-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_15/scaffold_15_6102169-6350589

-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: +)Couldn't classify 94948, 95003
Couldn't classify 95900, 96040
Sorry, prediction CodingQuarry_transcript_18025-T1 fails validation.
(ATG)	 TA	91625-91654	GT	TGG
(CCT)	 AG	93233-93334	GT	CGG
(CTG)	 AG	93922-94072	GT	AGG
(CAC)	 AG	94394-94458	GT	TGG
(AGT)	 AG	94777-94852	GT	AGG
(GTC)	 AG	94948-95003	CA	CCC
(CAG)	 CA	95900-96040	GT	AGG
(GAG)	 AG	96192-96281	GT	AGG
(ATC)	 AG	96472-96579	AG	AGA
-recovered CodingQuarry_transcript_18025-T1, initial, 91625, 91654
-recovered CodingQuarry_transcript_18025-T1, terminal, 96472, 96579
-recovered CodingQuarry_transcript_18025-T1, internal, 93233, 93334
-recovered CodingQuarry_transcript_18025-T1, internal, 93922, 94072
-recovered CodingQuarry_transcript_18025-T1, internal, 94394, 94458
-recovered CodingQuarry_transcript_18025-T1, internal, 94777, 94852
-recovered CodingQuarry_transcript_18025-T1, internal, 96192, 96281
Valid prediction for snap_scaffold_15-snap.1359-T1
Valid prediction for Augustus_model.g24179.t1
Valid prediction for HiQ_model.g24180.t1
Valid prediction for GlimmerHMM_glimmerT_36287-T1
Valid prediction for snap_scaffold_15-snap.1344-T1
Valid prediction for snap_scaffold_15-snap.1346-T1
Valid prediction for snap_scaffold_15-snap.1331-T1
Valid prediction for snap_scaffold_15-snap.1361-T1
Valid prediction for GlimmerHMM_glimmerT_36305-T1
Valid prediction for GlimmerHMM_glimmerT_36306-T1
Valid prediction for CodingQuarry_transcript_18024-T1
Valid prediction for snap_scaffold_15-snap.1356-T1
Valid prediction for snap_scaffold_15-snap.1341-T1
Valid prediction for snap_scaffold_15-snap.1335-T1
Valid prediction for GlimmerHMM_glimmerT_36290-T1
Valid prediction for Augustus_model.g24178.t1
Valid prediction for snap_scaffold_15-snap.1357-T1
Couldn't classify 78394, 78777
Sorry, prediction pasa_asmbl_15244.p3 fails validation.
(ATG)	 CC	78394-78777	AC	CAA
Valid prediction for GlimmerHMM_glimmerT_36288-T1
Couldn't classify 132967, 133338
Sorry, prediction pasa_asmbl_15250.p1 fails validation.
(TTT)	 GT	132967-133338	CT	GAC
Valid prediction for snap_scaffold_15-snap.1338-T1
Valid prediction for snap_scaffold_15-snap.1324-T1
Valid prediction for GlimmerHMM_glimmerT_36295-T1
Valid prediction for GlimmerHMM_glimmerT_36292-T1
Valid prediction for snap_scaffold_15-snap.1348-T1
Valid prediction for CodingQuarry_transcript_18023-T1
Couldn't classify 70211, 70346
Couldn't classify 71387, 71940
Sorry, prediction pasa_asmbl_15243.p1 fails validation.
(TCT)	 AT	70211-70346	GT	AAG
(TCA)	 AG	71387-71940	GT	AGG
-recovered pasa_asmbl_15243.p1, internal, 71387, 71940
Couldn't classify 58174, 58542
Sorry, prediction pasa_asmbl_15239.p1 fails validation.
(GAG)	 GA	58174-58542	GT	GAG
Valid prediction for GlimmerHMM_glimmerT_36291-T1
Valid prediction for GlimmerHMM_glimmerT_36304-T1
Valid prediction for HiQ_model.g24181.t1
Valid prediction for Augustus_model.g24183.t1
Valid prediction for snap_scaffold_15-snap.1328-T1
Valid prediction for GlimmerHMM_glimmerT_36286-T1
Valid prediction for Augustus_model.g24177.t1
Valid prediction for GlimmerHMM_glimmerT_36297-T1
Valid prediction for pasa_asmbl_15246.p1
Valid prediction for snap_scaffold_15-snap.1347-T1
Valid prediction for GlimmerHMM_glimmerT_36298-T1
Valid prediction for snap_scaffold_15-snap.1350-T1
Valid prediction for snap_scaffold_15-snap.1353-T1
Valid prediction for snap_scaffold_15-snap.1358-T1
Valid prediction for snap_scaffold_15-snap.1326-T1
Valid prediction for snap_scaffold_15-snap.1332-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 snap_scaffold_15-snap.1343-T1
Valid prediction for snap_scaffold_15-snap.1320-T1
Valid prediction for snap_scaffold_15-snap.1322-T1
Valid prediction for snap_scaffold_15-snap.1336-T1
Valid prediction for GlimmerHMM_glimmerT_36294-T1
Valid prediction for snap_scaffold_15-snap.1345-T1
Valid prediction for GlimmerHMM_glimmerT_36307-T1
Valid prediction for snap_scaffold_15-snap.1334-T1
Valid prediction for snap_scaffold_15-snap.1337-T1
Valid prediction for GlimmerHMM_glimmerT_36299-T1
Valid prediction for snap_scaffold_15-snap.1339-T1
Valid prediction for GlimmerHMM_glimmerT_36300-T1
Valid prediction for snap_scaffold_15-snap.1329-T1
Valid prediction for GlimmerHMM_glimmerT_36285-T1
Valid prediction for snap_scaffold_15-snap.1355-T1
Valid prediction for GlimmerHMM_glimmerT_36284-T1
Valid prediction for Augustus_model.g24185.t1
Valid prediction for GlimmerHMM_glimmerT_36296-T1
Valid prediction for Augustus_model.g24175.t1
Valid prediction for snap_scaffold_15-snap.1327-T1
Valid prediction for Augustus_model.g24173.t1
Valid prediction for HiQ_model.g24174.t1
Valid prediction for snap_scaffold_15-snap.1333-T1
Valid prediction for Augustus_model.g24182.t1
Valid prediction for Augustus_model.g24184.t1
Valid prediction for snap_scaffold_15-snap.1340-T1
Valid prediction for snap_scaffold_15-snap.1354-T1
Valid prediction for snap_scaffold_15-snap.1360-T1
Valid prediction for Augustus_model.g24189.t1
Valid prediction for Augustus_model.g24186.t1
Valid prediction for snap_scaffold_15-snap.1342-T1
Valid prediction for pasa_asmbl_14248.p1
Couldn't classify 242794, 242824
Sorry, prediction pasa_asmbl_14243.p1 fails validation.
(GCC)	 AG	242794-242824	GT	AGG
(AGT)	 AG	243405-243548	GT	CGG
(GCA)	 AG	245913-246019	GT	AGG
(GAT)	 AG	246306-246441	GT	AGG
(AGT)	 AG	247141-247169	AG	GAA
-recovered pasa_asmbl_14243.p1, terminal, 247141, 247169
-recovered pasa_asmbl_14243.p1, internal, 242794, 242824
-recovered pasa_asmbl_14243.p1, internal, 243405, 243548
-recovered pasa_asmbl_14243.p1, internal, 245913, 246019
-recovered pasa_asmbl_14243.p1, internal, 246306, 246441
Valid prediction for GlimmerHMM_glimmerT_36289-T1
Valid prediction for GlimmerHMM_glimmerT_36283-T1
Valid prediction for GlimmerHMM_glimmerT_36293-T1
Valid prediction for GlimmerHMM_glimmerT_36301-T1
Valid prediction for snap_scaffold_15-snap.1321-T1
Valid prediction for Augustus_model.g24188.t1
Valid prediction for snap_scaffold_15-snap.1318-T1
Valid prediction for Augustus_model.g24187.t1
Valid prediction for snap_scaffold_15-snap.1319-T1
Valid prediction for GlimmerHMM_glimmerT_36302-T1
Valid prediction for snap_scaffold_15-snap.1325-T1
Valid prediction for snap_scaffold_15-snap.1349-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_36282-T1
Valid prediction for snap_scaffold_15-snap.1330-T1
Valid prediction for snap_scaffold_15-snap.1351-T1
Valid prediction for GlimmerHMM_glimmerT_36303-T1
Valid prediction for snap_scaffold_15-snap.1323-T1
Valid prediction for snap_scaffold_15-snap.1352-T1
Valid prediction for Augustus_model.g24176.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 50885, rend_intergenic: 42006  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55294, rend_intergenic: 52248  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61191, rend_intergenic: 55917  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69931, rend_intergenic: 61275  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81610, rend_intergenic: 72598  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86123, rend_intergenic: 81924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97235, rend_intergenic: 93799  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111140, rend_intergenic: 107285  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133447, rend_intergenic: 120208  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151664, rend_intergenic: 149117  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158787, rend_intergenic: 151794  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167036, rend_intergenic: 159237  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178150, rend_intergenic: 172674  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184846, rend_intergenic: 179820  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196821, rend_intergenic: 194304  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 239766, rend_intergenic: 214837  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 248421
-exon list size: 393


building trellis

0.3    
0.5    
0.8    
1.0    
1.3    
1.5    
1.8    
2.0    
2.3    
2.5    
2.8    
3.0    
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3.5    
3.8    
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4.3    
4.6    
4.8    
5.1    
5.3    
5.6    
5.8    
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6.3    
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6.8    
7.1    
7.3    
7.6    
7.8    
8.1    
8.4    
8.6    
8.9    
9.1    
9.4    
9.6    
9.9    
10.1    
10.4    
10.6    
10.9    
11.1    
11.4    
11.6    
11.9    
12.2    
12.4    
12.7    
12.9    
13.2    
13.4    
13.7    
13.9    
14.2    
14.4    
14.7    
14.9    
15.2    
15.4    
15.7    
15.9    
16.2    
16.5    
16.7    
17.0    
17.2    
17.5    
17.7    
18.0    
18.2    
18.5    
18.7    
19.0    
19.2    
19.5    
19.7    
20.0    
20.3    
20.5    
20.8    
21.0    
21.3    
21.5    
21.8    
22.0    
22.3    
22.5    
22.8    
23.0    
23.3    
23.5    
23.8    
24.1    
24.3    
24.6    
24.8    
25.1    
25.3    
25.6    
25.8    
26.1    
26.3    
26.6    
26.8    
27.1    
27.3    
27.6    
27.8    
28.1    
28.4    
28.6    
28.9    
29.1    
29.4    
29.6    
29.9    
30.1    
30.4    
30.6    
30.9    
31.1    
31.4    
31.6    
31.9    
32.2    
32.4    
32.7    
32.9    
33.2    
33.4    
33.7    
33.9    
34.2    
34.4    
34.7    
34.9    
35.2    
35.4    
35.7    
35.9    
36.2    
36.5    
36.7    
37.0    
37.2    
37.5    
37.7    
38.0    
38.2    
38.5    
38.7    
39.0    
39.2    
39.5    
39.7    
40.0    
40.3    
40.5    
40.8    
41.0    
41.3    
41.5    
41.8    
42.0    
42.3    
42.5    
42.8    
43.0    
43.3    
43.5    
43.8    
44.1    
44.3    
44.6    
44.8    
45.1    
45.3    
45.6    
45.8    
46.1    
46.3    
46.6    
46.8    
47.1    
47.3    
47.6    
47.8    
48.1    
48.4    
48.6    
48.9    
49.1    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.9    
51.1    
51.4    
51.6    
51.9    
52.2    
52.4    
52.7    
52.9    
53.2    
53.4    
53.7    
53.9    
54.2    
54.4    
54.7    
54.9    
55.2    
55.4    
55.7    
55.9    
56.2    
56.5    
56.7    
57.0    
57.2    
57.5    
57.7    
58.0    
58.2    
58.5    
58.7    
59.0    
59.2    
59.5    
59.7    
60.0    
60.3    
60.5    
60.8    
61.0    
61.3    
61.5    
61.8    
62.0    
62.3    
62.5    
62.8    
63.0    
63.3    
63.5    
63.8    
64.1    
64.3    
64.6    
64.8    
65.1    
65.3    
65.6    
65.8    
66.1    
66.3    
66.6    
66.8    
67.1    
67.3    
67.6    
67.8    
68.1    
68.4    
68.6    
68.9    
69.1    
69.4    
69.6    
69.9    
70.1    
70.4    
70.6    
70.9    
71.1    
71.4    
71.6    
71.9    
72.2    
72.4    
72.7    
72.9    
73.2    
73.4    
73.7    
73.9    
74.2    
74.4    
74.7    
74.9    
75.2    
75.4    
75.7    
75.9    
76.2    
76.5    
76.7    
77.0    
77.2    
77.5    
77.7    
78.0    
78.2    
78.5    
78.7    
79.0    
79.2    
79.5    
79.7    
80.0    
80.3    
80.5    
80.8    
81.0    
81.3    
81.5    
81.8    
82.0    
82.3    
82.5    
82.8    
83.0    
83.3    
83.5    
83.8    
84.1    
84.3    
84.6    
84.8    
85.1    
85.3    
85.6    
85.8    
86.1    
86.3    
86.6    
86.8    
87.1    
87.3    
87.6    
87.8    
88.1    
88.4    
88.6    
88.9    
89.1    
89.4    
89.6    
89.9    
90.1    
90.4    
90.6    
90.9    
91.1    
91.4    
91.6    
91.9    
92.2    
92.4    
92.7    
92.9    
93.2    
93.4    
93.7    
93.9    
94.2    
94.4    
94.7    
94.9    
95.2    
95.4    
95.7    
95.9    
96.2    
96.5    
96.7    
97.0    
97.2    
97.5    
97.7    
98.0    
98.2    
98.5    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 50885, rend_intergenic: 42006  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55294, rend_intergenic: 52248  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61191, rend_intergenic: 55917  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69931, rend_intergenic: 61275  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81610, rend_intergenic: 72598  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86123, rend_intergenic: 81924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97235, rend_intergenic: 93799  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111140, rend_intergenic: 107285  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133447, rend_intergenic: 120208  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151664, rend_intergenic: 149117  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158787, rend_intergenic: 151794  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167036, rend_intergenic: 159237  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178150, rend_intergenic: 172674  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184846, rend_intergenic: 179820  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196821, rend_intergenic: 194304  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 239766, rend_intergenic: 214837  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 232517 - 248421
-exon list size: 15


building trellis

5.9    
11.8    
17.6    
23.5    
29.4    
35.3    
41.2    
47.1    
52.9    
58.8    
64.7    
70.6    
76.5    
82.4    
88.2    
94.1    
-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 232517 - 243555
-exon list size: 11


building trellis

7.7    
15.4    
23.1    
30.8    
38.5    
46.2    
53.8    
61.5    
69.2    
76.9    
84.6    
92.3    
-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