-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_23/scaffold_23_6716219-6883221

-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.g35272.t1
Valid prediction for GeneMark_model.90927_t
Valid prediction for GeneMark_model.90932_t
Valid prediction for GeneMark_model.90934_t
Valid prediction for GlimmerHMM_glimmerT_52450-T1
Valid prediction for snap_scaffold_23-snap.1231-T1
Valid prediction for GeneMark_model.90917_t
Valid prediction for GlimmerHMM_glimmerT_52453-T1
Valid prediction for snap_scaffold_23-snap.1218-T1
Valid prediction for GlimmerHMM_glimmerT_52445-T1
Valid prediction for HiQ_model.g35274.t1
Valid prediction for snap_scaffold_23-snap.1246-T1
Valid prediction for GeneMark_model.90912_t
Valid prediction for snap_scaffold_23-snap.1241-T1
Valid prediction for snap_scaffold_23-snap.1226-T1
Couldn't classify 60558, 61037
Sorry, prediction pasa_asmbl_30948.p1 fails validation.
(CAC)	 GG	60558-61037	CG	CGC
Valid prediction for GeneMark_model.90923_t
Valid prediction for snap_scaffold_23-snap.1224-T1
Valid prediction for GeneMark_model.90936_t
Valid prediction for snap_scaffold_23-snap.1234-T1
Valid prediction for Augustus_model.g35271.t1
Valid prediction for Augustus_model.g35268.t1
Valid prediction for GeneMark_model.90909_t
Valid prediction for GlimmerHMM_glimmerT_52442-T1
Valid prediction for snap_scaffold_23-snap.1230-T1
Couldn't classify 108764, 108857
Couldn't classify 111513, 111597
Sorry, prediction pasa_asmbl_31282.p1 fails validation.
(GTC)	 CA	108764-108857	GT	AGG
(GTC)	 AG	109121-109195	GT	CGG
(ATC)	 AG	109326-109457	GT	AGG
(AAA)	 AG	110800-111001	GT	AGG
(CTG)	 AG	111513-111597	GG	CAG
-recovered pasa_asmbl_31282.p1, internal, 109121, 109195
-recovered pasa_asmbl_31282.p1, internal, 109326, 109457
-recovered pasa_asmbl_31282.p1, internal, 110800, 111001
Couldn't classify 58306, 58533
Couldn't classify 59526, 59607
Sorry, prediction pasa_asmbl_30947.p1 fails validation.
(GAT)	 CA	58306-58533	GT	GGG
(AAT)	 AG	58652-58774	GT	AGG
(AGT)	 AG	59090-59226	GC	AGG
(GCG)	 AG	59526-59607	TC	GCT
-recovered pasa_asmbl_30947.p1, internal, 58652, 58774
-recovered pasa_asmbl_30947.p1, internal, 59090, 59226
Valid prediction for snap_scaffold_23-snap.1233-T1
Valid prediction for snap_scaffold_23-snap.1235-T1
Valid prediction for GlimmerHMM_glimmerT_52448-T1
Couldn't classify 98227, 98559
Sorry, prediction pasa_asmbl_30955.p1 fails validation.
(ATG)	 CC	98227-98559	GA	GTG
Valid prediction for Augustus_model.g35266.t1
Valid prediction for GeneMark_model.90915_t
Valid prediction for snap_scaffold_23-snap.1238-T1
Couldn't classify 61338, 61919
Sorry, prediction pasa_asmbl_30949.p1 fails validation.
(ATG)	 AG	61338-61919	GA	CTG
Valid prediction for Augustus_model.g35269.t1
Valid prediction for pasa_asmbl_30958.p1
Valid prediction for GeneMark_model.90921_t
Valid prediction for GlimmerHMM_glimmerT_52446-T1
Valid prediction for GeneMark_model.90907_t
Valid prediction for CodingQuarry_transcript_35630-T1
Valid prediction for GlimmerHMM_glimmerT_52443-T1
Valid prediction for snap_scaffold_23-snap.1223-T1
Valid prediction for GlimmerHMM_glimmerT_52436-T1
Valid prediction for snap_scaffold_23-snap.1219-T1
Couldn't classify 47385, 47594
Couldn't classify 48399, 48461
Sorry, prediction pasa_asmbl_31221.p1 fails validation.
(GCC)	 AG	47385-47594	GT	AGG
(TCC)	 AG	47876-47977	GT	TGG
(GAG)	 AG	48399-48461	CA	GCC
-recovered pasa_asmbl_31221.p1, internal, 47385, 47594
-recovered pasa_asmbl_31221.p1, internal, 47876, 47977
Couldn't classify 62139, 62765
Sorry, prediction pasa_asmbl_30950.p1 fails validation.
(CAG)	 TA	62139-62765	GT	CAG
(GCC)	 AG	62814-63641	GC	AAG
-recovered pasa_asmbl_30950.p1, terminal, 62814, 63641
-recovered pasa_asmbl_30950.p1, internal, 62814, 63641
Valid prediction for GlimmerHMM_glimmerT_52457-T1
Valid prediction for GlimmerHMM_glimmerT_52444-T1
Couldn't classify 80400, 80774
Sorry, prediction pasa_asmbl_30953.p1 fails validation.
(ATG)	 GC	80400-80774	TA	TGT
Valid prediction for snap_scaffold_23-snap.1240-T1
Valid prediction for GlimmerHMM_glimmerT_52440-T1
Valid prediction for GeneMark_model.90926_t
Valid prediction for GeneMark_model.90919_t
Valid prediction for Augustus_model.g35270.t1
Valid prediction for GeneMark_model.90906_t
Valid prediction for GeneMark_model.90929_t
Valid prediction for snap_scaffold_23-snap.1222-T1
Valid prediction for GeneMark_model.90913_t
Valid prediction for snap_scaffold_23-snap.1237-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 Augustus_model.g35275.t1
Valid prediction for GeneMark_model.90914_t
Valid prediction for snap_scaffold_23-snap.1243-T1
Valid prediction for snap_scaffold_23-snap.1229-T1
Valid prediction for snap_scaffold_23-snap.1225-T1
Valid prediction for GeneMark_model.90928_t
Valid prediction for CodingQuarry_transcript_35631-T1
Valid prediction for snap_scaffold_23-snap.1221-T1
Valid prediction for GlimmerHMM_glimmerT_52437-T1
Valid prediction for snap_scaffold_23-snap.1245-T1
Valid prediction for GeneMark_model.90920_t
Valid prediction for GeneMark_model.90911_t
Valid prediction for Augustus_model.g35267.t1
Valid prediction for GlimmerHMM_glimmerT_52441-T1
Valid prediction for GlimmerHMM_glimmerT_52452-T1
Valid prediction for snap_scaffold_23-snap.1220-T1
Valid prediction for Augustus_model.g35273.t1
Valid prediction for GlimmerHMM_glimmerT_52451-T1
Valid prediction for GeneMark_model.90910_t
Valid prediction for GlimmerHMM_glimmerT_52458-T1
Valid prediction for GlimmerHMM_glimmerT_52455-T1
Valid prediction for pasa_asmbl_31703.p1
Valid prediction for snap_scaffold_23-snap.1227-T1
Valid prediction for GeneMark_model.90935_t
Valid prediction for GeneMark_model.90937_t
Valid prediction for GeneMark_model.90916_t
Valid prediction for GeneMark_model.90931_t
Valid prediction for GlimmerHMM_glimmerT_52456-T1
Valid prediction for snap_scaffold_23-snap.1228-T1
Valid prediction for pasa_asmbl_31704.p1
Valid prediction for GeneMark_model.90933_t
Valid prediction for snap_scaffold_23-snap.1244-T1
Valid prediction for snap_scaffold_23-snap.1236-T1
Valid prediction for GlimmerHMM_glimmerT_52439-T1
Valid prediction for GlimmerHMM_glimmerT_52449-T1
Valid prediction for CodingQuarry_transcript_35632-T1
Valid prediction for snap_scaffold_23-snap.1242-T1
Valid prediction for GeneMark_model.90930_t
Valid prediction for GlimmerHMM_glimmerT_52447-T1
Valid prediction for snap_scaffold_23-snap.1232-T1
Valid prediction for GlimmerHMM_glimmerT_52454-T1
Valid prediction for GeneMark_model.90908_t
Valid prediction for GeneMark_model.90918_t
Valid prediction for GeneMark_model.90924_t
Valid prediction for snap_scaffold_23-snap.1239-T1
Valid prediction for GlimmerHMM_glimmerT_52438-T1
Valid prediction for GeneMark_model.90922_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11153, rend_intergenic: 9235  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14677, rend_intergenic: 11631  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22573, rend_intergenic: 20953  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31040, rend_intergenic: 27099  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43438, rend_intergenic: 41817  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63641, rend_intergenic: 49397  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101420, rend_intergenic: 100348  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112166, rend_intergenic: 108761  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114693, rend_intergenic: 112727  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 167003
-exon list size: 465


building trellis

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27.2    
27.4    
27.6    
27.8    
28.1    
28.3    
28.5    
28.7    
28.9    
29.1    
29.3    
29.6    
29.8    
30.0    
30.2    
30.4    
30.6    
30.8    
31.0    
31.3    
31.5    
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31.9    
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32.3    
32.5    
32.8    
33.0    
33.2    
33.4    
33.6    
33.8    
34.0    
34.3    
34.5    
34.7    
34.9    
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35.3    
35.5    
35.8    
36.0    
36.2    
36.4    
36.6    
36.8    
37.0    
37.3    
37.5    
37.7    
37.9    
38.1    
38.3    
38.5    
38.8    
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39.6    
39.8    
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40.3    
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40.7    
40.9    
41.1    
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41.5    
41.8    
42.0    
42.2    
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42.6    
42.8    
43.0    
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44.3    
44.5    
44.8    
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45.6    
45.8    
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46.7    
46.9    
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48.4    
48.6    
48.8    
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49.3    
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50.3    
50.5    
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51.6    
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52.9    
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54.8    
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59.3    
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60.4    
60.6    
60.8    
61.0    
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62.3    
62.5    
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63.0    
63.2    
63.4    
63.6    
63.8    
64.0    
64.2    
64.5    
64.7    
64.9    
65.1    
65.3    
65.5    
65.7    
66.0    
66.2    
66.4    
66.6    
66.8    
67.0    
67.2    
67.5    
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67.9    
68.1    
68.3    
68.5    
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69.0    
69.2    
69.4    
69.6    
69.8    
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72.2    
72.4    
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72.8    
73.0    
73.2    
73.4    
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73.9    
74.1    
74.3    
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74.9    
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75.4    
75.6    
75.8    
76.0    
76.2    
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77.9    
78.2    
78.4    
78.6    
78.8    
79.0    
79.2    
79.4    
79.7    
79.9    
80.1    
80.3    
80.5    
80.7    
80.9    
81.2    
81.4    
81.6    
81.8    
82.0    
82.2    
82.4    
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82.9    
83.1    
83.3    
83.5    
83.7    
83.9    
84.2    
84.4    
84.6    
84.8    
85.0    
85.2    
85.4    
85.7    
85.9    
86.1    
86.3    
86.5    
86.7    
86.9    
87.2    
87.4    
87.6    
87.8    
88.0    
88.2    
88.4    
88.7    
88.9    
89.1    
89.3    
89.5    
89.7    
89.9    
90.1    
90.4    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.9    
92.1    
92.3    
92.5    
92.7    
92.9    
93.1    
93.4    
93.6    
93.8    
94.0    
94.2    
94.4    
94.6    
94.9    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.4    
99.6    
99.8    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 11153, rend_intergenic: 9235  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14677, rend_intergenic: 11631  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22573, rend_intergenic: 20953  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31040, rend_intergenic: 27099  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43438, rend_intergenic: 41817  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63641, rend_intergenic: 49397  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101420, rend_intergenic: 100348  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112166, rend_intergenic: 108761  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114693, rend_intergenic: 112727  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support