-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_6/scaffold_6_2547527-2725473

-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_6-snap.609-T1
Valid prediction for snap_scaffold_6-snap.612-T1
Valid prediction for GlimmerHMM_glimmerT_14192-T1
Valid prediction for snap_scaffold_6-snap.600-T1
Valid prediction for snap_scaffold_6-snap.616-T1
Valid prediction for snap_scaffold_6-snap.596-T1
Couldn't classify 154442, 154597
Couldn't classify 156606, 156734
Sorry, prediction pasa_asmbl_46769.p1 fails validation.
(CTA)	 GT	154442-154597	GT	CGG
(GCG)	 AG	154778-154894	GT	GGG
(CCA)	 AG	155094-155184	GT	ACG
(TGA)	 AG	155309-155506	GT	AGG
(ATG)	 AG	155768-155860	GT	AGG
(AGT)	 AG	155990-156105	GT	TCG
(GTA)	 AG	156606-156734	AA	GGA
add_exon() Sorry, pasa_asmbl_46769.p1 155768-155860-initial-1 is invalid.
-recovered pasa_asmbl_46769.p1, initial, 155768, 155860
add_exon() Sorry, pasa_asmbl_46769.p1 155309-155506-terminal-1 is invalid.
-recovered pasa_asmbl_46769.p1, terminal, 155309, 155506
-recovered pasa_asmbl_46769.p1, internal, 154778, 154894
-recovered pasa_asmbl_46769.p1, internal, 155094, 155184
-recovered pasa_asmbl_46769.p1, internal, 155309, 155506
-recovered pasa_asmbl_46769.p1, internal, 155768, 155860
-recovered pasa_asmbl_46769.p1, internal, 155990, 156105
Valid prediction for GlimmerHMM_glimmerT_14196-T1
Valid prediction for GlimmerHMM_glimmerT_14204-T1
Valid prediction for snap_scaffold_6-snap.633-T1
Valid prediction for HiQ_model.g9410.t1
Valid prediction for snap_scaffold_6-snap.638-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_6-snap.637-T1
Valid prediction for snap_scaffold_6-snap.631-T1
Valid prediction for snap_scaffold_6-snap.614-T1
Valid prediction for snap_scaffold_6-snap.634-T1
Valid prediction for snap_scaffold_6-snap.619-T1
Valid prediction for Augustus_model.g9411.t1
Valid prediction for GlimmerHMM_glimmerT_14198-T1
Valid prediction for snap_scaffold_6-snap.627-T1
Valid prediction for snap_scaffold_6-snap.628-T1
Valid prediction for snap_scaffold_6-snap.625-T1
Valid prediction for snap_scaffold_6-snap.622-T1
Valid prediction for snap_scaffold_6-snap.603-T1
Valid prediction for GlimmerHMM_glimmerT_14205-T1
Valid prediction for snap_scaffold_6-snap.602-T1
Valid prediction for snap_scaffold_6-snap.630-T1
Valid prediction for GlimmerHMM_glimmerT_14200-T1
Valid prediction for snap_scaffold_6-snap.604-T1
Valid prediction for snap_scaffold_6-snap.598-T1
Valid prediction for snap_scaffold_6-snap.635-T1
Valid prediction for snap_scaffold_6-snap.595-T1
Valid prediction for GlimmerHMM_glimmerT_14188-T1
Valid prediction for GlimmerHMM_glimmerT_14197-T1
Valid prediction for snap_scaffold_6-snap.607-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: -)Couldn't classify 3957, 4112
Sorry, prediction pasa_asmbl_48152.p1 fails validation.
(CAA)	 CA	3957-4112	GT	CAG
(GTG)	 AG	4260-4353	GT	AGG
(GCT)	 AG	5378-5427	GT	AGG
(AAC)	 AG	5861-5902	CA	GAC
-recovered pasa_asmbl_48152.p1, terminal, 5861, 5902
-recovered pasa_asmbl_48152.p1, internal, 4260, 4353
-recovered pasa_asmbl_48152.p1, internal, 5378, 5427
Valid prediction for snap_scaffold_6-snap.610-T1
Valid prediction for snap_scaffold_6-snap.594-T1
Valid prediction for snap_scaffold_6-snap.615-T1
Valid prediction for Augustus_model.g9403.t1
Valid prediction for Augustus_model.g9405.t1
Valid prediction for GlimmerHMM_glimmerT_14187-T1
Valid prediction for GlimmerHMM_glimmerT_14201-T1
Valid prediction for GlimmerHMM_glimmerT_14190-T1
Valid prediction for GlimmerHMM_glimmerT_14195-T1
Valid prediction for snap_scaffold_6-snap.606-T1
Valid prediction for snap_scaffold_6-snap.623-T1
Valid prediction for pasa_asmbl_48149.p1
Valid prediction for GlimmerHMM_glimmerT_14194-T1
Valid prediction for HiQ_model.g9409.t1
Valid prediction for Augustus_model.g9406.t1
Valid prediction for GlimmerHMM_glimmerT_14193-T1
Valid prediction for snap_scaffold_6-snap.597-T1
Valid prediction for GlimmerHMM_glimmerT_14206-T1
Valid prediction for Augustus_model.g9402.t1
Valid prediction for snap_scaffold_6-snap.624-T1
Valid prediction for snap_scaffold_6-snap.639-T1
Valid prediction for snap_scaffold_6-snap.636-T1
Valid prediction for snap_scaffold_6-snap.620-T1
Valid prediction for GlimmerHMM_glimmerT_14203-T1
Valid prediction for snap_scaffold_6-snap.632-T1
Valid prediction for snap_scaffold_6-snap.618-T1
Valid prediction for snap_scaffold_6-snap.617-T1
Valid prediction for pasa_asmbl_48145.p1
Valid prediction for snap_scaffold_6-snap.621-T1
Valid prediction for snap_scaffold_6-snap.613-T1
Valid prediction for snap_scaffold_6-snap.599-T1
Valid prediction for snap_scaffold_6-snap.611-T1
Valid prediction for Augustus_model.g9404.t1
Valid prediction for GlimmerHMM_glimmerT_14191-T1
Valid prediction for snap_scaffold_6-snap.626-T1
Valid prediction for GlimmerHMM_glimmerT_14189-T1
Valid prediction for snap_scaffold_6-snap.629-T1
Valid prediction for Augustus_model.g9412.t1
Valid prediction for CodingQuarry_transcript_54943-T1
Valid prediction for Augustus_model.g9407.t1
Valid prediction for snap_scaffold_6-snap.608-T1
Couldn't classify 36624, 36693
Couldn't classify 39361, 39417
Sorry, prediction pasa_asmbl_49431.p1 fails validation.
(TTG)	 GG	36624-36693	GT	AGG
(GTT)	 AG	36870-36934	GT	TGG
(GAA)	 AG	37469-37526	GT	CGG
(CTG)	 AG	37763-37831	GT	TGG
(CCC)	 AG	38101-38262	GT	AGG
(GCA)	 AG	39169-39224	GT	AGG
(CTT)	 AG	39361-39417	GT	CTG
-recovered pasa_asmbl_49431.p1, internal, 36870, 36934
-recovered pasa_asmbl_49431.p1, internal, 37469, 37526
-recovered pasa_asmbl_49431.p1, internal, 37763, 37831
-recovered pasa_asmbl_49431.p1, internal, 38101, 38262
-recovered pasa_asmbl_49431.p1, internal, 39169, 39224
-recovered pasa_asmbl_49431.p1, internal, 39361, 39417
Valid prediction for GlimmerHMM_glimmerT_14202-T1
Valid prediction for GlimmerHMM_glimmerT_14199-T1
Valid prediction for snap_scaffold_6-snap.605-T1
Valid prediction for HiQ_model.g9408.t1
Valid prediction for snap_scaffold_6-snap.601-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8509, rend_intergenic: 4940  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13337, rend_intergenic: 11675  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24814, rend_intergenic: 14510  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35786, rend_intergenic: 30133  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39353, rend_intergenic: 36342  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42352, rend_intergenic: 40198  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49156, rend_intergenic: 43688  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64750, rend_intergenic: 49206  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72350, rend_intergenic: 69797  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84231, rend_intergenic: 78967  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95635, rend_intergenic: 87363  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106595, rend_intergenic: 102344  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113160, rend_intergenic: 107327  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131467, rend_intergenic: 115458  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134764, rend_intergenic: 133095  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141751, rend_intergenic: 134891  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166479, rend_intergenic: 158709  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175063, rend_intergenic: 171348  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 177947
-exon list size: 317


building trellis

0.3    
0.6    
0.9    
1.3    
1.6    
1.9    
2.2    
2.5    
2.8    
3.1    
3.4    
3.8    
4.1    
4.4    
4.7    
5.0    
5.3    
5.6    
6.0    
6.3    
6.6    
6.9    
7.2    
7.5    
7.8    
8.2    
8.5    
8.8    
9.1    
9.4    
9.7    
10.0    
10.3    
10.7    
11.0    
11.3    
11.6    
11.9    
12.2    
12.5    
12.9    
13.2    
13.5    
13.8    
14.1    
14.4    
14.7    
15.0    
15.4    
15.7    
16.0    
16.3    
16.6    
16.9    
17.2    
17.6    
17.9    
18.2    
18.5    
18.8    
19.1    
19.4    
19.7    
20.1    
20.4    
20.7    
21.0    
21.3    
21.6    
21.9    
22.3    
22.6    
22.9    
23.2    
23.5    
23.8    
24.1    
24.5    
24.8    
25.1    
25.4    
25.7    
26.0    
26.3    
26.6    
27.0    
27.3    
27.6    
27.9    
28.2    
28.5    
28.8    
29.2    
29.5    
29.8    
30.1    
30.4    
30.7    
31.0    
31.3    
31.7    
32.0    
32.3    
32.6    
32.9    
33.2    
33.5    
33.9    
34.2    
34.5    
34.8    
35.1    
35.4    
35.7    
36.1    
36.4    
36.7    
37.0    
37.3    
37.6    
37.9    
38.2    
38.6    
38.9    
39.2    
39.5    
39.8    
40.1    
40.4    
40.8    
41.1    
41.4    
41.7    
42.0    
42.3    
42.6    
42.9    
43.3    
43.6    
43.9    
44.2    
44.5    
44.8    
45.1    
45.5    
45.8    
46.1    
46.4    
46.7    
47.0    
47.3    
47.6    
48.0    
48.3    
48.6    
48.9    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.1    
51.4    
51.7    
52.0    
52.4    
52.7    
53.0    
53.3    
53.6    
53.9    
54.2    
54.5    
54.9    
55.2    
55.5    
55.8    
56.1    
56.4    
56.7    
57.1    
57.4    
57.7    
58.0    
58.3    
58.6    
58.9    
59.2    
59.6    
59.9    
60.2    
60.5    
60.8    
61.1    
61.4    
61.8    
62.1    
62.4    
62.7    
63.0    
63.3    
63.6    
63.9    
64.3    
64.6    
64.9    
65.2    
65.5    
65.8    
66.1    
66.5    
66.8    
67.1    
67.4    
67.7    
68.0    
68.3    
68.7    
69.0    
69.3    
69.6    
69.9    
70.2    
70.5    
70.8    
71.2    
71.5    
71.8    
72.1    
72.4    
72.7    
73.0    
73.4    
73.7    
74.0    
74.3    
74.6    
74.9    
75.2    
75.5    
75.9    
76.2    
76.5    
76.8    
77.1    
77.4    
77.7    
78.1    
78.4    
78.7    
79.0    
79.3    
79.6    
79.9    
80.3    
80.6    
80.9    
81.2    
81.5    
81.8    
82.1    
82.4    
82.8    
83.1    
83.4    
83.7    
84.0    
84.3    
84.6    
85.0    
85.3    
85.6    
85.9    
86.2    
86.5    
86.8    
87.1    
87.5    
87.8    
88.1    
88.4    
88.7    
89.0    
89.3    
89.7    
90.0    
90.3    
90.6    
90.9    
91.2    
91.5    
91.8    
92.2    
92.5    
92.8    
93.1    
93.4    
93.7    
94.0    
94.4    
94.7    
95.0    
95.3    
95.6    
95.9    
96.2    
96.6    
96.9    
97.2    
97.5    
97.8    
98.1    
98.4    
98.7    
99.1    
99.4    
99.7    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 8509, rend_intergenic: 4940  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13337, rend_intergenic: 11675  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24814, rend_intergenic: 14510  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35786, rend_intergenic: 30133  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39353, rend_intergenic: 36342  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42352, rend_intergenic: 40198  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49156, rend_intergenic: 43688  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64750, rend_intergenic: 49206  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72350, rend_intergenic: 69797  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84231, rend_intergenic: 78967  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95635, rend_intergenic: 87363  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106595, rend_intergenic: 102344  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113160, rend_intergenic: 107327  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131467, rend_intergenic: 115458  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134764, rend_intergenic: 133095  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141751, rend_intergenic: 134891  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166479, rend_intergenic: 158709  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175063, rend_intergenic: 171348  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

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