-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_28/scaffold_28_9191502-9368057

-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_28-snap.2078-T1
Valid prediction for HiQ_model.g40475.t1
Valid prediction for GeneMark_model.105955_t
Valid prediction for GeneMark_model.105972_t
Valid prediction for GlimmerHMM_glimmerT_60811-T1
Couldn't classify 76892, 76992
Sorry, prediction pasa_asmbl_38472.p1 fails validation.
(CCA)	 GC	76892-76992	GT	ATG
(AAT)	 AG	78191-78260	GT	AGG
(GCC)	 AG	78632-78757	GT	AGG
(ATT)	 AG	79014-79122	GT	AGG
(GTA)	 AG	79313-79392	CA	AAC
-recovered pasa_asmbl_38472.p1, terminal, 79313, 79392
-recovered pasa_asmbl_38472.p1, internal, 78191, 78260
-recovered pasa_asmbl_38472.p1, internal, 78632, 78757
-recovered pasa_asmbl_38472.p1, internal, 79014, 79122
Valid prediction for GeneMark_model.105970_t
Valid prediction for GeneMark_model.105991_t
Valid prediction for snap_scaffold_28-snap.2090-T1
Valid prediction for Augustus_model.g40479.t1
Valid prediction for GlimmerHMM_glimmerT_60807-T1
Valid prediction for snap_scaffold_28-snap.2093-T1
Valid prediction for CodingQuarry_transcript_43657-T1
Valid prediction for snap_scaffold_28-snap.2102-T1
Valid prediction for GeneMark_model.105973_t
Valid prediction for snap_scaffold_28-snap.2079-T1
Valid prediction for GlimmerHMM_glimmerT_60822-T1
Valid prediction for GlimmerHMM_glimmerT_60815-T1
Valid prediction for GeneMark_model.105982_t
Valid prediction for GeneMark_model.105967_t
Valid prediction for snap_scaffold_28-snap.2080-T1
Valid prediction for GeneMark_model.105957_t
Valid prediction for GeneMark_model.105983_t
Valid prediction for snap_scaffold_28-snap.2091-T1
Valid prediction for snap_scaffold_28-snap.2097-T1
Valid prediction for GeneMark_model.105976_t
Valid prediction for GlimmerHMM_glimmerT_60810-T1
Valid prediction for snap_scaffold_28-snap.2088-T1
Valid prediction for snap_scaffold_28-snap.2095-T1
Valid prediction for snap_scaffold_28-snap.2100-T1
Valid prediction for snap_scaffold_28-snap.2075-T1
Valid prediction for GlimmerHMM_glimmerT_60820-T1
Valid prediction for GeneMark_model.105988_t
Valid prediction for GlimmerHMM_glimmerT_60818-T1
Valid prediction for GeneMark_model.105960_t
Valid prediction for GlimmerHMM_glimmerT_60817-T1
Valid prediction for GeneMark_model.105979_t
Valid prediction for GeneMark_model.105965_t
Valid prediction for GeneMark_model.105980_t
Valid prediction for snap_scaffold_28-snap.2082-T1
Valid prediction for GeneMark_model.105974_t
Valid prediction for GeneMark_model.105977_t
Valid prediction for snap_scaffold_28-snap.2089-T1
Valid prediction for GeneMark_model.105986_t
Valid prediction for snap_scaffold_28-snap.2085-T1
Valid prediction for GeneMark_model.105962_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 GlimmerHMM_glimmerT_60808-T1
Valid prediction for GeneMark_model.105971_t
Valid prediction for GeneMark_model.105963_t
Valid prediction for snap_scaffold_28-snap.2096-T1
Valid prediction for GlimmerHMM_glimmerT_60823-T1
Valid prediction for GeneMark_model.105968_t
Valid prediction for snap_scaffold_28-snap.2094-T1
Valid prediction for GeneMark_model.105961_t
Valid prediction for snap_scaffold_28-snap.2101-T1
Valid prediction for snap_scaffold_28-snap.2092-T1
Valid prediction for snap_scaffold_28-snap.2103-T1
Valid prediction for GeneMark_model.105958_t
Valid prediction for CodingQuarry_transcript_43656-T1
Valid prediction for snap_scaffold_28-snap.2084-T1
Valid prediction for Augustus_model.g40477.t1
Valid prediction for GlimmerHMM_glimmerT_60816-T1
Valid prediction for GeneMark_model.105966_t
Valid prediction for Augustus_model.g40478.t1
Couldn't classify 111521, 111673
Sorry, prediction pasa_asmbl_37833.p1 fails validation.
(AGG)	 GC	111521-111673	GT	CGG
(CTG)	 AG	112086-112227	GT	AGG
(ATG)	 AG	114826-114923	GT	AGG
(GCG)	 AG	115880-115975	GT	GGG
(GCT)	 AG	116592-116703	GT	TGG
(GTG)	 AG	116816-116913	GT	AGG
(TTT)	 AG	118166-118348	GC	AGG
add_exon() Sorry, pasa_asmbl_37833.p1 114826-114923-initial-1 is invalid.
-recovered pasa_asmbl_37833.p1, initial, 114826, 114923
-recovered pasa_asmbl_37833.p1, terminal, 118166, 118348
-recovered pasa_asmbl_37833.p1, internal, 112086, 112227
-recovered pasa_asmbl_37833.p1, internal, 114826, 114923
-recovered pasa_asmbl_37833.p1, internal, 115880, 115975
-recovered pasa_asmbl_37833.p1, internal, 116592, 116703
-recovered pasa_asmbl_37833.p1, internal, 116816, 116913
-recovered pasa_asmbl_37833.p1, internal, 118166, 118348
Valid prediction for Augustus_model.g40474.t1
Valid prediction for GeneMark_model.105984_t
Valid prediction for snap_scaffold_28-snap.2076-T1
Valid prediction for GeneMark_model.105956_t
Valid prediction for snap_scaffold_28-snap.2077-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.105989_t
Couldn't classify 138947, 139078
Sorry, prediction pasa_asmbl_37826.p1 fails validation.
(GGC)	 AG	138947-139078	GT	AGG
(GTG)	 AG	139921-140035	GT	TGG
(GCG)	 AG	140916-141340	GG	GAG
-recovered pasa_asmbl_37826.p1, terminal, 140916, 141340
-recovered pasa_asmbl_37826.p1, internal, 138947, 139078
-recovered pasa_asmbl_37826.p1, internal, 139921, 140035
Valid prediction for snap_scaffold_28-snap.2099-T1
Valid prediction for GeneMark_model.105987_t
Valid prediction for GeneMark_model.105990_t
Valid prediction for GeneMark_model.105959_t
Valid prediction for Augustus_model.g40471.t1
Valid prediction for GeneMark_model.105992_t
Valid prediction for Augustus_model.g40472.t1
Valid prediction for GeneMark_model.105969_t
Valid prediction for snap_scaffold_28-snap.2086-T1
Valid prediction for Augustus_model.g40470.t1
Valid prediction for GlimmerHMM_glimmerT_60813-T1
Valid prediction for Augustus_model.g40476.t1
Couldn't classify 104741, 104830
Couldn't classify 107627, 107656
Sorry, prediction pasa_asmbl_37835.p1 fails validation.
(CCG)	 AG	104741-104830	GT	AGG
(GAC)	 AG	105582-105768	GT	AGG
(CTC)	 AG	106079-106291	GT	CGG
(GTA)	 AG	106430-106692	GT	AGG
(ACC)	 AG	106813-107022	GT	AGG
(GTG)	 AG	107627-107656	CC	AGC
-recovered pasa_asmbl_37835.p1, internal, 104741, 104830
-recovered pasa_asmbl_37835.p1, internal, 105582, 105768
-recovered pasa_asmbl_37835.p1, internal, 106079, 106291
-recovered pasa_asmbl_37835.p1, internal, 106430, 106692
-recovered pasa_asmbl_37835.p1, internal, 106813, 107022
Valid prediction for snap_scaffold_28-snap.2074-T1
Valid prediction for snap_scaffold_28-snap.2087-T1
Valid prediction for GeneMark_model.105978_t
Valid prediction for GeneMark_model.105981_t
Couldn't classify 107726, 107942
Couldn't classify 111121, 111300
Sorry, prediction pasa_asmbl_37834.p1 fails validation.
(ACT)	 AG	107726-107942	GT	GGG
(GAG)	 AG	108779-108960	GT	AGG
(GTA)	 AG	109064-109183	GT	AGG
(AAA)	 AG	110127-110272	GT	AGG
(GCG)	 AG	110679-110844	GT	TGG
(CCA)	 AG	111121-111300	AA	ACA
-recovered pasa_asmbl_37834.p1, internal, 107726, 107942
-recovered pasa_asmbl_37834.p1, internal, 108779, 108960
-recovered pasa_asmbl_37834.p1, internal, 109064, 109183
-recovered pasa_asmbl_37834.p1, internal, 110127, 110272
-recovered pasa_asmbl_37834.p1, internal, 110679, 110844
Valid prediction for GlimmerHMM_glimmerT_60812-T1
Valid prediction for snap_scaffold_28-snap.2083-T1
Valid prediction for GeneMark_model.105975_t
Valid prediction for GlimmerHMM_glimmerT_60814-T1
Valid prediction for GlimmerHMM_glimmerT_60809-T1
Valid prediction for Augustus_model.g40473.t1
Valid prediction for GeneMark_model.105985_t
Valid prediction for GlimmerHMM_glimmerT_60819-T1
Valid prediction for GlimmerHMM_glimmerT_60821-T1
Valid prediction for GeneMark_model.105964_t
Valid prediction for snap_scaffold_28-snap.2098-T1
Valid prediction for snap_scaffold_28-snap.2081-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15702, rend_intergenic: 10570  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27410, rend_intergenic: 15872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37608, rend_intergenic: 35217  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56537, rend_intergenic: 45763  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73961, rend_intergenic: 64316  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118354, rend_intergenic: 115815  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123349, rend_intergenic: 121258  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125193, rend_intergenic: 124182  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157325, rend_intergenic: 149416  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 176556
-exon list size: 443


building trellis

0.2    
0.4    
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1.6    
1.8    
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2.9    
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10.6    
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11.9    
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12.6    
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14.8    
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15.5    
15.7    
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17.5    
17.8    
18.0    
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22.9    
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23.4    
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23.8    
24.0    
24.3    
24.5    
24.7    
24.9    
25.2    
25.4    
25.6    
25.8    
26.1    
26.3    
26.5    
26.7    
27.0    
27.2    
27.4    
27.6    
27.9    
28.1    
28.3    
28.5    
28.8    
29.0    
29.2    
29.4    
29.7    
29.9    
30.1    
30.3    
30.6    
30.8    
31.0    
31.2    
31.5    
31.7    
31.9    
32.1    
32.4    
32.6    
32.8    
33.0    
33.3    
33.5    
33.7    
33.9    
34.2    
34.4    
34.6    
34.8    
35.1    
35.3    
35.5    
35.7    
36.0    
36.2    
36.4    
36.6    
36.9    
37.1    
37.3    
37.5    
37.8    
38.0    
38.2    
38.4    
38.7    
38.9    
39.1    
39.3    
39.6    
39.8    
40.0    
40.2    
40.4    
40.7    
40.9    
41.1    
41.3    
41.6    
41.8    
42.0    
42.2    
42.5    
42.7    
42.9    
43.1    
43.4    
43.6    
43.8    
44.0    
44.3    
44.5    
44.7    
44.9    
45.2    
45.4    
45.6    
45.8    
46.1    
46.3    
46.5    
46.7    
47.0    
47.2    
47.4    
47.6    
47.9    
48.1    
48.3    
48.5    
48.8    
49.0    
49.2    
49.4    
49.7    
49.9    
50.1    
50.3    
50.6    
50.8    
51.0    
51.2    
51.5    
51.7    
51.9    
52.1    
52.4    
52.6    
52.8    
53.0    
53.3    
53.5    
53.7    
53.9    
54.2    
54.4    
54.6    
54.8    
55.1    
55.3    
55.5    
55.7    
56.0    
56.2    
56.4    
56.6    
56.9    
57.1    
57.3    
57.5    
57.8    
58.0    
58.2    
58.4    
58.7    
58.9    
59.1    
59.3    
59.6    
59.8    
60.0    
60.2    
60.4    
60.7    
60.9    
61.1    
61.3    
61.6    
61.8    
62.0    
62.2    
62.5    
62.7    
62.9    
63.1    
63.4    
63.6    
63.8    
64.0    
64.3    
64.5    
64.7    
64.9    
65.2    
65.4    
65.6    
65.8    
66.1    
66.3    
66.5    
66.7    
67.0    
67.2    
67.4    
67.6    
67.9    
68.1    
68.3    
68.5    
68.8    
69.0    
69.2    
69.4    
69.7    
69.9    
70.1    
70.3    
70.6    
70.8    
71.0    
71.2    
71.5    
71.7    
71.9    
72.1    
72.4    
72.6    
72.8    
73.0    
73.3    
73.5    
73.7    
73.9    
74.2    
74.4    
74.6    
74.8    
75.1    
75.3    
75.5    
75.7    
76.0    
76.2    
76.4    
76.6    
76.9    
77.1    
77.3    
77.5    
77.8    
78.0    
78.2    
78.4    
78.7    
78.9    
79.1    
79.3    
79.6    
79.8    
80.0    
80.2    
80.4    
80.7    
80.9    
81.1    
81.3    
81.6    
81.8    
82.0    
82.2    
82.5    
82.7    
82.9    
83.1    
83.4    
83.6    
83.8    
84.0    
84.3    
84.5    
84.7    
84.9    
85.2    
85.4    
85.6    
85.8    
86.1    
86.3    
86.5    
86.7    
87.0    
87.2    
87.4    
87.6    
87.9    
88.1    
88.3    
88.5    
88.8    
89.0    
89.2    
89.4    
89.7    
89.9    
90.1    
90.3    
90.6    
90.8    
91.0    
91.2    
91.5    
91.7    
91.9    
92.1    
92.4    
92.6    
92.8    
93.0    
93.3    
93.5    
93.7    
93.9    
94.2    
94.4    
94.6    
94.8    
95.1    
95.3    
95.5    
95.7    
96.0    
96.2    
96.4    
96.6    
96.9    
97.1    
97.3    
97.5    
97.8    
98.0    
98.2    
98.4    
98.7    
98.9    
99.1    
99.3    
99.6    
99.8    
-found 19 predictions from path traversal
Error with prediction: snap lend_intergenic: 15702, rend_intergenic: 10570  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27410, rend_intergenic: 15872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37608, rend_intergenic: 35217  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56537, rend_intergenic: 45763  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73961, rend_intergenic: 64316  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118354, rend_intergenic: 115815  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123349, rend_intergenic: 121258  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125193, rend_intergenic: 124182  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157325, rend_intergenic: 149416  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 13 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 12247
-exon list size: 29


building trellis

3.2    
6.5    
9.7    
12.9    
16.1    
19.4    
22.6    
25.8    
29.0    
32.3    
35.5    
38.7    
41.9    
45.2    
48.4    
51.6    
54.8    
58.1    
61.3    
64.5    
67.7    
71.0    
74.2    
77.4    
80.6    
83.9    
87.1    
90.3    
93.5    
96.8    
-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 1 - 10750
-exon list size: 18


building trellis

5.0    
10.0    
15.0    
20.0    
25.0    
30.0    
35.0    
40.0    
45.0    
50.0    
55.0    
60.0    
65.0    
70.0    
75.0    
80.0    
85.0    
90.0    
95.0    
-found 1 predictions from path traversal

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

-building DP trellis

-building trellis in range 1 - 10347
-exon list size: 16


building trellis

5.6    
11.1    
16.7    
22.2    
27.8    
33.3    
38.9    
44.4    
50.0    
55.6    
61.1    
66.7    
72.2    
77.8    
83.3    
88.9    
94.4    
-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