-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_6/scaffold_6_12933934-13131771

-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 Augustus_model.g10822.t1
Valid prediction for snap_scaffold_6-snap.2717-T1
Couldn't classify 146704, 146890
Sorry, prediction pasa_asmbl_47407.p1 fails validation.
(AGA)	 TC	146704-146890	GT	GGG
(CTC)	 AG	147599-147708	GT	AGG
(CCA)	 AG	148189-148308	AA	GAA
-recovered pasa_asmbl_47407.p1, terminal, 148189, 148308
-recovered pasa_asmbl_47407.p1, internal, 147599, 147708
Valid prediction for GeneMark_model.26913_t
Valid prediction for snap_scaffold_6-snap.2723-T1
Valid prediction for snap_scaffold_6-snap.2718-T1
Valid prediction for GlimmerHMM_glimmerT_16093-T1
Valid prediction for GlimmerHMM_glimmerT_16105-T1
Valid prediction for GlimmerHMM_glimmerT_16089-T1
Valid prediction for GlimmerHMM_glimmerT_16102-T1
Valid prediction for Augustus_model.g10840.t1
Valid prediction for snap_scaffold_6-snap.2735-T1
Valid prediction for GlimmerHMM_glimmerT_16107-T1
Valid prediction for snap_scaffold_6-snap.2719-T1
Valid prediction for GeneMark_model.26925_t
Valid prediction for snap_scaffold_6-snap.2724-T1
Valid prediction for GlimmerHMM_glimmerT_16095-T1
Valid prediction for GlimmerHMM_glimmerT_16098-T1
Valid prediction for snap_scaffold_6-snap.2703-T1
Valid prediction for snap_scaffold_6-snap.2713-T1
Valid prediction for pasa_asmbl_47395.p1
Valid prediction for Augustus_model.g10841.t1
Valid prediction for GeneMark_model.26903_t
Valid prediction for GeneMark_model.26914_t
Valid prediction for Augustus_model.g10843.t1
Valid prediction for snap_scaffold_6-snap.2725-T1
Valid prediction for GlimmerHMM_glimmerT_16109-T1
Valid prediction for Augustus_model.g10833.t1
Valid prediction for CodingQuarry_transcript_55125-T1
Valid prediction for snap_scaffold_6-snap.2706-T1
Valid prediction for GlimmerHMM_glimmerT_16087-T1
Valid prediction for snap_scaffold_6-snap.2729-T1
Valid prediction for Augustus_model.g10826.t1
Valid prediction for GlimmerHMM_glimmerT_16111-T1
Valid prediction for Augustus_model.g10842.t1
Couldn't classify 3678, 3794
Couldn't classify 6709, 6918
Sorry, prediction pasa_asmbl_47392.p1 fails validation.
(CCT)	 AT	3678-3794	GT	ATG
(GTG)	 AG	3989-4044	GT	ATG
(CTA)	 AG	5973-6079	GT	AGG
(GAC)	 AG	6347-6432	GT	AGG
(ATC)	 AG	6709-6918	GT	AGG
-recovered pasa_asmbl_47392.p1, internal, 3989, 4044
-recovered pasa_asmbl_47392.p1, internal, 5973, 6079
-recovered pasa_asmbl_47392.p1, internal, 6347, 6432
-recovered pasa_asmbl_47392.p1, internal, 6709, 6918
Valid prediction for snap_scaffold_6-snap.2715-T1
Valid prediction for Augustus_model.g10824.t1
Valid prediction for Augustus_model.g10837.t1
Valid prediction for GeneMark_model.26923_t
Valid prediction for GeneMark_model.26919_t
Valid prediction for snap_scaffold_6-snap.2714-T1
Valid prediction for CodingQuarry_transcript_55124-T1
Valid prediction for GlimmerHMM_glimmerT_16085-T1
Valid prediction for GeneMark_model.26905_t
Valid prediction for Augustus_model.g10838.t1
Valid prediction for snap_scaffold_6-snap.2728-T1
Couldn't classify 48756, 48798
Sorry, prediction pasa_asmbl_47402.p1 fails validation.
(GTA)	 TT	48756-48798	GT	TGG
(AGG)	 AG	48915-48926	GT	AGG
(TGC)	 AG	49230-49384	GT	AGG
(GCA)	 AG	49727-49843	GT	AGG
(GTT)	 AG	50527-50631	GG	GAG
-recovered pasa_asmbl_47402.p1, terminal, 50527, 50631
-recovered pasa_asmbl_47402.p1, internal, 48915, 48926
-recovered pasa_asmbl_47402.p1, internal, 49230, 49384
-recovered pasa_asmbl_47402.p1, internal, 49727, 49843
Valid prediction for snap_scaffold_6-snap.2732-T1
Valid prediction for CodingQuarry_transcript_55123-T1
Valid prediction for GeneMark_model.26908_t
Valid prediction for snap_scaffold_6-snap.2731-T1
Couldn't classify 14648, 14749
Sorry, prediction pasa_asmbl_47394.p1 fails validation.
(TTG)	 AG	14648-14749	GT	CGG
(CCC)	 AG	14943-15029	GT	CTG
(TCT)	 AG	15142-15340	GT	AGG
(AGC)	 AG	15564-15657	GT	AGG
(GTC)	 AG	15759-15807	GA	GAG
add_exon() Sorry, pasa_asmbl_47394.p1 15564-15657-terminal-3 is invalid.
-recovered pasa_asmbl_47394.p1, terminal, 15564, 15657
-recovered pasa_asmbl_47394.p1, terminal, 15759, 15807
-recovered pasa_asmbl_47394.p1, internal, 14648, 14749
-recovered pasa_asmbl_47394.p1, internal, 14943, 15029
-recovered pasa_asmbl_47394.p1, internal, 15142, 15340
-recovered pasa_asmbl_47394.p1, internal, 15564, 15657
Valid prediction for Augustus_model.g10825.t1
Valid prediction for CodingQuarry_transcript_55132-T1
Valid prediction for Augustus_model.g10846.t1
Couldn't classify 140814, 140930
Sorry, prediction pasa_asmbl_47405.p1 fails validation.
(ATG)	 AC	134773-134984	GT	TGG
(CTC)	 AG	136402-136584	GT	GTG
(TTA)	 AG	137125-137314	GT	AGG
(ATC)	 AG	138275-138391	GT	AGG
(GGC)	 AG	140814-140930	AA	GTA
-recovered pasa_asmbl_47405.p1, initial, 134773, 134984
-recovered pasa_asmbl_47405.p1, internal, 136402, 136584
-recovered pasa_asmbl_47405.p1, internal, 137125, 137314
-recovered pasa_asmbl_47405.p1, internal, 138275, 138391
Valid prediction for HiQ_model.g10839.t1
Valid prediction for snap_scaffold_6-snap.2698-T1
Valid prediction for CodingQuarry_transcript_55122-T1
Valid prediction for GlimmerHMM_glimmerT_16090-T1
Valid prediction for GeneMark_model.26910_t
Valid prediction for HiQ_model.g10827.t1
Valid prediction for GeneMark_model.26904_t
Valid prediction for snap_scaffold_6-snap.2733-T1
Valid prediction for snap_scaffold_6-snap.2712-T1
Valid prediction for Augustus_model.g10829.t1
Valid prediction for snap_scaffold_6-snap.2730-T1
Valid prediction for GlimmerHMM_glimmerT_16104-T1
Valid prediction for GeneMark_model.26921_t
Valid prediction for GeneMark_model.26917_t
Valid prediction for GlimmerHMM_glimmerT_16106-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 GlimmerHMM_glimmerT_16091-T1
Valid prediction for Augustus_model.g10835.t1
Valid prediction for Augustus_model.g10828.t1
Valid prediction for Augustus_model.g10836.t1
Valid prediction for pasa_asmbl_48794.p1
Valid prediction for GeneMark_model.26902_t
Valid prediction for GeneMark_model.26922_t
Valid prediction for GlimmerHMM_glimmerT_16099-T1
Couldn't classify 5297, 5380
Sorry, prediction pasa_asmbl_48816.p1 fails validation.
(CTG)	 AG	5297-5380	GT	TGG
(TTC)	 AG	5575-5688	GT	AGG
(CCT)	 AG	6225-6308	GT	AGG
(ATC)	 AG	6667-6735	CC	GAC
-recovered pasa_asmbl_48816.p1, terminal, 6667, 6735
-recovered pasa_asmbl_48816.p1, internal, 5297, 5380
-recovered pasa_asmbl_48816.p1, internal, 5575, 5688
-recovered pasa_asmbl_48816.p1, internal, 6225, 6308
Couldn't classify 197003, 197311
Sorry, prediction pasa_asmbl_47391.p1 fails validation.
(CCC)	 GC	197003-197311	CA	AGC
Valid prediction for snap_scaffold_6-snap.2705-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_6-snap.2726-T1
Valid prediction for snap_scaffold_6-snap.2707-T1
Valid prediction for GeneMark_model.26907_t
Valid prediction for GlimmerHMM_glimmerT_16110-T1
Valid prediction for HiQ_model.g10830.t1
Valid prediction for Augustus_model.g10844.t1
Valid prediction for snap_scaffold_6-snap.2720-T1
Valid prediction for GeneMark_model.26906_t
Valid prediction for snap_scaffold_6-snap.2701-T1
Valid prediction for snap_scaffold_6-snap.2716-T1
Valid prediction for CodingQuarry_transcript_55131-T1
Valid prediction for GlimmerHMM_glimmerT_16100-T1
Valid prediction for snap_scaffold_6-snap.2710-T1
Valid prediction for GeneMark_model.26916_t
Valid prediction for GeneMark_model.26927_t
Valid prediction for GeneMark_model.26909_t
Valid prediction for GeneMark_model.26915_t
Valid prediction for GeneMark_model.26911_t
Valid prediction for snap_scaffold_6-snap.2722-T1
Couldn't classify 100747, 101550
Sorry, prediction pasa_asmbl_47404.p1 fails validation.
(CTG)	 CT	100747-101550	CC	AGC
Valid prediction for snap_scaffold_6-snap.2708-T1
Valid prediction for snap_scaffold_6-snap.2721-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_6-snap.2727-T1
Valid prediction for GeneMark_model.26926_t
Valid prediction for snap_scaffold_6-snap.2704-T1
Valid prediction for snap_scaffold_6-snap.2711-T1
Valid prediction for Augustus_model.g10832.t1
Valid prediction for snap_scaffold_6-snap.2699-T1
Valid prediction for GlimmerHMM_glimmerT_16084-T1
Valid prediction for snap_scaffold_6-snap.2702-T1
Valid prediction for Augustus_model.g10834.t1
Valid prediction for GlimmerHMM_glimmerT_16096-T1
Valid prediction for GlimmerHMM_glimmerT_16103-T1
Valid prediction for GlimmerHMM_glimmerT_16086-T1
Valid prediction for snap_scaffold_6-snap.2734-T1
Valid prediction for Augustus_model.g10831.t1
Couldn't classify 84437, 84554
Couldn't classify 85997, 86135
Sorry, prediction pasa_asmbl_48809.p1 fails validation.
(GAG)	 CA	84437-84554	GT	GGG
(GGG)	 AG	85053-85213	GT	AGG
(AGA)	 AG	85376-85474	GT	AGG
(CAA)	 AG	85678-85823	GT	AGG
(GCA)	 AG	85997-86135	GA	GGG
-recovered pasa_asmbl_48809.p1, internal, 85053, 85213
-recovered pasa_asmbl_48809.p1, internal, 85376, 85474
-recovered pasa_asmbl_48809.p1, internal, 85678, 85823
Valid prediction for GlimmerHMM_glimmerT_16101-T1
Valid prediction for snap_scaffold_6-snap.2700-T1
Valid prediction for CodingQuarry_transcript_55128-T1
Valid prediction for GeneMark_model.26912_t
Valid prediction for HiQ_model.g10845.t1
Valid prediction for GlimmerHMM_glimmerT_16094-T1
Valid prediction for GeneMark_model.26918_t
Valid prediction for GlimmerHMM_glimmerT_16097-T1
Valid prediction for GlimmerHMM_glimmerT_16088-T1
Valid prediction for CodingQuarry_transcript_55130-T1
Valid prediction for pasa_asmbl_48810.p1
Valid prediction for Augustus_model.g10823.t1
Valid prediction for GlimmerHMM_glimmerT_16108-T1
Valid prediction for CodingQuarry_transcript_55129-T1
Valid prediction for snap_scaffold_6-snap.2709-T1
Valid prediction for CodingQuarry_transcript_55127-T1
Valid prediction for GeneMark_model.26920_t
Valid prediction for CodingQuarry_transcript_55126-T1
Valid prediction for GlimmerHMM_glimmerT_16092-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)
-building DP trellis

-building trellis in range 1 - 197838
-exon list size: 431


building trellis

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1.6    
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2.3    
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2.8    
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3.7    
3.9    
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5.8    
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6.7    
6.9    
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7.9    
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8.3    
8.5    
8.8    
9.0    
9.2    
9.5    
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9.9    
10.2    
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10.6    
10.9    
11.1    
11.3    
11.5    
11.8    
12.0    
12.2    
12.5    
12.7    
12.9    
13.2    
13.4    
13.6    
13.9    
14.1    
14.3    
14.5    
14.8    
15.0    
15.2    
15.5    
15.7    
15.9    
16.2    
16.4    
16.6    
16.9    
17.1    
17.3    
17.6    
17.8    
18.0    
18.2    
18.5    
18.7    
18.9    
19.2    
19.4    
19.6    
19.9    
20.1    
20.3    
20.6    
20.8    
21.0    
21.2    
21.5    
21.7    
21.9    
22.2    
22.4    
22.6    
22.9    
23.1    
23.3    
23.6    
23.8    
24.0    
24.2    
24.5    
24.7    
24.9    
25.2    
25.4    
25.6    
25.9    
26.1    
26.3    
26.6    
26.8    
27.0    
27.3    
27.5    
27.7    
27.9    
28.2    
28.4    
28.6    
28.9    
29.1    
29.3    
29.6    
29.8    
30.0    
30.3    
30.5    
30.7    
30.9    
31.2    
31.4    
31.6    
31.9    
32.1    
32.3    
32.6    
32.8    
33.0    
33.3    
33.5    
33.7    
33.9    
34.2    
34.4    
34.6    
34.9    
35.1    
35.3    
35.6    
35.8    
36.0    
36.3    
36.5    
36.7    
37.0    
37.2    
37.4    
37.6    
37.9    
38.1    
38.3    
38.6    
38.8    
39.0    
39.3    
39.5    
39.7    
40.0    
40.2    
40.4    
40.6    
40.9    
41.1    
41.3    
41.6    
41.8    
42.0    
42.3    
42.5    
42.7    
43.0    
43.2    
43.4    
43.6    
43.9    
44.1    
44.3    
44.6    
44.8    
45.0    
45.3    
45.5    
45.7    
46.0    
46.2    
46.4    
46.7    
46.9    
47.1    
47.3    
47.6    
47.8    
48.0    
48.3    
48.5    
48.7    
49.0    
49.2    
49.4    
49.7    
49.9    
50.1    
50.3    
50.6    
50.8    
51.0    
51.3    
51.5    
51.7    
52.0    
52.2    
52.4    
52.7    
52.9    
53.1    
53.3    
53.6    
53.8    
54.0    
54.3    
54.5    
54.7    
55.0    
55.2    
55.4    
55.7    
55.9    
56.1    
56.4    
56.6    
56.8    
57.0    
57.3    
57.5    
57.7    
58.0    
58.2    
58.4    
58.7    
58.9    
59.1    
59.4    
59.6    
59.8    
60.0    
60.3    
60.5    
60.7    
61.0    
61.2    
61.4    
61.7    
61.9    
62.1    
62.4    
62.6    
62.8    
63.0    
63.3    
63.5    
63.7    
64.0    
64.2    
64.4    
64.7    
64.9    
65.1    
65.4    
65.6    
65.8    
66.1    
66.3    
66.5    
66.7    
67.0    
67.2    
67.4    
67.7    
67.9    
68.1    
68.4    
68.6    
68.8    
69.1    
69.3    
69.5    
69.7    
70.0    
70.2    
70.4    
70.7    
70.9    
71.1    
71.4    
71.6    
71.8    
72.1    
72.3    
72.5    
72.7    
73.0    
73.2    
73.4    
73.7    
73.9    
74.1    
74.4    
74.6    
74.8    
75.1    
75.3    
75.5    
75.8    
76.0    
76.2    
76.4    
76.7    
76.9    
77.1    
77.4    
77.6    
77.8    
78.1    
78.3    
78.5    
78.8    
79.0    
79.2    
79.4    
79.7    
79.9    
80.1    
80.4    
80.6    
80.8    
81.1    
81.3    
81.5    
81.8    
82.0    
82.2    
82.4    
82.7    
82.9    
83.1    
83.4    
83.6    
83.8    
84.1    
84.3    
84.5    
84.8    
85.0    
85.2    
85.5    
85.7    
85.9    
86.1    
86.4    
86.6    
86.8    
87.1    
87.3    
87.5    
87.8    
88.0    
88.2    
88.5    
88.7    
88.9    
89.1    
89.4    
89.6    
89.8    
90.1    
90.3    
90.5    
90.8    
91.0    
91.2    
91.5    
91.7    
91.9    
92.1    
92.4    
92.6    
92.8    
93.1    
93.3    
93.5    
93.8    
94.0    
94.2    
94.5    
94.7    
94.9    
95.2    
95.4    
95.6    
95.8    
96.1    
96.3    
96.5    
96.8    
97.0    
97.2    
97.5    
97.7    
97.9    
98.2    
98.4    
98.6    
98.8    
99.1    
99.3    
99.5    
99.8    
-found 31 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 30 predictions persist after filtering for low support