-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_14/scaffold_14_10008646-10274626

-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 GeneMark_model.60552_t
Valid prediction for snap_scaffold_14-snap.2119-T1
Valid prediction for snap_scaffold_14-snap.2079-T1
Valid prediction for GeneMark_model.60498_t
Valid prediction for snap_scaffold_14-snap.2110-T1
Valid prediction for snap_scaffold_14-snap.2104-T1
Valid prediction for GlimmerHMM_glimmerT_35272-T1
Valid prediction for snap_scaffold_14-snap.2078-T1
Valid prediction for GlimmerHMM_glimmerT_35265-T1
Valid prediction for snap_scaffold_14-snap.2123-T1
Valid prediction for Augustus_model.g23721.t1
Valid prediction for snap_scaffold_14-snap.2081-T1
Valid prediction for snap_scaffold_14-snap.2099-T1
Valid prediction for GeneMark_model.60520_t
Valid prediction for snap_scaffold_14-snap.2114-T1
Valid prediction for GeneMark_model.60563_t
Valid prediction for snap_scaffold_14-snap.2125-T1
Valid prediction for GeneMark_model.60501_t
Valid prediction for GeneMark_model.60549_t
Valid prediction for GlimmerHMM_glimmerT_35267-T1
Valid prediction for GeneMark_model.60559_t
Valid prediction for GeneMark_model.60543_t
Valid prediction for GeneMark_model.60554_t
Valid prediction for Augustus_model.g23723.t1
Valid prediction for GlimmerHMM_glimmerT_35288-T1
Valid prediction for GeneMark_model.60558_t
Valid prediction for GlimmerHMM_glimmerT_35263-T1
Valid prediction for GlimmerHMM_glimmerT_35283-T1
Valid prediction for Augustus_model.g23719.t1
Valid prediction for GeneMark_model.60508_t
Valid prediction for GlimmerHMM_glimmerT_35279-T1
Valid prediction for snap_scaffold_14-snap.2128-T1
Valid prediction for Augustus_model.g23715.t1
Valid prediction for GeneMark_model.60516_t
Valid prediction for snap_scaffold_14-snap.2106-T1
Valid prediction for snap_scaffold_14-snap.2129-T1
Valid prediction for GeneMark_model.60556_t
Valid prediction for Augustus_model.g23718.t1
Valid prediction for GeneMark_model.60533_t
Valid prediction for Augustus_model.g23724.t1
Valid prediction for GeneMark_model.60561_t
Valid prediction for snap_scaffold_14-snap.2083-T1
Valid prediction for GeneMark_model.60526_t
Valid prediction for snap_scaffold_14-snap.2122-T1
Valid prediction for GeneMark_model.60544_t
Valid prediction for GeneMark_model.60504_t
Valid prediction for GeneMark_model.60496_t
Valid prediction for GeneMark_model.60502_t
Valid prediction for GeneMark_model.60514_t
Valid prediction for Augustus_model.g23717.t1
Couldn't classify 35182, 35541
Sorry, prediction pasa_asmbl_12292.p1 fails validation.
(ATG)	 CA	35182-35541	CA	GCC
Valid prediction for snap_scaffold_14-snap.2131-T1
Valid prediction for GeneMark_model.60521_t
Valid prediction for GeneMark_model.60538_t
Valid prediction for GeneMark_model.60518_t
Valid prediction for snap_scaffold_14-snap.2088-T1
Valid prediction for GeneMark_model.60506_t
Valid prediction for GeneMark_model.60528_t
Valid prediction for GlimmerHMM_glimmerT_35261-T1
Valid prediction for snap_scaffold_14-snap.2080-T1
Valid prediction for GeneMark_model.60531_t
Valid prediction for Augustus_model.g23728.t1
Valid prediction for Augustus_model.g23726.t1
Valid prediction for snap_scaffold_14-snap.2117-T1
Valid prediction for snap_scaffold_14-snap.2094-T1
Valid prediction for GlimmerHMM_glimmerT_35277-T1
Valid prediction for snap_scaffold_14-snap.2130-T1
Valid prediction for GlimmerHMM_glimmerT_35281-T1
Valid prediction for GeneMark_model.60540_t
Valid prediction for GeneMark_model.60536_t
Valid prediction for GeneMark_model.60525_t
Valid prediction for GeneMark_model.60523_t
Valid prediction for snap_scaffold_14-snap.2089-T1
Valid prediction for GeneMark_model.60513_t
Valid prediction for GeneMark_model.60565_t
Valid prediction for GeneMark_model.60564_t
Valid prediction for GeneMark_model.60509_t
Valid prediction for snap_scaffold_14-snap.2103-T1
Valid prediction for snap_scaffold_14-snap.2115-T1
Valid prediction for Augustus_model.g23727.t1
Valid prediction for GeneMark_model.60547_t
Valid prediction for GlimmerHMM_glimmerT_35269-T1
Valid prediction for snap_scaffold_14-snap.2120-T1
Valid prediction for snap_scaffold_14-snap.2127-T1
Valid prediction for snap_scaffold_14-snap.2112-T1
Valid prediction for GlimmerHMM_glimmerT_35271-T1
Valid prediction for Augustus_model.g23725.t1
Valid prediction for Augustus_model.g23720.t1
Valid prediction for GeneMark_model.60529_t
Valid prediction for snap_scaffold_14-snap.2091-T1
Couldn't classify 38213, 38471
Sorry, prediction pasa_asmbl_12726.p1 fails validation.
(GAG)	 AG	38213-38471	GT	AGG
(ATG)	 AG	38566-38687	GT	AGG
(TCT)	 AG	40117-40212	GT	CGG
(GCC)	 AG	40968-41129	GT	AGG
(CTG)	 AG	41985-42121	GT	AGG
(TGT)	 AG	43252-43363	GT	CGG
(AAC)	 AG	43473-43703	GT	CGG
(ACA)	 AG	44510-44621	GT	AGG
(TGA)	 AG	44866-44963	GT	GCG
(GTG)	 AG	45554-45630	GT	AAG
(GGC)	 AG	46736-46908	GT	CGG
(AGT)	 AG	47103-47218	GT	TGG
(GGT)	 AG	47333-47494	GT	AGG
(CTC)	 AG	47673-47886	GT	GGG
(CCC)	 AG	48059-48147	GT	CGG
(ACG)	 AG	48279-48374	GT	CGG
(TGT)	 AG	48587-48652	AG	GAA
-recovered pasa_asmbl_12726.p1, initial, 38566, 38687
add_exon() Sorry, pasa_asmbl_12726.p1 41985-42121-terminal-2 is invalid.
-recovered pasa_asmbl_12726.p1, terminal, 41985, 42121
-recovered pasa_asmbl_12726.p1, terminal, 48587, 48652
-recovered pasa_asmbl_12726.p1, internal, 38213, 38471
-recovered pasa_asmbl_12726.p1, internal, 38566, 38687
-recovered pasa_asmbl_12726.p1, internal, 40117, 40212
-recovered pasa_asmbl_12726.p1, internal, 40968, 41129
-recovered pasa_asmbl_12726.p1, internal, 41985, 42121
-recovered pasa_asmbl_12726.p1, internal, 43252, 43363
-recovered pasa_asmbl_12726.p1, internal, 43473, 43703
-recovered pasa_asmbl_12726.p1, internal, 44510, 44621
-recovered pasa_asmbl_12726.p1, internal, 44866, 44963
-recovered pasa_asmbl_12726.p1, internal, 45554, 45630
-recovered pasa_asmbl_12726.p1, internal, 46736, 46908
-recovered pasa_asmbl_12726.p1, internal, 47103, 47218
-recovered pasa_asmbl_12726.p1, internal, 47333, 47494
-recovered pasa_asmbl_12726.p1, internal, 47673, 47886
-recovered pasa_asmbl_12726.p1, internal, 48059, 48147
-recovered pasa_asmbl_12726.p1, internal, 48279, 48374
Valid prediction for snap_scaffold_14-snap.2097-T1
Valid prediction for snap_scaffold_14-snap.2101-T1
Valid prediction for GlimmerHMM_glimmerT_35287-T1
Valid prediction for GeneMark_model.60535_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.60542_t
Valid prediction for GeneMark_model.60539_t
Valid prediction for snap_scaffold_14-snap.2093-T1
Valid prediction for GlimmerHMM_glimmerT_35278-T1
Valid prediction for GeneMark_model.60555_t
Valid prediction for GlimmerHMM_glimmerT_35273-T1
Valid prediction for HiQ_model.g23713.t1
Valid prediction for snap_scaffold_14-snap.2105-T1
Valid prediction for GlimmerHMM_glimmerT_35266-T1
Valid prediction for GlimmerHMM_glimmerT_35282-T1
Valid prediction for GeneMark_model.60530_t
Valid prediction for GeneMark_model.60511_t
Valid prediction for Augustus_model.g23722.t1
Valid prediction for GeneMark_model.60534_t
Valid prediction for GeneMark_model.60546_t
Valid prediction for Augustus_model.g23714.t1
Valid prediction for GeneMark_model.60551_t
Valid prediction for GlimmerHMM_glimmerT_35284-T1
Valid prediction for GeneMark_model.60562_t
Valid prediction for snap_scaffold_14-snap.2118-T1
Valid prediction for snap_scaffold_14-snap.2095-T1
Valid prediction for GeneMark_model.60548_t
Valid prediction for GeneMark_model.60519_t
Valid prediction for GlimmerHMM_glimmerT_35274-T1
Valid prediction for GeneMark_model.60545_t
Valid prediction for snap_scaffold_14-snap.2086-T1
Valid prediction for GeneMark_model.60497_t
Valid prediction for GeneMark_model.60505_t
Valid prediction for GlimmerHMM_glimmerT_35268-T1
Valid prediction for snap_scaffold_14-snap.2092-T1
Valid prediction for GlimmerHMM_glimmerT_35286-T1
Valid prediction for GeneMark_model.60553_t
Valid prediction for GeneMark_model.60512_t
Valid prediction for Augustus_model.g23716.t1
Valid prediction for GeneMark_model.60537_t
Valid prediction for CodingQuarry_transcript_15757-T1
Couldn't classify 264326, 264787
Sorry, prediction pasa_asmbl_13386.p1 fails validation.
(ATG)	 TT	264326-264787	AT	GTA
Valid prediction for CodingQuarry_transcript_15758-T1
Valid prediction for snap_scaffold_14-snap.2111-T1
Valid prediction for GeneMark_model.60522_t
Valid prediction for GeneMark_model.60503_t
Valid prediction for GlimmerHMM_glimmerT_35275-T1
Valid prediction for snap_scaffold_14-snap.2085-T1
Valid prediction for GeneMark_model.60500_t
Valid prediction for GlimmerHMM_glimmerT_35280-T1
Valid prediction for snap_scaffold_14-snap.2113-T1
Valid prediction for GlimmerHMM_glimmerT_35276-T1
Valid prediction for GeneMark_model.60560_t
Valid prediction for pasa_asmbl_13387.p1
Valid prediction for GeneMark_model.60541_t
Valid prediction for snap_scaffold_14-snap.2109-T1
Valid prediction for GeneMark_model.60515_t
Valid prediction for GeneMark_model.60524_t
Valid prediction for CodingQuarry_transcript_15756-T1
Valid prediction for snap_scaffold_14-snap.2090-T1
Valid prediction for GeneMark_model.60507_t
Valid prediction for snap_scaffold_14-snap.2100-T1
Valid prediction for snap_scaffold_14-snap.2098-T1
Valid prediction for GlimmerHMM_glimmerT_35260-T1
Valid prediction for GlimmerHMM_glimmerT_35264-T1
Valid prediction for snap_scaffold_14-snap.2096-T1
Valid prediction for snap_scaffold_14-snap.2121-T1
Valid prediction for GeneMark_model.60532_t
Valid prediction for snap_scaffold_14-snap.2126-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_35270-T1
Valid prediction for GeneMark_model.60499_t
Valid prediction for GeneMark_model.60517_t
Valid prediction for GeneMark_model.60510_t
Valid prediction for snap_scaffold_14-snap.2102-T1
Valid prediction for snap_scaffold_14-snap.2084-T1
Valid prediction for snap_scaffold_14-snap.2087-T1
Valid prediction for snap_scaffold_14-snap.2082-T1
Valid prediction for GeneMark_model.60495_t
Valid prediction for snap_scaffold_14-snap.2124-T1
Valid prediction for snap_scaffold_14-snap.2108-T1
Valid prediction for GeneMark_model.60557_t
Valid prediction for snap_scaffold_14-snap.2107-T1
Valid prediction for snap_scaffold_14-snap.2077-T1
Valid prediction for GeneMark_model.60550_t
Valid prediction for GlimmerHMM_glimmerT_35262-T1
Valid prediction for snap_scaffold_14-snap.2116-T1
Valid prediction for GlimmerHMM_glimmerT_35285-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 21503, rend_intergenic: 9539  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26785, rend_intergenic: 25710  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49478, rend_intergenic: 37230  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60766, rend_intergenic: 58392  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61529, rend_intergenic: 61206  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69971, rend_intergenic: 61607  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75722, rend_intergenic: 73436  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96306, rend_intergenic: 91029  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100829, rend_intergenic: 96423  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111682, rend_intergenic: 102052  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126389, rend_intergenic: 113966  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147262, rend_intergenic: 140083  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180516, rend_intergenic: 179301  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187779, rend_intergenic: 182753  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204770, rend_intergenic: 198949  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 210509, rend_intergenic: 206110  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 243914, rend_intergenic: 236952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 265981
-exon list size: 792


building trellis

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65.0    
65.1    
65.2    
65.4    
65.5    
65.6    
65.7    
65.9    
66.0    
66.1    
66.2    
66.4    
66.5    
66.6    
66.8    
66.9    
67.0    
67.1    
67.3    
67.4    
67.5    
67.6    
67.8    
67.9    
68.0    
68.1    
68.3    
68.4    
68.5    
68.6    
68.8    
68.9    
69.0    
69.1    
69.3    
69.4    
69.5    
69.6    
69.8    
69.9    
70.0    
70.2    
70.3    
70.4    
70.5    
70.7    
70.8    
70.9    
71.0    
71.2    
71.3    
71.4    
71.5    
71.7    
71.8    
71.9    
72.0    
72.2    
72.3    
72.4    
72.5    
72.7    
72.8    
72.9    
73.0    
73.2    
73.3    
73.4    
73.6    
73.7    
73.8    
73.9    
74.1    
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    
75.9    
76.1    
76.2    
76.3    
76.4    
76.6    
76.7    
76.8    
77.0    
77.1    
77.2    
77.3    
77.5    
77.6    
77.7    
77.8    
78.0    
78.1    
78.2    
78.3    
78.5    
78.6    
78.7    
78.8    
79.0    
79.1    
79.2    
79.3    
79.5    
79.6    
79.7    
79.8    
80.0    
80.1    
80.2    
80.4    
80.5    
80.6    
80.7    
80.9    
81.0    
81.1    
81.2    
81.4    
81.5    
81.6    
81.7    
81.9    
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    
84.6    
84.8    
84.9    
85.0    
85.1    
85.3    
85.4    
85.5    
85.6    
85.8    
85.9    
86.0    
86.1    
86.3    
86.4    
86.5    
86.6    
86.8    
86.9    
87.0    
87.2    
87.3    
87.4    
87.5    
87.7    
87.8    
87.9    
88.0    
88.2    
88.3    
88.4    
88.5    
88.7    
88.8    
88.9    
89.0    
89.2    
89.3    
89.4    
89.5    
89.7    
89.8    
89.9    
90.1    
90.2    
90.3    
90.4    
90.6    
90.7    
90.8    
90.9    
91.1    
91.2    
91.3    
91.4    
91.6    
91.7    
91.8    
91.9    
92.1    
92.2    
92.3    
92.4    
92.6    
92.7    
92.8    
92.9    
93.1    
93.2    
93.3    
93.5    
93.6    
93.7    
93.8    
94.0    
94.1    
94.2    
94.3    
94.5    
94.6    
94.7    
94.8    
95.0    
95.1    
95.2    
95.3    
95.5    
95.6    
95.7    
95.8    
96.0    
96.1    
96.2    
96.3    
96.5    
96.6    
96.7    
96.9    
97.0    
97.1    
97.2    
97.4    
97.5    
97.6    
97.7    
97.9    
98.0    
98.1    
98.2    
98.4    
98.5    
98.6    
98.7    
98.9    
99.0    
99.1    
99.2    
99.4    
99.5    
99.6    
99.7    
99.9    
-found 49 predictions from path traversal
Error with prediction: snap lend_intergenic: 21503, rend_intergenic: 9539  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26785, rend_intergenic: 25710  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49478, rend_intergenic: 37230  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60766, rend_intergenic: 58392  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61529, rend_intergenic: 61206  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69971, rend_intergenic: 61607  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75722, rend_intergenic: 73436  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96306, rend_intergenic: 91029  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100829, rend_intergenic: 96423  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111682, rend_intergenic: 102052  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126389, rend_intergenic: 113966  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147262, rend_intergenic: 140083  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180516, rend_intergenic: 179301  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187779, rend_intergenic: 182753  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204770, rend_intergenic: 198949  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 210509, rend_intergenic: 206110  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 243914, rend_intergenic: 236952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

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