-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_14/scaffold_14_11048982-11325988

-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 Augustus_model.g23810.t1
Valid prediction for Augustus_model.g23817.t1
Valid prediction for GeneMark_model.60766_t
Valid prediction for snap_scaffold_14-snap.2303-T1
Valid prediction for snap_scaffold_14-snap.2293-T1
Valid prediction for HiQ_model.g23820.t1
Valid prediction for snap_scaffold_14-snap.2288-T1
Valid prediction for pasa_asmbl_12348.p1
Valid prediction for GeneMark_model.60742_t
Valid prediction for GlimmerHMM_glimmerT_35398-T1
Valid prediction for GlimmerHMM_glimmerT_35413-T1
Valid prediction for GeneMark_model.60746_t
Valid prediction for GeneMark_model.60755_t
Valid prediction for snap_scaffold_14-snap.2308-T1
Valid prediction for GeneMark_model.60772_t
Valid prediction for GeneMark_model.60751_t
Valid prediction for Augustus_model.g23807.t1
Valid prediction for Augustus_model.g23815.t1
Valid prediction for Augustus_model.g23818.t1
Valid prediction for snap_scaffold_14-snap.2298-T1
Valid prediction for GlimmerHMM_glimmerT_35408-T1
Valid prediction for GeneMark_model.60754_t
Valid prediction for GlimmerHMM_glimmerT_35423-T1
Valid prediction for GlimmerHMM_glimmerT_35400-T1
Valid prediction for snap_scaffold_14-snap.2282-T1
Valid prediction for snap_scaffold_14-snap.2299-T1
Valid prediction for GeneMark_model.60739_t
Valid prediction for GlimmerHMM_glimmerT_35415-T1
Valid prediction for GlimmerHMM_glimmerT_35411-T1
Couldn't classify 78908, 79115
Sorry, prediction pasa_asmbl_12345.p1 fails validation.
(GTT)	 AG	78908-79115	GT	AGG
(GTG)	 AG	80871-81041	GT	CGG
(GAT)	 AG	81373-81462	GT	TGG
(GTG)	 AG	81666-81904	GT	AGG
(GTA)	 AG	83616-83804	GA	GAG
-recovered pasa_asmbl_12345.p1, terminal, 83616, 83804
-recovered pasa_asmbl_12345.p1, internal, 78908, 79115
-recovered pasa_asmbl_12345.p1, internal, 80871, 81041
-recovered pasa_asmbl_12345.p1, internal, 81373, 81462
-recovered pasa_asmbl_12345.p1, internal, 81666, 81904
Valid prediction for snap_scaffold_14-snap.2286-T1
Valid prediction for GeneMark_model.60744_t
Valid prediction for snap_scaffold_14-snap.2306-T1
Valid prediction for GeneMark_model.60757_t
Valid prediction for GeneMark_model.60734_t
Valid prediction for GeneMark_model.60779_t
Valid prediction for snap_scaffold_14-snap.2300-T1
Valid prediction for Augustus_model.g23809.t1
Valid prediction for GeneMark_model.60759_t
Valid prediction for GeneMark_model.60776_t
Valid prediction for Augustus_model.g23813.t1
Valid prediction for snap_scaffold_14-snap.2302-T1
Valid prediction for GlimmerHMM_glimmerT_35399-T1
Valid prediction for GlimmerHMM_glimmerT_35406-T1
Valid prediction for GeneMark_model.60735_t
Valid prediction for Augustus_model.g23816.t1
Valid prediction for GeneMark_model.60768_t
Valid prediction for GlimmerHMM_glimmerT_35401-T1
Valid prediction for pasa_asmbl_12341.p1
Valid prediction for Augustus_model.g23822.t1
Valid prediction for CodingQuarry_transcript_15779-T1
Valid prediction for GlimmerHMM_glimmerT_35410-T1
Valid prediction for snap_scaffold_14-snap.2285-T1
Valid prediction for GlimmerHMM_glimmerT_35409-T1
Valid prediction for pasa_asmbl_12344.p1
Valid prediction for snap_scaffold_14-snap.2291-T1
Valid prediction for GeneMark_model.60769_t
Valid prediction for Augustus_model.g23827.t1
Valid prediction for snap_scaffold_14-snap.2289-T1
Valid prediction for GeneMark_model.60737_t
Valid prediction for GlimmerHMM_glimmerT_35403-T1
Valid prediction for snap_scaffold_14-snap.2284-T1
Valid prediction for GlimmerHMM_glimmerT_35404-T1
Valid prediction for snap_scaffold_14-snap.2301-T1
Valid prediction for snap_scaffold_14-snap.2294-T1
Valid prediction for GeneMark_model.60750_t
Valid prediction for snap_scaffold_14-snap.2297-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: -)Couldn't classify 86841, 86904
Sorry, prediction pasa_asmbl_13443.p1 fails validation.
(CCA)	 AC	86841-86904	GT	AGG
(TCC)	 AG	87103-87162	GT	TGG
(AGA)	 AG	87301-87423	GT	AGG
(GTG)	 AG	87599-87661	GT	AGG
(GTC)	 AG	87910-87969	GT	CGG
(TGT)	 AG	88103-88174	GT	AGG
(AAT)	 AG	88286-88317	AG	GAA
-recovered pasa_asmbl_13443.p1, terminal, 88286, 88317
-recovered pasa_asmbl_13443.p1, internal, 87103, 87162
-recovered pasa_asmbl_13443.p1, internal, 87301, 87423
-recovered pasa_asmbl_13443.p1, internal, 87599, 87661
-recovered pasa_asmbl_13443.p1, internal, 87910, 87969
-recovered pasa_asmbl_13443.p1, internal, 88103, 88174
Valid prediction for snap_scaffold_14-snap.2290-T1
Valid prediction for GeneMark_model.60748_t
Valid prediction for snap_scaffold_14-snap.2287-T1
Valid prediction for GeneMark_model.60762_t
Valid prediction for GeneMark_model.60753_t
Valid prediction for snap_scaffold_14-snap.2318-T1
Valid prediction for Augustus_model.g23811.t1
Valid prediction for GlimmerHMM_glimmerT_35421-T1
Valid prediction for GeneMark_model.60740_t
Valid prediction for GeneMark_model.60738_t
Valid prediction for Augustus_model.g23821.t1
Valid prediction for HiQ_model.g23808.t1
Valid prediction for snap_scaffold_14-snap.2280-T1
Valid prediction for Augustus_model.g23828.t1
Valid prediction for Augustus_model.g23825.t1
Valid prediction for GeneMark_model.60761_t
Valid prediction for GeneMark_model.60745_t
Valid prediction for HiQ_model.g23824.t1
Valid prediction for GlimmerHMM_glimmerT_35419-T1
Couldn't classify 120267, 120270
Sorry, prediction pasa_asmbl_13435.p1 fails validation.
(CAC)	 CT	120267-120270	GT	CAG
(ATA)	 AG	120381-120427	GT	AGG
(ATG)	 AG	120547-120632	GT	TGG
(GTG)	 AG	120766-120855	GT	AGG
(GGA)	 AG	121061-121223	GT	GCG
(GGA)	 AG	121421-121618	GT	AGG
(GTA)	 AG	121809-121919	GG	GAG
-recovered pasa_asmbl_13435.p1, initial, 120547, 120632
-recovered pasa_asmbl_13435.p1, terminal, 121809, 121919
-recovered pasa_asmbl_13435.p1, internal, 120381, 120427
-recovered pasa_asmbl_13435.p1, internal, 120547, 120632
-recovered pasa_asmbl_13435.p1, internal, 120766, 120855
-recovered pasa_asmbl_13435.p1, internal, 121061, 121223
-recovered pasa_asmbl_13435.p1, internal, 121421, 121618
Valid prediction for GlimmerHMM_glimmerT_35424-T1
Valid prediction for snap_scaffold_14-snap.2311-T1
Couldn't classify 130189, 130311
Sorry, prediction pasa_asmbl_13434.p1 fails validation.
(CCC)	 CT	130189-130311	GT	TGG
(GAG)	 AG	130410-130493	GT	AGG
(GAC)	 AG	130711-130863	TC	AAT
-recovered pasa_asmbl_13434.p1, terminal, 130711, 130863
-recovered pasa_asmbl_13434.p1, internal, 130410, 130493
Valid prediction for snap_scaffold_14-snap.2312-T1
Valid prediction for GeneMark_model.60775_t
Valid prediction for snap_scaffold_14-snap.2281-T1
Valid prediction for Augustus_model.g23830.t1
Valid prediction for GeneMark_model.60774_t
Valid prediction for GlimmerHMM_glimmerT_35426-T1
Couldn't classify 111454, 111789
Sorry, prediction pasa_asmbl_13438.p1 fails validation.
(CTC)	 CG	111454-111789	GA	GAG
Valid prediction for pasa_asmbl_13430.p1
Couldn't classify 248584, 248617
Sorry, prediction pasa_asmbl_13426.p1 fails validation.
(ACA)	 AA	248584-248617	GT	TGG
(CAA)	 AG	249221-249349	GT	TGG
(CTC)	 AG	249460-249524	GT	AGG
(GAG)	 AG	249731-249789	GT	AGG
(AAT)	 AG	249920-250010	GT	AGG
(GTG)	 AG	250133-250269	GT	AAG
(GAA)	 AG	250415-250609	GT	CAG
(GCA)	 AG	250876-251022	GT	TGG
(GCA)	 AG	251200-251349	GT	AGG
(GTA)	 AG	251465-251525	GT	AGG
(GAG)	 AG	251638-251780	GT	AGG
(GAT)	 AG	252225-252393	GA	AAG
add_exon() Sorry, pasa_asmbl_13426.p1 250133-250269-terminal-2 is invalid.
-recovered pasa_asmbl_13426.p1, terminal, 250133, 250269
add_exon() Sorry, pasa_asmbl_13426.p1 251638-251780-terminal-2 is invalid.
-recovered pasa_asmbl_13426.p1, terminal, 251638, 251780
-recovered pasa_asmbl_13426.p1, terminal, 252225, 252393
-recovered pasa_asmbl_13426.p1, internal, 249221, 249349
-recovered pasa_asmbl_13426.p1, internal, 249460, 249524
-recovered pasa_asmbl_13426.p1, internal, 249731, 249789
-recovered pasa_asmbl_13426.p1, internal, 249920, 250010
-recovered pasa_asmbl_13426.p1, internal, 250133, 250269
-recovered pasa_asmbl_13426.p1, internal, 250415, 250609
-recovered pasa_asmbl_13426.p1, internal, 250876, 251022
-recovered pasa_asmbl_13426.p1, internal, 251200, 251349
-recovered pasa_asmbl_13426.p1, internal, 251465, 251525
-recovered pasa_asmbl_13426.p1, internal, 251638, 251780
Couldn't classify 76895, 77063
Sorry, prediction pasa_asmbl_13444.p1 fails validation.
(AAG)	 AC	76895-77063	GT	AGG
(TAG)	 AG	78127-78558	GT	TGG
(GTT)	 AG	78702-78895	GT	AGG
(CAC)	 AG	79221-79319	GT	CGG
(ACC)	 AG	80702-80932	CT	AGC
-recovered pasa_asmbl_13444.p1, terminal, 80702, 80932
-recovered pasa_asmbl_13444.p1, internal, 78127, 78558
-recovered pasa_asmbl_13444.p1, internal, 78702, 78895
-recovered pasa_asmbl_13444.p1, internal, 79221, 79319
Valid prediction for snap_scaffold_14-snap.2313-T1
Valid prediction for CodingQuarry_transcript_15780-T1
Valid prediction for GeneMark_model.60760_t
Valid prediction for snap_scaffold_14-snap.2316-T1
Valid prediction for HiQ_model.g23829.t1
Valid prediction for GeneMark_model.60758_t
Valid prediction for snap_scaffold_14-snap.2307-T1
Valid prediction for GlimmerHMM_glimmerT_35420-T1
Valid prediction for GlimmerHMM_glimmerT_35405-T1
Valid prediction for GlimmerHMM_glimmerT_35427-T1
Valid prediction for snap_scaffold_14-snap.2296-T1
Valid prediction for GeneMark_model.60743_t
Valid prediction for snap_scaffold_14-snap.2317-T1
Valid prediction for GlimmerHMM_glimmerT_35425-T1
Valid prediction for GlimmerHMM_glimmerT_35418-T1
Valid prediction for Augustus_model.g23832.t1
Valid prediction for GlimmerHMM_glimmerT_35414-T1
Valid prediction for Augustus_model.g23814.t1
Valid prediction for pasa_asmbl_13451.p1
Valid prediction for GeneMark_model.60778_t
Valid prediction for GeneMark_model.60773_t
Valid prediction for pasa_asmbl_13440.p1
Valid prediction for snap_scaffold_14-snap.2279-T1
Valid prediction for GeneMark_model.60777_t
Valid prediction for snap_scaffold_14-snap.2309-T1
Valid prediction for GeneMark_model.60756_t
Valid prediction for GlimmerHMM_glimmerT_35407-T1
Valid prediction for GeneMark_model.60733_t
Valid prediction for Augustus_model.g23812.t1
Valid prediction for GeneMark_model.60752_t
Valid prediction for Augustus_model.g23819.t1
Valid prediction for snap_scaffold_14-snap.2295-T1
Valid prediction for snap_scaffold_14-snap.2283-T1
Valid prediction for GeneMark_model.60741_t
Valid prediction for snap_scaffold_14-snap.2292-T1
Valid prediction for GlimmerHMM_glimmerT_35402-T1
Valid prediction for CodingQuarry_transcript_15776-T1
Couldn't classify 59922, 60272
Sorry, prediction pasa_asmbl_13449.p1 fails validation.
(GGA)	 CA	59922-60272	CC	GAC
Valid prediction for snap_scaffold_14-snap.2315-T1
Valid prediction for snap_scaffold_14-snap.2314-T1
Valid prediction for Augustus_model.g23826.t1
Couldn't classify 88822, 88904
Sorry, prediction pasa_asmbl_13441.p1 fails validation.
(CTC)	 TT	88822-88904	GT	CGG
(TGA)	 AG	90026-90114	GT	CGG
(ATG)	 AG	90485-90609	GT	AGG
(GGG)	 AG	90770-90883	GT	AGG
(CAT)	 AG	91075-91149	GT	AGG
(GTG)	 AG	91294-91412	GT	AGG
(TGA)	 AG	91586-91739	GT	GAG
(AAT)	 AG	91888-92052	GT	AGG
(CTG)	 AG	92298-92389	GT	TGG
(TTA)	 AG	92563-92636	GT	AGG
(AAC)	 AG	93052-93198	GT	AGG
(ACC)	 AG	93528-93680	GT	AGG
(ATT)	 AG	93935-94009	GT	AAG
(ACT)	 AG	94171-94208	AC	AAA
add_exon() Sorry, pasa_asmbl_13441.p1 90485-90609-initial-1 is invalid.
-recovered pasa_asmbl_13441.p1, initial, 90485, 90609
-recovered pasa_asmbl_13441.p1, terminal, 94171, 94208
-recovered pasa_asmbl_13441.p1, internal, 90026, 90114
-recovered pasa_asmbl_13441.p1, internal, 90485, 90609
-recovered pasa_asmbl_13441.p1, internal, 90770, 90883
-recovered pasa_asmbl_13441.p1, internal, 91075, 91149
-recovered pasa_asmbl_13441.p1, internal, 91294, 91412
-recovered pasa_asmbl_13441.p1, internal, 91586, 91739
-recovered pasa_asmbl_13441.p1, internal, 91888, 92052
-recovered pasa_asmbl_13441.p1, internal, 92298, 92389
-recovered pasa_asmbl_13441.p1, internal, 92563, 92636
-recovered pasa_asmbl_13441.p1, internal, 93052, 93198
-recovered pasa_asmbl_13441.p1, internal, 93528, 93680
-recovered pasa_asmbl_13441.p1, internal, 93935, 94009
Valid prediction for snap_scaffold_14-snap.2305-T1
Valid prediction for GlimmerHMM_glimmerT_35412-T1
Valid prediction for snap_scaffold_14-snap.2304-T1
Valid prediction for GeneMark_model.60763_t
Valid prediction for Augustus_model.g23823.t1
Valid prediction for Augustus_model.g23831.t1
Valid prediction for CodingQuarry_transcript_15774-T1
Valid prediction for CodingQuarry_transcript_15781-T1
Valid prediction for CodingQuarry_transcript_15778-T1
Valid prediction for GlimmerHMM_glimmerT_35422-T1
Valid prediction for GeneMark_model.60770_t
Valid prediction for GlimmerHMM_glimmerT_35416-T1
Valid prediction for GeneMark_model.60764_t
Valid prediction for GeneMark_model.60765_t
Valid prediction for snap_scaffold_14-snap.2310-T1
Valid prediction for GlimmerHMM_glimmerT_35417-T1
Valid prediction for GeneMark_model.60736_t
Valid prediction for Augustus_model.g23806.t1
Valid prediction for CodingQuarry_transcript_15775-T1
Valid prediction for GeneMark_model.60767_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 20688, rend_intergenic: 15496  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142406, rend_intergenic: 127817  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 277007
-exon list size: 636


building trellis

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62.9    
63.0    
63.2    
63.3    
63.5    
63.6    
63.8    
63.9    
64.1    
64.3    
64.4    
64.6    
64.7    
64.9    
65.0    
65.2    
65.4    
65.5    
65.7    
65.8    
66.0    
66.1    
66.3    
66.5    
66.6    
66.8    
66.9    
67.1    
67.2    
67.4    
67.6    
67.7    
67.9    
68.0    
68.2    
68.3    
68.5    
68.7    
68.8    
69.0    
69.1    
69.3    
69.4    
69.6    
69.7    
69.9    
70.1    
70.2    
70.4    
70.5    
70.7    
70.8    
71.0    
71.2    
71.3    
71.5    
71.6    
71.8    
71.9    
72.1    
72.3    
72.4    
72.6    
72.7    
72.9    
73.0    
73.2    
73.4    
73.5    
73.7    
73.8    
74.0    
74.1    
74.3    
74.5    
74.6    
74.8    
74.9    
75.1    
75.2    
75.4    
75.5    
75.7    
75.9    
76.0    
76.2    
76.3    
76.5    
76.6    
76.8    
77.0    
77.1    
77.3    
77.4    
77.6    
77.7    
77.9    
78.1    
78.2    
78.4    
78.5    
78.7    
78.8    
79.0    
79.2    
79.3    
79.5    
79.6    
79.8    
79.9    
80.1    
80.3    
80.4    
80.6    
80.7    
80.9    
81.0    
81.2    
81.3    
81.5    
81.7    
81.8    
82.0    
82.1    
82.3    
82.4    
82.6    
82.8    
82.9    
83.1    
83.2    
83.4    
83.5    
83.7    
83.9    
84.0    
84.2    
84.3    
84.5    
84.6    
84.8    
85.0    
85.1    
85.3    
85.4    
85.6    
85.7    
85.9    
86.1    
86.2    
86.4    
86.5    
86.7    
86.8    
87.0    
87.1    
87.3    
87.5    
87.6    
87.8    
87.9    
88.1    
88.2    
88.4    
88.6    
88.7    
88.9    
89.0    
89.2    
89.3    
89.5    
89.7    
89.8    
90.0    
90.1    
90.3    
90.4    
90.6    
90.8    
90.9    
91.1    
91.2    
91.4    
91.5    
91.7    
91.8    
92.0    
92.2    
92.3    
92.5    
92.6    
92.8    
92.9    
93.1    
93.3    
93.4    
93.6    
93.7    
93.9    
94.0    
94.2    
94.4    
94.5    
94.7    
94.8    
95.0    
95.1    
95.3    
95.5    
95.6    
95.8    
95.9    
96.1    
96.2    
96.4    
96.6    
96.7    
96.9    
97.0    
97.2    
97.3    
97.5    
97.6    
97.8    
98.0    
98.1    
98.3    
98.4    
98.6    
98.7    
98.9    
99.1    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 20688, rend_intergenic: 15496  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142406, rend_intergenic: 127817  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 31 predictions persist after filtering for low support