-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_4/scaffold_4_9557696-9713509

-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 GeneMark_model.16502_t
Valid prediction for GlimmerHMM_glimmerT_10152-T1
Valid prediction for GlimmerHMM_glimmerT_10157-T1
Valid prediction for GlimmerHMM_glimmerT_10173-T1
Valid prediction for GeneMark_model.16539_t
Valid prediction for GeneMark_model.16504_t
Valid prediction for GlimmerHMM_glimmerT_10175-T1
Valid prediction for GeneMark_model.16531_t
Valid prediction for Augustus_model.g6671.t1
Valid prediction for GeneMark_model.16499_t
Valid prediction for GlimmerHMM_glimmerT_10156-T1
Valid prediction for GlimmerHMM_glimmerT_10142-T1
Valid prediction for GeneMark_model.16529_t
Valid prediction for snap_scaffold_4-snap.2051-T1
Valid prediction for snap_scaffold_4-snap.2023-T1
Valid prediction for Augustus_model.g6660.t1
Valid prediction for GlimmerHMM_glimmerT_10171-T1
Couldn't classify 98201, 98632
Sorry, prediction pasa_asmbl_42952.p1 fails validation.
(CAT)	 CT	98201-98632	CC	AGC
Valid prediction for Augustus_model.g6665.t1
Valid prediction for GlimmerHMM_glimmerT_10160-T1
Valid prediction for snap_scaffold_4-snap.2028-T1
Valid prediction for snap_scaffold_4-snap.2037-T1
Valid prediction for snap_scaffold_4-snap.2050-T1
Valid prediction for GlimmerHMM_glimmerT_10158-T1
Valid prediction for GeneMark_model.16513_t
Valid prediction for snap_scaffold_4-snap.2056-T1
Valid prediction for snap_scaffold_4-snap.2044-T1
Valid prediction for Augustus_model.g6662.t1
Valid prediction for GlimmerHMM_glimmerT_10143-T1
Valid prediction for GeneMark_model.16518_t
Valid prediction for snap_scaffold_4-snap.2027-T1
Valid prediction for snap_scaffold_4-snap.2034-T1
Valid prediction for Augustus_model.g6654.t1
Valid prediction for snap_scaffold_4-snap.2029-T1
Valid prediction for CodingQuarry_transcript_48991-T1
Valid prediction for GeneMark_model.16535_t
Valid prediction for Augustus_model.g6656.t1
Valid prediction for GeneMark_model.16516_t
Valid prediction for snap_scaffold_4-snap.2046-T1
Valid prediction for GeneMark_model.16525_t
Valid prediction for Augustus_model.g6652.t1
Valid prediction for snap_scaffold_4-snap.2048-T1
Valid prediction for GlimmerHMM_glimmerT_10159-T1
Valid prediction for Augustus_model.g6663.t1
Valid prediction for GlimmerHMM_glimmerT_10148-T1
Valid prediction for GeneMark_model.16533_t
Valid prediction for GlimmerHMM_glimmerT_10145-T1
Valid prediction for GeneMark_model.16520_t
Valid prediction for GeneMark_model.16505_t
Valid prediction for GlimmerHMM_glimmerT_10167-T1
Valid prediction for snap_scaffold_4-snap.2031-T1
Valid prediction for GeneMark_model.16497_t
Valid prediction for Augustus_model.g6670.t1
Valid prediction for GlimmerHMM_glimmerT_10161-T1
Valid prediction for GeneMark_model.16511_t
Valid prediction for snap_scaffold_4-snap.2036-T1
Valid prediction for snap_scaffold_4-snap.2038-T1
Valid prediction for GeneMark_model.16522_t
Valid prediction for GlimmerHMM_glimmerT_10169-T1
Valid prediction for GlimmerHMM_glimmerT_10155-T1
Valid prediction for GlimmerHMM_glimmerT_10151-T1
Valid prediction for GlimmerHMM_glimmerT_10164-T1
Valid prediction for GeneMark_model.16538_t
Valid prediction for GeneMark_model.16523_t
Valid prediction for snap_scaffold_4-snap.2041-T1
Valid prediction for GeneMark_model.16507_t
Valid prediction for snap_scaffold_4-snap.2030-T1
Valid prediction for HiQ_model.g6661.t1
Valid prediction for GlimmerHMM_glimmerT_10144-T1
Valid prediction for GeneMark_model.16514_t
Valid prediction for snap_scaffold_4-snap.2054-T1
Valid prediction for Augustus_model.g6658.t1
Valid prediction for GeneMark_model.16527_t

-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_4-snap.2040-T1
Valid prediction for GeneMark_model.16524_t
Valid prediction for GeneMark_model.16530_t
Valid prediction for snap_scaffold_4-snap.2022-T1
Valid prediction for GeneMark_model.16506_t
Valid prediction for snap_scaffold_4-snap.2042-T1
Valid prediction for snap_scaffold_4-snap.2026-T1
Valid prediction for GeneMark_model.16515_t
Valid prediction for GeneMark_model.16501_t
Valid prediction for snap_scaffold_4-snap.2049-T1
Valid prediction for Augustus_model.g6666.t1
Valid prediction for Augustus_model.g6655.t1
Valid prediction for GlimmerHMM_glimmerT_10162-T1
Valid prediction for GlimmerHMM_glimmerT_10168-T1
Valid prediction for GeneMark_model.16512_t
Valid prediction for GlimmerHMM_glimmerT_10165-T1
Valid prediction for GeneMark_model.16500_t
Valid prediction for GeneMark_model.16510_t
Valid prediction for snap_scaffold_4-snap.2024-T1
Valid prediction for snap_scaffold_4-snap.2053-T1
Valid prediction for GeneMark_model.16498_t
Valid prediction for snap_scaffold_4-snap.2045-T1
Valid prediction for GlimmerHMM_glimmerT_10154-T1
Valid prediction for GlimmerHMM_glimmerT_10172-T1
Valid prediction for GlimmerHMM_glimmerT_10149-T1
Valid prediction for GlimmerHMM_glimmerT_10153-T1
Valid prediction for GeneMark_model.16496_t
Valid prediction for GeneMark_model.16503_t
Valid prediction for Augustus_model.g6669.t1
Valid prediction for Augustus_model.g6664.t1
Valid prediction for GlimmerHMM_glimmerT_10166-T1
Valid prediction for snap_scaffold_4-snap.2039-T1
Valid prediction for snap_scaffold_4-snap.2033-T1
Valid prediction for GeneMark_model.16528_t
Valid prediction for GeneMark_model.16536_t
Valid prediction for GeneMark_model.16526_t
Valid prediction for GeneMark_model.16519_t
Valid prediction for Augustus_model.g6657.t1
Valid prediction for snap_scaffold_4-snap.2025-T1
Valid prediction for GeneMark_model.16532_t
Valid prediction for snap_scaffold_4-snap.2043-T1
Valid prediction for GlimmerHMM_glimmerT_10163-T1
Valid prediction for GlimmerHMM_glimmerT_10150-T1
Valid prediction for snap_scaffold_4-snap.2055-T1
Valid prediction for GeneMark_model.16521_t
Valid prediction for snap_scaffold_4-snap.2052-T1
Valid prediction for GlimmerHMM_glimmerT_10174-T1
Valid prediction for snap_scaffold_4-snap.2047-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.16517_t
Valid prediction for Augustus_model.g6653.t1
Valid prediction for GeneMark_model.16534_t
Valid prediction for Augustus_model.g6668.t1
Valid prediction for GlimmerHMM_glimmerT_10146-T1
Valid prediction for snap_scaffold_4-snap.2035-T1
Valid prediction for GlimmerHMM_glimmerT_10147-T1
Valid prediction for Augustus_model.g6659.t1
Valid prediction for Augustus_model.g6667.t1
Valid prediction for snap_scaffold_4-snap.2032-T1
Valid prediction for GlimmerHMM_glimmerT_10170-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9205, rend_intergenic: 6506  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27765, rend_intergenic: 25952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53046, rend_intergenic: 48827  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64794, rend_intergenic: 62136  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84615, rend_intergenic: 78843  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93910, rend_intergenic: 84768  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103095, rend_intergenic: 94638  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104034, rend_intergenic: 103715  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119736, rend_intergenic: 104635  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122065, rend_intergenic: 119938  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123664, rend_intergenic: 123602  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126810, rend_intergenic: 124432  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127520, rend_intergenic: 127149  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132660, rend_intergenic: 127721  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151282, rend_intergenic: 146080  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 155814
-exon list size: 638


building trellis

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16.9    
17.0    
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18.8    
18.9    
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20.8    
20.9    
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21.9    
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22.8    
23.0    
23.1    
23.3    
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23.6    
23.8    
23.9    
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24.4    
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24.7    
24.8    
25.0    
25.2    
25.3    
25.5    
25.6    
25.8    
25.9    
26.1    
26.2    
26.4    
26.6    
26.7    
26.9    
27.0    
27.2    
27.3    
27.5    
27.7    
27.8    
28.0    
28.1    
28.3    
28.4    
28.6    
28.7    
28.9    
29.1    
29.2    
29.4    
29.5    
29.7    
29.8    
30.0    
30.2    
30.3    
30.5    
30.6    
30.8    
30.9    
31.1    
31.2    
31.4    
31.6    
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31.9    
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32.2    
32.3    
32.5    
32.7    
32.8    
33.0    
33.1    
33.3    
33.4    
33.6    
33.8    
33.9    
34.1    
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34.8    
35.0    
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36.9    
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38.8    
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40.9    
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42.7    
42.8    
43.0    
43.1    
43.3    
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43.6    
43.8    
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44.1    
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44.4    
44.5    
44.7    
44.8    
45.0    
45.2    
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45.8    
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46.1    
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46.4    
46.6    
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46.9    
47.0    
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48.0    
48.1    
48.3    
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48.6    
48.8    
48.9    
49.1    
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50.8    
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51.9    
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52.8    
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53.1    
53.3    
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53.6    
53.8    
53.9    
54.1    
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54.8    
55.0    
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55.3    
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55.8    
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56.1    
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56.9    
57.0    
57.2    
57.3    
57.5    
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57.8    
58.0    
58.1    
58.3    
58.4    
58.6    
58.8    
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59.8    
60.0    
60.2    
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60.6    
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61.1    
61.3    
61.4    
61.6    
61.7    
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62.0    
62.2    
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62.8    
63.0    
63.1    
63.3    
63.4    
63.6    
63.7    
63.9    
64.1    
64.2    
64.4    
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64.8    
65.0    
65.2    
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66.4    
66.6    
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66.9    
67.0    
67.2    
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68.0    
68.1    
68.3    
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68.6    
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69.1    
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71.1    
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71.4    
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73.8    
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79.1    
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80.5    
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80.8    
80.9    
81.1    
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81.4    
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81.9    
82.0    
82.2    
82.3    
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82.7    
82.8    
83.0    
83.1    
83.3    
83.4    
83.6    
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83.9    
84.1    
84.2    
84.4    
84.5    
84.7    
84.8    
85.0    
85.2    
85.3    
85.5    
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85.9    
86.1    
86.2    
86.4    
86.6    
86.7    
86.9    
87.0    
87.2    
87.3    
87.5    
87.7    
87.8    
88.0    
88.1    
88.3    
88.4    
88.6    
88.8    
88.9    
89.1    
89.2    
89.4    
89.5    
89.7    
89.8    
90.0    
90.2    
90.3    
90.5    
90.6    
90.8    
90.9    
91.1    
91.2    
91.4    
91.6    
91.7    
91.9    
92.0    
92.2    
92.3    
92.5    
92.7    
92.8    
93.0    
93.1    
93.3    
93.4    
93.6    
93.8    
93.9    
94.1    
94.2    
94.4    
94.5    
94.7    
94.8    
95.0    
95.2    
95.3    
95.5    
95.6    
95.8    
95.9    
96.1    
96.2    
96.4    
96.6    
96.7    
96.9    
97.0    
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97.3    
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97.8    
98.0    
98.1    
98.3    
98.4    
98.6    
98.8    
98.9    
99.1    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 9205, rend_intergenic: 6506  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27765, rend_intergenic: 25952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53046, rend_intergenic: 48827  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64794, rend_intergenic: 62136  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84615, rend_intergenic: 78843  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93910, rend_intergenic: 84768  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103095, rend_intergenic: 94638  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104034, rend_intergenic: 103715  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119736, rend_intergenic: 104635  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122065, rend_intergenic: 119938  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123664, rend_intergenic: 123602  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126810, rend_intergenic: 124432  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127520, rend_intergenic: 127149  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132660, rend_intergenic: 127721  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151282, rend_intergenic: 146080  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support