-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_25/scaffold_25_5319336-5520003

-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_25-snap.1125-T1
Valid prediction for HiQ_model.g35954.t1
Valid prediction for snap_scaffold_25-snap.1134-T1
Valid prediction for snap_scaffold_25-snap.1148-T1
Valid prediction for Augustus_model.g35951.t1
Valid prediction for snap_scaffold_25-snap.1128-T1
Valid prediction for snap_scaffold_25-snap.1131-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for snap_scaffold_25-snap.1150-T1
Valid prediction for snap_scaffold_25-snap.1130-T1
Valid prediction for GlimmerHMM_glimmerT_54182-T1
Valid prediction for GlimmerHMM_glimmerT_54151-T1
Valid prediction for CodingQuarry_transcript_38731-T1
Valid prediction for snap_scaffold_25-snap.1145-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_25-snap.1120-T1
Valid prediction for GlimmerHMM_glimmerT_54164-T1
Valid prediction for snap_scaffold_25-snap.1135-T1
Valid prediction for snap_scaffold_25-snap.1139-T1
Valid prediction for Augustus_model.g35963.t1
Valid prediction for GlimmerHMM_glimmerT_54176-T1
Valid prediction for pasa_asmbl_33563.p1
Valid prediction for snap_scaffold_25-snap.1112-T1
Valid prediction for snap_scaffold_25-snap.1157-T1
Valid prediction for snap_scaffold_25-snap.1153-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_25-snap.1116-T1
Valid prediction for snap_scaffold_25-snap.1123-T1
Valid prediction for Augustus_model.g35957.t1
Valid prediction for GlimmerHMM_glimmerT_54153-T1
Valid prediction for GlimmerHMM_glimmerT_54183-T1
Valid prediction for snap_scaffold_25-snap.1110-T1
Valid prediction for GlimmerHMM_glimmerT_54174-T1
Valid prediction for GlimmerHMM_glimmerT_54167-T1
Valid prediction for GlimmerHMM_glimmerT_54177-T1
Valid prediction for Augustus_model.g35959.t1
Valid prediction for snap_scaffold_25-snap.1142-T1
Valid prediction for snap_scaffold_25-snap.1113-T1
Valid prediction for snap_scaffold_25-snap.1155-T1
Valid prediction for snap_scaffold_25-snap.1122-T1
Valid prediction for GlimmerHMM_glimmerT_54179-T1
Valid prediction for snap_scaffold_25-snap.1146-T1
Valid prediction for GlimmerHMM_glimmerT_54172-T1
Valid prediction for GlimmerHMM_glimmerT_54165-T1
Valid prediction for Augustus_model.g35944.t1
Valid prediction for GlimmerHMM_glimmerT_54173-T1
Valid prediction for snap_scaffold_25-snap.1140-T1
Valid prediction for GlimmerHMM_glimmerT_54170-T1
Valid prediction for GlimmerHMM_glimmerT_54163-T1
Valid prediction for Augustus_model.g35964.t1
Valid prediction for HiQ_model.g35952.t1
Valid prediction for Augustus_model.g35958.t1
Valid prediction for snap_scaffold_25-snap.1144-T1
Valid prediction for snap_scaffold_25-snap.1143-T1
Valid prediction for GlimmerHMM_glimmerT_54162-T1
Valid prediction for snap_scaffold_25-snap.1119-T1
Valid prediction for snap_scaffold_25-snap.1141-T1
Couldn't classify 110749, 111043
Sorry, prediction pasa_asmbl_33564.p2 fails validation.
(GCT)	 AT	110749-111043	GT	GGG
(GGG)	 AG	111607-111791	AG	GAA
-recovered pasa_asmbl_33564.p2, terminal, 111607, 111791

-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_25-snap.1118-T1
Valid prediction for snap_scaffold_25-snap.1121-T1
Valid prediction for GlimmerHMM_glimmerT_54154-T1
Valid prediction for snap_scaffold_25-snap.1133-T1
Valid prediction for snap_scaffold_25-snap.1124-T1
Valid prediction for GlimmerHMM_glimmerT_54178-T1
Valid prediction for Augustus_model.g35956.t1
Valid prediction for Augustus_model.g35965.t1
Valid prediction for snap_scaffold_25-snap.1156-T1
Valid prediction for GlimmerHMM_glimmerT_54158-T1
Valid prediction for GlimmerHMM_glimmerT_54181-T1
Valid prediction for snap_scaffold_25-snap.1117-T1
Valid prediction for Augustus_model.g35960.t1
Couldn't classify 133416, 133645
Couldn't classify 134149, 134329
Sorry, prediction pasa_asmbl_34642.p2 fails validation.
(AAG)	 CA	133416-133645	GT	AGG
(GCC)	 AG	134149-134329	GG	CAG
Valid prediction for GlimmerHMM_glimmerT_54171-T1
Valid prediction for HiQ_model.g35953.t1
Couldn't classify 125493, 125544
Couldn't classify 129752, 129883
Sorry, prediction pasa_asmbl_34256.p1 fails validation.
(GCC)	 CG	125493-125544	GT	TGG
(TGA)	 AG	126814-126910	GT	AGG
(CCG)	 AG	127072-127230	GT	AGG
(GTT)	 AG	127329-127398	GT	AGG
(ATG)	 AG	129752-129883	GT	AGG
-recovered pasa_asmbl_34256.p1, initial, 129752, 129883
-recovered pasa_asmbl_34256.p1, internal, 126814, 126910
-recovered pasa_asmbl_34256.p1, internal, 127072, 127230
-recovered pasa_asmbl_34256.p1, internal, 127329, 127398
-recovered pasa_asmbl_34256.p1, internal, 129752, 129883
Valid prediction for snap_scaffold_25-snap.1151-T1
Valid prediction for GlimmerHMM_glimmerT_54175-T1
Valid prediction for GlimmerHMM_glimmerT_54152-T1
Valid prediction for snap_scaffold_25-snap.1158-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_25-snap.1132-T1
Valid prediction for GlimmerHMM_glimmerT_54161-T1
Valid prediction for snap_scaffold_25-snap.1152-T1
Valid prediction for snap_scaffold_25-snap.1154-T1
Valid prediction for Augustus_model.g35947.t1
Valid prediction for GlimmerHMM_glimmerT_54156-T1
Valid prediction for snap_scaffold_25-snap.1138-T1
Valid prediction for Augustus_model.g35955.t1
Valid prediction for snap_scaffold_25-snap.1114-T1
Valid prediction for Augustus_model.g35961.t1
Valid prediction for GlimmerHMM_glimmerT_54166-T1
Valid prediction for snap_scaffold_25-snap.1147-T1
Valid prediction for Augustus_model.g35950.t1
Valid prediction for Augustus_model.g35949.t1
Valid prediction for GlimmerHMM_glimmerT_54157-T1
Valid prediction for GlimmerHMM_glimmerT_54159-T1
Valid prediction for snap_scaffold_25-snap.1137-T1
Valid prediction for snap_scaffold_25-snap.1126-T1
Couldn't classify 94991, 95045
Couldn't classify 96779, 96986
Sorry, prediction pasa_asmbl_34257.p1 fails validation.
(GAC)	 TA	94991-95045	GT	AAG
(ATC)	 AG	95386-96547	GT	AGG
(TGG)	 AG	96779-96986	AG	GTA
-recovered pasa_asmbl_34257.p1, internal, 95386, 96547
Valid prediction for snap_scaffold_25-snap.1136-T1
Valid prediction for GlimmerHMM_glimmerT_54160-T1
Valid prediction for GlimmerHMM_glimmerT_54184-T1
Valid prediction for GlimmerHMM_glimmerT_54168-T1
Valid prediction for GlimmerHMM_glimmerT_54169-T1
Valid prediction for snap_scaffold_25-snap.1127-T1
Valid prediction for snap_scaffold_25-snap.1129-T1
Valid prediction for snap_scaffold_25-snap.1111-T1
Valid prediction for snap_scaffold_25-snap.1115-T1
Valid prediction for Augustus_model.g35945.t1
Valid prediction for Augustus_model.g35962.t1
Valid prediction for GlimmerHMM_glimmerT_54180-T1
Valid prediction for snap_scaffold_25-snap.1149-T1
Valid prediction for snap_scaffold_25-snap.1159-T1
Valid prediction for Augustus_model.g35948.t1
Valid prediction for Augustus_model.g35946.t1
Valid prediction for GlimmerHMM_glimmerT_54155-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 34972, rend_intergenic: 25477  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42316, rend_intergenic: 35501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46026, rend_intergenic: 43542  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46859, rend_intergenic: 46085  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69151, rend_intergenic: 59875  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80153, rend_intergenic: 70391  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92655, rend_intergenic: 82905  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97083, rend_intergenic: 93729  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105669, rend_intergenic: 99854  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111791, rend_intergenic: 111179  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161937, rend_intergenic: 153529  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184037, rend_intergenic: 179714  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 200668
-exon list size: 403


building trellis

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2.5    
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9.1    
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10.6    
10.9    
11.1    
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11.6    
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12.1    
12.3    
12.6    
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13.1    
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14.6    
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15.6    
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16.0    
16.3    
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17.0    
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17.5    
17.8    
18.0    
18.3    
18.5    
18.8    
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19.3    
19.5    
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20.2    
20.5    
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21.5    
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22.2    
22.5    
22.7    
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23.2    
23.5    
23.7    
24.0    
24.2    
24.4    
24.7    
24.9    
25.2    
25.4    
25.7    
25.9    
26.2    
26.4    
26.7    
26.9    
27.2    
27.4    
27.7    
27.9    
28.1    
28.4    
28.6    
28.9    
29.1    
29.4    
29.6    
29.9    
30.1    
30.4    
30.6    
30.9    
31.1    
31.4    
31.6    
31.9    
32.1    
32.3    
32.6    
32.8    
33.1    
33.3    
33.6    
33.8    
34.1    
34.3    
34.6    
34.8    
35.1    
35.3    
35.6    
35.8    
36.0    
36.3    
36.5    
36.8    
37.0    
37.3    
37.5    
37.8    
38.0    
38.3    
38.5    
38.8    
39.0    
39.3    
39.5    
39.8    
40.0    
40.2    
40.5    
40.7    
41.0    
41.2    
41.5    
41.7    
42.0    
42.2    
42.5    
42.7    
43.0    
43.2    
43.5    
43.7    
44.0    
44.2    
44.4    
44.7    
44.9    
45.2    
45.4    
45.7    
45.9    
46.2    
46.4    
46.7    
46.9    
47.2    
47.4    
47.7    
47.9    
48.1    
48.4    
48.6    
48.9    
49.1    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
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51.1    
51.4    
51.6    
51.9    
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52.3    
52.6    
52.8    
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53.3    
53.6    
53.8    
54.1    
54.3    
54.6    
54.8    
55.1    
55.3    
55.6    
55.8    
56.0    
56.3    
56.5    
56.8    
57.0    
57.3    
57.5    
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58.0    
58.3    
58.5    
58.8    
59.0    
59.3    
59.5    
59.8    
60.0    
60.2    
60.5    
60.7    
61.0    
61.2    
61.5    
61.7    
62.0    
62.2    
62.5    
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63.2    
63.5    
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64.0    
64.2    
64.4    
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65.4    
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66.2    
66.4    
66.7    
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67.2    
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68.1    
68.4    
68.6    
68.9    
69.1    
69.4    
69.6    
69.9    
70.1    
70.4    
70.6    
70.9    
71.1    
71.4    
71.6    
71.9    
72.1    
72.3    
72.6    
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73.3    
73.6    
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74.1    
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74.6    
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75.1    
75.3    
75.6    
75.8    
76.0    
76.3    
76.5    
76.8    
77.0    
77.3    
77.5    
77.8    
78.0    
78.3    
78.5    
78.8    
79.0    
79.3    
79.5    
79.8    
80.0    
80.2    
80.5    
80.7    
81.0    
81.2    
81.5    
81.7    
82.0    
82.2    
82.5    
82.7    
83.0    
83.2    
83.5    
83.7    
84.0    
84.2    
84.4    
84.7    
84.9    
85.2    
85.4    
85.7    
85.9    
86.2    
86.4    
86.7    
86.9    
87.2    
87.4    
87.7    
87.9    
88.1    
88.4    
88.6    
88.9    
89.1    
89.4    
89.6    
89.9    
90.1    
90.4    
90.6    
90.9    
91.1    
91.4    
91.6    
91.9    
92.1    
92.3    
92.6    
92.8    
93.1    
93.3    
93.6    
93.8    
94.1    
94.3    
94.6    
94.8    
95.1    
95.3    
95.6    
95.8    
96.0    
96.3    
96.5    
96.8    
97.0    
97.3    
97.5    
97.8    
98.0    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 38 predictions from path traversal
Error with prediction: snap lend_intergenic: 34972, rend_intergenic: 25477  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42316, rend_intergenic: 35501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46026, rend_intergenic: 43542  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46859, rend_intergenic: 46085  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69151, rend_intergenic: 59875  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80153, rend_intergenic: 70391  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92655, rend_intergenic: 82905  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97083, rend_intergenic: 93729  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105669, rend_intergenic: 99854  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111791, rend_intergenic: 111179  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161937, rend_intergenic: 153529  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184037, rend_intergenic: 179714  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 29 predictions persist after filtering for low support