-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_12/scaffold_12_11434554-11718190

-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.2156-T1
Valid prediction for snap_scaffold_12-snap.2152-T1
Valid prediction for snap_scaffold_12-snap.2131-T1
Valid prediction for pasa_asmbl_7964.p1
Valid prediction for GlimmerHMM_glimmerT_30075-T1
Valid prediction for snap_scaffold_12-snap.2136-T1
Valid prediction for GlimmerHMM_glimmerT_30074-T1
Valid prediction for snap_scaffold_12-snap.2151-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for Augustus_model.g19903.t1
Valid prediction for GlimmerHMM_glimmerT_30090-T1
Valid prediction for Augustus_model.g19904.t1
Valid prediction for Augustus_model.g19901.t1
Valid prediction for snap_scaffold_12-snap.2124-T1
Valid prediction for Augustus_model.g19900.t1
Valid prediction for HiQ_model.g19907.t1
Valid prediction for CodingQuarry_transcript_10394-T1
Valid prediction for Augustus_model.g19914.t1
Valid prediction for GlimmerHMM_glimmerT_30068-T1
Valid prediction for Augustus_model.g19898.t1
Valid prediction for snap_scaffold_12-snap.2125-T1
Valid prediction for snap_scaffold_12-snap.2133-T1
Valid prediction for Augustus_model.g19902.t1
Valid prediction for GlimmerHMM_glimmerT_30081-T1
Valid prediction for snap_scaffold_12-snap.2137-T1
Valid prediction for GlimmerHMM_glimmerT_30077-T1
Valid prediction for snap_scaffold_12-snap.2126-T1
Valid prediction for Augustus_model.g19905.t1
Valid prediction for snap_scaffold_12-snap.2155-T1
Valid prediction for snap_scaffold_12-snap.2141-T1
Valid prediction for GlimmerHMM_glimmerT_30071-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: -)Couldn't classify 60886, 61026
Sorry, prediction pasa_asmbl_9145.p1 fails validation.
(GCG)	 AA	60886-61026	GT	AGG
(GTG)	 AG	61182-61303	GT	AGG
(GAG)	 AG	61393-61462	GT	AGG
(GCC)	 AG	61739-61843	GT	AAG
(GGA)	 AG	62033-62095	GT	GGG
(TGG)	 AG	62205-62275	GT	AGG
(CTC)	 AG	62437-62543	GT	AGG
(AGA)	 AG	62786-62842	GT	CTG
(GTA)	 AG	62973-63067	GT	AGG
(GAG)	 AG	63527-63597	GT	AGG
(GGA)	 AG	64185-64335	TG	GAT
-recovered pasa_asmbl_9145.p1, terminal, 64185, 64335
-recovered pasa_asmbl_9145.p1, internal, 61182, 61303
-recovered pasa_asmbl_9145.p1, internal, 61393, 61462
-recovered pasa_asmbl_9145.p1, internal, 61739, 61843
-recovered pasa_asmbl_9145.p1, internal, 62033, 62095
-recovered pasa_asmbl_9145.p1, internal, 62205, 62275
-recovered pasa_asmbl_9145.p1, internal, 62437, 62543
-recovered pasa_asmbl_9145.p1, internal, 62786, 62842
-recovered pasa_asmbl_9145.p1, internal, 62973, 63067
-recovered pasa_asmbl_9145.p1, internal, 63527, 63597
Couldn't classify 24778, 24836
Sorry, prediction pasa_asmbl_8825.p1 fails validation.
(TGG)	 TC	24778-24836	GT	GTG
(GGT)	 AG	25277-25369	GT	AGG
(TTT)	 AG	26250-26341	GT	CCG
(ACG)	 AG	27599-27696	GA	GAG
-recovered pasa_asmbl_8825.p1, terminal, 27599, 27696
-recovered pasa_asmbl_8825.p1, internal, 25277, 25369
-recovered pasa_asmbl_8825.p1, internal, 26250, 26341
Valid prediction for Augustus_model.g19899.t1
Valid prediction for Augustus_model.g19912.t1
Valid prediction for snap_scaffold_12-snap.2148-T1
Valid prediction for GlimmerHMM_glimmerT_30080-T1
Valid prediction for CodingQuarry_transcript_10395-T1
Valid prediction for Augustus_model.g19913.t1
Valid prediction for GlimmerHMM_glimmerT_30091-T1
Valid prediction for snap_scaffold_12-snap.2134-T1
Valid prediction for snap_scaffold_12-snap.2139-T1
Valid prediction for snap_scaffold_12-snap.2154-T1
Valid prediction for GlimmerHMM_glimmerT_30083-T1
Couldn't classify 99198, 99303
Sorry, prediction pasa_asmbl_8819.p1 fails validation.
(AAC)	 AC	99198-99303	GT	CGG
(AAA)	 AG	101344-101483	GT	AGG
(GCC)	 AG	101801-101941	GG	AAG
-recovered pasa_asmbl_8819.p1, terminal, 101801, 101941
-recovered pasa_asmbl_8819.p1, internal, 101344, 101483
Valid prediction for snap_scaffold_12-snap.2129-T1
Valid prediction for pasa_asmbl_8817.p1
Valid prediction for GlimmerHMM_glimmerT_30093-T1
Valid prediction for GlimmerHMM_glimmerT_30089-T1
Valid prediction for GlimmerHMM_glimmerT_30085-T1
Valid prediction for snap_scaffold_12-snap.2145-T1
Valid prediction for GlimmerHMM_glimmerT_30078-T1
Valid prediction for snap_scaffold_12-snap.2146-T1
Valid prediction for Augustus_model.g19915.t1
Valid prediction for Augustus_model.g19909.t1
Valid prediction for snap_scaffold_12-snap.2143-T1
Valid prediction for Augustus_model.g19908.t1
Valid prediction for GlimmerHMM_glimmerT_30088-T1
Valid prediction for snap_scaffold_12-snap.2153-T1
Valid prediction for snap_scaffold_12-snap.2142-T1
Valid prediction for snap_scaffold_12-snap.2132-T1
Valid prediction for GlimmerHMM_glimmerT_30072-T1
Valid prediction for GlimmerHMM_glimmerT_30076-T1
Valid prediction for GlimmerHMM_glimmerT_30069-T1
Valid prediction for snap_scaffold_12-snap.2128-T1
Valid prediction for GlimmerHMM_glimmerT_30092-T1
Valid prediction for snap_scaffold_12-snap.2144-T1
Valid prediction for snap_scaffold_12-snap.2138-T1
Valid prediction for GlimmerHMM_glimmerT_30087-T1
Valid prediction for CodingQuarry_transcript_10393-T1
Valid prediction for Augustus_model.g19910.t1
Valid prediction for CodingQuarry_transcript_10396-T1
Valid prediction for GlimmerHMM_glimmerT_30084-T1
Valid prediction for GlimmerHMM_glimmerT_30082-T1
Valid prediction for snap_scaffold_12-snap.2130-T1
Valid prediction for snap_scaffold_12-snap.2123-T1
Valid prediction for snap_scaffold_12-snap.2140-T1
Valid prediction for GlimmerHMM_glimmerT_30079-T1
Couldn't classify 96149, 96257
Couldn't classify 97171, 97376
Sorry, prediction pasa_asmbl_8820.p1 fails validation.
(TCA)	 TG	96149-96257	GT	TGG
(GTC)	 AG	96574-96654	GT	TGG
(ACT)	 AG	97171-97376	CT	AGC
-recovered pasa_asmbl_8820.p1, internal, 96574, 96654
Valid prediction for GlimmerHMM_glimmerT_30094-T1
Valid prediction for GlimmerHMM_glimmerT_30070-T1
Valid prediction for GlimmerHMM_glimmerT_30086-T1
Valid prediction for snap_scaffold_12-snap.2149-T1
Valid prediction for snap_scaffold_12-snap.2135-T1
Valid prediction for snap_scaffold_12-snap.2127-T1
Valid prediction for snap_scaffold_12-snap.2147-T1
Valid prediction for snap_scaffold_12-snap.2150-T1
Valid prediction for Augustus_model.g19911.t1
Valid prediction for HiQ_model.g19906.t1
Valid prediction for Augustus_model.g19916.t1
Couldn't classify 2032, 2204
Couldn't classify 5252, 5347
Sorry, prediction pasa_asmbl_8827.p1 fails validation.
(GCC)	 AG	2032-2204	GT	AGG
(GGT)	 AG	3371-3554	GT	AGG
(TTC)	 AG	5252-5347	CT	TCC
-recovered pasa_asmbl_8827.p1, internal, 2032, 2204
-recovered pasa_asmbl_8827.p1, internal, 3371, 3554
Valid prediction for GlimmerHMM_glimmerT_30073-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 8456, rend_intergenic: 8453  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96362, rend_intergenic: 94415  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119481, rend_intergenic: 117548  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148210, rend_intergenic: 129453  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 281573, rend_intergenic: 271231  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 283637
-exon list size: 325


building trellis

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3.7    
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5.8    
6.1    
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7.0    
7.3    
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8.0    
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8.9    
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11.6    
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12.2    
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13.1    
13.5    
13.8    
14.1    
14.4    
14.7    
15.0    
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15.6    
15.9    
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17.4    
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18.0    
18.3    
18.7    
19.0    
19.3    
19.6    
19.9    
20.2    
20.5    
20.8    
21.1    
21.4    
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22.6    
22.9    
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24.5    
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25.4    
25.7    
26.0    
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26.6    
26.9    
27.2    
27.5    
27.8    
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28.4    
28.7    
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30.0    
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30.6    
30.9    
31.2    
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31.8    
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32.4    
32.7    
33.0    
33.3    
33.6    
33.9    
34.3    
34.6    
34.9    
35.2    
35.5    
35.8    
36.1    
36.4    
36.7    
37.0    
37.3    
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38.8    
39.1    
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40.1    
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40.7    
41.0    
41.3    
41.6    
41.9    
42.2    
42.5    
42.8    
43.1    
43.4    
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44.0    
44.3    
44.6    
45.0    
45.3    
45.6    
45.9    
46.2    
46.5    
46.8    
47.1    
47.4    
47.7    
48.0    
48.3    
48.6    
48.9    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.1    
51.4    
51.7    
52.0    
52.3    
52.6    
52.9    
53.2    
53.5    
53.8    
54.1    
54.4    
54.7    
55.0    
55.4    
55.7    
56.0    
56.3    
56.6    
56.9    
57.2    
57.5    
57.8    
58.1    
58.4    
58.7    
59.0    
59.3    
59.6    
59.9    
60.2    
60.6    
60.9    
61.2    
61.5    
61.8    
62.1    
62.4    
62.7    
63.0    
63.3    
63.6    
63.9    
64.2    
64.5    
64.8    
65.1    
65.4    
65.7    
66.1    
66.4    
66.7    
67.0    
67.3    
67.6    
67.9    
68.2    
68.5    
68.8    
69.1    
69.4    
69.7    
70.0    
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70.6    
70.9    
71.3    
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73.1    
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74.0    
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74.6    
74.9    
75.2    
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76.1    
76.5    
76.8    
77.1    
77.4    
77.7    
78.0    
78.3    
78.6    
78.9    
79.2    
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80.1    
80.4    
80.7    
81.0    
81.3    
81.7    
82.0    
82.3    
82.6    
82.9    
83.2    
83.5    
83.8    
84.1    
84.4    
84.7    
85.0    
85.3    
85.6    
85.9    
86.2    
86.5    
86.9    
87.2    
87.5    
87.8    
88.1    
88.4    
88.7    
89.0    
89.3    
89.6    
89.9    
90.2    
90.5    
90.8    
91.1    
91.4    
91.7    
92.0    
92.4    
92.7    
93.0    
93.3    
93.6    
93.9    
94.2    
94.5    
94.8    
95.1    
95.4    
95.7    
96.0    
96.3    
96.6    
96.9    
97.2    
97.6    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 31 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 8456, rend_intergenic: 8453  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96362, rend_intergenic: 94415  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119481, rend_intergenic: 117548  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148210, rend_intergenic: 129453  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 281573, rend_intergenic: 271231  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