-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_2/scaffold_2_968169-1184429

-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_2-snap.261-T1
Valid prediction for GlimmerHMM_glimmerT_3210-T1
Valid prediction for GeneMark_model.5195_t
Valid prediction for Augustus_model.g2180.t1
Valid prediction for GeneMark_model.5183_t
Valid prediction for GeneMark_model.5177_t
Valid prediction for GlimmerHMM_glimmerT_3219-T1
Valid prediction for GlimmerHMM_glimmerT_3225-T1
Valid prediction for GeneMark_model.5187_t
Valid prediction for snap_scaffold_2-snap.223-T1
Valid prediction for snap_scaffold_2-snap.228-T1
Valid prediction for snap_scaffold_2-snap.255-T1
Valid prediction for GeneMark_model.5214_t
Valid prediction for snap_scaffold_2-snap.224-T1
Valid prediction for GlimmerHMM_glimmerT_3224-T1
Valid prediction for GlimmerHMM_glimmerT_3215-T1
Valid prediction for snap_scaffold_2-snap.248-T1
Valid prediction for GeneMark_model.5218_t
Valid prediction for GeneMark_model.5193_t
Valid prediction for GlimmerHMM_glimmerT_3226-T1
Valid prediction for snap_scaffold_2-snap.230-T1
Valid prediction for GeneMark_model.5202_t
Valid prediction for snap_scaffold_2-snap.252-T1
Valid prediction for GeneMark_model.5216_t
Valid prediction for snap_scaffold_2-snap.229-T1
Valid prediction for GeneMark_model.5196_t
Valid prediction for snap_scaffold_2-snap.263-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_3218-T1
Valid prediction for GlimmerHMM_glimmerT_3205-T1
Valid prediction for GeneMark_model.5175_t
Valid prediction for GeneMark_model.5204_t
Valid prediction for snap_scaffold_2-snap.256-T1
Valid prediction for Augustus_model.g2177.t1
Valid prediction for snap_scaffold_2-snap.245-T1
Valid prediction for snap_scaffold_2-snap.250-T1
Valid prediction for snap_scaffold_2-snap.253-T1
Valid prediction for GeneMark_model.5222_t
Valid prediction for snap_scaffold_2-snap.242-T1
Valid prediction for GeneMark_model.5208_t
Valid prediction for GeneMark_model.5198_t
Valid prediction for snap_scaffold_2-snap.238-T1
Valid prediction for GeneMark_model.5178_t
Valid prediction for snap_scaffold_2-snap.243-T1
Valid prediction for GeneMark_model.5180_t
Valid prediction for Augustus_model.g2175.t1
Valid prediction for snap_scaffold_2-snap.232-T1
Valid prediction for snap_scaffold_2-snap.258-T1
Valid prediction for GeneMark_model.5224_t
Valid prediction for GeneMark_model.5211_t
Valid prediction for GlimmerHMM_glimmerT_3209-T1
Valid prediction for GlimmerHMM_glimmerT_3217-T1
Valid prediction for GlimmerHMM_glimmerT_3229-T1
Valid prediction for GlimmerHMM_glimmerT_3221-T1
Valid prediction for snap_scaffold_2-snap.260-T1
Valid prediction for GlimmerHMM_glimmerT_3207-T1
Valid prediction for GeneMark_model.5212_t
Valid prediction for Augustus_model.g2173.t1
Valid prediction for GeneMark_model.5188_t
Valid prediction for GlimmerHMM_glimmerT_3213-T1
Valid prediction for GeneMark_model.5206_t
Valid prediction for snap_scaffold_2-snap.264-T1
Valid prediction for snap_scaffold_2-snap.226-T1
Valid prediction for snap_scaffold_2-snap.233-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 snap_scaffold_2-snap.259-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GeneMark_model.5201_t
Valid prediction for snap_scaffold_2-snap.251-T1
Valid prediction for Augustus_model.g2181.t1
Couldn't classify 45783, 45801
Sorry, prediction GeneMark_model.5220_t fails validation.
(TAG)	 AG	45783-45801	GT	AGG
(GTG)	 AG	45822-45841	GT	AGG
(GCT)	 AG	45887-45901	GT	AGG
(TCT)	 AG	45937-45981	GT	AGG
(GCT)	 AG	46007-46021	GT	AGG
(GCT)	 AG	46047-46061	GT	AGG
(TCG)	 AG	46097-46142	AG	GAA
add_exon() Sorry, GeneMark_model.5220_t 45937-45981-terminal-1 is invalid.
-recovered GeneMark_model.5220_t, terminal, 45937, 45981
-recovered GeneMark_model.5220_t, terminal, 46047, 46061
-recovered GeneMark_model.5220_t, terminal, 46097, 46142
-recovered GeneMark_model.5220_t, internal, 45783, 45801
-recovered GeneMark_model.5220_t, internal, 45822, 45841
-recovered GeneMark_model.5220_t, internal, 45887, 45901
-recovered GeneMark_model.5220_t, internal, 45937, 45981
-recovered GeneMark_model.5220_t, internal, 46007, 46021
-recovered GeneMark_model.5220_t, internal, 46047, 46061
Valid prediction for GlimmerHMM_glimmerT_3231-T1
Valid prediction for GlimmerHMM_glimmerT_3227-T1
Valid prediction for GlimmerHMM_glimmerT_3208-T1
Valid prediction for GeneMark_model.5194_t
Valid prediction for snap_scaffold_2-snap.254-T1
Valid prediction for GeneMark_model.5225_t
Valid prediction for snap_scaffold_2-snap.222-T1
Valid prediction for GlimmerHMM_glimmerT_3228-T1
Couldn't classify 106023, 106148
Sorry, prediction pasa_asmbl_22861.p1 fails validation.
(ATG)	 GA	104174-104305	GT	GGG
(AAT)	 AG	104629-104710	GT	AGG
(ACG)	 AG	104933-105033	GT	AGG
(GGA)	 AG	105260-105409	GT	TGG
(GTC)	 AG	105506-105580	GT	CGG
(AAC)	 AG	106023-106148	TG	GGT
-recovered pasa_asmbl_22861.p1, initial, 104174, 104305
-recovered pasa_asmbl_22861.p1, internal, 104629, 104710
-recovered pasa_asmbl_22861.p1, internal, 104933, 105033
-recovered pasa_asmbl_22861.p1, internal, 105260, 105409
-recovered pasa_asmbl_22861.p1, internal, 105506, 105580
Valid prediction for GeneMark_model.5226_t
Valid prediction for snap_scaffold_2-snap.231-T1
Valid prediction for GeneMark_model.5215_t
Valid prediction for GlimmerHMM_glimmerT_3206-T1
Valid prediction for GlimmerHMM_glimmerT_3211-T1
Valid prediction for Augustus_model.g2171.t1
Valid prediction for GlimmerHMM_glimmerT_3216-T1
Valid prediction for snap_scaffold_2-snap.234-T1
Valid prediction for snap_scaffold_2-snap.262-T1
Valid prediction for GlimmerHMM_glimmerT_3230-T1
Valid prediction for GeneMark_model.5223_t
Valid prediction for GeneMark_model.5200_t
Valid prediction for GlimmerHMM_glimmerT_3233-T1
Valid prediction for snap_scaffold_2-snap.241-T1
Valid prediction for GeneMark_model.5191_t
Valid prediction for GeneMark_model.5205_t
Couldn't classify 48450, 48992
Sorry, prediction pasa_asmbl_22862.p1 fails validation.
(GCC)	 GT	48450-48992	GG	AAG
Valid prediction for snap_scaffold_2-snap.235-T1
Valid prediction for snap_scaffold_2-snap.240-T1
Valid prediction for GeneMark_model.5217_t
Valid prediction for Augustus_model.g2182.t1
Valid prediction for Augustus_model.g2172.t1
Valid prediction for Augustus_model.g2178.t1
Valid prediction for snap_scaffold_2-snap.227-T1
Valid prediction for snap_scaffold_2-snap.225-T1
Valid prediction for GeneMark_model.5182_t
Valid prediction for snap_scaffold_2-snap.239-T1
Valid prediction for snap_scaffold_2-snap.237-T1
Couldn't classify 33571, 33644
Couldn't classify 34720, 34843
Sorry, prediction pasa_asmbl_24007.p1 fails validation.
(GAC)	 TC	33571-33644	GT	ATG
(GAT)	 AG	34249-34350	GT	AAG
(GTT)	 AG	34720-34843	GC	ACG
-recovered pasa_asmbl_24007.p1, internal, 34249, 34350
-recovered pasa_asmbl_24007.p1, internal, 34720, 34843
Valid prediction for snap_scaffold_2-snap.247-T1
Valid prediction for GlimmerHMM_glimmerT_3232-T1
Valid prediction for GeneMark_model.5176_t
Valid prediction for GeneMark_model.5207_t
Valid prediction for GlimmerHMM_glimmerT_3214-T1
Valid prediction for Augustus_model.g2176.t1
Valid prediction for GeneMark_model.5179_t
Valid prediction for GeneMark_model.5209_t
Valid prediction for GeneMark_model.5213_t
Valid prediction for GlimmerHMM_glimmerT_3212-T1
Valid prediction for GlimmerHMM_glimmerT_3223-T1
Valid prediction for Augustus_model.g2174.t1
Valid prediction for snap_scaffold_2-snap.265-T1
Valid prediction for GeneMark_model.5190_t
Valid prediction for GeneMark_model.5199_t
Valid prediction for GeneMark_model.5192_t
Valid prediction for snap_scaffold_2-snap.249-T1
Couldn't classify 111905, 112013
Sorry, prediction pasa_asmbl_22860.p1 fails validation.
(GGG)	 TA	111905-112013	GT	TGG
(GTC)	 AG	112111-112236	GT	AGG
(GAG)	 AG	112737-112847	GT	AGG
(GTC)	 AG	113173-113288	GT	AGG
(GTG)	 AG	113974-114174	GT	AGG
(ATC)	 AG	115793-115969	AG	GAA
-recovered pasa_asmbl_22860.p1, terminal, 115793, 115969
-recovered pasa_asmbl_22860.p1, internal, 112111, 112236
-recovered pasa_asmbl_22860.p1, internal, 112737, 112847
-recovered pasa_asmbl_22860.p1, internal, 113173, 113288
-recovered pasa_asmbl_22860.p1, internal, 113974, 114174
Valid prediction for GeneMark_model.5185_t
Valid prediction for GeneMark_model.5197_t
Couldn't classify 34720, 34873
Sorry, prediction GeneMark_model.5221_t fails validation.
(ATG)	 AG	31765-31934	GT	CTG
(TAT)	 AG	32066-32095	GT	GAG
(TGT)	 AG	32118-32276	GT	GTG
(TAT)	 AG	32297-32404	GT	GGG
(ACT)	 AG	32453-32467	GT	GGG
(GGT)	 AG	32507-33154	GT	GGG
(ACA)	 AG	33182-33196	GT	GGG
(GGT)	 AG	33236-33331	GT	GTG
(GGT)	 AG	33360-33596	GT	GAG
(GAT)	 AG	34249-34350	GT	AAG
(GTT)	 AG	34720-34873	GT	GGG
-recovered GeneMark_model.5221_t, initial, 31765, 31934
add_exon() Sorry, GeneMark_model.5221_t 33360-33596-terminal-1 is invalid.
-recovered GeneMark_model.5221_t, terminal, 33360, 33596
-recovered GeneMark_model.5221_t, internal, 31765, 31934
-recovered GeneMark_model.5221_t, internal, 32066, 32095
-recovered GeneMark_model.5221_t, internal, 32118, 32276
-recovered GeneMark_model.5221_t, internal, 32297, 32404
-recovered GeneMark_model.5221_t, internal, 32453, 32467
-recovered GeneMark_model.5221_t, internal, 32507, 33154
-recovered GeneMark_model.5221_t, internal, 33182, 33196
-recovered GeneMark_model.5221_t, internal, 33236, 33331
-recovered GeneMark_model.5221_t, internal, 33360, 33596
-recovered GeneMark_model.5221_t, internal, 34249, 34350
-recovered GeneMark_model.5221_t, internal, 34720, 34873
Valid prediction for snap_scaffold_2-snap.244-T1
Valid prediction for GeneMark_model.5184_t
Valid prediction for GeneMark_model.5186_t
Valid prediction for GlimmerHMM_glimmerT_3222-T1
Valid prediction for GeneMark_model.5210_t
Valid prediction for snap_scaffold_2-snap.257-T1
Valid prediction for snap_scaffold_2-snap.236-T1
Valid prediction for GeneMark_model.5189_t
Valid prediction for GeneMark_model.5181_t
Valid prediction for snap_scaffold_2-snap.246-T1
Valid prediction for GlimmerHMM_glimmerT_3220-T1
Valid prediction for Augustus_model.g2179.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6701, rend_intergenic: 4029  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12637, rend_intergenic: 11498  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18443, rend_intergenic: 13823  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38112, rend_intergenic: 31738  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67811, rend_intergenic: 54441  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73526, rend_intergenic: 70739  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84220, rend_intergenic: 74111  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87009, rend_intergenic: 85997  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94207, rend_intergenic: 92032  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123145, rend_intergenic: 115741  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125770, rend_intergenic: 123479  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137054, rend_intergenic: 131283  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144876, rend_intergenic: 141786  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146866, rend_intergenic: 145243  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161123, rend_intergenic: 159275  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170701, rend_intergenic: 161161  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189783, rend_intergenic: 180776  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211158, rend_intergenic: 195494  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 216261
-exon list size: 846


building trellis

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58.8    
59.0    
59.1    
59.2    
59.3    
59.4    
59.6    
59.7    
59.8    
59.9    
60.0    
60.1    
60.3    
60.4    
60.5    
60.6    
60.7    
60.8    
61.0    
61.1    
61.2    
61.3    
61.4    
61.6    
61.7    
61.8    
61.9    
62.0    
62.1    
62.3    
62.4    
62.5    
62.6    
62.7    
62.9    
63.0    
63.1    
63.2    
63.3    
63.4    
63.6    
63.7    
63.8    
63.9    
64.0    
64.2    
64.3    
64.4    
64.5    
64.6    
64.7    
64.9    
65.0    
65.1    
65.2    
65.3    
65.4    
65.6    
65.7    
65.8    
65.9    
66.0    
66.2    
66.3    
66.4    
66.5    
66.6    
66.7    
66.9    
67.0    
67.1    
67.2    
67.3    
67.5    
67.6    
67.7    
67.8    
67.9    
68.0    
68.2    
68.3    
68.4    
68.5    
68.6    
68.8    
68.9    
69.0    
69.1    
69.2    
69.3    
69.5    
69.6    
69.7    
69.8    
69.9    
70.0    
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    
72.1    
72.2    
72.3    
72.4    
72.5    
72.6    
72.8    
72.9    
73.0    
73.1    
73.2    
73.3    
73.5    
73.6    
73.7    
73.8    
73.9    
74.1    
74.2    
74.3    
74.4    
74.5    
74.6    
74.8    
74.9    
75.0    
75.1    
75.2    
75.4    
75.5    
75.6    
75.7    
75.8    
75.9    
76.1    
76.2    
76.3    
76.4    
76.5    
76.7    
76.8    
76.9    
77.0    
77.1    
77.2    
77.4    
77.5    
77.6    
77.7    
77.8    
77.9    
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    
80.0    
80.1    
80.2    
80.3    
80.4    
80.5    
80.7    
80.8    
80.9    
81.0    
81.1    
81.2    
81.4    
81.5    
81.6    
81.7    
81.8    
82.0    
82.1    
82.2    
82.3    
82.4    
82.5    
82.7    
82.8    
82.9    
83.0    
83.1    
83.3    
83.4    
83.5    
83.6    
83.7    
83.8    
84.0    
84.1    
84.2    
84.3    
84.4    
84.6    
84.7    
84.8    
84.9    
85.0    
85.1    
85.3    
85.4    
85.5    
85.6    
85.7    
85.8    
86.0    
86.1    
86.2    
86.3    
86.4    
86.6    
86.7    
86.8    
86.9    
87.0    
87.1    
87.3    
87.4    
87.5    
87.6    
87.7    
87.9    
88.0    
88.1    
88.2    
88.3    
88.4    
88.6    
88.7    
88.8    
88.9    
89.0    
89.2    
89.3    
89.4    
89.5    
89.6    
89.7    
89.9    
90.0    
90.1    
90.2    
90.3    
90.4    
90.6    
90.7    
90.8    
90.9    
91.0    
91.2    
91.3    
91.4    
91.5    
91.6    
91.7    
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    
93.8    
93.9    
94.0    
94.1    
94.2    
94.3    
94.5    
94.6    
94.7    
94.8    
94.9    
95.0    
95.2    
95.3    
95.4    
95.5    
95.6    
95.8    
95.9    
96.0    
96.1    
96.2    
96.3    
96.5    
96.6    
96.7    
96.8    
96.9    
97.1    
97.2    
97.3    
97.4    
97.5    
97.6    
97.8    
97.9    
98.0    
98.1    
98.2    
98.3    
98.5    
98.6    
98.7    
98.8    
98.9    
99.1    
99.2    
99.3    
99.4    
99.5    
99.6    
99.8    
99.9    
-found 38 predictions from path traversal
Error with prediction: snap lend_intergenic: 6701, rend_intergenic: 4029  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12637, rend_intergenic: 11498  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18443, rend_intergenic: 13823  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38112, rend_intergenic: 31738  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67811, rend_intergenic: 54441  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73526, rend_intergenic: 70739  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84220, rend_intergenic: 74111  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87009, rend_intergenic: 85997  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94207, rend_intergenic: 92032  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123145, rend_intergenic: 115741  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125770, rend_intergenic: 123479  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137054, rend_intergenic: 131283  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144876, rend_intergenic: 141786  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146866, rend_intergenic: 145243  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161123, rend_intergenic: 159275  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170701, rend_intergenic: 161161  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189783, rend_intergenic: 180776  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211158, rend_intergenic: 195494  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support