-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_6/scaffold_6_16071476-16255223

-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.27782_t
Valid prediction for snap_scaffold_6-snap.3417-T1
Valid prediction for GlimmerHMM_glimmerT_16625-T1
Couldn't classify 94653, 94679
Sorry, prediction GeneMark_model.27800_t fails validation.
(ATG)	 CG	94060-94259	GT	TGG
(GAG)	 AG	94290-94412	GT	CAG
(AGC)	 AG	94437-94595	GC	GAG
(AGA)	 AG	94619-94627	GT	GAG
(AGA)	 AG	94653-94679	GT	AAG
-recovered GeneMark_model.27800_t, initial, 94060, 94259
-recovered GeneMark_model.27800_t, internal, 94290, 94412
-recovered GeneMark_model.27800_t, internal, 94437, 94595
-recovered GeneMark_model.27800_t, internal, 94619, 94627
-recovered GeneMark_model.27800_t, internal, 94653, 94679
Valid prediction for GlimmerHMM_glimmerT_16626-T1
Valid prediction for snap_scaffold_6-snap.3410-T1
Valid prediction for GeneMark_model.27787_t
Valid prediction for GeneMark_model.27812_t
Valid prediction for GeneMark_model.27785_t
Valid prediction for GeneMark_model.27809_t
Valid prediction for snap_scaffold_6-snap.3402-T1
Valid prediction for snap_scaffold_6-snap.3406-T1
Valid prediction for GlimmerHMM_glimmerT_16611-T1
Valid prediction for GeneMark_model.27798_t
Valid prediction for Augustus_model.g11194.t1
Valid prediction for Augustus_model.g11185.t1
Valid prediction for GlimmerHMM_glimmerT_16636-T1
Valid prediction for GeneMark_model.27772_t
Valid prediction for GeneMark_model.27774_t
Valid prediction for snap_scaffold_6-snap.3391-T1
Valid prediction for GlimmerHMM_glimmerT_16628-T1
Valid prediction for GeneMark_model.27816_t
Valid prediction for snap_scaffold_6-snap.3400-T1
Valid prediction for Augustus_model.g11193.t1
Valid prediction for GlimmerHMM_glimmerT_16606-T1
Valid prediction for GlimmerHMM_glimmerT_16623-T1
Valid prediction for snap_scaffold_6-snap.3408-T1
Valid prediction for GeneMark_model.27803_t
Valid prediction for snap_scaffold_6-snap.3423-T1
Valid prediction for GlimmerHMM_glimmerT_16614-T1
Valid prediction for GeneMark_model.27789_t
Valid prediction for GeneMark_model.27806_t
Couldn't classify 103391, 103480
Sorry, prediction GeneMark_model.27801_t fails validation.
(GTT)	 AG	103391-103480	GT	GAG
(AGA)	 AG	103518-103575	CA	GAC
-recovered GeneMark_model.27801_t, terminal, 103518, 103575
-recovered GeneMark_model.27801_t, internal, 103391, 103480
Valid prediction for GeneMark_model.27825_t
Valid prediction for GeneMark_model.27796_t
Valid prediction for GeneMark_model.27819_t
Valid prediction for GlimmerHMM_glimmerT_16630-T1
Valid prediction for GeneMark_model.27764_t
Valid prediction for GeneMark_model.27804_t
Valid prediction for snap_scaffold_6-snap.3415-T1
Valid prediction for GeneMark_model.27765_t
Valid prediction for GeneMark_model.27793_t
Valid prediction for GlimmerHMM_glimmerT_16631-T1
Valid prediction for snap_scaffold_6-snap.3393-T1
Valid prediction for snap_scaffold_6-snap.3409-T1
Valid prediction for GlimmerHMM_glimmerT_16607-T1
Valid prediction for GlimmerHMM_glimmerT_16605-T1
Valid prediction for GeneMark_model.27823_t
Valid prediction for GeneMark_model.27767_t
Valid prediction for GeneMark_model.27791_t
Valid prediction for Augustus_model.g11191.t1
Valid prediction for GlimmerHMM_glimmerT_16622-T1
Valid prediction for snap_scaffold_6-snap.3413-T1
Valid prediction for GeneMark_model.27769_t
Valid prediction for GlimmerHMM_glimmerT_16608-T1
Valid prediction for snap_scaffold_6-snap.3388-T1
Valid prediction for GlimmerHMM_glimmerT_16632-T1
Valid prediction for GeneMark_model.27811_t
Valid prediction for GlimmerHMM_glimmerT_16620-T1
Valid prediction for Augustus_model.g11189.t1
Valid prediction for GlimmerHMM_glimmerT_16604-T1
Valid prediction for GlimmerHMM_glimmerT_16609-T1
Valid prediction for GlimmerHMM_glimmerT_16615-T1
Valid prediction for GeneMark_model.27814_t
Valid prediction for snap_scaffold_6-snap.3419-T1
Valid prediction for GeneMark_model.27777_t
Valid prediction for Augustus_model.g11192.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 Augustus_model.g11184.t1
Valid prediction for GeneMark_model.27794_t
Valid prediction for snap_scaffold_6-snap.3418-T1
Valid prediction for GeneMark_model.27788_t
Valid prediction for snap_scaffold_6-snap.3405-T1
Valid prediction for snap_scaffold_6-snap.3397-T1
Valid prediction for GeneMark_model.27784_t
Valid prediction for snap_scaffold_6-snap.3396-T1
Valid prediction for snap_scaffold_6-snap.3398-T1
Valid prediction for GeneMark_model.27824_t
Valid prediction for GeneMark_model.27768_t
Valid prediction for GeneMark_model.27813_t
Valid prediction for GeneMark_model.27778_t
Valid prediction for GeneMark_model.27771_t
Valid prediction for GeneMark_model.27797_t
Valid prediction for GeneMark_model.27770_t
Valid prediction for GeneMark_model.27780_t
Valid prediction for GlimmerHMM_glimmerT_16619-T1
Valid prediction for snap_scaffold_6-snap.3403-T1
Valid prediction for snap_scaffold_6-snap.3420-T1
Valid prediction for GeneMark_model.27807_t
Valid prediction for GeneMark_model.27766_t
Valid prediction for GlimmerHMM_glimmerT_16627-T1
Valid prediction for GeneMark_model.27773_t
Valid prediction for snap_scaffold_6-snap.3395-T1
Valid prediction for snap_scaffold_6-snap.3394-T1
Valid prediction for GeneMark_model.27818_t
Valid prediction for snap_scaffold_6-snap.3411-T1
Valid prediction for snap_scaffold_6-snap.3401-T1
Valid prediction for GeneMark_model.27802_t
Valid prediction for GlimmerHMM_glimmerT_16612-T1
Valid prediction for GeneMark_model.27810_t
Valid prediction for snap_scaffold_6-snap.3392-T1
Valid prediction for snap_scaffold_6-snap.3424-T1
Valid prediction for GlimmerHMM_glimmerT_16616-T1
Valid prediction for GeneMark_model.27783_t
Valid prediction for GeneMark_model.27775_t
Valid prediction for GlimmerHMM_glimmerT_16621-T1
Valid prediction for GlimmerHMM_glimmerT_16610-T1
Valid prediction for Augustus_model.g11190.t1
Valid prediction for GeneMark_model.27776_t
Valid prediction for Augustus_model.g11183.t1
Valid prediction for snap_scaffold_6-snap.3414-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_6-snap.3425-T1
Valid prediction for snap_scaffold_6-snap.3404-T1
Valid prediction for GeneMark_model.27763_t
Valid prediction for GeneMark_model.27821_t
Valid prediction for GeneMark_model.27815_t
Valid prediction for GeneMark_model.27792_t
Valid prediction for GeneMark_model.27781_t
Valid prediction for GeneMark_model.27795_t
Valid prediction for GeneMark_model.27786_t
Valid prediction for GeneMark_model.27808_t
Valid prediction for GlimmerHMM_glimmerT_16618-T1
Valid prediction for snap_scaffold_6-snap.3387-T1
Valid prediction for GeneMark_model.27779_t
Valid prediction for GeneMark_model.27820_t
Couldn't classify 151279, 151848
Sorry, prediction pasa_asmbl_49039.p1 fails validation.
(ATG)	 AT	151279-151848	CT	GCC
Valid prediction for Augustus_model.g11186.t1
Valid prediction for GlimmerHMM_glimmerT_16613-T1
Valid prediction for snap_scaffold_6-snap.3399-T1
Valid prediction for GeneMark_model.27799_t
Valid prediction for GeneMark_model.27822_t
Valid prediction for snap_scaffold_6-snap.3416-T1
Valid prediction for GeneMark_model.27805_t
Valid prediction for snap_scaffold_6-snap.3426-T1
Valid prediction for GlimmerHMM_glimmerT_16635-T1
Couldn't classify 175268, 175443
Sorry, prediction pasa_asmbl_49291.p1 fails validation.
(CAG)	 CT	175268-175443	GT	ACG
(GTA)	 AG	176829-177049	GT	AGG
(GTA)	 AG	178026-178270	GT	GAG
add_exon() Sorry, pasa_asmbl_49291.p1 176829-177049-terminal-2 is invalid.
-recovered pasa_asmbl_49291.p1, terminal, 176829, 177049
-recovered pasa_asmbl_49291.p1, terminal, 178026, 178270
-recovered pasa_asmbl_49291.p1, internal, 176829, 177049
-recovered pasa_asmbl_49291.p1, internal, 178026, 178270
Valid prediction for GlimmerHMM_glimmerT_16633-T1
Valid prediction for snap_scaffold_6-snap.3421-T1
Valid prediction for snap_scaffold_6-snap.3407-T1
Valid prediction for snap_scaffold_6-snap.3389-T1
Valid prediction for snap_scaffold_6-snap.3390-T1
Valid prediction for snap_scaffold_6-snap.3412-T1
Valid prediction for GlimmerHMM_glimmerT_16634-T1
Couldn't classify 31381, 31569
Sorry, prediction GeneMark_model.27817_t fails validation.
(AGA)	 AG	31381-31569	GT	GAG
(AAG)	 AG	31594-31764	GT	GAG
(AGA)	 AG	31790-31990	GT	GAG
(AGG)	 AG	32023-32124	GT	CAG
(GAC)	 AG	32145-32198	GT	AGG
(AGG)	 AG	32228-32590	GT	AGG
(GAC)	 AG	32616-32855	GT	GAG
(AGA)	 AG	32882-33013	GT	AGG
(AGG)	 AG	33088-33441	GT	GAG
(AGG)	 AG	33472-33678	GT	AGG
(GAC)	 AG	33711-33767	GT	GAG
(AGG)	 AG	33790-33891	GC	AGG
(AGG)	 AG	33914-34210	GT	GAG
(GAC)	 AG	34243-34281	GT	AGG
(AGA)	 AG	34309-34338	GT	GAG
(AGG)	 AG	34362-34535	GT	CAG
(AAA)	 AG	34660-34803	GT	CAG
(AGA)	 AG	34829-34834	GT	ACG
(AGA)	 AG	34901-34978	GT	CTG
(AGT)	 AG	35797-35885	GT	TGG
(TGG)	 AG	36716-36824	GT	ATG
(GAG)	 AG	36851-36985	GT	GCG
(AGA)	 AG	37013-37075	GT	AGG
(AGA)	 AG	37141-37170	GT	ATG
(ACT)	 AG	37221-37229	GC	CAG
(ACA)	 AG	37255-37347	GT	GAG
(AGA)	 AG	37383-37412	GC	GAG
(AGA)	 AG	37502-37564	GT	GAG
(GAG)	 AG	37597-37756	GC	AAG
-recovered GeneMark_model.27817_t, terminal, 37597, 37756
-recovered GeneMark_model.27817_t, internal, 31381, 31569
-recovered GeneMark_model.27817_t, internal, 31594, 31764
-recovered GeneMark_model.27817_t, internal, 31790, 31990
-recovered GeneMark_model.27817_t, internal, 32023, 32124
-recovered GeneMark_model.27817_t, internal, 32145, 32198
-recovered GeneMark_model.27817_t, internal, 32228, 32590
-recovered GeneMark_model.27817_t, internal, 32616, 32855
-recovered GeneMark_model.27817_t, internal, 32882, 33013
-recovered GeneMark_model.27817_t, internal, 33088, 33441
-recovered GeneMark_model.27817_t, internal, 33472, 33678
-recovered GeneMark_model.27817_t, internal, 33711, 33767
-recovered GeneMark_model.27817_t, internal, 33790, 33891
-recovered GeneMark_model.27817_t, internal, 33914, 34210
-recovered GeneMark_model.27817_t, internal, 34243, 34281
-recovered GeneMark_model.27817_t, internal, 34309, 34338
-recovered GeneMark_model.27817_t, internal, 34362, 34535
-recovered GeneMark_model.27817_t, internal, 34660, 34803
-recovered GeneMark_model.27817_t, internal, 34829, 34834
-recovered GeneMark_model.27817_t, internal, 34901, 34978
-recovered GeneMark_model.27817_t, internal, 35797, 35885
-recovered GeneMark_model.27817_t, internal, 36716, 36824
-recovered GeneMark_model.27817_t, internal, 36851, 36985
-recovered GeneMark_model.27817_t, internal, 37013, 37075
-recovered GeneMark_model.27817_t, internal, 37141, 37170
-recovered GeneMark_model.27817_t, internal, 37221, 37229
-recovered GeneMark_model.27817_t, internal, 37255, 37347
-recovered GeneMark_model.27817_t, internal, 37383, 37412
-recovered GeneMark_model.27817_t, internal, 37502, 37564
-recovered GeneMark_model.27817_t, internal, 37597, 37756
Valid prediction for GlimmerHMM_glimmerT_16617-T1
Valid prediction for GeneMark_model.27790_t
Valid prediction for GlimmerHMM_glimmerT_16629-T1
Valid prediction for GlimmerHMM_glimmerT_16624-T1
Valid prediction for Augustus_model.g11188.t1
Valid prediction for snap_scaffold_6-snap.3422-T1
Valid prediction for Augustus_model.g11187.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10836, rend_intergenic: 9400  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16314, rend_intergenic: 11551  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19378, rend_intergenic: 16743  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25747, rend_intergenic: 23929  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53060, rend_intergenic: 47710  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57539, rend_intergenic: 53141  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62877, rend_intergenic: 58058  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76135, rend_intergenic: 72475  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92357, rend_intergenic: 78845  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113777, rend_intergenic: 92400  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118799, rend_intergenic: 118586  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139181, rend_intergenic: 136860  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147986, rend_intergenic: 144552  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172632, rend_intergenic: 165774  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176020, rend_intergenic: 173471  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 24871, rend_intergenic: 24868  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 183748
-exon list size: 792


building trellis

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57.1    
57.2    
57.3    
57.4    
57.6    
57.7    
57.8    
57.9    
58.1    
58.2    
58.3    
58.4    
58.6    
58.7    
58.8    
58.9    
59.1    
59.2    
59.3    
59.4    
59.6    
59.7    
59.8    
59.9    
60.1    
60.2    
60.3    
60.5    
60.6    
60.7    
60.8    
61.0    
61.1    
61.2    
61.3    
61.5    
61.6    
61.7    
61.8    
62.0    
62.1    
62.2    
62.3    
62.5    
62.6    
62.7    
62.8    
63.0    
63.1    
63.2    
63.4    
63.5    
63.6    
63.7    
63.9    
64.0    
64.1    
64.2    
64.4    
64.5    
64.6    
64.7    
64.9    
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 45 predictions from path traversal
Error with prediction: snap lend_intergenic: 10836, rend_intergenic: 9400  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16314, rend_intergenic: 11551  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19378, rend_intergenic: 16743  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25747, rend_intergenic: 23929  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53060, rend_intergenic: 47710  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57539, rend_intergenic: 53141  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62877, rend_intergenic: 58058  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76135, rend_intergenic: 72475  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92357, rend_intergenic: 78845  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113777, rend_intergenic: 92400  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118799, rend_intergenic: 118586  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139181, rend_intergenic: 136860  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147986, rend_intergenic: 144552  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172632, rend_intergenic: 165774  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176020, rend_intergenic: 173471  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 24871, rend_intergenic: 24868  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support