-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_17/scaffold_17_8284470-8442265

-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 GlimmerHMM_glimmerT_40684-T1
Valid prediction for CodingQuarry_transcript_22057-T1
Valid prediction for Augustus_model.g27135.t1
Valid prediction for CodingQuarry_transcript_22059-T1
Valid prediction for GlimmerHMM_glimmerT_40678-T1
Valid prediction for snap_scaffold_17-snap.1650-T1
Valid prediction for snap_scaffold_17-snap.1651-T1
Valid prediction for pasa_asmbl_18969.p1
Valid prediction for snap_scaffold_17-snap.1640-T1
Valid prediction for Augustus_model.g27120.t1
Valid prediction for CodingQuarry_transcript_22060-T1
Valid prediction for HiQ_model.g27126.t1
Valid prediction for snap_scaffold_17-snap.1673-T1
Couldn't classify 48207, 48758
Sorry, prediction pasa_asmbl_18980.p1 fails validation.
(AAC)	 CC	48207-48758	AA	ACA
Valid prediction for Augustus_model.g27130.t1
Valid prediction for GlimmerHMM_glimmerT_40686-T1
Valid prediction for snap_scaffold_17-snap.1654-T1
Valid prediction for pasa_asmbl_18974.p1
Valid prediction for snap_scaffold_17-snap.1660-T1
Valid prediction for CodingQuarry_transcript_22063-T1
Valid prediction for snap_scaffold_17-snap.1646-T1
Couldn't classify 55915, 56049
Couldn't classify 56760, 56877
Sorry, prediction pasa_asmbl_18984.p1 fails validation.
(GGC)	 GT	55915-56049	GT	GAG
(GAG)	 AG	56581-56651	GT	AGG
(GAA)	 AG	56760-56877	AC	ACA
-recovered pasa_asmbl_18984.p1, internal, 56581, 56651
Couldn't classify 52478, 52605
Couldn't classify 56760, 56877
Sorry, prediction pasa_asmbl_18983.p1 fails validation.
(GGA)	 TG	52478-52605	GT	AGG
(TGC)	 AG	52857-53030	GT	GAG
(CCC)	 AG	53155-53249	GT	CGG
(GGA)	 AG	53383-53456	GT	AGG
(CTA)	 AG	53629-53674	GT	AAG
(ATG)	 AG	53790-53898	GT	AGG
(GAT)	 AG	54109-54315	GT	CGG
(GAG)	 AG	54407-54553	GT	TGG
(GTC)	 AG	55391-55499	GT	AGG
(CAA)	 AG	55614-55763	GT	GAG
(GAG)	 AG	56581-56651	GT	AGG
(GAA)	 AG	56760-56877	AC	ACA
add_exon() Sorry, pasa_asmbl_18983.p1 53790-53898-initial-1 is invalid.
-recovered pasa_asmbl_18983.p1, initial, 53790, 53898
-recovered pasa_asmbl_18983.p1, internal, 52857, 53030
-recovered pasa_asmbl_18983.p1, internal, 53155, 53249
-recovered pasa_asmbl_18983.p1, internal, 53383, 53456
-recovered pasa_asmbl_18983.p1, internal, 53629, 53674
-recovered pasa_asmbl_18983.p1, internal, 53790, 53898
-recovered pasa_asmbl_18983.p1, internal, 54109, 54315
-recovered pasa_asmbl_18983.p1, internal, 54407, 54553
-recovered pasa_asmbl_18983.p1, internal, 55391, 55499
-recovered pasa_asmbl_18983.p1, internal, 55614, 55763
-recovered pasa_asmbl_18983.p1, internal, 56581, 56651
Couldn't classify 48762, 49253
Sorry, prediction pasa_asmbl_18981.p1 fails validation.
(TGC)	 AA	48762-49253	GG	GGG
Valid prediction for GlimmerHMM_glimmerT_40699-T1
Valid prediction for CodingQuarry_transcript_22062-T1
Valid prediction for snap_scaffold_17-snap.1652-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_17-snap.1672-T1
Valid prediction for GlimmerHMM_glimmerT_40698-T1
Valid prediction for GlimmerHMM_glimmerT_40685-T1
Couldn't classify 57096, 57252
Sorry, prediction pasa_asmbl_18985.p1 fails validation.
(TCA)	 TT	57096-57252	GT	AGG
(ATT)	 AG	57591-57645	GT	AGG
(GAA)	 AG	58097-58229	GT	AGG
(AAG)	 AG	58771-59055	GT	TGG
(GTA)	 AG	59143-59229	GT	GGG
(GAA)	 AG	59422-59512	GT	AGG
(GTG)	 AG	59719-59857	GT	AAG
(GGG)	 AG	59989-60161	GT	GGG
(GTC)	 AG	60361-60527	GT	CGG
(CCG)	 AG	60751-61222	GT	AGG
(CTA)	 AG	61447-61538	TG	GAT
-recovered pasa_asmbl_18985.p1, terminal, 61447, 61538
-recovered pasa_asmbl_18985.p1, internal, 57591, 57645
-recovered pasa_asmbl_18985.p1, internal, 58097, 58229
-recovered pasa_asmbl_18985.p1, internal, 58771, 59055
-recovered pasa_asmbl_18985.p1, internal, 59143, 59229
-recovered pasa_asmbl_18985.p1, internal, 59422, 59512
-recovered pasa_asmbl_18985.p1, internal, 59719, 59857
-recovered pasa_asmbl_18985.p1, internal, 59989, 60161
-recovered pasa_asmbl_18985.p1, internal, 60361, 60527
-recovered pasa_asmbl_18985.p1, internal, 60751, 61222
Valid prediction for snap_scaffold_17-snap.1645-T1
Valid prediction for GlimmerHMM_glimmerT_40701-T1
Valid prediction for GlimmerHMM_glimmerT_40692-T1
Valid prediction for snap_scaffold_17-snap.1641-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g27131.t1
Valid prediction for Augustus_model.g27128.t1
Valid prediction for snap_scaffold_17-snap.1658-T1
Valid prediction for snap_scaffold_17-snap.1647-T1
Valid prediction for CodingQuarry_transcript_22064-T1
Valid prediction for GlimmerHMM_glimmerT_40693-T1
Valid prediction for snap_scaffold_17-snap.1639-T1
Valid prediction for GlimmerHMM_glimmerT_40683-T1
Valid prediction for snap_scaffold_17-snap.1669-T1
Couldn't classify 46530, 46844
Sorry, prediction pasa_asmbl_18978.p1 fails validation.
(CCA)	 TG	46530-46844	AA	GTA
Valid prediction for snap_scaffold_17-snap.1666-T1
Valid prediction for Augustus_model.g27127.t1
Couldn't classify 46911, 48137
Sorry, prediction pasa_asmbl_18979.p1 fails validation.
(GAC)	 GA	46911-48137	CC	ACC
Valid prediction for CodingQuarry_transcript_22061-T1
Couldn't classify 44031, 44666
Couldn't classify 45768, 46433
Sorry, prediction pasa_asmbl_18977.p1 fails validation.
(TCC)	 TA	44031-44666	GT	GGG
(GGT)	 AG	45768-46433	CG	GTC
Valid prediction for snap_scaffold_17-snap.1665-T1
Valid prediction for snap_scaffold_17-snap.1648-T1
Valid prediction for CodingQuarry_transcript_22058-T1
Valid prediction for Augustus_model.g27137.t1
Valid prediction for snap_scaffold_17-snap.1656-T1
Valid prediction for GlimmerHMM_glimmerT_40702-T1
Couldn't classify 49473, 50295
Couldn't classify 51852, 52021
Sorry, prediction pasa_asmbl_18982.p1 fails validation.
(CCC)	 AC	49473-50295	GT	GGG
(GTT)	 AG	51852-52021	TC	CCT
Valid prediction for HiQ_model.g27125.t1
Valid prediction for GlimmerHMM_glimmerT_40700-T1
Valid prediction for Augustus_model.g27136.t1
Valid prediction for CodingQuarry_transcript_22056-T1
Valid prediction for snap_scaffold_17-snap.1670-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 HiQ_model.g27132.t1
Valid prediction for snap_scaffold_17-snap.1661-T1
Valid prediction for pasa_asmbl_18092.p1
Valid prediction for GlimmerHMM_glimmerT_40690-T1
Valid prediction for Augustus_model.g27122.t1
Valid prediction for snap_scaffold_17-snap.1653-T1
Valid prediction for CodingQuarry_transcript_22055-T1
Valid prediction for snap_scaffold_17-snap.1663-T1
Valid prediction for Augustus_model.g27129.t1
Valid prediction for snap_scaffold_17-snap.1649-T1
Valid prediction for GlimmerHMM_glimmerT_40688-T1
Valid prediction for snap_scaffold_17-snap.1662-T1
Valid prediction for snap_scaffold_17-snap.1667-T1
Valid prediction for snap_scaffold_17-snap.1642-T1
Valid prediction for GlimmerHMM_glimmerT_40681-T1
Couldn't classify 136199, 136219
Couldn't classify 139361, 139420
Sorry, prediction pasa_asmbl_18084.p1 fails validation.
(AAA)	 GG	136199-136219	GT	TGG
(GTC)	 AG	136309-136441	GT	AGG
(GGC)	 AG	137879-137967	GT	AGG
(ATC)	 AG	138201-138416	GT	AGG
(ATC)	 AG	138580-138701	GT	TGG
(GCA)	 AG	138837-138927	GT	AGG
(GTA)	 AG	139361-139420	CT	CCC
-recovered pasa_asmbl_18084.p1, internal, 136309, 136441
-recovered pasa_asmbl_18084.p1, internal, 137879, 137967
-recovered pasa_asmbl_18084.p1, internal, 138201, 138416
-recovered pasa_asmbl_18084.p1, internal, 138580, 138701
-recovered pasa_asmbl_18084.p1, internal, 138837, 138927
Valid prediction for GlimmerHMM_glimmerT_40696-T1
Valid prediction for GlimmerHMM_glimmerT_40679-T1
Valid prediction for GlimmerHMM_glimmerT_40697-T1
Valid prediction for HiQ_model.g27134.t1
Valid prediction for snap_scaffold_17-snap.1671-T1
Valid prediction for GlimmerHMM_glimmerT_40695-T1
Valid prediction for GlimmerHMM_glimmerT_40691-T1
Valid prediction for Augustus_model.g27121.t1
Valid prediction for GlimmerHMM_glimmerT_40682-T1
Valid prediction for GlimmerHMM_glimmerT_40689-T1
Valid prediction for GlimmerHMM_glimmerT_40680-T1
Valid prediction for snap_scaffold_17-snap.1659-T1
Valid prediction for CodingQuarry_transcript_22053-T1
Valid prediction for GlimmerHMM_glimmerT_40687-T1
Valid prediction for CodingQuarry_transcript_22065-T1
Valid prediction for CodingQuarry_transcript_22054-T1
Valid prediction for snap_scaffold_17-snap.1664-T1
Valid prediction for GlimmerHMM_glimmerT_40694-T1
Valid prediction for Augustus_model.g27123.t1
Valid prediction for snap_scaffold_17-snap.1655-T1
Valid prediction for snap_scaffold_17-snap.1657-T1
Valid prediction for snap_scaffold_17-snap.1644-T1
Valid prediction for GlimmerHMM_glimmerT_40703-T1
Valid prediction for snap_scaffold_17-snap.1638-T1
Couldn't classify 11867, 12152
Sorry, prediction pasa_asmbl_18097.p1 fails validation.
(GAC)	 GG	11867-12152	GT	CTG
(CCA)	 AG	12606-12671	GT	CGG
(GCT)	 AG	12803-12925	GT	AGG
(ATG)	 AG	13025-13149	GA	AAG
-recovered pasa_asmbl_18097.p1, terminal, 13025, 13149
-recovered pasa_asmbl_18097.p1, internal, 12606, 12671
-recovered pasa_asmbl_18097.p1, internal, 12803, 12925
Valid prediction for snap_scaffold_17-snap.1643-T1
Valid prediction for Augustus_model.g27138.t1
Valid prediction for HiQ_model.g27124.t1
Valid prediction for CodingQuarry_transcript_22066-T1
Valid prediction for Augustus_model.g27133.t1
Valid prediction for snap_scaffold_17-snap.1668-T1
Couldn't classify 139832, 139901
Sorry, prediction pasa_asmbl_18083.p1 fails validation.
(CAG)	 AG	139832-139901	GT	AGG
(CGG)	 AG	140009-140127	GT	TTG
(ATT)	 AG	140292-140369	GT	AGG
(GTG)	 AG	140496-140556	GT	TGG
(CCA)	 AG	140796-140965	TG	AAT
-recovered pasa_asmbl_18083.p1, terminal, 140796, 140965
-recovered pasa_asmbl_18083.p1, internal, 139832, 139901
-recovered pasa_asmbl_18083.p1, internal, 140009, 140127
-recovered pasa_asmbl_18083.p1, internal, 140292, 140369
-recovered pasa_asmbl_18083.p1, internal, 140496, 140556
Valid prediction for pasa_asmbl_18087.p1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 61860, rend_intergenic: 55888  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74230, rend_intergenic: 71790  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85957, rend_intergenic: 83827  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90802, rend_intergenic: 90251  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94605, rend_intergenic: 92335  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100362, rend_intergenic: 97526  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104088, rend_intergenic: 100589  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128461, rend_intergenic: 120088  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129395, rend_intergenic: 128760  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147708, rend_intergenic: 146521  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 99900, rend_intergenic: 99897  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 157796
-exon list size: 388


building trellis

0.3    
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1.0    
1.3    
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2.3    
2.6    
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3.6    
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5.1    
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5.9    
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6.7    
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9.5    
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10.0    
10.3    
10.5    
10.8    
11.0    
11.3    
11.5    
11.8    
12.1    
12.3    
12.6    
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13.3    
13.6    
13.8    
14.1    
14.4    
14.6    
14.9    
15.1    
15.4    
15.6    
15.9    
16.2    
16.4    
16.7    
16.9    
17.2    
17.4    
17.7    
17.9    
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    
22.1    
22.3    
22.6    
22.8    
23.1    
23.3    
23.6    
23.8    
24.1    
24.4    
24.6    
24.9    
25.1    
25.4    
25.6    
25.9    
26.2    
26.4    
26.7    
26.9    
27.2    
27.4    
27.7    
27.9    
28.2    
28.5    
28.7    
29.0    
29.2    
29.5    
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30.0    
30.3    
30.5    
30.8    
31.0    
31.3    
31.5    
31.8    
32.1    
32.3    
32.6    
32.8    
33.1    
33.3    
33.6    
33.8    
34.1    
34.4    
34.6    
34.9    
35.1    
35.4    
35.6    
35.9    
36.2    
36.4    
36.7    
36.9    
37.2    
37.4    
37.7    
37.9    
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    
42.1    
42.3    
42.6    
42.8    
43.1    
43.3    
43.6    
43.8    
44.1    
44.4    
44.6    
44.9    
45.1    
45.4    
45.6    
45.9    
46.2    
46.4    
46.7    
46.9    
47.2    
47.4    
47.7    
47.9    
48.2    
48.5    
48.7    
49.0    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.0    
51.3    
51.5    
51.8    
52.1    
52.3    
52.6    
52.8    
53.1    
53.3    
53.6    
53.8    
54.1    
54.4    
54.6    
54.9    
55.1    
55.4    
55.6    
55.9    
56.2    
56.4    
56.7    
56.9    
57.2    
57.4    
57.7    
57.9    
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    
62.1    
62.3    
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62.8    
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63.6    
63.8    
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65.6    
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66.2    
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67.4    
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68.2    
68.5    
68.7    
69.0    
69.2    
69.5    
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70.3    
70.5    
70.8    
71.0    
71.3    
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72.1    
72.3    
72.6    
72.8    
73.1    
73.3    
73.6    
73.8    
74.1    
74.4    
74.6    
74.9    
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75.4    
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77.9    
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    
82.1    
82.3    
82.6    
82.8    
83.1    
83.3    
83.6    
83.8    
84.1    
84.4    
84.6    
84.9    
85.1    
85.4    
85.6    
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86.2    
86.4    
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86.9    
87.2    
87.4    
87.7    
87.9    
88.2    
88.5    
88.7    
89.0    
89.2    
89.5    
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90.0    
90.3    
90.5    
90.8    
91.0    
91.3    
91.5    
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92.3    
92.6    
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93.1    
93.3    
93.6    
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96.4    
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96.9    
97.2    
97.4    
97.7    
97.9    
98.2    
98.5    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 61860, rend_intergenic: 55888  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74230, rend_intergenic: 71790  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85957, rend_intergenic: 83827  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90802, rend_intergenic: 90251  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94605, rend_intergenic: 92335  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100362, rend_intergenic: 97526  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104088, rend_intergenic: 100589  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128461, rend_intergenic: 120088  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129395, rend_intergenic: 128760  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147708, rend_intergenic: 146521  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 99900, rend_intergenic: 99897  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support