-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_2/scaffold_2_17900119-18096426

-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_5584-T1
Valid prediction for GlimmerHMM_glimmerT_5600-T1
Couldn't classify 146120, 147050
Sorry, prediction pasa_asmbl_25255.p1 fails validation.
(AGC)	 AA	146120-147050	GT	AGG
(GGA)	 AG	147352-147407	CA	AAC
-recovered pasa_asmbl_25255.p1, terminal, 147352, 147407
Valid prediction for HiQ_model.g3795.t1
Couldn't classify 21778, 22085
Couldn't classify 23494, 23510
Sorry, prediction pasa_asmbl_25238.p1 fails validation.
(CCC)	 CC	21778-22085	GT	AGG
(CCC)	 AG	22394-22611	GT	AGG
(GAG)	 AG	22945-23088	GT	GGG
(GTG)	 AG	23494-23510	CA	GGC
-recovered pasa_asmbl_25238.p1, internal, 22394, 22611
-recovered pasa_asmbl_25238.p1, internal, 22945, 23088
Valid prediction for GeneMark_model.9012_t
Couldn't classify 6127, 6183
Couldn't classify 7321, 7332
Sorry, prediction pasa_asmbl_25233.p1 fails validation.
(AGC)	 AG	6127-6183	GT	GGG
(GCA)	 AG	6814-6938	GT	CAG
(GGA)	 AG	7067-7169	GT	TCG
(ACC)	 AG	7321-7332	AA	GGA
-recovered pasa_asmbl_25233.p1, internal, 6127, 6183
-recovered pasa_asmbl_25233.p1, internal, 6814, 6938
-recovered pasa_asmbl_25233.p1, internal, 7067, 7169
Couldn't classify 13897, 13953
Couldn't classify 17317, 17333
Sorry, prediction pasa_asmbl_25234.p1 fails validation.
(CTG)	 TG	13897-13953	GT	GGG
(GTA)	 AG	14937-15045	GT	TGG
(TGT)	 AG	15406-15625	GT	AGG
(AGC)	 AG	16135-16319	GT	GGG
(CCG)	 AG	16450-16545	GT	CAG
(AGA)	 AG	16632-16714	GT	GAG
(GAC)	 AG	16876-17086	GT	CAG
(CCA)	 AG	17317-17333	AA	ACA
-recovered pasa_asmbl_25234.p1, internal, 14937, 15045
-recovered pasa_asmbl_25234.p1, internal, 15406, 15625
-recovered pasa_asmbl_25234.p1, internal, 16135, 16319
-recovered pasa_asmbl_25234.p1, internal, 16450, 16545
-recovered pasa_asmbl_25234.p1, internal, 16632, 16714
-recovered pasa_asmbl_25234.p1, internal, 16876, 17086
Valid prediction for GeneMark_model.8990_t
Valid prediction for snap_scaffold_2-snap.3518-T1
Couldn't classify 84003, 84030
Sorry, prediction pasa_asmbl_25250.p1 fails validation.
(GTT)	 CA	84003-84030	GT	GGG
(ATG)	 AG	84151-84239	GT	AGG
(GAC)	 AG	84775-84826	GT	AGG
(TTT)	 AG	84934-85031	GT	GGG
(TTA)	 AG	85161-85275	GT	TGG
(GTA)	 AG	85391-85552	GT	GCG
(TGG)	 AG	85663-85736	GT	AGG
(CAA)	 AG	85826-85957	CA	AAC
add_exon() Sorry, pasa_asmbl_25250.p1 84151-84239-initial-1 is invalid.
-recovered pasa_asmbl_25250.p1, initial, 84151, 84239
-recovered pasa_asmbl_25250.p1, terminal, 85826, 85957
-recovered pasa_asmbl_25250.p1, internal, 84151, 84239
-recovered pasa_asmbl_25250.p1, internal, 84775, 84826
-recovered pasa_asmbl_25250.p1, internal, 84934, 85031
-recovered pasa_asmbl_25250.p1, internal, 85161, 85275
-recovered pasa_asmbl_25250.p1, internal, 85391, 85552
-recovered pasa_asmbl_25250.p1, internal, 85663, 85736
Valid prediction for GlimmerHMM_glimmerT_5607-T1
Valid prediction for GeneMark_model.8978_t
Valid prediction for HiQ_model.g3796.t1
Valid prediction for GlimmerHMM_glimmerT_5597-T1
Valid prediction for pasa_asmbl_25247.p1
Valid prediction for snap_scaffold_2-snap.3540-T1
Valid prediction for GeneMark_model.8994_t
Valid prediction for GeneMark_model.8981_t
Valid prediction for snap_scaffold_2-snap.3526-T1
Valid prediction for GlimmerHMM_glimmerT_5613-T1
Valid prediction for GeneMark_model.9019_t
Valid prediction for snap_scaffold_2-snap.3531-T1
Valid prediction for GeneMark_model.9021_t
Valid prediction for GeneMark_model.8992_t
Valid prediction for GeneMark_model.9004_t
Valid prediction for GeneMark_model.8998_t
Valid prediction for GeneMark_model.9026_t
Valid prediction for GeneMark_model.9023_t
Valid prediction for snap_scaffold_2-snap.3530-T1
Valid prediction for GeneMark_model.9008_t
Valid prediction for GeneMark_model.8985_t
Valid prediction for snap_scaffold_2-snap.3517-T1
Valid prediction for GlimmerHMM_glimmerT_5594-T1
Valid prediction for CodingQuarry_transcript_28784-T1
Valid prediction for snap_scaffold_2-snap.3536-T1
Valid prediction for GeneMark_model.9006_t
Valid prediction for GeneMark_model.9017_t
Valid prediction for GlimmerHMM_glimmerT_5596-T1
Valid prediction for snap_scaffold_2-snap.3532-T1
Valid prediction for snap_scaffold_2-snap.3538-T1
Valid prediction for GlimmerHMM_glimmerT_5608-T1
Valid prediction for Augustus_model.g3801.t1
Valid prediction for GlimmerHMM_glimmerT_5611-T1
Valid prediction for Augustus_model.g3797.t1
Valid prediction for snap_scaffold_2-snap.3537-T1
Valid prediction for CodingQuarry_transcript_28787-T1
Valid prediction for Augustus_model.g3788.t1
Valid prediction for GeneMark_model.8980_t
Valid prediction for GlimmerHMM_glimmerT_5590-T1
Valid prediction for GlimmerHMM_glimmerT_5603-T1
Valid prediction for pasa_asmbl_25246.p1
Valid prediction for snap_scaffold_2-snap.3543-T1
Valid prediction for snap_scaffold_2-snap.3547-T1
Valid prediction for snap_scaffold_2-snap.3516-T1
Valid prediction for Augustus_model.g3793.t1
Valid prediction for GeneMark_model.8976_t
Valid prediction for snap_scaffold_2-snap.3542-T1
Valid prediction for snap_scaffold_2-snap.3529-T1
Valid prediction for HiQ_model.g3803.t1
Valid prediction for CodingQuarry_transcript_28785-T1
Valid prediction for GeneMark_model.8996_t
Valid prediction for GeneMark_model.8987_t
Valid prediction for HiQ_model.g3789.t1
Valid prediction for GeneMark_model.9014_t
Valid prediction for GeneMark_model.9002_t
Valid prediction for GlimmerHMM_glimmerT_5583-T1
Valid prediction for GlimmerHMM_glimmerT_5604-T1
Valid prediction for CodingQuarry_transcript_28786-T1
Valid prediction for snap_scaffold_2-snap.3523-T1
Valid prediction for GeneMark_model.9010_t
Valid prediction for pasa_asmbl_25257.p1
Valid prediction for GlimmerHMM_glimmerT_5595-T1
Couldn't classify 53503, 53658
Sorry, prediction pasa_asmbl_25241.p1 fails validation.
(CAG)	 CC	53503-53658	GT	AGG
(ATG)	 AG	53886-54096	GT	TGG
(TGA)	 AG	54606-54807	GT	CTG
(GCA)	 AG	55109-55316	AA	GAA
-recovered pasa_asmbl_25241.p1, initial, 53886, 54096
-recovered pasa_asmbl_25241.p1, terminal, 55109, 55316
-recovered pasa_asmbl_25241.p1, internal, 53886, 54096
-recovered pasa_asmbl_25241.p1, internal, 54606, 54807
Valid prediction for GeneMark_model.9028_t
Valid prediction for snap_scaffold_2-snap.3534-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.9000_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.9027_t
Valid prediction for GeneMark_model.9007_t
Valid prediction for snap_scaffold_2-snap.3548-T1
Valid prediction for snap_scaffold_2-snap.3527-T1
Valid prediction for GeneMark_model.8983_t
Valid prediction for GeneMark_model.9025_t
Valid prediction for GlimmerHMM_glimmerT_5593-T1
Valid prediction for GeneMark_model.9003_t
Valid prediction for GlimmerHMM_glimmerT_5599-T1
Valid prediction for GeneMark_model.8984_t
Valid prediction for GeneMark_model.9005_t
Valid prediction for GeneMark_model.9011_t
Valid prediction for CodingQuarry_transcript_28782-T1
Valid prediction for snap_scaffold_2-snap.3545-T1
Valid prediction for GeneMark_model.9009_t
Valid prediction for CodingQuarry_transcript_28781-T1
Valid prediction for Augustus_model.g3799.t1
Valid prediction for Augustus_model.g3794.t1
Valid prediction for CodingQuarry_transcript_28783-T1
Valid prediction for snap_scaffold_2-snap.3533-T1
Valid prediction for GlimmerHMM_glimmerT_5589-T1
Valid prediction for snap_scaffold_2-snap.3528-T1
Valid prediction for GlimmerHMM_glimmerT_5602-T1
Valid prediction for GlimmerHMM_glimmerT_5588-T1
Valid prediction for CodingQuarry_transcript_28788-T1
Valid prediction for GlimmerHMM_glimmerT_5586-T1
Valid prediction for GeneMark_model.9015_t
Valid prediction for GeneMark_model.8997_t
Valid prediction for GlimmerHMM_glimmerT_5585-T1
Valid prediction for GeneMark_model.9001_t
Valid prediction for snap_scaffold_2-snap.3519-T1
Valid prediction for GeneMark_model.8982_t
Valid prediction for GeneMark_model.8999_t
Valid prediction for GlimmerHMM_glimmerT_5591-T1
Valid prediction for Augustus_model.g3800.t1
Valid prediction for snap_scaffold_2-snap.3546-T1
Valid prediction for HiQ_model.g3802.t1
Valid prediction for GeneMark_model.9020_t
Valid prediction for GlimmerHMM_glimmerT_5609-T1
Valid prediction for GeneMark_model.8988_t
Valid prediction for pasa_asmbl_23777.p1
Valid prediction for snap_scaffold_2-snap.3525-T1
Valid prediction for Augustus_model.g3798.t1
Valid prediction for GeneMark_model.8979_t
Valid prediction for GeneMark_model.8975_t
Valid prediction for GlimmerHMM_glimmerT_5601-T1
Valid prediction for HiQ_model.g3792.t1
Valid prediction for GlimmerHMM_glimmerT_5605-T1
Valid prediction for GlimmerHMM_glimmerT_5592-T1
Valid prediction for pasa_asmbl_23774.p1
Valid prediction for GeneMark_model.9018_t
Valid prediction for snap_scaffold_2-snap.3541-T1
Valid prediction for snap_scaffold_2-snap.3520-T1
Valid prediction for GeneMark_model.8986_t
Valid prediction for pasa_asmbl_23773.p1
Valid prediction for GeneMark_model.8989_t
Valid prediction for GeneMark_model.9016_t
Valid prediction for Augustus_model.g3790.t1
Valid prediction for snap_scaffold_2-snap.3539-T1
Valid prediction for GeneMark_model.8995_t
Valid prediction for GeneMark_model.9022_t
Valid prediction for GlimmerHMM_glimmerT_5614-T1
Valid prediction for GeneMark_model.9024_t
Valid prediction for snap_scaffold_2-snap.3522-T1
Valid prediction for GeneMark_model.8991_t
Valid prediction for GlimmerHMM_glimmerT_5598-T1
Valid prediction for GeneMark_model.9013_t
Couldn't classify 104182, 104202
Couldn't classify 105483, 105538
Sorry, prediction pasa_asmbl_24023.p1 fails validation.
(TAC)	 CC	104182-104202	GT	AGG
(GTG)	 AG	104538-104643	GT	AGG
(CGG)	 AG	104765-104925	GT	TGG
(TAT)	 AG	105148-105208	GT	AGG
(TGA)	 AG	105483-105538	GC	TGG
-recovered pasa_asmbl_24023.p1, internal, 104538, 104643
-recovered pasa_asmbl_24023.p1, internal, 104765, 104925
-recovered pasa_asmbl_24023.p1, internal, 105148, 105208
-recovered pasa_asmbl_24023.p1, internal, 105483, 105538
Valid prediction for snap_scaffold_2-snap.3524-T1
Valid prediction for GlimmerHMM_glimmerT_5606-T1
Valid prediction for snap_scaffold_2-snap.3521-T1
Valid prediction for snap_scaffold_2-snap.3535-T1
Valid prediction for GlimmerHMM_glimmerT_5612-T1
Valid prediction for pasa_asmbl_23782.p2
Valid prediction for snap_scaffold_2-snap.3544-T1
Valid prediction for GeneMark_model.8993_t
Valid prediction for snap_scaffold_2-snap.3549-T1
Valid prediction for GlimmerHMM_glimmerT_5610-T1
Valid prediction for Augustus_model.g3787.t1
Valid prediction for Augustus_model.g3791.t1
Valid prediction for GeneMark_model.8977_t
Valid prediction for GlimmerHMM_glimmerT_5587-T1
Valid prediction for snap_scaffold_2-snap.3515-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 23588, rend_intergenic: 12920  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44627, rend_intergenic: 38420  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93769, rend_intergenic: 90947  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100698, rend_intergenic: 94103  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122987, rend_intergenic: 103344  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129136, rend_intergenic: 124287  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131487, rend_intergenic: 129269  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146478, rend_intergenic: 133473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193956, rend_intergenic: 183012  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 196308
-exon list size: 860


building trellis

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61.3    
61.4    
61.5    
61.6    
61.7    
61.8    
61.9    
62.1    
62.2    
62.3    
62.4    
62.5    
62.6    
62.8    
62.9    
63.0    
63.1    
63.2    
63.3    
63.5    
63.6    
63.7    
63.8    
63.9    
64.0    
64.2    
64.3    
64.4    
64.5    
64.6    
64.7    
64.8    
65.0    
65.1    
65.2    
65.3    
65.4    
65.5    
65.7    
65.8    
65.9    
66.0    
66.1    
66.2    
66.4    
66.5    
66.6    
66.7    
66.8    
66.9    
67.1    
67.2    
67.3    
67.4    
67.5    
67.6    
67.7    
67.9    
68.0    
68.1    
68.2    
68.3    
68.4    
68.6    
68.7    
68.8    
68.9    
69.0    
69.1    
69.3    
69.4    
69.5    
69.6    
69.7    
69.8    
70.0    
70.1    
70.2    
70.3    
70.4    
70.5    
70.6    
70.8    
70.9    
71.0    
71.1    
71.2    
71.3    
71.5    
71.6    
71.7    
71.8    
71.9    
72.0    
72.2    
72.3    
72.4    
72.5    
72.6    
72.7    
72.9    
73.0    
73.1    
73.2    
73.3    
73.4    
73.5    
73.7    
73.8    
73.9    
74.0    
74.1    
74.2    
74.4    
74.5    
74.6    
74.7    
74.8    
74.9    
75.1    
75.2    
75.3    
75.4    
75.5    
75.6    
75.8    
75.9    
76.0    
76.1    
76.2    
76.3    
76.5    
76.6    
76.7    
76.8    
76.9    
77.0    
77.1    
77.3    
77.4    
77.5    
77.6    
77.7    
77.8    
78.0    
78.1    
78.2    
78.3    
78.4    
78.5    
78.7    
78.8    
78.9    
79.0    
79.1    
79.2    
79.4    
79.5    
79.6    
79.7    
79.8    
79.9    
80.0    
80.2    
80.3    
80.4    
80.5    
80.6    
80.7    
80.9    
81.0    
81.1    
81.2    
81.3    
81.4    
81.6    
81.7    
81.8    
81.9    
82.0    
82.1    
82.3    
82.4    
82.5    
82.6    
82.7    
82.8    
82.9    
83.1    
83.2    
83.3    
83.4    
83.5    
83.6    
83.8    
83.9    
84.0    
84.1    
84.2    
84.3    
84.5    
84.6    
84.7    
84.8    
84.9    
85.0    
85.2    
85.3    
85.4    
85.5    
85.6    
85.7    
85.8    
86.0    
86.1    
86.2    
86.3    
86.4    
86.5    
86.7    
86.8    
86.9    
87.0    
87.1    
87.2    
87.4    
87.5    
87.6    
87.7    
87.8    
87.9    
88.1    
88.2    
88.3    
88.4    
88.5    
88.6    
88.7    
88.9    
89.0    
89.1    
89.2    
89.3    
89.4    
89.6    
89.7    
89.8    
89.9    
90.0    
90.1    
90.3    
90.4    
90.5    
90.6    
90.7    
90.8    
91.0    
91.1    
91.2    
91.3    
91.4    
91.5    
91.6    
91.8    
91.9    
92.0    
92.1    
92.2    
92.3    
92.5    
92.6    
92.7    
92.8    
92.9    
93.0    
93.2    
93.3    
93.4    
93.5    
93.6    
93.7    
93.9    
94.0    
94.1    
94.2    
94.3    
94.4    
94.5    
94.7    
94.8    
94.9    
95.0    
95.1    
95.2    
95.4    
95.5    
95.6    
95.7    
95.8    
95.9    
96.1    
96.2    
96.3    
96.4    
96.5    
96.6    
96.8    
96.9    
97.0    
97.1    
97.2    
97.3    
97.4    
97.6    
97.7    
97.8    
97.9    
98.0    
98.1    
98.3    
98.4    
98.5    
98.6    
98.7    
98.8    
99.0    
99.1    
99.2    
99.3    
99.4    
99.5    
99.7    
99.8    
99.9    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 23588, rend_intergenic: 12920  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44627, rend_intergenic: 38420  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93769, rend_intergenic: 90947  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100698, rend_intergenic: 94103  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122987, rend_intergenic: 103344  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129136, rend_intergenic: 124287  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131487, rend_intergenic: 129269  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146478, rend_intergenic: 133473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193956, rend_intergenic: 183012  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.
GOT 5prime partial gene.

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