-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_7/scaffold_7_3776687-3998912

-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_17659-T1
Valid prediction for pasa_asmbl_50582.p1
Valid prediction for GeneMark_model.29755_t
Valid prediction for snap_scaffold_7-snap.908-T1
Valid prediction for snap_scaffold_7-snap.936-T1
Valid prediction for GeneMark_model.29738_t
Valid prediction for GlimmerHMM_glimmerT_17662-T1
Valid prediction for GeneMark_model.29740_t
Valid prediction for snap_scaffold_7-snap.929-T1
Valid prediction for HiQ_model.g11823.t1
Valid prediction for CodingQuarry_transcript_57312-T1
Valid prediction for CodingQuarry_transcript_57315-T1
Valid prediction for GlimmerHMM_glimmerT_17644-T1
Valid prediction for GlimmerHMM_glimmerT_17641-T1
Valid prediction for GlimmerHMM_glimmerT_17658-T1
Valid prediction for GeneMark_model.29742_t
Valid prediction for snap_scaffold_7-snap.937-T1
Valid prediction for GeneMark_model.29764_t
Valid prediction for GlimmerHMM_glimmerT_17654-T1
Valid prediction for snap_scaffold_7-snap.919-T1
Valid prediction for snap_scaffold_7-snap.921-T1
Couldn't classify 35743, 35815
Couldn't classify 39012, 39083
Sorry, prediction pasa_asmbl_50579.p1 fails validation.
(CCA)	 CA	35743-35815	GT	AGG
(AAC)	 AG	38389-38546	GT	AGG
(ATC)	 AG	38664-38822	GT	AGG
(GCG)	 AG	39012-39083	TC	GGT
-recovered pasa_asmbl_50579.p1, internal, 38389, 38546
-recovered pasa_asmbl_50579.p1, internal, 38664, 38822
Valid prediction for GlimmerHMM_glimmerT_17651-T1
Valid prediction for GeneMark_model.29736_t
Valid prediction for GeneMark_model.29733_t
Valid prediction for Augustus_model.g11827.t1
Valid prediction for GlimmerHMM_glimmerT_17639-T1
Valid prediction for snap_scaffold_7-snap.905-T1
Valid prediction for Augustus_model.g11829.t1
Valid prediction for snap_scaffold_7-snap.941-T1
Valid prediction for snap_scaffold_7-snap.943-T1
Valid prediction for snap_scaffold_7-snap.930-T1
Valid prediction for snap_scaffold_7-snap.926-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_7-snap.938-T1
Valid prediction for snap_scaffold_7-snap.932-T1
Valid prediction for GeneMark_model.29761_t
Valid prediction for Augustus_model.g11811.t1
Valid prediction for GeneMark_model.29754_t
Valid prediction for snap_scaffold_7-snap.910-T1
Valid prediction for GlimmerHMM_glimmerT_17648-T1
Valid prediction for CodingQuarry_transcript_57322-T1
Valid prediction for GeneMark_model.29735_t
Valid prediction for GlimmerHMM_glimmerT_17660-T1
Valid prediction for GeneMark_model.29765_t
Valid prediction for GeneMark_model.29747_t
Valid prediction for snap_scaffold_7-snap.935-T1
Valid prediction for GlimmerHMM_glimmerT_17661-T1
Valid prediction for Augustus_model.g11813.t1
Couldn't classify 39472, 39540
Sorry, prediction pasa_asmbl_50581.p1 fails validation.
(TTC)	 GC	39472-39540	GT	GGG
(ATC)	 AG	40055-40157	GT	GGG
(AGG)	 AG	41234-41360	GT	AGG
(GAC)	 AG	41637-41700	CA	GAC
-recovered pasa_asmbl_50581.p1, terminal, 41637, 41700
-recovered pasa_asmbl_50581.p1, internal, 40055, 40157
-recovered pasa_asmbl_50581.p1, internal, 41234, 41360
Valid prediction for snap_scaffold_7-snap.942-T1
Valid prediction for Augustus_model.g11828.t1
Valid prediction for snap_scaffold_7-snap.925-T1
Valid prediction for pasa_asmbl_50584.p1

-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 HiQ_model.g11824.t1
Valid prediction for GlimmerHMM_glimmerT_17650-T1
Valid prediction for Augustus_model.g11815.t1
Valid prediction for GeneMark_model.29759_t
Valid prediction for pasa_asmbl_49646.p1
Valid prediction for CodingQuarry_transcript_57316-T1
Valid prediction for Augustus_model.g11810.t1
Valid prediction for GlimmerHMM_glimmerT_17653-T1
Valid prediction for CodingQuarry_transcript_57321-T1
Valid prediction for snap_scaffold_7-snap.924-T1
Valid prediction for HiQ_model.g11826.t1
Valid prediction for Augustus_model.g11816.t1
Valid prediction for snap_scaffold_7-snap.927-T1
Couldn't classify 124627, 124660
Couldn't classify 127425, 127482
Sorry, prediction pasa_asmbl_49634.p1 fails validation.
(GCT)	 AG	124627-124660	GT	AGG
(AGC)	 AG	124907-125633	GT	AGG
(GAA)	 AG	126793-126924	GT	AAG
(GTA)	 AG	127425-127482	AT	GGA
-recovered pasa_asmbl_49634.p1, internal, 124627, 124660
-recovered pasa_asmbl_49634.p1, internal, 124907, 125633
-recovered pasa_asmbl_49634.p1, internal, 126793, 126924
Valid prediction for Augustus_model.g11818.t1
Valid prediction for GeneMark_model.29746_t
Valid prediction for GeneMark_model.29744_t
Valid prediction for snap_scaffold_7-snap.922-T1
Valid prediction for snap_scaffold_7-snap.920-T1
Valid prediction for GeneMark_model.29758_t
Valid prediction for snap_scaffold_7-snap.915-T1
Valid prediction for CodingQuarry_transcript_57317-T1
Valid prediction for snap_scaffold_7-snap.928-T1
Valid prediction for Augustus_model.g11821.t1
Valid prediction for snap_scaffold_7-snap.940-T1
Valid prediction for snap_scaffold_7-snap.907-T1
Valid prediction for CodingQuarry_transcript_57318-T1
Valid prediction for Augustus_model.g11822.t1
Valid prediction for GeneMark_model.29763_t
Valid prediction for snap_scaffold_7-snap.914-T1
Valid prediction for GeneMark_model.29737_t
Valid prediction for HiQ_model.g11819.t1
Valid prediction for GeneMark_model.29751_t
Valid prediction for pasa_asmbl_49651.p1
Valid prediction for GeneMark_model.29753_t
Valid prediction for GeneMark_model.29760_t
Valid prediction for snap_scaffold_7-snap.906-T1
Valid prediction for Augustus_model.g11812.t1
Valid prediction for snap_scaffold_7-snap.911-T1
Valid prediction for snap_scaffold_7-snap.913-T1
Valid prediction for GlimmerHMM_glimmerT_17655-T1
Valid prediction for GlimmerHMM_glimmerT_17646-T1
Valid prediction for snap_scaffold_7-snap.931-T1
Valid prediction for GeneMark_model.29756_t
Valid prediction for CodingQuarry_transcript_57320-T1
Couldn't classify 176300, 176447
Sorry, prediction pasa_asmbl_49628.p1 fails validation.
(GGT)	 CT	176300-176447	GT	AGG
(CAC)	 AG	176653-176720	GT	CAG
(CCT)	 AG	177528-177725	AG	AGA
-recovered pasa_asmbl_49628.p1, terminal, 177528, 177725
-recovered pasa_asmbl_49628.p1, internal, 176653, 176720
Valid prediction for Augustus_model.g11817.t1
Valid prediction for GeneMark_model.29748_t
Valid prediction for GeneMark_model.29739_t
Valid prediction for snap_scaffold_7-snap.934-T1
Valid prediction for CodingQuarry_transcript_57319-T1
Valid prediction for GlimmerHMM_glimmerT_17645-T1
Valid prediction for pasa_asmbl_49641.p1
Valid prediction for GeneMark_model.29745_t
Valid prediction for snap_scaffold_7-snap.933-T1
Valid prediction for snap_scaffold_7-snap.916-T1
Valid prediction for snap_scaffold_7-snap.918-T1
Valid prediction for HiQ_model.g11825.t1
Valid prediction for GlimmerHMM_glimmerT_17647-T1
Valid prediction for snap_scaffold_7-snap.909-T1
Valid prediction for GeneMark_model.29762_t
Couldn't classify 136896, 136991
Couldn't classify 137614, 137709
Sorry, prediction pasa_asmbl_49633.p1 fails validation.
(GAG)	 TG	136896-136991	GT	AGG
(GAC)	 AG	137376-137495	GT	AGG
(GCT)	 AG	137614-137709	TG	GGT
-recovered pasa_asmbl_49633.p1, internal, 137376, 137495
Valid prediction for snap_scaffold_7-snap.939-T1
Valid prediction for GeneMark_model.29757_t
Valid prediction for GlimmerHMM_glimmerT_17656-T1
Valid prediction for GlimmerHMM_glimmerT_17642-T1
Valid prediction for GeneMark_model.29743_t
Valid prediction for snap_scaffold_7-snap.917-T1
Valid prediction for Augustus_model.g11820.t1
Valid prediction for CodingQuarry_transcript_57314-T1
Valid prediction for GeneMark_model.29750_t
Valid prediction for GlimmerHMM_glimmerT_17640-T1
Valid prediction for GlimmerHMM_glimmerT_17649-T1
Valid prediction for GeneMark_model.29749_t
Valid prediction for GlimmerHMM_glimmerT_17657-T1
Valid prediction for snap_scaffold_7-snap.923-T1
Valid prediction for GeneMark_model.29741_t
Couldn't classify 138538, 139006
Couldn't classify 140363, 140420
Sorry, prediction pasa_asmbl_49632.p1 fails validation.
(GAA)	 CT	138538-139006	GT	TGG
(GCA)	 AG	139420-139588	GT	AGG
(GAA)	 AG	140363-140420	CC	CTC
-recovered pasa_asmbl_49632.p1, internal, 139420, 139588
Valid prediction for GlimmerHMM_glimmerT_17643-T1
Valid prediction for GeneMark_model.29734_t
Valid prediction for GeneMark_model.29752_t
Valid prediction for Augustus_model.g11814.t1
Valid prediction for GeneMark_model.29732_t
Valid prediction for GlimmerHMM_glimmerT_17652-T1
Valid prediction for snap_scaffold_7-snap.912-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10208, rend_intergenic: 1652  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15773, rend_intergenic: 11774  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43919, rend_intergenic: 17301  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62607, rend_intergenic: 55991  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64039, rend_intergenic: 63606  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65724, rend_intergenic: 65129  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71456, rend_intergenic: 65738  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91767, rend_intergenic: 82889  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97844, rend_intergenic: 92547  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121876, rend_intergenic: 117917  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128495, rend_intergenic: 125979  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140099, rend_intergenic: 137539  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179110, rend_intergenic: 177324  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 222226
-exon list size: 513


building trellis

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9.1    
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10.9    
11.1    
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14.0    
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14.8    
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15.5    
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16.1    
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17.7    
17.9    
18.1    
18.3    
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18.6    
18.8    
19.0    
19.2    
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19.6    
19.8    
20.0    
20.2    
20.4    
20.6    
20.8    
21.0    
21.2    
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21.6    
21.7    
21.9    
22.1    
22.3    
22.5    
22.7    
22.9    
23.1    
23.3    
23.5    
23.7    
23.9    
24.1    
24.3    
24.5    
24.7    
24.9    
25.0    
25.2    
25.4    
25.6    
25.8    
26.0    
26.2    
26.4    
26.6    
26.8    
27.0    
27.2    
27.4    
27.6    
27.8    
28.0    
28.2    
28.3    
28.5    
28.7    
28.9    
29.1    
29.3    
29.5    
29.7    
29.9    
30.1    
30.3    
30.5    
30.7    
30.9    
31.1    
31.3    
31.5    
31.7    
31.8    
32.0    
32.2    
32.4    
32.6    
32.8    
33.0    
33.2    
33.4    
33.6    
33.8    
34.0    
34.2    
34.4    
34.6    
34.8    
35.0    
35.1    
35.3    
35.5    
35.7    
35.9    
36.1    
36.3    
36.5    
36.7    
36.9    
37.1    
37.3    
37.5    
37.7    
37.9    
38.1    
38.3    
38.4    
38.6    
38.8    
39.0    
39.2    
39.4    
39.6    
39.8    
40.0    
40.2    
40.4    
40.6    
40.8    
41.0    
41.2    
41.4    
41.6    
41.7    
41.9    
42.1    
42.3    
42.5    
42.7    
42.9    
43.1    
43.3    
43.5    
43.7    
43.9    
44.1    
44.3    
44.5    
44.7    
44.9    
45.0    
45.2    
45.4    
45.6    
45.8    
46.0    
46.2    
46.4    
46.6    
46.8    
47.0    
47.2    
47.4    
47.6    
47.8    
48.0    
48.2    
48.3    
48.5    
48.7    
48.9    
49.1    
49.3    
49.5    
49.7    
49.9    
50.1    
50.3    
50.5    
50.7    
50.9    
51.1    
51.3    
51.5    
51.7    
51.8    
52.0    
52.2    
52.4    
52.6    
52.8    
53.0    
53.2    
53.4    
53.6    
53.8    
54.0    
54.2    
54.4    
54.6    
54.8    
55.0    
55.1    
55.3    
55.5    
55.7    
55.9    
56.1    
56.3    
56.5    
56.7    
56.9    
57.1    
57.3    
57.5    
57.7    
57.9    
58.1    
58.3    
58.4    
58.6    
58.8    
59.0    
59.2    
59.4    
59.6    
59.8    
60.0    
60.2    
60.4    
60.6    
60.8    
61.0    
61.2    
61.4    
61.6    
61.7    
61.9    
62.1    
62.3    
62.5    
62.7    
62.9    
63.1    
63.3    
63.5    
63.7    
63.9    
64.1    
64.3    
64.5    
64.7    
64.9    
65.0    
65.2    
65.4    
65.6    
65.8    
66.0    
66.2    
66.4    
66.6    
66.8    
67.0    
67.2    
67.4    
67.6    
67.8    
68.0    
68.2    
68.3    
68.5    
68.7    
68.9    
69.1    
69.3    
69.5    
69.7    
69.9    
70.1    
70.3    
70.5    
70.7    
70.9    
71.1    
71.3    
71.5    
71.7    
71.8    
72.0    
72.2    
72.4    
72.6    
72.8    
73.0    
73.2    
73.4    
73.6    
73.8    
74.0    
74.2    
74.4    
74.6    
74.8    
75.0    
75.1    
75.3    
75.5    
75.7    
75.9    
76.1    
76.3    
76.5    
76.7    
76.9    
77.1    
77.3    
77.5    
77.7    
77.9    
78.1    
78.3    
78.4    
78.6    
78.8    
79.0    
79.2    
79.4    
79.6    
79.8    
80.0    
80.2    
80.4    
80.6    
80.8    
81.0    
81.2    
81.4    
81.6    
81.7    
81.9    
82.1    
82.3    
82.5    
82.7    
82.9    
83.1    
83.3    
83.5    
83.7    
83.9    
84.1    
84.3    
84.5    
84.7    
84.9    
85.0    
85.2    
85.4    
85.6    
85.8    
86.0    
86.2    
86.4    
86.6    
86.8    
87.0    
87.2    
87.4    
87.6    
87.8    
88.0    
88.2    
88.3    
88.5    
88.7    
88.9    
89.1    
89.3    
89.5    
89.7    
89.9    
90.1    
90.3    
90.5    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
91.8    
92.0    
92.2    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
94.0    
94.2    
94.4    
94.6    
94.8    
95.0    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 10208, rend_intergenic: 1652  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15773, rend_intergenic: 11774  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43919, rend_intergenic: 17301  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62607, rend_intergenic: 55991  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64039, rend_intergenic: 63606  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65724, rend_intergenic: 65129  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71456, rend_intergenic: 65738  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91767, rend_intergenic: 82889  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97844, rend_intergenic: 92547  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121876, rend_intergenic: 117917  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128495, rend_intergenic: 125979  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140099, rend_intergenic: 137539  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179110, rend_intergenic: 177324  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 200555 - 222226
-exon list size: 6


building trellis

12.5    
25.0    
37.5    
50.0    
62.5    
75.0    
87.5    
-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 206918 - 222226
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-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

-building DP trellis

-building trellis in range 206918 - 220531
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-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