-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_19/scaffold_19_11904846-12038756

-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_19-snap.2332-T1
Valid prediction for GlimmerHMM_glimmerT_44991-T1
Valid prediction for snap_scaffold_19-snap.2337-T1
Valid prediction for snap_scaffold_19-snap.2316-T1
Valid prediction for pasa_asmbl_21734.p1
Valid prediction for snap_scaffold_19-snap.2312-T1
Valid prediction for Augustus_model.g29847.t1
Couldn't classify 88333, 88353
Sorry, prediction pasa_asmbl_21733.p2 fails validation.
(GCC)	 GA	88333-88353	GT	AGG
(GCG)	 AG	88558-88758	GT	CCG
(GTG)	 AG	89854-89991	GG	GAG
-recovered pasa_asmbl_21733.p2, terminal, 89854, 89991
-recovered pasa_asmbl_21733.p2, internal, 88558, 88758
Valid prediction for HiQ_model.g29851.t1
Valid prediction for snap_scaffold_19-snap.2313-T1
Valid prediction for snap_scaffold_19-snap.2320-T1
Valid prediction for CodingQuarry_transcript_25816-T1
Valid prediction for pasa_asmbl_21728.p1
Valid prediction for snap_scaffold_19-snap.2322-T1
Valid prediction for GlimmerHMM_glimmerT_44998-T1
Couldn't classify 84392, 84676
Couldn't classify 84866, 84913
Sorry, prediction pasa_asmbl_21949.p1 fails validation.
(CTA)	 CC	84392-84676	GT	AGG
(AAA)	 AG	84866-84913	GA	AGG
Valid prediction for snap_scaffold_19-snap.2334-T1
Valid prediction for GlimmerHMM_glimmerT_45001-T1
Valid prediction for CodingQuarry_transcript_25818-T1
Valid prediction for snap_scaffold_19-snap.2326-T1
Valid prediction for Augustus_model.g29839.t1
Valid prediction for CodingQuarry_transcript_25814-T1
Valid prediction for GlimmerHMM_glimmerT_44984-T1
Valid prediction for CodingQuarry_transcript_25815-T1
Valid prediction for GlimmerHMM_glimmerT_44983-T1
Valid prediction for snap_scaffold_19-snap.2314-T1
Valid prediction for HiQ_model.g29835.t1
Valid prediction for pasa_asmbl_21729.p1
Valid prediction for Augustus_model.g29844.t1
Valid prediction for Augustus_model.g29841.t1
Valid prediction for GlimmerHMM_glimmerT_44995-T1
Valid prediction for snap_scaffold_19-snap.2318-T1
Valid prediction for snap_scaffold_19-snap.2329-T1
Valid prediction for Augustus_model.g29846.t1
Valid prediction for HiQ_model.g29843.t1
Valid prediction for GlimmerHMM_glimmerT_44997-T1
Valid prediction for Augustus_model.g29842.t1
Valid prediction for GlimmerHMM_glimmerT_44999-T1
Valid prediction for Augustus_model.g29836.t1
Valid prediction for HiQ_model.g29837.t1
Valid prediction for snap_scaffold_19-snap.2323-T1
Valid prediction for GlimmerHMM_glimmerT_44982-T1
Couldn't classify 73422, 73577
Sorry, prediction pasa_asmbl_21731.p1 fails validation.
(ATG)	 AA	70761-70788	GT	CGG
(ACC)	 AG	71778-72034	GT	AGG
(GTG)	 AG	73422-73577	GG	GAG
-recovered pasa_asmbl_21731.p1, initial, 70761, 70788
-recovered pasa_asmbl_21731.p1, internal, 71778, 72034
Couldn't classify 80843, 80990
Sorry, prediction pasa_asmbl_21732.p1 fails validation.
(GAC)	 TA	80843-80990	GT	AGG
(GCC)	 AG	81128-81651	AA	GAA
-recovered pasa_asmbl_21732.p1, terminal, 81128, 81651
Valid prediction for snap_scaffold_19-snap.2336-T1
Valid prediction for snap_scaffold_19-snap.2330-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 Augustus_model.g29852.t1
Valid prediction for snap_scaffold_19-snap.2321-T1
Valid prediction for CodingQuarry_transcript_25817-T1
Valid prediction for Augustus_model.g29840.t1
Valid prediction for snap_scaffold_19-snap.2339-T1
Valid prediction for snap_scaffold_19-snap.2319-T1
Couldn't classify 31091, 31562
Sorry, prediction pasa_asmbl_22442.p1 fails validation.
(ATG)	 AC	29489-29565	GT	AGG
(TCC)	 AG	30119-30192	GT	AGG
(ATA)	 AG	30288-30462	GT	AGG
(CAA)	 AG	30566-30612	GT	TGG
(GGG)	 AG	30718-31060	GT	AGG
(GTC)	 AG	31091-31562	AG	CCA
-recovered pasa_asmbl_22442.p1, initial, 29489, 29565
-recovered pasa_asmbl_22442.p1, internal, 30119, 30192
-recovered pasa_asmbl_22442.p1, internal, 30288, 30462
-recovered pasa_asmbl_22442.p1, internal, 30566, 30612
-recovered pasa_asmbl_22442.p1, internal, 30718, 31060
Valid prediction for GlimmerHMM_glimmerT_44985-T1
Valid prediction for GlimmerHMM_glimmerT_44990-T1
Valid prediction for HiQ_model.g29849.t1
Valid prediction for snap_scaffold_19-snap.2325-T1
Valid prediction for GlimmerHMM_glimmerT_44993-T1
Valid prediction for snap_scaffold_19-snap.2324-T1
Valid prediction for GlimmerHMM_glimmerT_45000-T1
Valid prediction for Augustus_model.g29845.t1
Valid prediction for snap_scaffold_19-snap.2315-T1
Valid prediction for pasa_asmbl_22439.p2
Valid prediction for Augustus_model.g29848.t1
Valid prediction for snap_scaffold_19-snap.2317-T1
Valid prediction for GlimmerHMM_glimmerT_44981-T1
Valid prediction for GlimmerHMM_glimmerT_44994-T1
Valid prediction for GlimmerHMM_glimmerT_44996-T1
Valid prediction for GlimmerHMM_glimmerT_44988-T1
Valid prediction for snap_scaffold_19-snap.2335-T1
Valid prediction for Augustus_model.g29838.t1
Valid prediction for snap_scaffold_19-snap.2331-T1
Valid prediction for GlimmerHMM_glimmerT_44989-T1
Valid prediction for GlimmerHMM_glimmerT_45002-T1
Valid prediction for GlimmerHMM_glimmerT_44986-T1
Valid prediction for snap_scaffold_19-snap.2328-T1
Valid prediction for snap_scaffold_19-snap.2327-T1
Valid prediction for snap_scaffold_19-snap.2338-T1
Valid prediction for Augustus_model.g29850.t1
Valid prediction for GlimmerHMM_glimmerT_44992-T1
Valid prediction for snap_scaffold_19-snap.2333-T1
Valid prediction for GlimmerHMM_glimmerT_44987-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13656, rend_intergenic: 12126  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15636, rend_intergenic: 14544  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23578, rend_intergenic: 22487  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26858, rend_intergenic: 23640  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29518, rend_intergenic: 26903  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37444, rend_intergenic: 29831  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55281, rend_intergenic: 37883  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62110, rend_intergenic: 55281  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63741, rend_intergenic: 62110  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67106, rend_intergenic: 64028  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81227, rend_intergenic: 71678  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89991, rend_intergenic: 85408  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103883, rend_intergenic: 95837  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 42523, rend_intergenic: 42520  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 133911
-exon list size: 302


building trellis

0.3    
0.7    
1.0    
1.3    
1.6    
2.0    
2.3    
2.6    
3.0    
3.3    
3.6    
3.9    
4.3    
4.6    
4.9    
5.3    
5.6    
5.9    
6.2    
6.6    
6.9    
7.2    
7.6    
7.9    
8.2    
8.6    
8.9    
9.2    
9.5    
9.9    
10.2    
10.5    
10.9    
11.2    
11.5    
11.8    
12.2    
12.5    
12.8    
13.2    
13.5    
13.8    
14.1    
14.5    
14.8    
15.1    
15.5    
15.8    
16.1    
16.4    
16.8    
17.1    
17.4    
17.8    
18.1    
18.4    
18.8    
19.1    
19.4    
19.7    
20.1    
20.4    
20.7    
21.1    
21.4    
21.7    
22.0    
22.4    
22.7    
23.0    
23.4    
23.7    
24.0    
24.3    
24.7    
25.0    
25.3    
25.7    
26.0    
26.3    
26.6    
27.0    
27.3    
27.6    
28.0    
28.3    
28.6    
28.9    
29.3    
29.6    
29.9    
30.3    
30.6    
30.9    
31.2    
31.6    
31.9    
32.2    
32.6    
32.9    
33.2    
33.6    
33.9    
34.2    
34.5    
34.9    
35.2    
35.5    
35.9    
36.2    
36.5    
36.8    
37.2    
37.5    
37.8    
38.2    
38.5    
38.8    
39.1    
39.5    
39.8    
40.1    
40.5    
40.8    
41.1    
41.4    
41.8    
42.1    
42.4    
42.8    
43.1    
43.4    
43.8    
44.1    
44.4    
44.7    
45.1    
45.4    
45.7    
46.1    
46.4    
46.7    
47.0    
47.4    
47.7    
48.0    
48.4    
48.7    
49.0    
49.3    
49.7    
50.0    
50.3    
50.7    
51.0    
51.3    
51.6    
52.0    
52.3    
52.6    
53.0    
53.3    
53.6    
53.9    
54.3    
54.6    
54.9    
55.3    
55.6    
55.9    
56.2    
56.6    
56.9    
57.2    
57.6    
57.9    
58.2    
58.6    
58.9    
59.2    
59.5    
59.9    
60.2    
60.5    
60.9    
61.2    
61.5    
61.8    
62.2    
62.5    
62.8    
63.2    
63.5    
63.8    
64.1    
64.5    
64.8    
65.1    
65.5    
65.8    
66.1    
66.4    
66.8    
67.1    
67.4    
67.8    
68.1    
68.4    
68.8    
69.1    
69.4    
69.7    
70.1    
70.4    
70.7    
71.1    
71.4    
71.7    
72.0    
72.4    
72.7    
73.0    
73.4    
73.7    
74.0    
74.3    
74.7    
75.0    
75.3    
75.7    
76.0    
76.3    
76.6    
77.0    
77.3    
77.6    
78.0    
78.3    
78.6    
78.9    
79.3    
79.6    
79.9    
80.3    
80.6    
80.9    
81.2    
81.6    
81.9    
82.2    
82.6    
82.9    
83.2    
83.6    
83.9    
84.2    
84.5    
84.9    
85.2    
85.5    
85.9    
86.2    
86.5    
86.8    
87.2    
87.5    
87.8    
88.2    
88.5    
88.8    
89.1    
89.5    
89.8    
90.1    
90.5    
90.8    
91.1    
91.4    
91.8    
92.1    
92.4    
92.8    
93.1    
93.4    
93.8    
94.1    
94.4    
94.7    
95.1    
95.4    
95.7    
96.1    
96.4    
96.7    
97.0    
97.4    
97.7    
98.0    
98.4    
98.7    
99.0    
99.3    
99.7    
-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 13656, rend_intergenic: 12126  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15636, rend_intergenic: 14544  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23578, rend_intergenic: 22487  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26858, rend_intergenic: 23640  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29518, rend_intergenic: 26903  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37444, rend_intergenic: 29831  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55281, rend_intergenic: 37883  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62110, rend_intergenic: 55281  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63741, rend_intergenic: 62110  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67106, rend_intergenic: 64028  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81227, rend_intergenic: 71678  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89991, rend_intergenic: 85408  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103883, rend_intergenic: 95837  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 42523, rend_intergenic: 42520  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support