-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_9/scaffold_9_1391365-1577509

-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_9-snap.321-T1
Valid prediction for Augustus_model.g14372.t1
Valid prediction for GlimmerHMM_glimmerT_21623-T1
Couldn't classify 175010, 175051
Couldn't classify 177568, 177684
Sorry, prediction pasa_asmbl_54678.p1 fails validation.
(GAC)	 TC	175010-175051	GT	AGG
(AGC)	 AG	176825-176971	GT	AGG
(GTG)	 AG	177059-177124	GT	AGG
(GTT)	 AG	177568-177684	AT	ACA
-recovered pasa_asmbl_54678.p1, internal, 176825, 176971
-recovered pasa_asmbl_54678.p1, internal, 177059, 177124
Valid prediction for Augustus_model.g14371.t1
Couldn't classify 145741, 145905
Sorry, prediction pasa_asmbl_53819.p1 fails validation.
(GGC)	 AG	145741-145905	GT	AGG
(GCG)	 AG	146437-146531	GT	AGG
(GTT)	 AG	146771-146903	AC	AAA
-recovered pasa_asmbl_53819.p1, terminal, 146771, 146903
-recovered pasa_asmbl_53819.p1, internal, 145741, 145905
-recovered pasa_asmbl_53819.p1, internal, 146437, 146531
Valid prediction for Augustus_model.g14380.t1
Valid prediction for snap_scaffold_9-snap.325-T1
Valid prediction for GlimmerHMM_glimmerT_21629-T1
Couldn't classify 133144, 133193
Couldn't classify 134137, 134284
Sorry, prediction pasa_asmbl_53815.p1 fails validation.
(GTG)	 AG	133144-133193	GT	AAG
(GAG)	 AG	133627-133734	GT	AGG
(GCA)	 AG	134137-134284	CA	ACC
-recovered pasa_asmbl_53815.p1, internal, 133144, 133193
-recovered pasa_asmbl_53815.p1, internal, 133627, 133734
Valid prediction for snap_scaffold_9-snap.302-T1
Valid prediction for GlimmerHMM_glimmerT_21620-T1
Valid prediction for GlimmerHMM_glimmerT_21625-T1
Valid prediction for Augustus_model.g14382.t1
Valid prediction for snap_scaffold_9-snap.318-T1
Valid prediction for snap_scaffold_9-snap.334-T1
Couldn't classify 139608, 139740
Couldn't classify 141420, 141475
Sorry, prediction pasa_asmbl_53817.p1 fails validation.
(GAG)	 GG	139608-139740	GT	AGG
(CTG)	 AG	140063-140230	GT	CGG
(GTA)	 AG	140588-140811	GT	AGG
(GCC)	 AG	141068-141254	GT	TGG
(CTC)	 AG	141420-141475	GC	CTG
-recovered pasa_asmbl_53817.p1, internal, 140063, 140230
-recovered pasa_asmbl_53817.p1, internal, 140588, 140811
-recovered pasa_asmbl_53817.p1, internal, 141068, 141254
-recovered pasa_asmbl_53817.p1, internal, 141420, 141475
Valid prediction for snap_scaffold_9-snap.308-T1
Valid prediction for snap_scaffold_9-snap.333-T1
Valid prediction for GlimmerHMM_glimmerT_21607-T1
Couldn't classify 134714, 134844
Couldn't classify 135128, 135341
Sorry, prediction pasa_asmbl_53816.p1 fails validation.
(GCC)	 CA	134714-134844	GT	GAG
(GTT)	 AG	135128-135341	GT	AGG
-recovered pasa_asmbl_53816.p1, internal, 135128, 135341
Valid prediction for snap_scaffold_9-snap.323-T1
Valid prediction for snap_scaffold_9-snap.316-T1
Valid prediction for snap_scaffold_9-snap.315-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_9-snap.299-T1
Valid prediction for snap_scaffold_9-snap.307-T1
Valid prediction for Augustus_model.g14374.t1
Valid prediction for GlimmerHMM_glimmerT_21627-T1
Valid prediction for Augustus_model.g14381.t1
Valid prediction for Augustus_model.g14375.t1
Couldn't classify 144965, 145041
Sorry, prediction pasa_asmbl_53818.p1 fails validation.
(ATG)	 CC	142181-142381	GT	AGG
(ATC)	 AG	142619-142810	GT	AGG
(CGT)	 AG	143241-143464	GT	AGG
(GGC)	 AG	143736-143878	GT	AGG
(ACT)	 AG	144081-144239	GT	AGG
(ACT)	 AG	144526-144705	GT	TGG
(ATG)	 AG	144965-145041	AG	CCA
-recovered pasa_asmbl_53818.p1, initial, 142181, 142381
-recovered pasa_asmbl_53818.p1, internal, 142619, 142810
-recovered pasa_asmbl_53818.p1, internal, 143241, 143464
-recovered pasa_asmbl_53818.p1, internal, 143736, 143878
-recovered pasa_asmbl_53818.p1, internal, 144081, 144239
-recovered pasa_asmbl_53818.p1, internal, 144526, 144705
Valid prediction for snap_scaffold_9-snap.306-T1
Valid prediction for GlimmerHMM_glimmerT_21618-T1
Valid prediction for GlimmerHMM_glimmerT_21626-T1
Valid prediction for snap_scaffold_9-snap.320-T1
Valid prediction for GlimmerHMM_glimmerT_21628-T1
Valid prediction for GlimmerHMM_glimmerT_21608-T1
Valid prediction for GlimmerHMM_glimmerT_21624-T1
Valid prediction for snap_scaffold_9-snap.305-T1
Couldn't classify 180875, 180973
Couldn't classify 183358, 183530
Sorry, prediction pasa_asmbl_53822.p1 fails validation.
(GCT)	 AG	180875-180973	GT	AGG
(GCG)	 AG	181141-181218	GT	GGG
(TAT)	 AG	182457-182560	GT	CAG
(GTG)	 AG	182834-182944	GT	AAG
(AGC)	 AG	183045-183112	GT	GGG
(GAC)	 AG	183358-183530	CT	GAC
-recovered pasa_asmbl_53822.p1, internal, 180875, 180973
-recovered pasa_asmbl_53822.p1, internal, 181141, 181218
-recovered pasa_asmbl_53822.p1, internal, 182457, 182560
-recovered pasa_asmbl_53822.p1, internal, 182834, 182944
-recovered pasa_asmbl_53822.p1, internal, 183045, 183112
Valid prediction for GlimmerHMM_glimmerT_21611-T1
Valid prediction for snap_scaffold_9-snap.332-T1
Valid prediction for CodingQuarry_transcript_62107-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_9-snap.335-T1
Valid prediction for snap_scaffold_9-snap.310-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_21615-T1
Valid prediction for snap_scaffold_9-snap.326-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_21616-T1
Valid prediction for snap_scaffold_9-snap.336-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g14379.t1
Valid prediction for Augustus_model.g14378.t1
Valid prediction for Augustus_model.g14376.t1
Valid prediction for snap_scaffold_9-snap.313-T1
Valid prediction for GlimmerHMM_glimmerT_21613-T1
Valid prediction for snap_scaffold_9-snap.303-T1
Valid prediction for snap_scaffold_9-snap.319-T1
Valid prediction for GlimmerHMM_glimmerT_21619-T1
Valid prediction for snap_scaffold_9-snap.312-T1
Valid prediction for GlimmerHMM_glimmerT_21614-T1
Valid prediction for snap_scaffold_9-snap.327-T1
Sorry, intron length (7) is less than minimum required (10)
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_9-snap.300-T1
Valid prediction for GlimmerHMM_glimmerT_21617-T1
Valid prediction for snap_scaffold_9-snap.317-T1
Valid prediction for snap_scaffold_9-snap.331-T1
Valid prediction for Augustus_model.g14377.t1
Valid prediction for GlimmerHMM_glimmerT_21612-T1
Valid prediction for snap_scaffold_9-snap.324-T1
Valid prediction for GlimmerHMM_glimmerT_21621-T1
Valid prediction for GlimmerHMM_glimmerT_21610-T1
Valid prediction for snap_scaffold_9-snap.311-T1
Valid prediction for snap_scaffold_9-snap.322-T1
Valid prediction for snap_scaffold_9-snap.329-T1
Valid prediction for snap_scaffold_9-snap.304-T1
Valid prediction for snap_scaffold_9-snap.301-T1
Valid prediction for snap_scaffold_9-snap.314-T1
Valid prediction for Augustus_model.g14373.t1
Valid prediction for snap_scaffold_9-snap.330-T1
Valid prediction for GlimmerHMM_glimmerT_21622-T1
Valid prediction for GlimmerHMM_glimmerT_21609-T1
Valid prediction for snap_scaffold_9-snap.328-T1
Valid prediction for snap_scaffold_9-snap.309-T1
Valid prediction for snap_scaffold_9-snap.298-T1
Couldn't classify 64154, 64234
Sorry, prediction pasa_asmbl_54820.p1 fails validation.
(CTG)	 AC	64154-64234	GT	AAG
(GGG)	 AG	65117-65371	TG	GAT
-recovered pasa_asmbl_54820.p1, terminal, 65117, 65371

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12470, rend_intergenic: 4318  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20538, rend_intergenic: 14801  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30185, rend_intergenic: 23256  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83700, rend_intergenic: 57207  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86712, rend_intergenic: 83700  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93990, rend_intergenic: 87081  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99280, rend_intergenic: 94167  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116066, rend_intergenic: 110863  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123484, rend_intergenic: 117560  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146903, rend_intergenic: 126150  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169111, rend_intergenic: 152760  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178312, rend_intergenic: 170413  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 186145
-exon list size: 418


building trellis

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1.9    
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2.9    
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3.6    
3.8    
4.0    
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5.0    
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7.1    
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8.1    
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8.6    
8.8    
9.0    
9.3    
9.5    
9.8    
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10.2    
10.5    
10.7    
11.0    
11.2    
11.4    
11.7    
11.9    
12.1    
12.4    
12.6    
12.9    
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13.3    
13.6    
13.8    
14.0    
14.3    
14.5    
14.8    
15.0    
15.2    
15.5    
15.7    
16.0    
16.2    
16.4    
16.7    
16.9    
17.1    
17.4    
17.6    
17.9    
18.1    
18.3    
18.6    
18.8    
19.0    
19.3    
19.5    
19.8    
20.0    
20.2    
20.5    
20.7    
21.0    
21.2    
21.4    
21.7    
21.9    
22.1    
22.4    
22.6    
22.9    
23.1    
23.3    
23.6    
23.8    
24.0    
24.3    
24.5    
24.8    
25.0    
25.2    
25.5    
25.7    
26.0    
26.2    
26.4    
26.7    
26.9    
27.1    
27.4    
27.6    
27.9    
28.1    
28.3    
28.6    
28.8    
29.0    
29.3    
29.5    
29.8    
30.0    
30.2    
30.5    
30.7    
31.0    
31.2    
31.4    
31.7    
31.9    
32.1    
32.4    
32.6    
32.9    
33.1    
33.3    
33.6    
33.8    
34.0    
34.3    
34.5    
34.8    
35.0    
35.2    
35.5    
35.7    
36.0    
36.2    
36.4    
36.7    
36.9    
37.1    
37.4    
37.6    
37.9    
38.1    
38.3    
38.6    
38.8    
39.0    
39.3    
39.5    
39.8    
40.0    
40.2    
40.5    
40.7    
41.0    
41.2    
41.4    
41.7    
41.9    
42.1    
42.4    
42.6    
42.9    
43.1    
43.3    
43.6    
43.8    
44.0    
44.3    
44.5    
44.8    
45.0    
45.2    
45.5    
45.7    
46.0    
46.2    
46.4    
46.7    
46.9    
47.1    
47.4    
47.6    
47.9    
48.1    
48.3    
48.6    
48.8    
49.0    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
50.7    
51.0    
51.2    
51.4    
51.7    
51.9    
52.1    
52.4    
52.6    
52.9    
53.1    
53.3    
53.6    
53.8    
54.0    
54.3    
54.5    
54.8    
55.0    
55.2    
55.5    
55.7    
56.0    
56.2    
56.4    
56.7    
56.9    
57.1    
57.4    
57.6    
57.9    
58.1    
58.3    
58.6    
58.8    
59.0    
59.3    
59.5    
59.8    
60.0    
60.2    
60.5    
60.7    
61.0    
61.2    
61.4    
61.7    
61.9    
62.1    
62.4    
62.6    
62.9    
63.1    
63.3    
63.6    
63.8    
64.0    
64.3    
64.5    
64.8    
65.0    
65.2    
65.5    
65.7    
66.0    
66.2    
66.4    
66.7    
66.9    
67.1    
67.4    
67.6    
67.9    
68.1    
68.3    
68.6    
68.8    
69.0    
69.3    
69.5    
69.8    
70.0    
70.2    
70.5    
70.7    
71.0    
71.2    
71.4    
71.7    
71.9    
72.1    
72.4    
72.6    
72.9    
73.1    
73.3    
73.6    
73.8    
74.0    
74.3    
74.5    
74.8    
75.0    
75.2    
75.5    
75.7    
76.0    
76.2    
76.4    
76.7    
76.9    
77.1    
77.4    
77.6    
77.9    
78.1    
78.3    
78.6    
78.8    
79.0    
79.3    
79.5    
79.8    
80.0    
80.2    
80.5    
80.7    
81.0    
81.2    
81.4    
81.7    
81.9    
82.1    
82.4    
82.6    
82.9    
83.1    
83.3    
83.6    
83.8    
84.0    
84.3    
84.5    
84.8    
85.0    
85.2    
85.5    
85.7    
86.0    
86.2    
86.4    
86.7    
86.9    
87.1    
87.4    
87.6    
87.9    
88.1    
88.3    
88.6    
88.8    
89.0    
89.3    
89.5    
89.8    
90.0    
90.2    
90.5    
90.7    
91.0    
91.2    
91.4    
91.7    
91.9    
92.1    
92.4    
92.6    
92.9    
93.1    
93.3    
93.6    
93.8    
94.0    
94.3    
94.5    
94.8    
95.0    
95.2    
95.5    
95.7    
96.0    
96.2    
96.4    
96.7    
96.9    
97.1    
97.4    
97.6    
97.9    
98.1    
98.3    
98.6    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 21 predictions from path traversal
Error with prediction: snap lend_intergenic: 12470, rend_intergenic: 4318  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20538, rend_intergenic: 14801  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30185, rend_intergenic: 23256  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83700, rend_intergenic: 57207  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86712, rend_intergenic: 83700  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93990, rend_intergenic: 87081  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99280, rend_intergenic: 94167  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116066, rend_intergenic: 110863  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123484, rend_intergenic: 117560  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146903, rend_intergenic: 126150  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169111, rend_intergenic: 152760  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178312, rend_intergenic: 170413  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support