-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_27/scaffold_27_4689265-4882456

-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_27-snap.1131-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for snap_scaffold_27-snap.1128-T1
Valid prediction for snap_scaffold_27-snap.1116-T1
Valid prediction for CodingQuarry_transcript_41795-T1
Valid prediction for snap_scaffold_27-snap.1148-T1
Valid prediction for Augustus_model.g39071.t1
Valid prediction for snap_scaffold_27-snap.1154-T1
Valid prediction for GlimmerHMM_glimmerT_58613-T1
Valid prediction for GeneMark_model.101911_t
Valid prediction for GeneMark_model.101919_t
Valid prediction for GeneMark_model.101921_t
Valid prediction for GeneMark_model.101957_t
Valid prediction for snap_scaffold_27-snap.1133-T1
Valid prediction for GeneMark_model.101933_t
Valid prediction for GlimmerHMM_glimmerT_58609-T1
Valid prediction for pasa_asmbl_36272.p1
Valid prediction for snap_scaffold_27-snap.1137-T1
Valid prediction for snap_scaffold_27-snap.1153-T1
Valid prediction for snap_scaffold_27-snap.1119-T1
Valid prediction for pasa_asmbl_36276.p1
Valid prediction for GlimmerHMM_glimmerT_58616-T1
Valid prediction for snap_scaffold_27-snap.1140-T1
Valid prediction for snap_scaffold_27-snap.1121-T1
Valid prediction for GeneMark_model.101952_t
Valid prediction for GeneMark_model.101904_t
Valid prediction for GlimmerHMM_glimmerT_58617-T1
Valid prediction for GlimmerHMM_glimmerT_58621-T1
Valid prediction for Augustus_model.g39059.t1
Valid prediction for GeneMark_model.101947_t
Valid prediction for HiQ_model.g39068.t1
Valid prediction for snap_scaffold_27-snap.1120-T1
Valid prediction for GeneMark_model.101936_t
Valid prediction for GeneMark_model.101905_t
Valid prediction for Augustus_model.g39062.t1
Valid prediction for snap_scaffold_27-snap.1118-T1
Valid prediction for GeneMark_model.101940_t
Valid prediction for GlimmerHMM_glimmerT_58623-T1
Valid prediction for GeneMark_model.101950_t
Valid prediction for GeneMark_model.101916_t
Couldn't classify 43178, 43263
Sorry, prediction pasa_asmbl_36268.p1 fails validation.
(GGA)	 GT	43178-43263	GT	CGG
(AGT)	 AG	43650-43766	GT	CGG
(CTG)	 AG	44140-44341	GT	AGG
(GGT)	 AG	44621-44819	GT	AGG
(AGG)	 AG	45100-45587	GT	AGG
(GTG)	 AG	45720-45867	GT	CGG
(ATA)	 AG	46191-46321	AC	AGA
-recovered pasa_asmbl_36268.p1, terminal, 46191, 46321
-recovered pasa_asmbl_36268.p1, internal, 43650, 43766
-recovered pasa_asmbl_36268.p1, internal, 44140, 44341
-recovered pasa_asmbl_36268.p1, internal, 44621, 44819
-recovered pasa_asmbl_36268.p1, internal, 45100, 45587
-recovered pasa_asmbl_36268.p1, internal, 45720, 45867
Valid prediction for Augustus_model.g39063.t1
Valid prediction for GeneMark_model.101914_t
Valid prediction for CodingQuarry_transcript_41792-T1
Valid prediction for snap_scaffold_27-snap.1124-T1
Valid prediction for GeneMark_model.101925_t
Valid prediction for GeneMark_model.101920_t
Valid prediction for snap_scaffold_27-snap.1145-T1
Valid prediction for snap_scaffold_27-snap.1147-T1
Valid prediction for GeneMark_model.101951_t
Valid prediction for GeneMark_model.101913_t
Valid prediction for GlimmerHMM_glimmerT_58606-T1
Valid prediction for Augustus_model.g39061.t1
Valid prediction for GlimmerHMM_glimmerT_58611-T1
Valid prediction for GeneMark_model.101939_t
Valid prediction for GeneMark_model.101923_t
Valid prediction for snap_scaffold_27-snap.1151-T1
Valid prediction for GlimmerHMM_glimmerT_58622-T1
Valid prediction for snap_scaffold_27-snap.1138-T1
Valid prediction for GeneMark_model.101929_t
Valid prediction for GeneMark_model.101927_t
Valid prediction for GeneMark_model.101955_t
Valid prediction for GlimmerHMM_glimmerT_58608-T1
Valid prediction for snap_scaffold_27-snap.1134-T1
Valid prediction for snap_scaffold_27-snap.1130-T1
Valid prediction for GeneMark_model.101908_t
Valid prediction for snap_scaffold_27-snap.1125-T1
Valid prediction for GeneMark_model.101932_t
Valid prediction for Augustus_model.g39070.t1
Valid prediction for snap_scaffold_27-snap.1143-T1
Valid prediction for snap_scaffold_27-snap.1127-T1
Valid prediction for GeneMark_model.101942_t
Valid prediction for GeneMark_model.101958_t
Valid prediction for GeneMark_model.101906_t
Valid prediction for GeneMark_model.101910_t
Valid prediction for GeneMark_model.101945_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: -)Couldn't classify 65213, 65361
Couldn't classify 65990, 66176
Sorry, prediction pasa_asmbl_37161.p1 fails validation.
(CTA)	 GC	65213-65361	GT	AGG
(GTG)	 AG	65990-66176	GA	TCG
Valid prediction for GlimmerHMM_glimmerT_58612-T1
Valid prediction for Augustus_model.g39058.t1
Valid prediction for GlimmerHMM_glimmerT_58620-T1
Valid prediction for GeneMark_model.101937_t
Valid prediction for GeneMark_model.101943_t
Couldn't classify 108211, 108507
Sorry, prediction pasa_asmbl_36922.p1 fails validation.
(GGG)	 GC	108211-108507	GG	GTG
Valid prediction for pasa_asmbl_36929.p1
Valid prediction for CodingQuarry_transcript_41794-T1
Valid prediction for GeneMark_model.101949_t
Valid prediction for Augustus_model.g39057.t1
Valid prediction for CodingQuarry_transcript_41796-T1
Valid prediction for GeneMark_model.101909_t
Valid prediction for GeneMark_model.101953_t
Valid prediction for GeneMark_model.101907_t
Valid prediction for GlimmerHMM_glimmerT_58625-T1
Valid prediction for CodingQuarry_transcript_41793-T1
Valid prediction for GeneMark_model.101930_t
Valid prediction for snap_scaffold_27-snap.1126-T1
Valid prediction for GlimmerHMM_glimmerT_58624-T1
Valid prediction for GlimmerHMM_glimmerT_58615-T1
Valid prediction for GeneMark_model.101928_t
Valid prediction for snap_scaffold_27-snap.1146-T1
Valid prediction for snap_scaffold_27-snap.1150-T1
Valid prediction for snap_scaffold_27-snap.1117-T1
Valid prediction for GlimmerHMM_glimmerT_58618-T1
Couldn't classify 109487, 109542
Sorry, prediction pasa_asmbl_36919.p1 fails validation.
(AGC)	 AC	109487-109542	GT	AGG
(GTC)	 AG	110591-111203	GT	AGG
(CTG)	 AG	111478-111622	GT	AGG
(AGC)	 AG	112940-113032	GT	GAG
(ACA)	 AG	113674-113819	GT	AGG
(CTG)	 AG	115808-115957	GT	AGG
(CGG)	 AG	116550-116749	GT	AGG
(GGA)	 AG	116982-117107	GT	AGG
(GAT)	 AG	117338-117570	GT	GGG
(GCC)	 AG	118139-118393	GT	AGG
(ATG)	 AG	118851-118966	CA	GAC
-recovered pasa_asmbl_36919.p1, terminal, 118851, 118966
-recovered pasa_asmbl_36919.p1, internal, 110591, 111203
-recovered pasa_asmbl_36919.p1, internal, 111478, 111622
-recovered pasa_asmbl_36919.p1, internal, 112940, 113032
-recovered pasa_asmbl_36919.p1, internal, 113674, 113819
-recovered pasa_asmbl_36919.p1, internal, 115808, 115957
-recovered pasa_asmbl_36919.p1, internal, 116550, 116749
-recovered pasa_asmbl_36919.p1, internal, 116982, 117107
-recovered pasa_asmbl_36919.p1, internal, 117338, 117570
-recovered pasa_asmbl_36919.p1, internal, 118139, 118393
Valid prediction for snap_scaffold_27-snap.1141-T1
Valid prediction for snap_scaffold_27-snap.1132-T1
Valid prediction for Augustus_model.g39064.t1
Valid prediction for GeneMark_model.101934_t
Valid prediction for GlimmerHMM_glimmerT_58605-T1
Valid prediction for HiQ_model.g39067.t1
Valid prediction for snap_scaffold_27-snap.1139-T1
Valid prediction for GlimmerHMM_glimmerT_58610-T1
Valid prediction for GeneMark_model.101931_t
Valid prediction for snap_scaffold_27-snap.1129-T1
Valid prediction for GeneMark_model.101941_t
Valid prediction for GlimmerHMM_glimmerT_58604-T1
Valid prediction for HiQ_model.g39065.t1
Valid prediction for GlimmerHMM_glimmerT_58607-T1
Couldn't classify 172083, 172134
Sorry, prediction pasa_asmbl_36916.p1 fails validation.
(GCA)	 CG	172083-172134	GT	AGG
(TGC)	 AG	173354-173465	GT	GGG
(GTC)	 AG	175335-175477	GT	AGG
(GTG)	 AG	176431-176612	AC	GAA
-recovered pasa_asmbl_36916.p1, terminal, 176431, 176612
-recovered pasa_asmbl_36916.p1, internal, 173354, 173465
-recovered pasa_asmbl_36916.p1, internal, 175335, 175477
Valid prediction for snap_scaffold_27-snap.1115-T1
Valid prediction for snap_scaffold_27-snap.1135-T1
Valid prediction for GeneMark_model.101954_t
Valid prediction for HiQ_model.g39066.t1
Valid prediction for GeneMark_model.101918_t
Valid prediction for GeneMark_model.101938_t
Valid prediction for pasa_asmbl_36923.p1
Valid prediction for snap_scaffold_27-snap.1122-T1
Valid prediction for GeneMark_model.101926_t
Valid prediction for Augustus_model.g39069.t1
Valid prediction for GeneMark_model.101922_t
Valid prediction for GeneMark_model.101944_t
Valid prediction for GeneMark_model.101915_t
Valid prediction for GeneMark_model.101924_t
Valid prediction for GlimmerHMM_glimmerT_58619-T1
Couldn't classify 67526, 67667
Couldn't classify 68858, 68908
Sorry, prediction pasa_asmbl_37172.p1 fails validation.
(GAC)	 AG	67526-67667	GT	AGG
(GGA)	 AG	68394-68500	GT	AGG
(AAC)	 AG	68858-68908	GT	AGG
-recovered pasa_asmbl_37172.p1, internal, 67526, 67667
-recovered pasa_asmbl_37172.p1, internal, 68394, 68500
-recovered pasa_asmbl_37172.p1, internal, 68858, 68908
Valid prediction for GeneMark_model.101912_t
Valid prediction for GlimmerHMM_glimmerT_58614-T1
Valid prediction for GeneMark_model.101917_t
Valid prediction for GeneMark_model.101948_t
Valid prediction for GeneMark_model.101946_t
Valid prediction for GeneMark_model.101935_t
Valid prediction for snap_scaffold_27-snap.1152-T1
Valid prediction for snap_scaffold_27-snap.1123-T1
Valid prediction for snap_scaffold_27-snap.1149-T1
Valid prediction for snap_scaffold_27-snap.1136-T1
Valid prediction for snap_scaffold_27-snap.1142-T1
Valid prediction for Augustus_model.g39060.t1
Valid prediction for snap_scaffold_27-snap.1144-T1
Valid prediction for GeneMark_model.101956_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 23435, rend_intergenic: 16399  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42213, rend_intergenic: 23603  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48936, rend_intergenic: 43626  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52395, rend_intergenic: 48979  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56242, rend_intergenic: 54892  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71485, rend_intergenic: 67361  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80838, rend_intergenic: 74227  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97968, rend_intergenic: 84379  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125880, rend_intergenic: 123173  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137703, rend_intergenic: 131326  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144020, rend_intergenic: 142824  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146230, rend_intergenic: 145715  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151517, rend_intergenic: 146548  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161906, rend_intergenic: 153318  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171653, rend_intergenic: 162853  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172167, rend_intergenic: 171808  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190615, rend_intergenic: 172550  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 193192
-exon list size: 831


building trellis

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65.9    
66.0    
66.1    
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    
68.1    
68.2    
68.3    
68.4    
68.5    
68.7    
68.8    
68.9    
69.0    
69.1    
69.3    
69.4    
69.5    
69.6    
69.7    
69.9    
70.0    
70.1    
70.2    
70.3    
70.5    
70.6    
70.7    
70.8    
70.9    
71.1    
71.2    
71.3    
71.4    
71.5    
71.7    
71.8    
71.9    
72.0    
72.1    
72.3    
72.4    
72.5    
72.6    
72.7    
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    
74.7    
74.8    
74.9    
75.0    
75.2    
75.3    
75.4    
75.5    
75.6    
75.8    
75.9    
76.0    
76.1    
76.2    
76.4    
76.5    
76.6    
76.7    
76.8    
77.0    
77.1    
77.2    
77.3    
77.4    
77.6    
77.7    
77.8    
77.9    
78.0    
78.2    
78.3    
78.4    
78.5    
78.6    
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    
80.6    
80.7    
80.8    
80.9    
81.0    
81.2    
81.3    
81.4    
81.5    
81.6    
81.8    
81.9    
82.0    
82.1    
82.2    
82.4    
82.5    
82.6    
82.7    
82.8    
83.0    
83.1    
83.2    
83.3    
83.4    
83.6    
83.7    
83.8    
83.9    
84.0    
84.2    
84.3    
84.4    
84.5    
84.6    
84.8    
84.9    
85.0    
85.1    
85.2    
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    
87.2    
87.3    
87.4    
87.5    
87.6    
87.8    
87.9    
88.0    
88.1    
88.2    
88.4    
88.5    
88.6    
88.7    
88.8    
89.0    
89.1    
89.2    
89.3    
89.4    
89.6    
89.7    
89.8    
89.9    
90.0    
90.2    
90.3    
90.4    
90.5    
90.6    
90.8    
90.9    
91.0    
91.1    
91.2    
91.4    
91.5    
91.6    
91.7    
91.8    
92.0    
92.1    
92.2    
92.3    
92.4    
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    
94.4    
94.5    
94.6    
94.7    
94.8    
95.0    
95.1    
95.2    
95.3    
95.4    
95.6    
95.7    
95.8    
95.9    
96.0    
96.2    
96.3    
96.4    
96.5    
96.6    
96.8    
96.9    
97.0    
97.1    
97.2    
97.4    
97.5    
97.6    
97.7    
97.8    
98.0    
98.1    
98.2    
98.3    
98.4    
98.6    
98.7    
98.8    
98.9    
99.0    
99.2    
99.3    
99.4    
99.5    
99.6    
99.8    
99.9    
-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 23435, rend_intergenic: 16399  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42213, rend_intergenic: 23603  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48936, rend_intergenic: 43626  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52395, rend_intergenic: 48979  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56242, rend_intergenic: 54892  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71485, rend_intergenic: 67361  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80838, rend_intergenic: 74227  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97968, rend_intergenic: 84379  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125880, rend_intergenic: 123173  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137703, rend_intergenic: 131326  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144020, rend_intergenic: 142824  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146230, rend_intergenic: 145715  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151517, rend_intergenic: 146548  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161906, rend_intergenic: 153318  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171653, rend_intergenic: 162853  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172167, rend_intergenic: 171808  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190615, rend_intergenic: 172550  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 16328
-exon list size: 19


building trellis

4.8    
9.5    
14.3    
19.0    
23.8    
28.6    
33.3    
38.1    
42.9    
47.6    
52.4    
57.1    
61.9    
66.7    
71.4    
76.2    
81.0    
85.7    
90.5    
95.2    
-found 2 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 177336 - 193192
-exon list size: 53


building trellis

1.8    
3.6    
5.5    
7.3    
9.1    
10.9    
12.7    
14.5    
16.4    
18.2    
20.0    
21.8    
23.6    
25.5    
27.3    
29.1    
30.9    
32.7    
34.5    
36.4    
38.2    
40.0    
41.8    
43.6    
45.5    
47.3    
49.1    
50.9    
52.7    
54.5    
56.4    
58.2    
60.0    
61.8    
63.6    
65.5    
67.3    
69.1    
70.9    
72.7    
74.5    
76.4    
78.2    
80.0    
81.8    
83.6    
85.5    
87.3    
89.1    
90.9    
92.7    
94.5    
96.4    
98.2    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support