-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_22/scaffold_22_10883606-10996956

-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_22-snap.2273-T1
Valid prediction for GeneMark_model.89394_t
Valid prediction for GlimmerHMM_glimmerT_51404-T1
Valid prediction for GeneMark_model.89398_t
Valid prediction for Augustus_model.g34489.t1
Valid prediction for snap_scaffold_22-snap.2255-T1
Valid prediction for pasa_asmbl_29736.p2
Valid prediction for snap_scaffold_22-snap.2254-T1
Valid prediction for GeneMark_model.89396_t
Valid prediction for snap_scaffold_22-snap.2274-T1
Valid prediction for GeneMark_model.89425_t
Couldn't classify 57115, 57120
Sorry, prediction GeneMark_model.89408_t fails validation.
(AGG)	 AG	57115-57120	GT	AGG
(GAC)	 AG	57145-57156	GT	ATG
(AGG)	 AG	57398-57523	GT	AGG
(AGG)	 AG	57552-57575	GT	GTG
(GAC)	 AG	57599-57757	GT	GAG
(TGG)	 AG	57793-57801	GT	GGG
(GGA)	 AG	57823-57892	GT	GAG
(GCG)	 AG	58038-58112	TC	AGT
-recovered GeneMark_model.89408_t, terminal, 58038, 58112
-recovered GeneMark_model.89408_t, internal, 57115, 57120
-recovered GeneMark_model.89408_t, internal, 57145, 57156
-recovered GeneMark_model.89408_t, internal, 57398, 57523
-recovered GeneMark_model.89408_t, internal, 57552, 57575
-recovered GeneMark_model.89408_t, internal, 57599, 57757
-recovered GeneMark_model.89408_t, internal, 57793, 57801
-recovered GeneMark_model.89408_t, internal, 57823, 57892
Couldn't classify 26844, 26962
Sorry, prediction pasa_asmbl_29657.p1 fails validation.
(ATG)	 GG	24633-24816	GT	CAG
(GCC)	 AG	25661-25876	GT	CAG
(TGC)	 AG	26844-26962	CC	ACC
-recovered pasa_asmbl_29657.p1, initial, 24633, 24816
-recovered pasa_asmbl_29657.p1, internal, 25661, 25876
Valid prediction for GlimmerHMM_glimmerT_51408-T1
Valid prediction for snap_scaffold_22-snap.2263-T1
Valid prediction for GeneMark_model.89400_t
Valid prediction for Augustus_model.g34495.t1
Valid prediction for snap_scaffold_22-snap.2258-T1
Valid prediction for GeneMark_model.89420_t
Valid prediction for GlimmerHMM_glimmerT_51406-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.89418_t
Valid prediction for snap_scaffold_22-snap.2277-T1
Valid prediction for snap_scaffold_22-snap.2268-T1
Valid prediction for GlimmerHMM_glimmerT_51409-T1
Valid prediction for snap_scaffold_22-snap.2262-T1
Valid prediction for Augustus_model.g34487.t1
Valid prediction for GeneMark_model.89424_t
Valid prediction for GeneMark_model.89415_t
Valid prediction for GeneMark_model.89401_t
Valid prediction for Augustus_model.g34493.t1
Valid prediction for GeneMark_model.89422_t
Valid prediction for snap_scaffold_22-snap.2280-T1
Valid prediction for snap_scaffold_22-snap.2265-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.89405_t
Valid prediction for snap_scaffold_22-snap.2260-T1
Valid prediction for snap_scaffold_22-snap.2269-T1
Couldn't classify 48888, 48930
Sorry, prediction GeneMark_model.89407_t fails validation.
(ATG)	 TG	48053-48056	GT	GGG
(GGG)	 AG	48340-48349	GT	CGG
(AGA)	 AG	48372-48458	GT	GGG
(GAG)	 AG	48485-48547	GT	TGG
(CGA)	 AG	48888-48930	GT	AGG
-recovered GeneMark_model.89407_t, initial, 48053, 48056
-recovered GeneMark_model.89407_t, internal, 48340, 48349
-recovered GeneMark_model.89407_t, internal, 48372, 48458
-recovered GeneMark_model.89407_t, internal, 48485, 48547
-recovered GeneMark_model.89407_t, internal, 48888, 48930
Valid prediction for GeneMark_model.89412_t
Valid prediction for GlimmerHMM_glimmerT_51403-T1
Valid prediction for CodingQuarry_transcript_34227-T1
Valid prediction for GeneMark_model.89428_t
Valid prediction for GeneMark_model.89427_t
Valid prediction for snap_scaffold_22-snap.2257-T1
Valid prediction for snap_scaffold_22-snap.2251-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for GeneMark_model.89429_t
Valid prediction for GeneMark_model.89410_t
Valid prediction for snap_scaffold_22-snap.2278-T1
Valid prediction for GeneMark_model.89403_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 GeneMark_model.89402_t
Valid prediction for pasa_asmbl_30402.p1
Valid prediction for Augustus_model.g34488.t1
Valid prediction for GlimmerHMM_glimmerT_51405-T1
Valid prediction for CodingQuarry_transcript_34230-T1
Valid prediction for GlimmerHMM_glimmerT_51401-T1
Valid prediction for CodingQuarry_transcript_34225-T1
Valid prediction for GeneMark_model.89406_t
Valid prediction for GeneMark_model.89404_t
Valid prediction for snap_scaffold_22-snap.2275-T1
Valid prediction for snap_scaffold_22-snap.2252-T1
Valid prediction for snap_scaffold_22-snap.2266-T1
Valid prediction for Augustus_model.g34486.t1
Valid prediction for Augustus_model.g34491.t1
Valid prediction for Augustus_model.g34483.t1
Valid prediction for snap_scaffold_22-snap.2264-T1
Valid prediction for GlimmerHMM_glimmerT_51410-T1
Valid prediction for snap_scaffold_22-snap.2279-T1
Valid prediction for GeneMark_model.89416_t
Couldn't classify 98045, 98281
Sorry, prediction pasa_asmbl_30401.p1 fails validation.
(CTT)	 AC	98045-98281	GT	AGG
(GTA)	 AG	98532-99086	GT	GAG
-recovered pasa_asmbl_30401.p1, terminal, 98532, 99086
-recovered pasa_asmbl_30401.p1, internal, 98532, 99086
Valid prediction for GlimmerHMM_glimmerT_51399-T1
Valid prediction for GeneMark_model.89426_t
Valid prediction for HiQ_model.g34492.t1
Valid prediction for GeneMark_model.89417_t
Couldn't classify 10206, 10372
Sorry, prediction pasa_asmbl_30405.p1 fails validation.
(GCC)	 CA	10206-10372	GT	AGG
(GTC)	 AG	10466-10643	GT	TGG
(AAA)	 AG	10987-11238	GT	AGG
(CCT)	 AG	11329-11387	GT	AGG
(TGG)	 AG	11661-11919	GT	AGG
(GAG)	 AG	12464-12638	GT	AGG
(CTC)	 AG	12848-12939	GT	AGG
(GCT)	 AG	13025-13135	GG	GAG
add_exon() Sorry, pasa_asmbl_30405.p1 11329-11387-terminal-2 is invalid.
-recovered pasa_asmbl_30405.p1, terminal, 11329, 11387
-recovered pasa_asmbl_30405.p1, terminal, 13025, 13135
-recovered pasa_asmbl_30405.p1, internal, 10466, 10643
-recovered pasa_asmbl_30405.p1, internal, 10987, 11238
-recovered pasa_asmbl_30405.p1, internal, 11329, 11387
-recovered pasa_asmbl_30405.p1, internal, 11661, 11919
-recovered pasa_asmbl_30405.p1, internal, 12464, 12638
-recovered pasa_asmbl_30405.p1, internal, 12848, 12939
Valid prediction for snap_scaffold_22-snap.2253-T1
Valid prediction for GlimmerHMM_glimmerT_51400-T1
Valid prediction for CodingQuarry_transcript_34226-T1
Valid prediction for snap_scaffold_22-snap.2271-T1
Valid prediction for Augustus_model.g34494.t1
Valid prediction for snap_scaffold_22-snap.2259-T1
Valid prediction for GeneMark_model.89411_t
Valid prediction for GeneMark_model.89421_t
Couldn't classify 52370, 52450
Couldn't classify 52708, 52842
Sorry, prediction CodingQuarry_transcript_34228-T1 fails validation.
(ATG)	 CA	50036-50058	GT	AGG
(GTC)	 AG	50206-50369	GT	AGG
(GAG)	 AG	50543-50728	GT	GGG
(GTC)	 AG	51046-51258	GT	AGG
(CGG)	 AG	51601-51686	GT	AGG
(TTC)	 AG	52370-52450	CT	ATC
(TGT)	 TG	52708-52842	GT	TGG
(GGC)	 AG	53605-53826	GT	GCG
(TCA)	 AG	53973-53981	CA	GAC
-recovered CodingQuarry_transcript_34228-T1, initial, 50036, 50058
-recovered CodingQuarry_transcript_34228-T1, terminal, 53973, 53981
-recovered CodingQuarry_transcript_34228-T1, internal, 50206, 50369
-recovered CodingQuarry_transcript_34228-T1, internal, 50543, 50728
-recovered CodingQuarry_transcript_34228-T1, internal, 51046, 51258
-recovered CodingQuarry_transcript_34228-T1, internal, 51601, 51686
-recovered CodingQuarry_transcript_34228-T1, internal, 53605, 53826
Valid prediction for GeneMark_model.89409_t
Valid prediction for snap_scaffold_22-snap.2261-T1
Valid prediction for snap_scaffold_22-snap.2270-T1
Valid prediction for GeneMark_model.89419_t
Valid prediction for GlimmerHMM_glimmerT_51402-T1
Valid prediction for GeneMark_model.89397_t
Valid prediction for GeneMark_model.89414_t
Valid prediction for snap_scaffold_22-snap.2272-T1
Valid prediction for snap_scaffold_22-snap.2276-T1
Valid prediction for GeneMark_model.89395_t
Valid prediction for CodingQuarry_transcript_34229-T1
Valid prediction for GeneMark_model.89393_t
Valid prediction for GlimmerHMM_glimmerT_51407-T1
Valid prediction for HiQ_model.g34485.t1
Valid prediction for pasa_asmbl_30399.p1
Valid prediction for Augustus_model.g34490.t1
Valid prediction for GeneMark_model.89399_t
Valid prediction for Augustus_model.g34484.t1
Valid prediction for snap_scaffold_22-snap.2267-T1
Valid prediction for GeneMark_model.89413_t
Valid prediction for Augustus_model.g34496.t1
Valid prediction for snap_scaffold_22-snap.2256-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6022, rend_intergenic: 4859  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13000, rend_intergenic: 8791  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22465, rend_intergenic: 14404  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26898, rend_intergenic: 24633  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30551, rend_intergenic: 28030  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39848, rend_intergenic: 31120  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45322, rend_intergenic: 42260  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48496, rend_intergenic: 45451  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72334, rend_intergenic: 59320  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79472, rend_intergenic: 72886  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85252, rend_intergenic: 79541  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99264, rend_intergenic: 91894  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104364, rend_intergenic: 100217  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110022, rend_intergenic: 104399  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 113351
-exon list size: 576


building trellis

0.2    
0.3    
0.5    
0.7    
0.9    
1.0    
1.2    
1.4    
1.6    
1.7    
1.9    
2.1    
2.2    
2.4    
2.6    
2.8    
2.9    
3.1    
3.3    
3.5    
3.6    
3.8    
4.0    
4.2    
4.3    
4.5    
4.7    
4.8    
5.0    
5.2    
5.4    
5.5    
5.7    
5.9    
6.1    
6.2    
6.4    
6.6    
6.7    
6.9    
7.1    
7.3    
7.4    
7.6    
7.8    
8.0    
8.1    
8.3    
8.5    
8.7    
8.8    
9.0    
9.2    
9.3    
9.5    
9.7    
9.9    
10.0    
10.2    
10.4    
10.6    
10.7    
10.9    
11.1    
11.2    
11.4    
11.6    
11.8    
11.9    
12.1    
12.3    
12.5    
12.6    
12.8    
13.0    
13.1    
13.3    
13.5    
13.7    
13.8    
14.0    
14.2    
14.4    
14.5    
14.7    
14.9    
15.1    
15.2    
15.4    
15.6    
15.7    
15.9    
16.1    
16.3    
16.4    
16.6    
16.8    
17.0    
17.1    
17.3    
17.5    
17.6    
17.8    
18.0    
18.2    
18.3    
18.5    
18.7    
18.9    
19.0    
19.2    
19.4    
19.6    
19.7    
19.9    
20.1    
20.2    
20.4    
20.6    
20.8    
20.9    
21.1    
21.3    
21.5    
21.6    
21.8    
22.0    
22.1    
22.3    
22.5    
22.7    
22.8    
23.0    
23.2    
23.4    
23.5    
23.7    
23.9    
24.0    
24.2    
24.4    
24.6    
24.7    
24.9    
25.1    
25.3    
25.4    
25.6    
25.8    
26.0    
26.1    
26.3    
26.5    
26.6    
26.8    
27.0    
27.2    
27.3    
27.5    
27.7    
27.9    
28.0    
28.2    
28.4    
28.5    
28.7    
28.9    
29.1    
29.2    
29.4    
29.6    
29.8    
29.9    
30.1    
30.3    
30.4    
30.6    
30.8    
31.0    
31.1    
31.3    
31.5    
31.7    
31.8    
32.0    
32.2    
32.4    
32.5    
32.7    
32.9    
33.0    
33.2    
33.4    
33.6    
33.7    
33.9    
34.1    
34.3    
34.4    
34.6    
34.8    
34.9    
35.1    
35.3    
35.5    
35.6    
35.8    
36.0    
36.2    
36.3    
36.5    
36.7    
36.9    
37.0    
37.2    
37.4    
37.5    
37.7    
37.9    
38.1    
38.2    
38.4    
38.6    
38.8    
38.9    
39.1    
39.3    
39.4    
39.6    
39.8    
40.0    
40.1    
40.3    
40.5    
40.7    
40.8    
41.0    
41.2    
41.3    
41.5    
41.7    
41.9    
42.0    
42.2    
42.4    
42.6    
42.7    
42.9    
43.1    
43.3    
43.4    
43.6    
43.8    
43.9    
44.1    
44.3    
44.5    
44.6    
44.8    
45.0    
45.2    
45.3    
45.5    
45.7    
45.8    
46.0    
46.2    
46.4    
46.5    
46.7    
46.9    
47.1    
47.2    
47.4    
47.6    
47.8    
47.9    
48.1    
48.3    
48.4    
48.6    
48.8    
49.0    
49.1    
49.3    
49.5    
49.7    
49.8    
50.0    
50.2    
50.3    
50.5    
50.7    
50.9    
51.0    
51.2    
51.4    
51.6    
51.7    
51.9    
52.1    
52.2    
52.4    
52.6    
52.8    
52.9    
53.1    
53.3    
53.5    
53.6    
53.8    
54.0    
54.2    
54.3    
54.5    
54.7    
54.8    
55.0    
55.2    
55.4    
55.5    
55.7    
55.9    
56.1    
56.2    
56.4    
56.6    
56.7    
56.9    
57.1    
57.3    
57.4    
57.6    
57.8    
58.0    
58.1    
58.3    
58.5    
58.7    
58.8    
59.0    
59.2    
59.3    
59.5    
59.7    
59.9    
60.0    
60.2    
60.4    
60.6    
60.7    
60.9    
61.1    
61.2    
61.4    
61.6    
61.8    
61.9    
62.1    
62.3    
62.5    
62.6    
62.8    
63.0    
63.1    
63.3    
63.5    
63.7    
63.8    
64.0    
64.2    
64.4    
64.5    
64.7    
64.9    
65.1    
65.2    
65.4    
65.6    
65.7    
65.9    
66.1    
66.3    
66.4    
66.6    
66.8    
67.0    
67.1    
67.3    
67.5    
67.6    
67.8    
68.0    
68.2    
68.3    
68.5    
68.7    
68.9    
69.0    
69.2    
69.4    
69.6    
69.7    
69.9    
70.1    
70.2    
70.4    
70.6    
70.8    
70.9    
71.1    
71.3    
71.5    
71.6    
71.8    
72.0    
72.1    
72.3    
72.5    
72.7    
72.8    
73.0    
73.2    
73.4    
73.5    
73.7    
73.9    
74.0    
74.2    
74.4    
74.6    
74.7    
74.9    
75.1    
75.3    
75.4    
75.6    
75.8    
76.0    
76.1    
76.3    
76.5    
76.6    
76.8    
77.0    
77.2    
77.3    
77.5    
77.7    
77.9    
78.0    
78.2    
78.4    
78.5    
78.7    
78.9    
79.1    
79.2    
79.4    
79.6    
79.8    
79.9    
80.1    
80.3    
80.4    
80.6    
80.8    
81.0    
81.1    
81.3    
81.5    
81.7    
81.8    
82.0    
82.2    
82.4    
82.5    
82.7    
82.9    
83.0    
83.2    
83.4    
83.6    
83.7    
83.9    
84.1    
84.3    
84.4    
84.6    
84.8    
84.9    
85.1    
85.3    
85.5    
85.6    
85.8    
86.0    
86.2    
86.3    
86.5    
86.7    
86.9    
87.0    
87.2    
87.4    
87.5    
87.7    
87.9    
88.1    
88.2    
88.4    
88.6    
88.8    
88.9    
89.1    
89.3    
89.4    
89.6    
89.8    
90.0    
90.1    
90.3    
90.5    
90.7    
90.8    
91.0    
91.2    
91.3    
91.5    
91.7    
91.9    
92.0    
92.2    
92.4    
92.6    
92.7    
92.9    
93.1    
93.3    
93.4    
93.6    
93.8    
93.9    
94.1    
94.3    
94.5    
94.6    
94.8    
95.0    
95.2    
95.3    
95.5    
95.7    
95.8    
96.0    
96.2    
96.4    
96.5    
96.7    
96.9    
97.1    
97.2    
97.4    
97.6    
97.8    
97.9    
98.1    
98.3    
98.4    
98.6    
98.8    
99.0    
99.1    
99.3    
99.5    
99.7    
99.8    
-found 18 predictions from path traversal
Error with prediction: snap lend_intergenic: 6022, rend_intergenic: 4859  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13000, rend_intergenic: 8791  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22465, rend_intergenic: 14404  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26898, rend_intergenic: 24633  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30551, rend_intergenic: 28030  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39848, rend_intergenic: 31120  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45322, rend_intergenic: 42260  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48496, rend_intergenic: 45451  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72334, rend_intergenic: 59320  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79472, rend_intergenic: 72886  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85252, rend_intergenic: 79541  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99264, rend_intergenic: 91894  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104364, rend_intergenic: 100217  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110022, rend_intergenic: 104399  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 12 predictions persist after filtering for low support