-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_5518394-5760991

-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 GlimmerHMM_glimmerT_54209-T1
Valid prediction for pasa_asmbl_33566.p1
Valid prediction for snap_scaffold_25-snap.1182-T1
Valid prediction for GlimmerHMM_glimmerT_54185-T1
Valid prediction for snap_scaffold_25-snap.1174-T1
Valid prediction for HiQ_model.g35975.t1
Valid prediction for HiQ_model.g35967.t1
Valid prediction for GlimmerHMM_glimmerT_54194-T1
Valid prediction for CodingQuarry_transcript_38737-T1
Valid prediction for pasa_asmbl_33568.p1
Valid prediction for snap_scaffold_25-snap.1184-T1
Valid prediction for GlimmerHMM_glimmerT_54199-T1
Valid prediction for Augustus_model.g35972.t1
Valid prediction for snap_scaffold_25-snap.1196-T1
Valid prediction for Augustus_model.g35979.t1
Valid prediction for snap_scaffold_25-snap.1173-T1
Valid prediction for snap_scaffold_25-snap.1164-T1
Valid prediction for pasa_asmbl_33575.p1
Valid prediction for GlimmerHMM_glimmerT_54204-T1
Valid prediction for CodingQuarry_transcript_38743-T1
Valid prediction for HiQ_model.g35985.t1
Valid prediction for snap_scaffold_25-snap.1178-T1
Valid prediction for GlimmerHMM_glimmerT_54189-T1
Valid prediction for CodingQuarry_transcript_38732-T1
Valid prediction for snap_scaffold_25-snap.1166-T1
Valid prediction for CodingQuarry_transcript_38739-T1
Couldn't classify 51808, 52033
Sorry, prediction pasa_asmbl_33567.p1 fails validation.
(TTC)	 GT	51808-52033	GT	AGG
(AGT)	 AG	52350-52513	CA	AAC
-recovered pasa_asmbl_33567.p1, terminal, 52350, 52513
Valid prediction for GlimmerHMM_glimmerT_54211-T1
Valid prediction for snap_scaffold_25-snap.1183-T1
Valid prediction for snap_scaffold_25-snap.1176-T1
Valid prediction for GlimmerHMM_glimmerT_54202-T1
Valid prediction for snap_scaffold_25-snap.1172-T1
Valid prediction for snap_scaffold_25-snap.1171-T1
Valid prediction for Augustus_model.g35986.t1
Valid prediction for HiQ_model.g35970.t1
Valid prediction for GlimmerHMM_glimmerT_54190-T1
Valid prediction for GlimmerHMM_glimmerT_54213-T1
Valid prediction for GlimmerHMM_glimmerT_54198-T1
Valid prediction for GlimmerHMM_glimmerT_54196-T1
Valid prediction for snap_scaffold_25-snap.1167-T1
Valid prediction for GlimmerHMM_glimmerT_54210-T1
Valid prediction for snap_scaffold_25-snap.1190-T1
Valid prediction for Augustus_model.g35966.t1
Valid prediction for snap_scaffold_25-snap.1162-T1
Valid prediction for snap_scaffold_25-snap.1160-T1
Valid prediction for GlimmerHMM_glimmerT_54191-T1
Valid prediction for Augustus_model.g35978.t1
Valid prediction for snap_scaffold_25-snap.1181-T1
Valid prediction for GlimmerHMM_glimmerT_54197-T1
Valid prediction for snap_scaffold_25-snap.1195-T1
Valid prediction for snap_scaffold_25-snap.1185-T1
Valid prediction for snap_scaffold_25-snap.1170-T1
Couldn't classify 122081, 122202
Couldn't classify 125193, 125222
Sorry, prediction pasa_asmbl_33572.p1 fails validation.
(GGG)	 AG	122081-122202	GT	AGG
(TGG)	 AG	122670-122710	GT	AGG
(TGA)	 AG	122809-122933	GT	AGG
(GTG)	 AG	123078-123203	GT	CGG
(TTG)	 AG	123889-123986	GT	TTG
(GAA)	 AG	124172-124271	GT	TGG
(TTT)	 AG	124437-124480	GT	AGG
(CAC)	 AG	125023-125062	GT	AGG
(GAG)	 AG	125193-125222	AG	GGA
add_exon() Sorry, pasa_asmbl_33572.p1 124437-124480-terminal-2 is invalid.
-recovered pasa_asmbl_33572.p1, terminal, 124437, 124480
-recovered pasa_asmbl_33572.p1, internal, 122081, 122202
-recovered pasa_asmbl_33572.p1, internal, 122670, 122710
-recovered pasa_asmbl_33572.p1, internal, 122809, 122933
-recovered pasa_asmbl_33572.p1, internal, 123078, 123203
-recovered pasa_asmbl_33572.p1, internal, 123889, 123986
-recovered pasa_asmbl_33572.p1, internal, 124172, 124271
-recovered pasa_asmbl_33572.p1, internal, 124437, 124480
-recovered pasa_asmbl_33572.p1, internal, 125023, 125062
Valid prediction for snap_scaffold_25-snap.1197-T1
Valid prediction for snap_scaffold_25-snap.1165-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 141263, 141381
Sorry, prediction pasa_asmbl_34268.p1 fails validation.
(AAA)	 AC	141263-141381	GT	AGG
(CCA)	 AG	141810-141909	GT	AGG
(GAT)	 AG	142273-142402	GT	AGG
(CGA)	 AG	142649-142728	GT	CGG
(GCT)	 AG	144344-144439	AG	GAA
-recovered pasa_asmbl_34268.p1, terminal, 144344, 144439
-recovered pasa_asmbl_34268.p1, internal, 141810, 141909
-recovered pasa_asmbl_34268.p1, internal, 142273, 142402
-recovered pasa_asmbl_34268.p1, internal, 142649, 142728
Valid prediction for pasa_asmbl_34280.p1
Valid prediction for GlimmerHMM_glimmerT_54208-T1
Valid prediction for pasa_asmbl_34265.p1
Valid prediction for GlimmerHMM_glimmerT_54206-T1
Valid prediction for snap_scaffold_25-snap.1193-T1
Valid prediction for snap_scaffold_25-snap.1168-T1
Valid prediction for snap_scaffold_25-snap.1199-T1
Valid prediction for Augustus_model.g35990.t1
Valid prediction for snap_scaffold_25-snap.1192-T1
Valid prediction for GlimmerHMM_glimmerT_54205-T1
Valid prediction for snap_scaffold_25-snap.1169-T1
Couldn't classify 201117, 201327
Sorry, prediction pasa_asmbl_34259.p1 fails validation.
(CCC)	 CA	201117-201327	GT	AGG
(ATC)	 AG	201477-201524	GT	AAG
(TGA)	 AG	201804-201886	GT	CGG
(GAC)	 AG	202163-202278	GT	AGG
(GAT)	 AG	202379-202530	GT	AGG
(TCC)	 AG	203000-203097	GT	GTG
(TCA)	 AG	203294-203834	GT	AGG
(AGT)	 AG	204431-204601	GT	AGG
(GTT)	 AG	204749-204837	AT	GAA
-recovered pasa_asmbl_34259.p1, terminal, 204749, 204837
-recovered pasa_asmbl_34259.p1, internal, 201477, 201524
-recovered pasa_asmbl_34259.p1, internal, 201804, 201886
-recovered pasa_asmbl_34259.p1, internal, 202163, 202278
-recovered pasa_asmbl_34259.p1, internal, 202379, 202530
-recovered pasa_asmbl_34259.p1, internal, 203000, 203097
-recovered pasa_asmbl_34259.p1, internal, 203294, 203834
-recovered pasa_asmbl_34259.p1, internal, 204431, 204601
Valid prediction for snap_scaffold_25-snap.1191-T1
Valid prediction for snap_scaffold_25-snap.1188-T1
Couldn't classify 66152, 66559
Sorry, prediction pasa_asmbl_34274.p1 fails validation.
(CAT)	 TG	66152-66559	TT	GAT
Valid prediction for HiQ_model.g35988.t1
Valid prediction for snap_scaffold_25-snap.1175-T1
Valid prediction for pasa_asmbl_34275.p1
Valid prediction for HiQ_model.g35974.t1
Valid prediction for pasa_asmbl_34270.p1
Valid prediction for snap_scaffold_25-snap.1194-T1
Valid prediction for GlimmerHMM_glimmerT_54186-T1
Valid prediction for HiQ_model.g35984.t1
Valid prediction for GlimmerHMM_glimmerT_54203-T1
Valid prediction for Augustus_model.g35981.t1
Valid prediction for pasa_asmbl_34279.p1
Valid prediction for snap_scaffold_25-snap.1186-T1
Valid prediction for GlimmerHMM_glimmerT_54215-T1
Valid prediction for Augustus_model.g35982.t1
Valid prediction for GlimmerHMM_glimmerT_54192-T1
Valid prediction for CodingQuarry_transcript_38735-T1
Valid prediction for HiQ_model.g35983.t1
Valid prediction for snap_scaffold_25-snap.1189-T1
Valid prediction for snap_scaffold_25-snap.1163-T1
Couldn't classify 186523, 186632
Sorry, prediction pasa_asmbl_34264.p1 fails validation.
(GAC)	 CG	186523-186632	GT	AGG
(TCT)	 AG	187243-187379	GT	AGG
(GTA)	 AG	188453-188637	AC	AAA
-recovered pasa_asmbl_34264.p1, terminal, 188453, 188637
-recovered pasa_asmbl_34264.p1, internal, 187243, 187379
Valid prediction for CodingQuarry_transcript_38741-T1
Valid prediction for HiQ_model.g35973.t1
Valid prediction for HiQ_model.g35977.t1
Valid prediction for GlimmerHMM_glimmerT_54212-T1
Valid prediction for CodingQuarry_transcript_38736-T1
Valid prediction for Augustus_model.g35987.t1
Valid prediction for snap_scaffold_25-snap.1200-T1
Valid prediction for snap_scaffold_25-snap.1187-T1
Valid prediction for GlimmerHMM_glimmerT_54193-T1
Valid prediction for snap_scaffold_25-snap.1202-T1
Valid prediction for snap_scaffold_25-snap.1198-T1
Couldn't classify 200065, 200136
Sorry, prediction pasa_asmbl_34262.p1 fails validation.
(ATG)	 GC	193728-194187	GT	CGG
(GTG)	 AG	194367-194521	GT	AGG
(CAG)	 AG	194733-194849	GT	TGG
(GAG)	 AG	194969-195146	GT	AGG
(CAT)	 AG	195602-195690	GT	CCG
(ATG)	 AG	195928-195979	GT	TGG
(CTC)	 AG	196247-196316	GT	AGG
(CGG)	 AG	196543-196669	GT	GGG
(TTG)	 AG	196779-196898	GT	GGG
(ATC)	 AG	196996-197172	GT	TGG
(ACT)	 AG	197545-197719	GT	AGG
(ATC)	 AG	197868-198448	GT	AGG
(CCT)	 AG	198636-198786	GT	CCG
(ATG)	 AG	198961-199047	GT	CGG
(ACA)	 AG	199153-199256	GT	AGG
(TTG)	 AG	199349-199406	GT	GGG
(GAC)	 AG	199539-199642	GT	TGG
(GCT)	 AG	200065-200136	TC	CCT
-recovered pasa_asmbl_34262.p1, initial, 193728, 194187
-recovered pasa_asmbl_34262.p1, initial, 195928, 195979
-recovered pasa_asmbl_34262.p1, initial, 198961, 199047
add_exon() Sorry, pasa_asmbl_34262.p1 196247-196316-terminal-3 is invalid.
-recovered pasa_asmbl_34262.p1, terminal, 196247, 196316
-recovered pasa_asmbl_34262.p1, internal, 194367, 194521
-recovered pasa_asmbl_34262.p1, internal, 194733, 194849
-recovered pasa_asmbl_34262.p1, internal, 194969, 195146
-recovered pasa_asmbl_34262.p1, internal, 195602, 195690
-recovered pasa_asmbl_34262.p1, internal, 195928, 195979
-recovered pasa_asmbl_34262.p1, internal, 196247, 196316
-recovered pasa_asmbl_34262.p1, internal, 196543, 196669
-recovered pasa_asmbl_34262.p1, internal, 196779, 196898
-recovered pasa_asmbl_34262.p1, internal, 196996, 197172
-recovered pasa_asmbl_34262.p1, internal, 197545, 197719
-recovered pasa_asmbl_34262.p1, internal, 197868, 198448
-recovered pasa_asmbl_34262.p1, internal, 198636, 198786
-recovered pasa_asmbl_34262.p1, internal, 198961, 199047
-recovered pasa_asmbl_34262.p1, internal, 199153, 199256
-recovered pasa_asmbl_34262.p1, internal, 199349, 199406
-recovered pasa_asmbl_34262.p1, internal, 199539, 199642
Valid prediction for snap_scaffold_25-snap.1201-T1
Valid prediction for HiQ_model.g35976.t1
Valid prediction for GlimmerHMM_glimmerT_54207-T1
Valid prediction for Augustus_model.g35980.t1
Valid prediction for CodingQuarry_transcript_38738-T1
Valid prediction for Augustus_model.g35968.t1
Valid prediction for Augustus_model.g35989.t1
Valid prediction for HiQ_model.g35971.t1
Valid prediction for GlimmerHMM_glimmerT_54187-T1
Valid prediction for snap_scaffold_25-snap.1161-T1
Valid prediction for HiQ_model.g35969.t1
Valid prediction for CodingQuarry_transcript_38742-T1
Valid prediction for CodingQuarry_transcript_38734-T1
Valid prediction for GlimmerHMM_glimmerT_54201-T1
Valid prediction for GlimmerHMM_glimmerT_54188-T1
Valid prediction for snap_scaffold_25-snap.1177-T1
Valid prediction for GlimmerHMM_glimmerT_54200-T1
Valid prediction for snap_scaffold_25-snap.1179-T1
Valid prediction for GlimmerHMM_glimmerT_54216-T1
Valid prediction for GlimmerHMM_glimmerT_54214-T1
Valid prediction for snap_scaffold_25-snap.1180-T1
Valid prediction for CodingQuarry_transcript_38733-T1
Valid prediction for GlimmerHMM_glimmerT_54195-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9147, rend_intergenic: 7224  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93040, rend_intergenic: 88629  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 242598
-exon list size: 370


building trellis

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15.6    
15.9    
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18.5    
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19.1    
19.4    
19.6    
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20.4    
20.7    
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21.2    
21.5    
21.8    
22.0    
22.3    
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23.4    
23.7    
23.9    
24.2    
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25.0    
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25.5    
25.8    
26.1    
26.3    
26.6    
26.9    
27.2    
27.4    
27.7    
28.0    
28.2    
28.5    
28.8    
29.0    
29.3    
29.6    
29.8    
30.1    
30.4    
30.6    
30.9    
31.2    
31.5    
31.7    
32.0    
32.3    
32.5    
32.8    
33.1    
33.3    
33.6    
33.9    
34.1    
34.4    
34.7    
34.9    
35.2    
35.5    
35.8    
36.0    
36.3    
36.6    
36.8    
37.1    
37.4    
37.6    
37.9    
38.2    
38.4    
38.7    
39.0    
39.2    
39.5    
39.8    
40.1    
40.3    
40.6    
40.9    
41.1    
41.4    
41.7    
41.9    
42.2    
42.5    
42.7    
43.0    
43.3    
43.5    
43.8    
44.1    
44.4    
44.6    
44.9    
45.2    
45.4    
45.7    
46.0    
46.2    
46.5    
46.8    
47.0    
47.3    
47.6    
47.8    
48.1    
48.4    
48.7    
48.9    
49.2    
49.5    
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50.0    
50.3    
50.5    
50.8    
51.1    
51.3    
51.6    
51.9    
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52.4    
52.7    
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53.2    
53.5    
53.8    
54.0    
54.3    
54.6    
54.8    
55.1    
55.4    
55.6    
55.9    
56.2    
56.5    
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57.8    
58.1    
58.3    
58.6    
58.9    
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59.4    
59.7    
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60.2    
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61.0    
61.3    
61.6    
61.8    
62.1    
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63.4    
63.7    
64.0    
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64.5    
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65.1    
65.3    
65.6    
65.9    
66.1    
66.4    
66.7    
66.9    
67.2    
67.5    
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68.0    
68.3    
68.5    
68.8    
69.1    
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69.6    
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70.7    
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71.8    
72.0    
72.3    
72.6    
72.8    
73.1    
73.4    
73.7    
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74.2    
74.5    
74.7    
75.0    
75.3    
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75.8    
76.1    
76.3    
76.6    
76.9    
77.2    
77.4    
77.7    
78.0    
78.2    
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78.8    
79.0    
79.3    
79.6    
79.8    
80.1    
80.4    
80.6    
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81.5    
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82.0    
82.3    
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82.8    
83.1    
83.3    
83.6    
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84.7    
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85.2    
85.5    
85.8    
86.0    
86.3    
86.6    
86.8    
87.1    
87.4    
87.6    
87.9    
88.2    
88.4    
88.7    
89.0    
89.2    
89.5    
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90.1    
90.3    
90.6    
90.9    
91.1    
91.4    
91.7    
91.9    
92.2    
92.5    
92.7    
93.0    
93.3    
93.5    
93.8    
94.1    
94.4    
94.6    
94.9    
95.2    
95.4    
95.7    
96.0    
96.2    
96.5    
96.8    
97.0    
97.3    
97.6    
97.8    
98.1    
98.4    
98.7    
98.9    
99.2    
99.5    
99.7    
-found 38 predictions from path traversal
Error with prediction: snap lend_intergenic: 9147, rend_intergenic: 7224  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93040, rend_intergenic: 88629  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 34 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 228438 - 242598
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 228438 - 239720
-exon list size: 1


building trellis

33.3    
66.7    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support