-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_6/scaffold_6_11581374-11842054

-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 Augustus_model.g10656.t1
Valid prediction for GeneMark_model.26727_t
Valid prediction for Augustus_model.g10651.t1
Valid prediction for GlimmerHMM_glimmerT_15892-T1
Valid prediction for GeneMark_model.26747_t
Valid prediction for GlimmerHMM_glimmerT_15906-T1
Valid prediction for GlimmerHMM_glimmerT_15908-T1
Valid prediction for GlimmerHMM_glimmerT_15904-T1
Valid prediction for snap_scaffold_6-snap.2453-T1
Valid prediction for GlimmerHMM_glimmerT_15889-T1
Valid prediction for Augustus_model.g10667.t1
Valid prediction for Augustus_model.g10654.t1
Valid prediction for snap_scaffold_6-snap.2483-T1
Valid prediction for snap_scaffold_6-snap.2463-T1
Valid prediction for GeneMark_model.26735_t
Valid prediction for snap_scaffold_6-snap.2465-T1
Valid prediction for snap_scaffold_6-snap.2461-T1
Valid prediction for GlimmerHMM_glimmerT_15910-T1
Valid prediction for GlimmerHMM_glimmerT_15890-T1
Valid prediction for snap_scaffold_6-snap.2478-T1
Valid prediction for GeneMark_model.26731_t
Valid prediction for snap_scaffold_6-snap.2472-T1
Valid prediction for GeneMark_model.26732_t
Valid prediction for snap_scaffold_6-snap.2459-T1
Valid prediction for GeneMark_model.26724_t
Valid prediction for GeneMark_model.26715_t
Valid prediction for GlimmerHMM_glimmerT_15903-T1
Valid prediction for GlimmerHMM_glimmerT_15902-T1
Valid prediction for GlimmerHMM_glimmerT_15899-T1
Valid prediction for GeneMark_model.26712_t
Valid prediction for snap_scaffold_6-snap.2455-T1
Valid prediction for snap_scaffold_6-snap.2482-T1
Valid prediction for GlimmerHMM_glimmerT_15897-T1
Valid prediction for snap_scaffold_6-snap.2492-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g10669.t1
Valid prediction for Augustus_model.g10665.t1
Valid prediction for GeneMark_model.26714_t
Valid prediction for GlimmerHMM_glimmerT_15886-T1
Valid prediction for Augustus_model.g10664.t1
Valid prediction for snap_scaffold_6-snap.2454-T1
Valid prediction for GlimmerHMM_glimmerT_15893-T1
Valid prediction for GeneMark_model.26738_t
Valid prediction for GeneMark_model.26740_t
Couldn't classify 122608, 122907
Sorry, prediction pasa_asmbl_47295.p1 fails validation.
(TGC)	 GC	122608-122907	CT	GAC
Valid prediction for snap_scaffold_6-snap.2458-T1
Valid prediction for snap_scaffold_6-snap.2456-T1
Valid prediction for GeneMark_model.26716_t
Valid prediction for snap_scaffold_6-snap.2476-T1
Valid prediction for GeneMark_model.26730_t
Valid prediction for GeneMark_model.26739_t
Valid prediction for GeneMark_model.26711_t
Valid prediction for Augustus_model.g10668.t1
Valid prediction for Augustus_model.g10659.t1
Valid prediction for snap_scaffold_6-snap.2491-T1
Valid prediction for snap_scaffold_6-snap.2466-T1
Valid prediction for Augustus_model.g10650.t1
Valid prediction for GlimmerHMM_glimmerT_15896-T1
Valid prediction for snap_scaffold_6-snap.2460-T1
Couldn't classify 13922, 13937
Couldn't classify 17758, 17826
Sorry, prediction pasa_asmbl_47291.p1 fails validation.
(GGT)	 AG	13922-13937	GT	GGG
(GTA)	 AG	15227-15284	GT	AAG
(AAA)	 AG	15397-15549	GT	AAG
(AGT)	 AG	15666-15717	GT	AGG
(AGT)	 AG	17758-17826	AA	GGA
add_exon() Sorry, pasa_asmbl_47291.p1 15227-15284-terminal-3 is invalid.
-recovered pasa_asmbl_47291.p1, terminal, 15227, 15284
-recovered pasa_asmbl_47291.p1, internal, 13922, 13937
-recovered pasa_asmbl_47291.p1, internal, 15227, 15284
-recovered pasa_asmbl_47291.p1, internal, 15397, 15549
-recovered pasa_asmbl_47291.p1, internal, 15666, 15717
Valid prediction for HiQ_model.g10663.t1
Valid prediction for GeneMark_model.26725_t
Valid prediction for snap_scaffold_6-snap.2494-T1
Valid prediction for CodingQuarry_transcript_55093-T1
Valid prediction for GeneMark_model.26744_t
Valid prediction for pasa_asmbl_47296.p1
Valid prediction for Augustus_model.g10657.t1
Valid prediction for GlimmerHMM_glimmerT_15905-T1
Valid prediction for snap_scaffold_6-snap.2470-T1
Valid prediction for snap_scaffold_6-snap.2484-T1
Valid prediction for snap_scaffold_6-snap.2477-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_15887-T1
Valid prediction for GlimmerHMM_glimmerT_15894-T1
Valid prediction for snap_scaffold_6-snap.2473-T1
Valid prediction for GlimmerHMM_glimmerT_15912-T1
Valid prediction for snap_scaffold_6-snap.2493-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_15911-T1
Valid prediction for snap_scaffold_6-snap.2485-T1
Valid prediction for snap_scaffold_6-snap.2479-T1
Valid prediction for HiQ_model.g10662.t1
Valid prediction for Augustus_model.g10673.t1
Valid prediction for GlimmerHMM_glimmerT_15895-T1
Valid prediction for CodingQuarry_transcript_55092-T1
Valid prediction for snap_scaffold_6-snap.2462-T1
Valid prediction for GeneMark_model.26718_t
Valid prediction for GeneMark_model.26750_t
Valid prediction for GeneMark_model.26719_t
Valid prediction for Augustus_model.g10655.t1
Valid prediction for Augustus_model.g10666.t1
Valid prediction for GeneMark_model.26723_t
Valid prediction for Augustus_model.g10671.t1
Valid prediction for snap_scaffold_6-snap.2475-T1
Valid prediction for Augustus_model.g10652.t1
Valid prediction for GeneMark_model.26721_t
Valid prediction for snap_scaffold_6-snap.2464-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.26726_t
Valid prediction for GeneMark_model.26743_t
Valid prediction for snap_scaffold_6-snap.2486-T1
Valid prediction for GlimmerHMM_glimmerT_15891-T1
Valid prediction for GeneMark_model.26734_t
Valid prediction for GlimmerHMM_glimmerT_15901-T1
Valid prediction for GeneMark_model.26742_t
Valid prediction for GlimmerHMM_glimmerT_15900-T1
Valid prediction for GlimmerHMM_glimmerT_15913-T1
Valid prediction for Augustus_model.g10661.t1
Valid prediction for snap_scaffold_6-snap.2467-T1
Valid prediction for GeneMark_model.26736_t
Valid prediction for snap_scaffold_6-snap.2481-T1
Valid prediction for GeneMark_model.26748_t
Valid prediction for snap_scaffold_6-snap.2495-T1
Couldn't classify 110744, 110868
Sorry, prediction pasa_asmbl_48705.p1 fails validation.
(ACT)	 CA	110744-110868	GT	TGG
(GAC)	 AG	111396-111544	GC	AGG
(TCG)	 AG	111641-112261	GT	AGG
(AGC)	 AG	112413-112594	GT	AGG
(GAC)	 AG	113364-113507	AG	AGA
-recovered pasa_asmbl_48705.p1, terminal, 113364, 113507
-recovered pasa_asmbl_48705.p1, internal, 111396, 111544
-recovered pasa_asmbl_48705.p1, internal, 111641, 112261
-recovered pasa_asmbl_48705.p1, internal, 112413, 112594
Valid prediction for GeneMark_model.26741_t
Valid prediction for snap_scaffold_6-snap.2457-T1
Valid prediction for GlimmerHMM_glimmerT_15888-T1
Valid prediction for Augustus_model.g10670.t1
Valid prediction for GeneMark_model.26717_t
Valid prediction for GeneMark_model.26713_t
Valid prediction for snap_scaffold_6-snap.2490-T1
Valid prediction for GeneMark_model.26720_t
Valid prediction for snap_scaffold_6-snap.2474-T1
Valid prediction for snap_scaffold_6-snap.2487-T1
Valid prediction for snap_scaffold_6-snap.2489-T1
Valid prediction for Augustus_model.g10658.t1
Valid prediction for Augustus_model.g10672.t1
Valid prediction for GeneMark_model.26729_t
Valid prediction for snap_scaffold_6-snap.2488-T1
Valid prediction for Augustus_model.g10660.t1
Valid prediction for GeneMark_model.26745_t
Valid prediction for Augustus_model.g10653.t1
Valid prediction for GlimmerHMM_glimmerT_15898-T1
Valid prediction for snap_scaffold_6-snap.2468-T1
Valid prediction for snap_scaffold_6-snap.2480-T1
Valid prediction for GlimmerHMM_glimmerT_15907-T1
Valid prediction for GeneMark_model.26746_t
Couldn't classify 72147, 72608
Sorry, prediction pasa_asmbl_48708.p1 fails validation.
(CTC)	 CT	72147-72608	AA	GAA
Valid prediction for GeneMark_model.26728_t
Valid prediction for GeneMark_model.26749_t
Valid prediction for snap_scaffold_6-snap.2496-T1
Valid prediction for snap_scaffold_6-snap.2471-T1
Valid prediction for GeneMark_model.26737_t
Valid prediction for snap_scaffold_6-snap.2469-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_15909-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 97855, rend_intergenic: 97852  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67716, rend_intergenic: 67128  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195864, rend_intergenic: 193433  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 225256, rend_intergenic: 219658  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 260681
-exon list size: 450


building trellis

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0.4    
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0.9    
1.1    
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1.5    
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2.9    
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17.9    
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20.1    
20.4    
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21.9    
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24.3    
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27.9    
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28.8    
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29.9    
30.1    
30.3    
30.5    
30.8    
31.0    
31.2    
31.4    
31.6    
31.9    
32.1    
32.3    
32.5    
32.7    
33.0    
33.2    
33.4    
33.6    
33.8    
34.1    
34.3    
34.5    
34.7    
35.0    
35.2    
35.4    
35.6    
35.8    
36.1    
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36.5    
36.7    
36.9    
37.2    
37.4    
37.6    
37.8    
38.1    
38.3    
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38.9    
39.2    
39.4    
39.6    
39.8    
40.0    
40.3    
40.5    
40.7    
40.9    
41.2    
41.4    
41.6    
41.8    
42.0    
42.3    
42.5    
42.7    
42.9    
43.1    
43.4    
43.6    
43.8    
44.0    
44.2    
44.5    
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44.9    
45.1    
45.4    
45.6    
45.8    
46.0    
46.2    
46.5    
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46.9    
47.1    
47.3    
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48.2    
48.5    
48.7    
48.9    
49.1    
49.3    
49.6    
49.8    
50.0    
50.2    
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50.9    
51.1    
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52.9    
53.1    
53.3    
53.5    
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54.0    
54.2    
54.4    
54.6    
54.9    
55.1    
55.3    
55.5    
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56.0    
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56.6    
56.9    
57.1    
57.3    
57.5    
57.7    
58.0    
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58.6    
58.8    
59.1    
59.3    
59.5    
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60.0    
60.2    
60.4    
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60.8    
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62.2    
62.4    
62.6    
62.8    
63.1    
63.3    
63.5    
63.7    
63.9    
64.2    
64.4    
64.6    
64.8    
65.0    
65.3    
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65.7    
65.9    
66.2    
66.4    
66.6    
66.8    
67.0    
67.3    
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67.9    
68.1    
68.4    
68.6    
68.8    
69.0    
69.2    
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70.1    
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71.0    
71.2    
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72.1    
72.3    
72.6    
72.8    
73.0    
73.2    
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74.1    
74.3    
74.6    
74.8    
75.0    
75.2    
75.4    
75.7    
75.9    
76.1    
76.3    
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77.0    
77.2    
77.4    
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77.9    
78.1    
78.3    
78.5    
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79.0    
79.2    
79.4    
79.6    
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80.1    
80.3    
80.5    
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81.0    
81.2    
81.4    
81.6    
81.9    
82.1    
82.3    
82.5    
82.7    
83.0    
83.2    
83.4    
83.6    
83.8    
84.1    
84.3    
84.5    
84.7    
85.0    
85.2    
85.4    
85.6    
85.8    
86.1    
86.3    
86.5    
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86.9    
87.2    
87.4    
87.6    
87.8    
88.1    
88.3    
88.5    
88.7    
88.9    
89.2    
89.4    
89.6    
89.8    
90.0    
90.3    
90.5    
90.7    
90.9    
91.2    
91.4    
91.6    
91.8    
92.0    
92.3    
92.5    
92.7    
92.9    
93.1    
93.4    
93.6    
93.8    
94.0    
94.2    
94.5    
94.7    
94.9    
95.1    
95.4    
95.6    
95.8    
96.0    
96.2    
96.5    
96.7    
96.9    
97.1    
97.3    
97.6    
97.8    
98.0    
98.2    
98.5    
98.7    
98.9    
99.1    
99.3    
99.6    
99.8    
-found 35 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 97855, rend_intergenic: 97852  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67716, rend_intergenic: 67128  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195864, rend_intergenic: 193433  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 225256, rend_intergenic: 219658  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 32 predictions persist after filtering for low support