-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_16/scaffold_16_8223801-8415692

-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_16-snap.1519-T1
Valid prediction for Augustus_model.g25808.t1
Valid prediction for Augustus_model.g25812.t1
Valid prediction for HiQ_model.g25814.t1
Valid prediction for snap_scaffold_16-snap.1527-T1
Valid prediction for snap_scaffold_16-snap.1538-T1
Valid prediction for Augustus_model.g25809.t1
Valid prediction for GlimmerHMM_glimmerT_38660-T1
Valid prediction for snap_scaffold_16-snap.1508-T1
Valid prediction for pasa_asmbl_16388.p1
Valid prediction for CodingQuarry_transcript_20024-T1
Valid prediction for snap_scaffold_16-snap.1511-T1
Valid prediction for Augustus_model.g25817.t1
Valid prediction for CodingQuarry_transcript_20025-T1
Valid prediction for CodingQuarry_transcript_20027-T1
Valid prediction for snap_scaffold_16-snap.1532-T1
Valid prediction for GlimmerHMM_glimmerT_38670-T1
Valid prediction for Augustus_model.g25811.t1
Valid prediction for GlimmerHMM_glimmerT_38662-T1
Valid prediction for pasa_asmbl_16385.p1
Valid prediction for snap_scaffold_16-snap.1517-T1
Valid prediction for CodingQuarry_transcript_20026-T1
Valid prediction for snap_scaffold_16-snap.1509-T1
Valid prediction for snap_scaffold_16-snap.1534-T1
Valid prediction for snap_scaffold_16-snap.1526-T1
Valid prediction for GlimmerHMM_glimmerT_38668-T1
Valid prediction for Augustus_model.g25824.t1
Valid prediction for snap_scaffold_16-snap.1515-T1
Valid prediction for snap_scaffold_16-snap.1510-T1
Valid prediction for snap_scaffold_16-snap.1505-T1
Valid prediction for snap_scaffold_16-snap.1530-T1
Valid prediction for GlimmerHMM_glimmerT_38663-T1
Valid prediction for HiQ_model.g25813.t1
Valid prediction for snap_scaffold_16-snap.1500-T1
Valid prediction for GlimmerHMM_glimmerT_38672-T1
Valid prediction for GlimmerHMM_glimmerT_38664-T1
Valid prediction for snap_scaffold_16-snap.1518-T1
Couldn't classify 88074, 88722
Sorry, prediction pasa_asmbl_16389.p1 fails validation.
(ACA)	 TA	88074-88722	GT	AGG
(AAG)	 AG	89125-89720	GC	AAG
-recovered pasa_asmbl_16389.p1, terminal, 89125, 89720
-recovered pasa_asmbl_16389.p1, internal, 89125, 89720
Valid prediction for snap_scaffold_16-snap.1513-T1
Valid prediction for Augustus_model.g25820.t1
Valid prediction for HiQ_model.g25816.t1
Valid prediction for GlimmerHMM_glimmerT_38667-T1
Valid prediction for snap_scaffold_16-snap.1516-T1
Valid prediction for snap_scaffold_16-snap.1524-T1
Valid prediction for Augustus_model.g25807.t1
Valid prediction for snap_scaffold_16-snap.1501-T1
Valid prediction for snap_scaffold_16-snap.1521-T1
Valid prediction for snap_scaffold_16-snap.1506-T1
Valid prediction for snap_scaffold_16-snap.1528-T1
Valid prediction for Augustus_model.g25819.t1
Valid prediction for snap_scaffold_16-snap.1512-T1
Valid prediction for snap_scaffold_16-snap.1536-T1
Valid prediction for GlimmerHMM_glimmerT_38665-T1
Valid prediction for Augustus_model.g25818.t1
Valid prediction for snap_scaffold_16-snap.1504-T1
Valid prediction for GlimmerHMM_glimmerT_38676-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 GlimmerHMM_glimmerT_38671-T1
Valid prediction for snap_scaffold_16-snap.1522-T1
Valid prediction for snap_scaffold_16-snap.1502-T1
Couldn't classify 109985, 110098
Sorry, prediction pasa_asmbl_17240.p1 fails validation.
(GGG)	 GG	109985-110098	GT	AGG
(GTT)	 AG	110426-110596	GT	GGG
(GGT)	 AG	110849-110986	GT	AGG
(GCT)	 AG	111863-111955	GT	AGG
(AAC)	 AG	112103-112195	GT	CCG
(CTT)	 AG	113624-113753	GT	TGG
(TGA)	 AG	113905-114028	GT	GGG
(GGT)	 AG	114304-114403	GT	AGG
(AGA)	 AG	114581-114703	GA	AGG
-recovered pasa_asmbl_17240.p1, terminal, 114581, 114703
-recovered pasa_asmbl_17240.p1, internal, 110426, 110596
-recovered pasa_asmbl_17240.p1, internal, 110849, 110986
-recovered pasa_asmbl_17240.p1, internal, 111863, 111955
-recovered pasa_asmbl_17240.p1, internal, 112103, 112195
-recovered pasa_asmbl_17240.p1, internal, 113624, 113753
-recovered pasa_asmbl_17240.p1, internal, 113905, 114028
-recovered pasa_asmbl_17240.p1, internal, 114304, 114403
Valid prediction for snap_scaffold_16-snap.1535-T1
Valid prediction for GlimmerHMM_glimmerT_38669-T1
Valid prediction for snap_scaffold_16-snap.1503-T1
Valid prediction for GlimmerHMM_glimmerT_38674-T1
Valid prediction for snap_scaffold_16-snap.1499-T1
Valid prediction for snap_scaffold_16-snap.1507-T1
Valid prediction for snap_scaffold_16-snap.1529-T1
Valid prediction for Augustus_model.g25823.t1
Valid prediction for HiQ_model.g25815.t1
Valid prediction for GlimmerHMM_glimmerT_38666-T1
Valid prediction for GlimmerHMM_glimmerT_38675-T1
Valid prediction for snap_scaffold_16-snap.1537-T1
Valid prediction for GlimmerHMM_glimmerT_38673-T1
Valid prediction for snap_scaffold_16-snap.1533-T1
Valid prediction for Augustus_model.g25810.t1
Valid prediction for GlimmerHMM_glimmerT_38659-T1
Valid prediction for snap_scaffold_16-snap.1514-T1
Couldn't classify 23663, 23803
Sorry, prediction pasa_asmbl_17242.p1 fails validation.
(GAG)	 CA	23663-23803	GT	AGG
(ATG)	 AG	25957-26034	GT	CGG
(GCA)	 AG	27729-27845	GT	AGG
(AAC)	 AG	27965-28044	GT	CCG
(GGA)	 AG	28177-28303	GT	ACG
(ATG)	 AG	28784-28854	GT	AGG
(GTA)	 AG	29337-29400	AA	AAA
-recovered pasa_asmbl_17242.p1, initial, 25957, 26034
-recovered pasa_asmbl_17242.p1, initial, 28784, 28854
-recovered pasa_asmbl_17242.p1, terminal, 29337, 29400
-recovered pasa_asmbl_17242.p1, internal, 25957, 26034
-recovered pasa_asmbl_17242.p1, internal, 27729, 27845
-recovered pasa_asmbl_17242.p1, internal, 27965, 28044
-recovered pasa_asmbl_17242.p1, internal, 28177, 28303
-recovered pasa_asmbl_17242.p1, internal, 28784, 28854
Valid prediction for Augustus_model.g25806.t1
Valid prediction for Augustus_model.g25821.t1
Valid prediction for GlimmerHMM_glimmerT_38661-T1
Valid prediction for snap_scaffold_16-snap.1520-T1
Valid prediction for CodingQuarry_transcript_20029-T1
Valid prediction for CodingQuarry_transcript_20028-T1
Valid prediction for GlimmerHMM_glimmerT_38677-T1
Valid prediction for HiQ_model.g25822.t1
Valid prediction for snap_scaffold_16-snap.1525-T1
Valid prediction for snap_scaffold_16-snap.1531-T1
Valid prediction for snap_scaffold_16-snap.1523-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 50706, rend_intergenic: 48626  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125267, rend_intergenic: 114458  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133618, rend_intergenic: 127327  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142172, rend_intergenic: 140944  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148639, rend_intergenic: 147822  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152783, rend_intergenic: 150728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158899, rend_intergenic: 154251  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163728, rend_intergenic: 162493  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169487, rend_intergenic: 165116  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172231, rend_intergenic: 169613  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177785, rend_intergenic: 172527  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184408, rend_intergenic: 180892  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 191892
-exon list size: 276


building trellis

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25.9    
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30.6    
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34.9    
35.3    
35.6    
36.0    
36.3    
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37.8    
38.1    
38.5    
38.8    
39.2    
39.6    
39.9    
40.3    
40.6    
41.0    
41.4    
41.7    
42.1    
42.4    
42.8    
43.2    
43.5    
43.9    
44.2    
44.6    
45.0    
45.3    
45.7    
46.0    
46.4    
46.8    
47.1    
47.5    
47.8    
48.2    
48.6    
48.9    
49.3    
49.6    
50.0    
50.4    
50.7    
51.1    
51.4    
51.8    
52.2    
52.5    
52.9    
53.2    
53.6    
54.0    
54.3    
54.7    
55.0    
55.4    
55.8    
56.1    
56.5    
56.8    
57.2    
57.6    
57.9    
58.3    
58.6    
59.0    
59.4    
59.7    
60.1    
60.4    
60.8    
61.2    
61.5    
61.9    
62.2    
62.6    
62.9    
63.3    
63.7    
64.0    
64.4    
64.7    
65.1    
65.5    
65.8    
66.2    
66.5    
66.9    
67.3    
67.6    
68.0    
68.3    
68.7    
69.1    
69.4    
69.8    
70.1    
70.5    
70.9    
71.2    
71.6    
71.9    
72.3    
72.7    
73.0    
73.4    
73.7    
74.1    
74.5    
74.8    
75.2    
75.5    
75.9    
76.3    
76.6    
77.0    
77.3    
77.7    
78.1    
78.4    
78.8    
79.1    
79.5    
79.9    
80.2    
80.6    
80.9    
81.3    
81.7    
82.0    
82.4    
82.7    
83.1    
83.5    
83.8    
84.2    
84.5    
84.9    
85.3    
85.6    
86.0    
86.3    
86.7    
87.1    
87.4    
87.8    
88.1    
88.5    
88.8    
89.2    
89.6    
89.9    
90.3    
90.6    
91.0    
91.4    
91.7    
92.1    
92.4    
92.8    
93.2    
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94.6    
95.0    
95.3    
95.7    
96.0    
96.4    
96.8    
97.1    
97.5    
97.8    
98.2    
98.6    
98.9    
99.3    
99.6    
-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 50706, rend_intergenic: 48626  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125267, rend_intergenic: 114458  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133618, rend_intergenic: 127327  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142172, rend_intergenic: 140944  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148639, rend_intergenic: 147822  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152783, rend_intergenic: 150728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158899, rend_intergenic: 154251  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163728, rend_intergenic: 162493  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169487, rend_intergenic: 165116  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172231, rend_intergenic: 169613  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177785, rend_intergenic: 172527  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184408, rend_intergenic: 180892  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

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

-building DP trellis

-building trellis in range 181076 - 191892
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-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