-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_12/scaffold_12_13244684-13378457

-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_12-snap.2479-T1
Valid prediction for snap_scaffold_12-snap.2477-T1
Valid prediction for GeneMark_model.53418_t
Valid prediction for snap_scaffold_12-snap.2487-T1
Valid prediction for GeneMark_model.53416_t
Valid prediction for GlimmerHMM_glimmerT_30972-T1
Valid prediction for GeneMark_model.53427_t
Valid prediction for GeneMark_model.53441_t
Valid prediction for snap_scaffold_12-snap.2485-T1
Valid prediction for GlimmerHMM_glimmerT_30979-T1
Valid prediction for snap_scaffold_12-snap.2481-T1
Valid prediction for GeneMark_model.53431_t
Valid prediction for GlimmerHMM_glimmerT_30968-T1
Valid prediction for GeneMark_model.53438_t
Valid prediction for GlimmerHMM_glimmerT_30973-T1
Valid prediction for snap_scaffold_12-snap.2475-T1
Valid prediction for snap_scaffold_12-snap.2472-T1
Valid prediction for GeneMark_model.53405_t
Valid prediction for snap_scaffold_12-snap.2488-T1
Valid prediction for Augustus_model.g20663.t1
Valid prediction for GeneMark_model.53410_t
Valid prediction for snap_scaffold_12-snap.2474-T1
Valid prediction for Augustus_model.g20668.t1
Valid prediction for Augustus_model.g20671.t1
Valid prediction for snap_scaffold_12-snap.2470-T1
Valid prediction for snap_scaffold_12-snap.2483-T1
Valid prediction for GeneMark_model.53414_t
Valid prediction for GeneMark_model.53440_t
Valid prediction for Augustus_model.g20670.t1
Valid prediction for GeneMark_model.53412_t
Valid prediction for GeneMark_model.53433_t
Valid prediction for GeneMark_model.53437_t
Valid prediction for GeneMark_model.53424_t
Valid prediction for snap_scaffold_12-snap.2492-T1
Valid prediction for GeneMark_model.53408_t
Valid prediction for GeneMark_model.53422_t
Valid prediction for snap_scaffold_12-snap.2484-T1
Valid prediction for GeneMark_model.53420_t
Valid prediction for GeneMark_model.53426_t
Valid prediction for GeneMark_model.53407_t
Valid prediction for GlimmerHMM_glimmerT_30980-T1
Valid prediction for GlimmerHMM_glimmerT_30977-T1
Valid prediction for Augustus_model.g20672.t1
Valid prediction for GlimmerHMM_glimmerT_30975-T1
Valid prediction for GeneMark_model.53429_t
Valid prediction for GeneMark_model.53404_t
Valid prediction for snap_scaffold_12-snap.2471-T1
Valid prediction for snap_scaffold_12-snap.2482-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.53439_t
Valid prediction for GeneMark_model.53419_t
Couldn't classify 99566, 99701
Couldn't classify 101122, 101300
Sorry, prediction pasa_asmbl_8294.p1 fails validation.
(GAC)	 CG	99566-99701	GT	GGG
(GTT)	 AG	101122-101300	AG	CCA
Valid prediction for Augustus_model.g20664.t1
Valid prediction for GlimmerHMM_glimmerT_30976-T1
Valid prediction for Augustus_model.g20665.t1
Valid prediction for snap_scaffold_12-snap.2486-T1
Valid prediction for GeneMark_model.53435_t
Couldn't classify 49247, 49479
Sorry, prediction pasa_asmbl_8067.p1 fails validation.
(AGT)	 AG	49247-49479	GT	AGG
(CGG)	 AG	50351-50507	GT	AGG
(GAA)	 AG	51237-51300	GT	CGG
(GAA)	 AG	52124-52179	GT	AGG
(TCT)	 AG	52565-52621	TA	GAT
-recovered pasa_asmbl_8067.p1, terminal, 52565, 52621
-recovered pasa_asmbl_8067.p1, internal, 49247, 49479
-recovered pasa_asmbl_8067.p1, internal, 50351, 50507
-recovered pasa_asmbl_8067.p1, internal, 51237, 51300
-recovered pasa_asmbl_8067.p1, internal, 52124, 52179
Valid prediction for GlimmerHMM_glimmerT_30971-T1
Valid prediction for GeneMark_model.53406_t
Valid prediction for GeneMark_model.53423_t
Valid prediction for snap_scaffold_12-snap.2489-T1
Valid prediction for GeneMark_model.53434_t
Valid prediction for GeneMark_model.53432_t
Valid prediction for snap_scaffold_12-snap.2490-T1
Valid prediction for GeneMark_model.53425_t
Valid prediction for GeneMark_model.53411_t
Valid prediction for Augustus_model.g20666.t1
Valid prediction for snap_scaffold_12-snap.2473-T1
Valid prediction for GeneMark_model.53415_t
Valid prediction for CodingQuarry_transcript_10416-T1
Valid prediction for GeneMark_model.53409_t
Valid prediction for snap_scaffold_12-snap.2476-T1
Valid prediction for Augustus_model.g20669.t1
Valid prediction for snap_scaffold_12-snap.2491-T1
Valid prediction for snap_scaffold_12-snap.2469-T1
Valid prediction for GeneMark_model.53436_t
Valid prediction for GeneMark_model.53417_t
Valid prediction for GeneMark_model.53442_t
Valid prediction for snap_scaffold_12-snap.2480-T1
Valid prediction for GeneMark_model.53430_t
Valid prediction for GeneMark_model.53413_t
Valid prediction for HiQ_model.g20667.t1
Valid prediction for GeneMark_model.53428_t
Valid prediction for GlimmerHMM_glimmerT_30970-T1
Valid prediction for GlimmerHMM_glimmerT_30974-T1
Valid prediction for GlimmerHMM_glimmerT_30978-T1
Valid prediction for snap_scaffold_12-snap.2478-T1
Valid prediction for GeneMark_model.53421_t
Valid prediction for GlimmerHMM_glimmerT_30969-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 23632, rend_intergenic: 4787  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36362, rend_intergenic: 28113  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41769, rend_intergenic: 37567  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52321, rend_intergenic: 42051  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64039, rend_intergenic: 52458  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81685, rend_intergenic: 66806  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115188, rend_intergenic: 108589  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 133774
-exon list size: 493


building trellis

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27.9    
28.1    
28.3    
28.5    
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28.9    
29.1    
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29.7    
29.9    
30.1    
30.3    
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30.9    
31.1    
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31.7    
31.9    
32.1    
32.3    
32.5    
32.7    
32.9    
33.1    
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33.5    
33.7    
33.9    
34.1    
34.3    
34.5    
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34.9    
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35.6    
35.8    
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36.2    
36.4    
36.6    
36.8    
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37.6    
37.8    
38.0    
38.2    
38.4    
38.6    
38.8    
39.0    
39.2    
39.4    
39.6    
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40.0    
40.2    
40.4    
40.6    
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42.0    
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45.5    
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45.9    
46.1    
46.3    
46.5    
46.7    
46.9    
47.1    
47.3    
47.5    
47.7    
47.9    
48.1    
48.3    
48.5    
48.7    
48.9    
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49.9    
50.1    
50.3    
50.5    
50.7    
50.9    
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51.3    
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51.9    
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55.6    
55.8    
56.0    
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56.6    
56.8    
57.0    
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57.6    
57.8    
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58.2    
58.4    
58.6    
58.8    
59.0    
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59.6    
59.8    
60.0    
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60.4    
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60.8    
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62.2    
62.4    
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63.0    
63.2    
63.4    
63.6    
63.8    
64.0    
64.2    
64.4    
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64.8    
65.1    
65.3    
65.5    
65.7    
65.9    
66.1    
66.3    
66.5    
66.7    
66.9    
67.1    
67.3    
67.5    
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67.9    
68.1    
68.3    
68.5    
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68.9    
69.1    
69.3    
69.5    
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70.3    
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72.1    
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72.9    
73.1    
73.3    
73.5    
73.7    
73.9    
74.1    
74.3    
74.5    
74.7    
74.9    
75.2    
75.4    
75.6    
75.8    
76.0    
76.2    
76.4    
76.6    
76.8    
77.0    
77.2    
77.4    
77.6    
77.8    
78.0    
78.2    
78.4    
78.6    
78.8    
79.0    
79.2    
79.4    
79.6    
79.8    
80.0    
80.2    
80.4    
80.6    
80.8    
81.0    
81.2    
81.4    
81.6    
81.8    
82.0    
82.2    
82.4    
82.6    
82.8    
83.0    
83.2    
83.4    
83.6    
83.8    
84.0    
84.2    
84.4    
84.6    
84.8    
85.1    
85.3    
85.5    
85.7    
85.9    
86.1    
86.3    
86.5    
86.7    
86.9    
87.1    
87.3    
87.5    
87.7    
87.9    
88.1    
88.3    
88.5    
88.7    
88.9    
89.1    
89.3    
89.5    
89.7    
89.9    
90.1    
90.3    
90.5    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
91.9    
92.1    
92.3    
92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.7    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.2    
95.4    
95.6    
95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.8    
98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 23632, rend_intergenic: 4787  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36362, rend_intergenic: 28113  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41769, rend_intergenic: 37567  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52321, rend_intergenic: 42051  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64039, rend_intergenic: 52458  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81685, rend_intergenic: 66806  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115188, rend_intergenic: 108589  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 10 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 13240
-exon list size: 27


building trellis

3.4    
6.9    
10.3    
13.8    
17.2    
20.7    
24.1    
27.6    
31.0    
34.5    
37.9    
41.4    
44.8    
48.3    
51.7    
55.2    
58.6    
62.1    
65.5    
69.0    
72.4    
75.9    
79.3    
82.8    
86.2    
89.7    
93.1    
96.6    
-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 1 - 13100
-exon list size: 25


building trellis

3.7    
7.4    
11.1    
14.8    
18.5    
22.2    
25.9    
29.6    
33.3    
37.0    
40.7    
44.4    
48.1    
51.9    
55.6    
59.3    
63.0    
66.7    
70.4    
74.1    
77.8    
81.5    
85.2    
88.9    
92.6    
96.3    
-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

-building DP trellis

-building trellis in range 1 - 12697
-exon list size: 22


building trellis

4.2    
8.3    
12.5    
16.7    
20.8    
25.0    
29.2    
33.3    
37.5    
41.7    
45.8    
50.0    
54.2    
58.3    
62.5    
66.7    
70.8    
75.0    
79.2    
83.3    
87.5    
91.7    
95.8    
-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