-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_6/scaffold_6_16253613-16407167

-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_6-snap.3462-T1
Valid prediction for GeneMark_model.27853_t
Valid prediction for GeneMark_model.27829_t
Valid prediction for snap_scaffold_6-snap.3449-T1
Valid prediction for GeneMark_model.27857_t
Valid prediction for GlimmerHMM_glimmerT_16649-T1
Valid prediction for GeneMark_model.27860_t
Valid prediction for GeneMark_model.27837_t
Valid prediction for snap_scaffold_6-snap.3460-T1
Valid prediction for GlimmerHMM_glimmerT_16644-T1
Valid prediction for snap_scaffold_6-snap.3454-T1
Valid prediction for snap_scaffold_6-snap.3446-T1
Valid prediction for GeneMark_model.27845_t
Valid prediction for GlimmerHMM_glimmerT_16647-T1
Valid prediction for snap_scaffold_6-snap.3450-T1
Valid prediction for snap_scaffold_6-snap.3427-T1
Valid prediction for GeneMark_model.27831_t
Valid prediction for snap_scaffold_6-snap.3440-T1
Valid prediction for GlimmerHMM_glimmerT_16641-T1
Valid prediction for GlimmerHMM_glimmerT_16657-T1
Valid prediction for snap_scaffold_6-snap.3457-T1
Valid prediction for Augustus_model.g11195.t1
Valid prediction for GlimmerHMM_glimmerT_16638-T1
Valid prediction for GeneMark_model.27833_t
Valid prediction for GeneMark_model.27859_t
Valid prediction for GeneMark_model.27850_t
Valid prediction for Augustus_model.g11202.t1
Valid prediction for GeneMark_model.27862_t
Valid prediction for GeneMark_model.27843_t
Valid prediction for snap_scaffold_6-snap.3428-T1
Valid prediction for GeneMark_model.27863_t
Valid prediction for GeneMark_model.27847_t
Valid prediction for snap_scaffold_6-snap.3441-T1
Valid prediction for GeneMark_model.27827_t
Valid prediction for snap_scaffold_6-snap.3442-T1
Couldn't classify 11988, 12056
Couldn't classify 15852, 15912
Sorry, prediction pasa_asmbl_47627.p1 fails validation.
(TAT)	 CC	11988-12056	GT	AGG
(GTG)	 AG	12419-12601	GT	CCG
(GAG)	 AG	13153-13308	GT	CTG
(ATC)	 AG	13427-13481	GT	AGG
(GCT)	 AG	13595-13644	GT	AGG
(TAC)	 AG	14073-14225	GT	AGG
(GCT)	 AG	14461-14531	GT	AGG
(GTT)	 AG	14703-14751	GT	GAG
(GCG)	 AG	14905-14990	GT	AAG
(TGA)	 AG	15256-15378	GT	AGG
(AGT)	 AG	15852-15912	GT	AGG
-recovered pasa_asmbl_47627.p1, internal, 12419, 12601
-recovered pasa_asmbl_47627.p1, internal, 13153, 13308
-recovered pasa_asmbl_47627.p1, internal, 13427, 13481
-recovered pasa_asmbl_47627.p1, internal, 13595, 13644
-recovered pasa_asmbl_47627.p1, internal, 14073, 14225
-recovered pasa_asmbl_47627.p1, internal, 14461, 14531
-recovered pasa_asmbl_47627.p1, internal, 14703, 14751
-recovered pasa_asmbl_47627.p1, internal, 14905, 14990
-recovered pasa_asmbl_47627.p1, internal, 15256, 15378
-recovered pasa_asmbl_47627.p1, internal, 15852, 15912
Valid prediction for GeneMark_model.27855_t
Valid prediction for CodingQuarry_transcript_55224-T1
Valid prediction for GeneMark_model.27841_t
Valid prediction for snap_scaffold_6-snap.3435-T1
Valid prediction for Augustus_model.g11198.t1
Valid prediction for GlimmerHMM_glimmerT_16652-T1
Valid prediction for GeneMark_model.27835_t
Valid prediction for snap_scaffold_6-snap.3455-T1
Valid prediction for GlimmerHMM_glimmerT_16654-T1
Valid prediction for snap_scaffold_6-snap.3436-T1
Valid prediction for GlimmerHMM_glimmerT_16639-T1
Valid prediction for snap_scaffold_6-snap.3443-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_6-snap.3431-T1
Valid prediction for GlimmerHMM_glimmerT_16650-T1
Couldn't classify 90696, 90874
Sorry, prediction pasa_asmbl_47631.p1 fails validation.
(GCT)	 CA	90696-90874	GT	AGG
(CTG)	 AG	92227-92320	GT	AGG
(GAG)	 AG	92585-92717	GT	CGG
(CAC)	 AG	93177-93253	AT	AGA
-recovered pasa_asmbl_47631.p1, terminal, 93177, 93253
-recovered pasa_asmbl_47631.p1, internal, 92227, 92320
-recovered pasa_asmbl_47631.p1, internal, 92585, 92717
Couldn't classify 34735, 34848
Sorry, prediction pasa_asmbl_47629.p2 fails validation.
(GAT)	 GA	34735-34848	GT	CGG
(CCT)	 AG	35326-35527	GT	AGG
(GGG)	 AG	35611-35717	AC	GAA
-recovered pasa_asmbl_47629.p2, terminal, 35611, 35717
-recovered pasa_asmbl_47629.p2, internal, 35326, 35527
Valid prediction for snap_scaffold_6-snap.3453-T1
Valid prediction for GeneMark_model.27839_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_6-snap.3448-T1
Couldn't classify 90682, 90818
Couldn't classify 91815, 92037
Sorry, prediction pasa_asmbl_49309.p1 fails validation.
(GAG)	 GG	90682-90818	GT	AAG
(GGA)	 AG	91815-92037	GT	AGG
-recovered pasa_asmbl_49309.p1, internal, 91815, 92037
Valid prediction for GlimmerHMM_glimmerT_16653-T1
Valid prediction for GeneMark_model.27846_t
Valid prediction for GlimmerHMM_glimmerT_16640-T1
Couldn't classify 28245, 28604
Sorry, prediction pasa_asmbl_49060.p3 fails validation.
(CCG)	 CC	28245-28604	CT	GAC
Valid prediction for snap_scaffold_6-snap.3433-T1
Couldn't classify 87796, 87892
Couldn't classify 88848, 88883
Sorry, prediction pasa_asmbl_49354.p2 fails validation.
(GCA)	 CT	87796-87892	GT	CGG
(TGA)	 AG	88090-88234	GT	AGG
(CCA)	 AG	88457-88595	GT	AGG
(GAC)	 AG	88848-88883	GA	AGG
-recovered pasa_asmbl_49354.p2, internal, 88090, 88234
-recovered pasa_asmbl_49354.p2, internal, 88457, 88595
Valid prediction for GeneMark_model.27852_t
Valid prediction for Augustus_model.g11196.t1
Valid prediction for GlimmerHMM_glimmerT_16658-T1
Valid prediction for CodingQuarry_transcript_55226-T1
Valid prediction for pasa_asmbl_49046.p1
Valid prediction for snap_scaffold_6-snap.3459-T1
Valid prediction for GeneMark_model.27861_t
Valid prediction for GlimmerHMM_glimmerT_16637-T1
Valid prediction for GlimmerHMM_glimmerT_16646-T1
Valid prediction for Augustus_model.g11204.t1
Couldn't classify 104961, 105143
Couldn't classify 105277, 105504
Sorry, prediction pasa_asmbl_49054.p1 fails validation.
(CAG)	 TC	104961-105143	GT	TGG
(AGC)	 AG	105277-105504	GT	AGG
-recovered pasa_asmbl_49054.p1, internal, 105277, 105504
Valid prediction for snap_scaffold_6-snap.3445-T1
Valid prediction for snap_scaffold_6-snap.3463-T1
Valid prediction for snap_scaffold_6-snap.3432-T1
Valid prediction for GeneMark_model.27840_t
Valid prediction for Augustus_model.g11201.t1
Valid prediction for GeneMark_model.27826_t
Valid prediction for Augustus_model.g11199.t1
Valid prediction for snap_scaffold_6-snap.3458-T1
Valid prediction for GeneMark_model.27851_t
Couldn't classify 93375, 93425
Couldn't classify 95539, 95558
Sorry, prediction pasa_asmbl_49056.p1 fails validation.
(GAA)	 AG	93375-93425	GT	AGG
(GCC)	 AG	93506-93644	GT	AGG
(GGA)	 AG	93786-93895	GT	AGG
(GTG)	 AG	93990-94208	GT	AGG
(GTG)	 AG	94500-94693	GT	CGG
(TTA)	 AG	95046-95218	GT	GGG
(GCC)	 AG	95539-95558	GC	CAG
-recovered pasa_asmbl_49056.p1, internal, 93375, 93425
-recovered pasa_asmbl_49056.p1, internal, 93506, 93644
-recovered pasa_asmbl_49056.p1, internal, 93786, 93895
-recovered pasa_asmbl_49056.p1, internal, 93990, 94208
-recovered pasa_asmbl_49056.p1, internal, 94500, 94693
-recovered pasa_asmbl_49056.p1, internal, 95046, 95218
-recovered pasa_asmbl_49056.p1, internal, 95539, 95558
Valid prediction for Augustus_model.g11197.t1
Valid prediction for GeneMark_model.27856_t
Valid prediction for GeneMark_model.27858_t
Valid prediction for GlimmerHMM_glimmerT_16651-T1
Valid prediction for snap_scaffold_6-snap.3437-T1
Valid prediction for GeneMark_model.27848_t
Valid prediction for snap_scaffold_6-snap.3461-T1
Valid prediction for GeneMark_model.27830_t
Valid prediction for GeneMark_model.27844_t
Valid prediction for snap_scaffold_6-snap.3447-T1
Couldn't classify 105750, 105843
Sorry, prediction pasa_asmbl_49053.p1 fails validation.
(AAC)	 AC	105750-105843	GT	GGG
(CTG)	 AG	106214-106393	GT	AGG
(CTG)	 AG	106508-106614	GT	AGG
(GTG)	 AG	106798-106875	AC	GAA
-recovered pasa_asmbl_49053.p1, terminal, 106798, 106875
-recovered pasa_asmbl_49053.p1, internal, 106214, 106393
-recovered pasa_asmbl_49053.p1, internal, 106508, 106614
Valid prediction for GlimmerHMM_glimmerT_16643-T1
Valid prediction for HiQ_model.g11206.t1
Couldn't classify 27459, 28217
Sorry, prediction pasa_asmbl_49061.p1 fails validation.
(AAG)	 TG	27459-28217	TG	CCT
Valid prediction for snap_scaffold_6-snap.3439-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GeneMark_model.27849_t
Valid prediction for GlimmerHMM_glimmerT_16656-T1
Valid prediction for GlimmerHMM_glimmerT_16648-T1
Valid prediction for HiQ_model.g11205.t1
Valid prediction for Augustus_model.g11207.t1
Valid prediction for snap_scaffold_6-snap.3434-T1
Valid prediction for snap_scaffold_6-snap.3456-T1
Valid prediction for GeneMark_model.27838_t
Valid prediction for GeneMark_model.27834_t
Valid prediction for snap_scaffold_6-snap.3452-T1
Valid prediction for CodingQuarry_transcript_55225-T1
Valid prediction for GlimmerHMM_glimmerT_16642-T1
Couldn't classify 25422, 25802
Sorry, prediction pasa_asmbl_49063.p1 fails validation.
(ATG)	 GC	25422-25802	CA	CAC
Valid prediction for GeneMark_model.27836_t
Valid prediction for snap_scaffold_6-snap.3451-T1
Couldn't classify 101341, 101613
Couldn't classify 104359, 104430
Sorry, prediction pasa_asmbl_49055.p1 fails validation.
(GGC)	 CA	101341-101613	GT	AGG
(GTG)	 AG	101953-102162	GT	AGG
(TGG)	 AG	102356-102487	GT	AGG
(GAG)	 AG	104359-104430	GC	TGG
-recovered pasa_asmbl_49055.p1, internal, 101953, 102162
-recovered pasa_asmbl_49055.p1, internal, 102356, 102487
-recovered pasa_asmbl_49055.p1, internal, 104359, 104430
Valid prediction for GlimmerHMM_glimmerT_16655-T1
Valid prediction for snap_scaffold_6-snap.3430-T1
Valid prediction for GeneMark_model.27828_t
Valid prediction for GeneMark_model.27854_t
Valid prediction for GeneMark_model.27832_t
Valid prediction for GeneMark_model.27842_t
Couldn't classify 124596, 124753
Couldn't classify 127661, 127805
Sorry, prediction pasa_asmbl_49044.p1 fails validation.
(GAG)	 AG	124596-124753	GT	AGG
(GGT)	 AG	124926-125109	GT	AGG
(GTG)	 AG	125358-125522	GT	TGG
(GTG)	 AG	125633-125756	GT	GGG
(AAA)	 AG	125986-126100	GT	AGG
(GAT)	 AG	127661-127805	GT	CGG
-recovered pasa_asmbl_49044.p1, internal, 124596, 124753
-recovered pasa_asmbl_49044.p1, internal, 124926, 125109
-recovered pasa_asmbl_49044.p1, internal, 125358, 125522
-recovered pasa_asmbl_49044.p1, internal, 125633, 125756
-recovered pasa_asmbl_49044.p1, internal, 125986, 126100
-recovered pasa_asmbl_49044.p1, internal, 127661, 127805
Valid prediction for snap_scaffold_6-snap.3438-T1
Valid prediction for GlimmerHMM_glimmerT_16645-T1
Valid prediction for Augustus_model.g11203.t1
Valid prediction for snap_scaffold_6-snap.3444-T1
Valid prediction for snap_scaffold_6-snap.3429-T1
Valid prediction for Augustus_model.g11200.t1
Valid prediction for pasa_asmbl_49064.p1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 39373, rend_intergenic: 39370  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17274, rend_intergenic: 6179  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28973, rend_intergenic: 19357  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41496, rend_intergenic: 37422  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81002, rend_intergenic: 50300  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96506, rend_intergenic: 90475  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110812, rend_intergenic: 102703  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121608, rend_intergenic: 112382  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123969, rend_intergenic: 122327  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127179, rend_intergenic: 124952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133488, rend_intergenic: 130124  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139743, rend_intergenic: 134954  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 153555
-exon list size: 725


building trellis

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66.0    
66.2    
66.3    
66.4    
66.6    
66.7    
66.9    
67.0    
67.1    
67.3    
67.4    
67.5    
67.7    
67.8    
68.0    
68.1    
68.2    
68.4    
68.5    
68.6    
68.8    
68.9    
69.1    
69.2    
69.3    
69.5    
69.6    
69.7    
69.9    
70.0    
70.2    
70.3    
70.4    
70.6    
70.7    
70.8    
71.0    
71.1    
71.3    
71.4    
71.5    
71.7    
71.8    
71.9    
72.1    
72.2    
72.4    
72.5    
72.6    
72.8    
72.9    
73.0    
73.2    
73.3    
73.5    
73.6    
73.7    
73.9    
74.0    
74.1    
74.3    
74.4    
74.6    
74.7    
74.8    
75.0    
75.1    
75.2    
75.4    
75.5    
75.7    
75.8    
75.9    
76.1    
76.2    
76.3    
76.5    
76.6    
76.8    
76.9    
77.0    
77.2    
77.3    
77.4    
77.6    
77.7    
77.9    
78.0    
78.1    
78.3    
78.4    
78.5    
78.7    
78.8    
79.0    
79.1    
79.2    
79.4    
79.5    
79.6    
79.8    
79.9    
80.1    
80.2    
80.3    
80.5    
80.6    
80.7    
80.9    
81.0    
81.2    
81.3    
81.4    
81.6    
81.7    
81.8    
82.0    
82.1    
82.3    
82.4    
82.5    
82.7    
82.8    
82.9    
83.1    
83.2    
83.4    
83.5    
83.6    
83.8    
83.9    
84.0    
84.2    
84.3    
84.5    
84.6    
84.7    
84.9    
85.0    
85.1    
85.3    
85.4    
85.6    
85.7    
85.8    
86.0    
86.1    
86.2    
86.4    
86.5    
86.7    
86.8    
86.9    
87.1    
87.2    
87.3    
87.5    
87.6    
87.8    
87.9    
88.0    
88.2    
88.3    
88.4    
88.6    
88.7    
88.9    
89.0    
89.1    
89.3    
89.4    
89.5    
89.7    
89.8    
90.0    
90.1    
90.2    
90.4    
90.5    
90.6    
90.8    
90.9    
91.1    
91.2    
91.3    
91.5    
91.6    
91.7    
91.9    
92.0    
92.2    
92.3    
92.4    
92.6    
92.7    
92.8    
93.0    
93.1    
93.3    
93.4    
93.5    
93.7    
93.8    
93.9    
94.1    
94.2    
94.4    
94.5    
94.6    
94.8    
94.9    
95.0    
95.2    
95.3    
95.5    
95.6    
95.7    
95.9    
96.0    
96.1    
96.3    
96.4    
96.6    
96.7    
96.8    
97.0    
97.1    
97.2    
97.4    
97.5    
97.7    
97.8    
97.9    
98.1    
98.2    
98.3    
98.5    
98.6    
98.8    
98.9    
99.0    
99.2    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 21 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 39373, rend_intergenic: 39370  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17274, rend_intergenic: 6179  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28973, rend_intergenic: 19357  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41496, rend_intergenic: 37422  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81002, rend_intergenic: 50300  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96506, rend_intergenic: 90475  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110812, rend_intergenic: 102703  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121608, rend_intergenic: 112382  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123969, rend_intergenic: 122327  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127179, rend_intergenic: 124952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133488, rend_intergenic: 130124  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139743, rend_intergenic: 134954  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 12 predictions persist after filtering for low support