glimmerT_13079-T1
Valid prediction for GeneMark_model.22071_t
Valid prediction for GeneMark_model.22040_t
Valid prediction for GeneMark_model.22033_t
Valid prediction for GeneMark_model.22050_t
Valid prediction for CodingQuarry_transcript_52154-T1
Valid prediction for GlimmerHMM_glimmerT_13068-T1
Valid prediction for GlimmerHMM_glimmerT_13069-T1
Valid prediction for snap_scaffold_5-snap.2294-T1
Valid prediction for snap_scaffold_5-snap.2309-T1
Valid prediction for GeneMark_model.22064_t
Valid prediction for HiQ_model.g8717.t1
Valid prediction for snap_scaffold_5-snap.2295-T1
Valid prediction for GeneMark_model.22032_t
Valid prediction for pasa_asmbl_44470.p1
Valid prediction for GeneMark_model.22055_t
Valid prediction for HiQ_model.g8713.t1
Valid prediction for GeneMark_model.22048_t
Valid prediction for GeneMark_model.22057_t
Valid prediction for snap_scaffold_5-snap.2285-T1
Valid prediction for Augustus_model.g8712.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.22054_t
Valid prediction for GeneMark_model.22060_t
Valid prediction for HiQ_model.g8709.t1
Valid prediction for Augustus_model.g8720.t1
Couldn't classify 30415, 30519
Couldn't classify 31074, 31168
Sorry, prediction pasa_asmbl_45834.p1 fails validation.
(GAT)	 AG	30415-30519	GT	TGG
(ACA)	 AG	30685-30738	GT	CGG
(GAC)	 AG	30845-30983	GT	AGG
(GAG)	 AG	31074-31168	GG	AGG
-recovered pasa_asmbl_45834.p1, internal, 30415, 30519
-recovered pasa_asmbl_45834.p1, internal, 30685, 30738
-recovered pasa_asmbl_45834.p1, internal, 30845, 30983
Valid prediction for snap_scaffold_5-snap.2311-T1
Valid prediction for snap_scaffold_5-snap.2315-T1
Couldn't classify 84280, 84306
Sorry, prediction pasa_asmbl_45829.p1 fails validation.
(GTT)	 AT	84280-84306	GT	CGG
(GAT)	 AG	85267-85367	GT	GTG
(TAA)	 AG	86400-86565	GT	AGG
(GAC)	 AG	86749-86860	GT	TGG
(AGG)	 AG	87020-87148	GT	GGG
(AAT)	 AG	87577-87653	GT	AGG
(CAG)	 AG	87787-87951	GT	AGG
(ATG)	 AG	88089-88175	TC	GAT
-recovered pasa_asmbl_45829.p1, terminal, 88089, 88175
-recovered pasa_asmbl_45829.p1, internal, 85267, 85367
-recovered pasa_asmbl_45829.p1, internal, 86400, 86565
-recovered pasa_asmbl_45829.p1, internal, 86749, 86860
-recovered pasa_asmbl_45829.p1, internal, 87020, 87148
-recovered pasa_asmbl_45829.p1, internal, 87577, 87653
-recovered pasa_asmbl_45829.p1, internal, 87787, 87951
Couldn't classify 44631, 44760
Sorry, prediction pasa_asmbl_45831.p1 fails validation.
(ACT)	 CC	44631-44760	GT	CTG
(TGC)	 AG	44884-44996	GT	TGG
(ATC)	 AG	45082-45236	GT	TGG
(GCA)	 AG	45541-45724	AC	GAA
-recovered pasa_asmbl_45831.p1, terminal, 45541, 45724
-recovered pasa_asmbl_45831.p1, internal, 44884, 44996
-recovered pasa_asmbl_45831.p1, internal, 45082, 45236
Couldn't classify 199303, 199436
Sorry, prediction pasa_asmbl_45828.p1 fails validation.
(ATG)	 CC	198959-199121	GT	GAG
(GTC)	 AG	199303-199436	GG	TGG
-recovered pasa_asmbl_45828.p1, initial, 198959, 199121
Valid prediction for Augustus_model.g8722.t1
Valid prediction for GlimmerHMM_glimmerT_13080-T1
Valid prediction for GeneMark_model.22049_t
Valid prediction for GeneMark_model.22066_t
Valid prediction for snap_scaffold_5-snap.2292-T1
Valid prediction for snap_scaffold_5-snap.2314-T1
Valid prediction for GlimmerHMM_glimmerT_13081-T1
Valid prediction for snap_scaffold_5-snap.2303-T1
Valid prediction for snap_scaffold_5-snap.2304-T1
Valid prediction for pasa_asmbl_45835.p1
Valid prediction for snap_scaffold_5-snap.2316-T1
Valid prediction for GeneMark_model.22041_t
Valid prediction for snap_scaffold_5-snap.2313-T1
Valid prediction for GeneMark_model.22042_t
Valid prediction for GeneMark_model.22061_t
Valid prediction for GeneMark_model.22068_t
Valid prediction for GlimmerHMM_glimmerT_13071-T1
Valid prediction for GeneMark_model.22072_t
Valid prediction for GlimmerHMM_glimmerT_13077-T1
Valid prediction for snap_scaffold_5-snap.2302-T1
Valid prediction for GeneMark_model.22039_t
Valid prediction for snap_scaffold_5-snap.2300-T1
Valid prediction for GlimmerHMM_glimmerT_13075-T1
Valid prediction for GlimmerHMM_glimmerT_13084-T1
Valid prediction for GeneMark_model.22063_t
Valid prediction for Augustus_model.g8710.t1
Valid prediction for snap_scaffold_5-snap.2306-T1
Valid prediction for snap_scaffold_5-snap.2318-T1
Valid prediction for Augustus_model.g8719.t1
Valid prediction for pasa_asmbl_45827.p1
Valid prediction for snap_scaffold_5-snap.2283-T1
Valid prediction for GeneMark_model.22043_t
Valid prediction for GeneMark_model.22069_t
Valid prediction for GlimmerHMM_glimmerT_13082-T1
Valid prediction for GeneMark_model.22067_t
Couldn't classify 77676, 77807
Couldn't classify 78297, 78332
Sorry, prediction pasa_asmbl_45830.p1 fails validation.
(GGT)	 GT	77676-77807	GT	AGG
(TCC)	 AG	77987-78127	GT	AGG
(GCT)	 AG	78297-78332	CT	AGC
-recovered pasa_asmbl_45830.p1, internal, 77987, 78127
Valid prediction for snap_scaffold_5-snap.2308-T1
Valid prediction for snap_scaffold_5-snap.2319-T1
Valid prediction for GlimmerHMM_glimmerT_13065-T1
Valid prediction for GeneMark_model.22065_t
Valid prediction for Augustus_model.g8716.t1
Valid prediction for GeneMark_model.22035_t
Valid prediction for GeneMark_model.22034_t
Valid prediction for Augustus_model.g8724.t1
Valid prediction for GlimmerHMM_glimmerT_13083-T1
Valid prediction for snap_scaffold_5-snap.2301-T1
Valid prediction for snap_scaffold_5-snap.2298-T1
Valid prediction for GeneMark_model.22047_t
Valid prediction for GeneMark_model.22073_t
Valid prediction for GlimmerHMM_glimmerT_13086-T1
Valid prediction for GeneMark_model.22059_t
Valid prediction for snap_scaffold_5-snap.2317-T1
Valid prediction for snap_scaffold_5-snap.2290-T1
Valid prediction for GlimmerHMM_glimmerT_13076-T1
Valid prediction for GeneMark_model.22051_t
Couldn't classify 4142, 4293
Couldn't classify 4493, 4697
Sorry, prediction pasa_asmbl_45838.p1 fails validation.
(GGT)	 CT	4142-4293	GT	AAG
(ATG)	 AG	4493-4697	AG	AAA
Valid prediction for GlimmerHMM_glimmerT_13067-T1
Valid prediction for Augustus_model.g8721.t1
Valid prediction for snap_scaffold_5-snap.2296-T1
Valid prediction for snap_scaffold_5-snap.2321-T1
Valid prediction for snap_scaffold_5-snap.2293-T1
Valid prediction for Augustus_model.g8715.t1
Valid prediction for GeneMark_model.22056_t
Valid prediction for snap_scaffold_5-snap.2288-T1
Valid prediction for GlimmerHMM_glimmerT_13073-T1
Valid prediction for GeneMark_model.22038_t
Couldn't classify 32449, 32554
Couldn't classify 34105, 34115
Sorry, prediction pasa_asmbl_45833.p1 fails validation.
(CCA)	 CT	32449-32554	GC	AGG
(GAT)	 AG	32642-32794	GT	AGG
(GGA)	 AG	32883-33005	GT	AGG
(GTC)	 AG	33184-33450	GT	AGG
(TGG)	 AG	33626-33763	GT	AGG
(GTG)	 AG	33867-33974	GT	AGG
(GCC)	 AG	34105-34115	AC	TGA
-recovered pasa_asmbl_45833.p1, internal, 32642, 32794
-recovered pasa_asmbl_45833.p1, internal, 32883, 33005
-recovered pasa_asmbl_45833.p1, internal, 33184, 33450
-recovered pasa_asmbl_45833.p1, internal, 33626, 33763
-recovered pasa_asmbl_45833.p1, internal, 33867, 33974
Valid prediction for GlimmerHMM_glimmerT_13066-T1
Valid prediction for GlimmerHMM_glimmerT_13078-T1
Valid prediction for snap_scaffold_5-snap.2284-T1
Valid prediction for snap_scaffold_5-snap.2312-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 16610, rend_intergenic: 12643  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51580, rend_intergenic: 39125  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55652, rend_intergenic: 51580  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70401, rend_intergenic: 66715  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92731, rend_intergenic: 82128  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98072, rend_intergenic: 97502  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100016, rend_intergenic: 98727  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122930, rend_intergenic: 100289  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142013, rend_intergenic: 134418  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 215562
-exon list size: 690


building trellis

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67.6    
67.8    
67.9    
68.1    
68.2    
68.4    
68.5    
68.6    
68.8    
68.9    
69.1    
69.2    
69.4    
69.5    
69.7    
69.8    
69.9    
70.1    
70.2    
70.4    
70.5    
70.7    
70.8    
71.0    
71.1    
71.2    
71.4    
71.5    
71.7    
71.8    
72.0    
72.1    
72.3    
72.4    
72.5    
72.7    
72.8    
73.0    
73.1    
73.3    
73.4    
73.6    
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    
76.4    
76.6    
76.7    
76.9    
77.0    
77.2    
77.3    
77.5    
77.6    
77.7    
77.9    
78.0    
78.2    
78.3    
78.5    
78.6    
78.8    
78.9    
79.0    
79.2    
79.3    
79.5    
79.6    
79.8    
79.9    
80.1    
80.2    
80.3    
80.5    
80.6    
80.8    
80.9    
81.1    
81.2    
81.4    
81.5    
81.6    
81.8    
81.9    
82.1    
82.2    
82.4    
82.5    
82.7    
82.8    
82.9    
83.1    
83.2    
83.4    
83.5    
83.7    
83.8    
84.0    
84.1    
84.2    
84.4    
84.5    
84.7    
84.8    
85.0    
85.1    
85.3    
85.4    
85.5    
85.7    
85.8    
86.0    
86.1    
86.3    
86.4    
86.6    
86.7    
86.8    
87.0    
87.1    
87.3    
87.4    
87.6    
87.7    
87.9    
88.0    
88.2    
88.3    
88.4    
88.6    
88.7    
88.9    
89.0    
89.2    
89.3    
89.5    
89.6    
89.7    
89.9    
90.0    
90.2    
90.3    
90.5    
90.6    
90.8    
90.9    
91.0    
91.2    
91.3    
91.5    
91.6    
91.8    
91.9    
92.1    
92.2    
92.3    
92.5    
92.6    
92.8    
92.9    
93.1    
93.2    
93.4    
93.5    
93.6    
93.8    
93.9    
94.1    
94.2    
94.4    
94.5    
94.7    
94.8    
94.9    
95.1    
95.2    
95.4    
95.5    
95.7    
95.8    
96.0    
96.1    
96.2    
96.4    
96.5    
96.7    
96.8    
97.0    
97.1    
97.3    
97.4    
97.5    
97.7    
97.8    
98.0    
98.1    
98.3    
98.4    
98.6    
98.7    
98.8    
99.0    
99.1    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 16610, rend_intergenic: 12643  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51580, rend_intergenic: 39125  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55652, rend_intergenic: 51580  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70401, rend_intergenic: 66715  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92731, rend_intergenic: 82128  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98072, rend_intergenic: 97502  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100016, rend_intergenic: 98727  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122930, rend_intergenic: 100289  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142013, rend_intergenic: 134418  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support