-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_5/scaffold_5_13970496-14141995

-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_5-snap.2604-T1
Valid prediction for snap_scaffold_5-snap.2624-T1
Valid prediction for GeneMark_model.22405_t
Couldn't classify 81258, 81350
Sorry, prediction pasa_asmbl_44566.p1 fails validation.
(AAC)	 AT	81258-81350	GT	TGG
(CCT)	 AG	81572-81683	GT	AGG
(AGG)	 AG	82163-82344	GT	CAG
(CCC)	 AG	83143-83251	GT	CGG
(ACC)	 AG	83329-83422	GT	ACG
(GTC)	 AG	84614-84692	GT	AGG
(GCG)	 AG	84853-84951	CC	AGC
-recovered pasa_asmbl_44566.p1, terminal, 84853, 84951
-recovered pasa_asmbl_44566.p1, internal, 81572, 81683
-recovered pasa_asmbl_44566.p1, internal, 82163, 82344
-recovered pasa_asmbl_44566.p1, internal, 83143, 83251
-recovered pasa_asmbl_44566.p1, internal, 83329, 83422
-recovered pasa_asmbl_44566.p1, internal, 84614, 84692
Valid prediction for snap_scaffold_5-snap.2613-T1
Valid prediction for snap_scaffold_5-snap.2618-T1
Valid prediction for snap_scaffold_5-snap.2611-T1
Valid prediction for GlimmerHMM_glimmerT_13326-T1
Valid prediction for GlimmerHMM_glimmerT_13323-T1
Valid prediction for snap_scaffold_5-snap.2631-T1
Valid prediction for GlimmerHMM_glimmerT_13321-T1
Valid prediction for HiQ_model.g8917.t1
Valid prediction for GeneMark_model.22407_t
Valid prediction for Augustus_model.g8904.t1
Valid prediction for GlimmerHMM_glimmerT_13312-T1
Valid prediction for pasa_asmbl_44575.p1
Valid prediction for GeneMark_model.22398_t
Valid prediction for GeneMark_model.22402_t
Valid prediction for GlimmerHMM_glimmerT_13318-T1
Valid prediction for snap_scaffold_5-snap.2619-T1
Valid prediction for GeneMark_model.22410_t
Valid prediction for GlimmerHMM_glimmerT_13329-T1
Valid prediction for GlimmerHMM_glimmerT_13316-T1
Valid prediction for HiQ_model.g8915.t1
Valid prediction for GlimmerHMM_glimmerT_13333-T1
Valid prediction for GeneMark_model.22391_t
Valid prediction for GeneMark_model.22421_t
Valid prediction for GlimmerHMM_glimmerT_13339-T1
Valid prediction for Augustus_model.g8911.t1
Valid prediction for snap_scaffold_5-snap.2615-T1
Valid prediction for GeneMark_model.22409_t
Valid prediction for snap_scaffold_5-snap.2606-T1
Valid prediction for HiQ_model.g8912.t1
Valid prediction for GlimmerHMM_glimmerT_13337-T1
Valid prediction for Augustus_model.g8902.t1
Valid prediction for GlimmerHMM_glimmerT_13319-T1
Valid prediction for Augustus_model.g8901.t1
Valid prediction for Augustus_model.g8908.t1
Valid prediction for CodingQuarry_transcript_52215-T1
Valid prediction for CodingQuarry_transcript_52214-T1
Valid prediction for snap_scaffold_5-snap.2610-T1
Valid prediction for snap_scaffold_5-snap.2612-T1
Valid prediction for GlimmerHMM_glimmerT_13315-T1
Valid prediction for GeneMark_model.22412_t
Valid prediction for GlimmerHMM_glimmerT_13314-T1
Valid prediction for Augustus_model.g8905.t1
Couldn't classify 102273, 102746
Sorry, prediction pasa_asmbl_44568.p1 fails validation.
(GCT)	 AC	102273-102746	GA	GAG
Valid prediction for GeneMark_model.22418_t
Valid prediction for snap_scaffold_5-snap.2625-T1
Valid prediction for GeneMark_model.22404_t
Valid prediction for snap_scaffold_5-snap.2620-T1
Couldn't classify 101962, 102095
Sorry, prediction pasa_asmbl_44567.p1 fails validation.
(ATG)	 CC	98638-98748	GT	AGG
(GAT)	 AG	100414-100726	GT	TGG
(ATT)	 AG	101962-102095	CA	TGC
-recovered pasa_asmbl_44567.p1, initial, 98638, 98748
-recovered pasa_asmbl_44567.p1, internal, 100414, 100726
Valid prediction for GlimmerHMM_glimmerT_13340-T1
Valid prediction for GeneMark_model.22396_t
Valid prediction for snap_scaffold_5-snap.2628-T1
Valid prediction for snap_scaffold_5-snap.2630-T1
Valid prediction for Augustus_model.g8903.t1
Valid prediction for CodingQuarry_transcript_52213-T1
Valid prediction for snap_scaffold_5-snap.2607-T1
Valid prediction for GeneMark_model.22406_t
Valid prediction for GeneMark_model.22393_t
Valid prediction for GeneMark_model.22401_t
Valid prediction for GeneMark_model.22414_t
Valid prediction for GlimmerHMM_glimmerT_13330-T1
Valid prediction for GeneMark_model.22416_t
Valid prediction for pasa_asmbl_44570.p1
Valid prediction for GeneMark_model.22394_t
Valid prediction for GeneMark_model.22419_t
Valid prediction for Augustus_model.g8909.t1
Valid prediction for snap_scaffold_5-snap.2621-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 GeneMark_model.22400_t
Valid prediction for Augustus_model.g8900.t1
Valid prediction for GeneMark_model.22413_t
Valid prediction for GeneMark_model.22417_t
Valid prediction for GlimmerHMM_glimmerT_13313-T1
Couldn't classify 99593, 99705
Sorry, prediction pasa_asmbl_45966.p1 fails validation.
(ATC)	 GC	99593-99705	GT	AGG
(GAA)	 AG	100292-100618	GT	AAG
(AGT)	 AG	101047-101183	GT	CGG
(GTC)	 AG	101351-101464	GT	AAG
(CTC)	 AG	101831-101989	GT	GGG
(ACC)	 AG	102127-102302	GT	AGG
(GAG)	 AG	102520-102696	AA	GAA
-recovered pasa_asmbl_45966.p1, terminal, 102520, 102696
-recovered pasa_asmbl_45966.p1, internal, 100292, 100618
-recovered pasa_asmbl_45966.p1, internal, 101047, 101183
-recovered pasa_asmbl_45966.p1, internal, 101351, 101464
-recovered pasa_asmbl_45966.p1, internal, 101831, 101989
-recovered pasa_asmbl_45966.p1, internal, 102127, 102302
Valid prediction for GlimmerHMM_glimmerT_13317-T1
Valid prediction for Augustus_model.g8913.t1
Valid prediction for GlimmerHMM_glimmerT_13328-T1
Valid prediction for snap_scaffold_5-snap.2629-T1
Valid prediction for GlimmerHMM_glimmerT_13325-T1
Valid prediction for GlimmerHMM_glimmerT_13334-T1
Valid prediction for GlimmerHMM_glimmerT_13331-T1
Valid prediction for GeneMark_model.22411_t
Valid prediction for Augustus_model.g8916.t1
Valid prediction for snap_scaffold_5-snap.2616-T1
Valid prediction for snap_scaffold_5-snap.2626-T1
Valid prediction for GeneMark_model.22397_t
Valid prediction for snap_scaffold_5-snap.2609-T1
Valid prediction for Augustus_model.g8910.t1
Valid prediction for snap_scaffold_5-snap.2614-T1
Valid prediction for GeneMark_model.22395_t
Valid prediction for GeneMark_model.22403_t
Valid prediction for GlimmerHMM_glimmerT_13322-T1
Valid prediction for snap_scaffold_5-snap.2605-T1
Valid prediction for GlimmerHMM_glimmerT_13336-T1
Valid prediction for GlimmerHMM_glimmerT_13335-T1
Valid prediction for Augustus_model.g8914.t1
Valid prediction for GlimmerHMM_glimmerT_13324-T1
Valid prediction for snap_scaffold_5-snap.2627-T1
Valid prediction for GeneMark_model.22408_t
Valid prediction for GeneMark_model.22392_t
Valid prediction for GeneMark_model.22399_t
Valid prediction for GlimmerHMM_glimmerT_13332-T1
Valid prediction for snap_scaffold_5-snap.2623-T1
Valid prediction for Augustus_model.g8906.t1
Valid prediction for GlimmerHMM_glimmerT_13327-T1
Valid prediction for pasa_asmbl_45968.p1
Valid prediction for HiQ_model.g8907.t1
Valid prediction for CodingQuarry_transcript_52212-T1
Valid prediction for snap_scaffold_5-snap.2608-T1
Valid prediction for GeneMark_model.22415_t
Valid prediction for GlimmerHMM_glimmerT_13338-T1
Valid prediction for snap_scaffold_5-snap.2622-T1
Valid prediction for GlimmerHMM_glimmerT_13320-T1
Valid prediction for GeneMark_model.22420_t
Valid prediction for GeneMark_model.22422_t
Valid prediction for snap_scaffold_5-snap.2617-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14923, rend_intergenic: 12230  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19133, rend_intergenic: 17418  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48628, rend_intergenic: 43125  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114921, rend_intergenic: 108795  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122954, rend_intergenic: 120771  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 171500
-exon list size: 417


building trellis

0.2    
0.5    
0.7    
1.0    
1.2    
1.4    
1.7    
1.9    
2.1    
2.4    
2.6    
2.9    
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3.3    
3.6    
3.8    
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5.0    
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8.8    
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9.5    
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10.3    
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10.7    
11.0    
11.2    
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11.9    
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13.8    
14.1    
14.3    
14.6    
14.8    
15.0    
15.3    
15.5    
15.8    
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16.5    
16.7    
16.9    
17.2    
17.4    
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17.9    
18.1    
18.4    
18.6    
18.9    
19.1    
19.3    
19.6    
19.8    
20.0    
20.3    
20.5    
20.8    
21.0    
21.2    
21.5    
21.7    
22.0    
22.2    
22.4    
22.7    
22.9    
23.2    
23.4    
23.6    
23.9    
24.1    
24.3    
24.6    
24.8    
25.1    
25.3    
25.5    
25.8    
26.0    
26.3    
26.5    
26.7    
27.0    
27.2    
27.4    
27.7    
27.9    
28.2    
28.4    
28.6    
28.9    
29.1    
29.4    
29.6    
29.8    
30.1    
30.3    
30.5    
30.8    
31.0    
31.3    
31.5    
31.7    
32.0    
32.2    
32.5    
32.7    
32.9    
33.2    
33.4    
33.7    
33.9    
34.1    
34.4    
34.6    
34.8    
35.1    
35.3    
35.6    
35.8    
36.0    
36.3    
36.5    
36.8    
37.0    
37.2    
37.5    
37.7    
37.9    
38.2    
38.4    
38.7    
38.9    
39.1    
39.4    
39.6    
39.9    
40.1    
40.3    
40.6    
40.8    
41.1    
41.3    
41.5    
41.8    
42.0    
42.2    
42.5    
42.7    
43.0    
43.2    
43.4    
43.7    
43.9    
44.2    
44.4    
44.6    
44.9    
45.1    
45.3    
45.6    
45.8    
46.1    
46.3    
46.5    
46.8    
47.0    
47.3    
47.5    
47.7    
48.0    
48.2    
48.4    
48.7    
48.9    
49.2    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.8    
51.1    
51.3    
51.6    
51.8    
52.0    
52.3    
52.5    
52.7    
53.0    
53.2    
53.5    
53.7    
53.9    
54.2    
54.4    
54.7    
54.9    
55.1    
55.4    
55.6    
55.8    
56.1    
56.3    
56.6    
56.8    
57.0    
57.3    
57.5    
57.8    
58.0    
58.2    
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58.7    
58.9    
59.2    
59.4    
59.7    
59.9    
60.1    
60.4    
60.6    
60.9    
61.1    
61.3    
61.6    
61.8    
62.1    
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62.5    
62.8    
63.0    
63.2    
63.5    
63.7    
64.0    
64.2    
64.4    
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65.4    
65.6    
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66.1    
66.3    
66.6    
66.8    
67.1    
67.3    
67.5    
67.8    
68.0    
68.3    
68.5    
68.7    
69.0    
69.2    
69.5    
69.7    
69.9    
70.2    
70.4    
70.6    
70.9    
71.1    
71.4    
71.6    
71.8    
72.1    
72.3    
72.6    
72.8    
73.0    
73.3    
73.5    
73.7    
74.0    
74.2    
74.5    
74.7    
74.9    
75.2    
75.4    
75.7    
75.9    
76.1    
76.4    
76.6    
76.8    
77.1    
77.3    
77.6    
77.8    
78.0    
78.3    
78.5    
78.8    
79.0    
79.2    
79.5    
79.7    
80.0    
80.2    
80.4    
80.7    
80.9    
81.1    
81.4    
81.6    
81.9    
82.1    
82.3    
82.6    
82.8    
83.1    
83.3    
83.5    
83.8    
84.0    
84.2    
84.5    
84.7    
85.0    
85.2    
85.4    
85.7    
85.9    
86.2    
86.4    
86.6    
86.9    
87.1    
87.4    
87.6    
87.8    
88.1    
88.3    
88.5    
88.8    
89.0    
89.3    
89.5    
89.7    
90.0    
90.2    
90.5    
90.7    
90.9    
91.2    
91.4    
91.6    
91.9    
92.1    
92.4    
92.6    
92.8    
93.1    
93.3    
93.6    
93.8    
94.0    
94.3    
94.5    
94.7    
95.0    
95.2    
95.5    
95.7    
95.9    
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 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 14923, rend_intergenic: 12230  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19133, rend_intergenic: 17418  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48628, rend_intergenic: 43125  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114921, rend_intergenic: 108795  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122954, rend_intergenic: 120771  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

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