-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_11987216-12214277

-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.2223-T1
Valid prediction for GlimmerHMM_glimmerT_30134-T1
Valid prediction for HiQ_model.g19939.t1
Couldn't classify 78001, 78225
Couldn't classify 78457, 78460
Sorry, prediction CodingQuarry_transcript_10406-T1 fails validation.
(ATG)	 AA	77641-77732	GT	AGG
(TAA)	 AG	78001-78225	GG	ATG
(GTA)	 TG	78457-78460	TC	AGT
-recovered CodingQuarry_transcript_10406-T1, initial, 77641, 77732
Valid prediction for GlimmerHMM_glimmerT_30126-T1
Valid prediction for snap_scaffold_12-snap.2199-T1
Valid prediction for GlimmerHMM_glimmerT_30147-T1
Couldn't classify 99791, 100618
Sorry, prediction pasa_asmbl_7982.p1 fails validation.
(CAG)	 AT	99791-100618	TT	AAT
Valid prediction for pasa_asmbl_7973.p1
Valid prediction for GlimmerHMM_glimmerT_30144-T1
Valid prediction for GlimmerHMM_glimmerT_30149-T1
Valid prediction for snap_scaffold_12-snap.2226-T1
Valid prediction for Augustus_model.g19949.t1
Valid prediction for Augustus_model.g19946.t1
Valid prediction for GlimmerHMM_glimmerT_30137-T1
Valid prediction for CodingQuarry_transcript_10402-T1
Couldn't classify 89505, 90075
Sorry, prediction pasa_asmbl_7979.p1 fails validation.
(CGC)	 TC	89505-90075	GT	TGG
(ATG)	 AG	90171-90246	GT	AGG
(GTT)	 AG	90378-90474	CT	AAC
-recovered pasa_asmbl_7979.p1, initial, 90171, 90246
-recovered pasa_asmbl_7979.p1, terminal, 90378, 90474
-recovered pasa_asmbl_7979.p1, internal, 90171, 90246
Valid prediction for GlimmerHMM_glimmerT_30146-T1
Couldn't classify 88808, 88840
Couldn't classify 89004, 89426
Sorry, prediction pasa_asmbl_7978.p1 fails validation.
(GCC)	 CA	88808-88840	GT	AGG
(GAG)	 AG	89004-89426	AC	CAA
Valid prediction for snap_scaffold_12-snap.2221-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g19951.t1
Valid prediction for snap_scaffold_12-snap.2211-T1
Valid prediction for snap_scaffold_12-snap.2208-T1
Valid prediction for CodingQuarry_transcript_10407-T1
Valid prediction for GlimmerHMM_glimmerT_30145-T1
Valid prediction for HiQ_model.g19945.t1
Valid prediction for snap_scaffold_12-snap.2202-T1
Valid prediction for snap_scaffold_12-snap.2207-T1
Valid prediction for snap_scaffold_12-snap.2218-T1
Valid prediction for GlimmerHMM_glimmerT_30136-T1
Valid prediction for snap_scaffold_12-snap.2210-T1
Valid prediction for snap_scaffold_12-snap.2220-T1
Valid prediction for GlimmerHMM_glimmerT_30140-T1
Valid prediction for CodingQuarry_transcript_10405-T1
Valid prediction for pasa_asmbl_7980.p1
Valid prediction for GlimmerHMM_glimmerT_30128-T1
Valid prediction for snap_scaffold_12-snap.2219-T1
Valid prediction for snap_scaffold_12-snap.2204-T1
Valid prediction for snap_scaffold_12-snap.2196-T1
Valid prediction for Augustus_model.g19942.t1
Valid prediction for snap_scaffold_12-snap.2201-T1
Couldn't classify 29743, 29925
Sorry, prediction pasa_asmbl_7971.p1 fails validation.
(TCC)	 CT	29743-29925	GT	AGG
(GTG)	 AG	30694-30798	GT	CGG
(GTA)	 AG	30910-30970	GT	CCG
(CTC)	 AG	31171-31271	GT	AGG
(GAG)	 AG	31635-31757	GT	CGG
(ATC)	 AG	32096-32203	GG	GAG
-recovered pasa_asmbl_7971.p1, terminal, 32096, 32203
-recovered pasa_asmbl_7971.p1, internal, 30694, 30798
-recovered pasa_asmbl_7971.p1, internal, 30910, 30970
-recovered pasa_asmbl_7971.p1, internal, 31171, 31271
-recovered pasa_asmbl_7971.p1, internal, 31635, 31757
Valid prediction for GlimmerHMM_glimmerT_30133-T1
Valid prediction for snap_scaffold_12-snap.2225-T1
Valid prediction for GlimmerHMM_glimmerT_30141-T1
Valid prediction for Augustus_model.g19953.t1
Valid prediction for GlimmerHMM_glimmerT_30130-T1
Valid prediction for snap_scaffold_12-snap.2212-T1
Valid prediction for Augustus_model.g19944.t1
Valid prediction for snap_scaffold_12-snap.2205-T1
Valid prediction for GlimmerHMM_glimmerT_30125-T1
Valid prediction for GlimmerHMM_glimmerT_30138-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 snap_scaffold_12-snap.2206-T1
Valid prediction for HiQ_model.g19938.t1
Valid prediction for snap_scaffold_12-snap.2203-T1
Valid prediction for GlimmerHMM_glimmerT_30150-T1
Valid prediction for CodingQuarry_transcript_10404-T1
Valid prediction for GlimmerHMM_glimmerT_30153-T1
Valid prediction for Augustus_model.g19941.t1
Valid prediction for Augustus_model.g19943.t1
Valid prediction for GlimmerHMM_glimmerT_30152-T1
Valid prediction for GlimmerHMM_glimmerT_30154-T1
Valid prediction for GlimmerHMM_glimmerT_30131-T1
Valid prediction for pasa_asmbl_8845.p1
Valid prediction for CodingQuarry_transcript_10403-T1
Valid prediction for snap_scaffold_12-snap.2200-T1
Valid prediction for snap_scaffold_12-snap.2227-T1
Valid prediction for GlimmerHMM_glimmerT_30142-T1
Valid prediction for GlimmerHMM_glimmerT_30151-T1
Valid prediction for CodingQuarry_transcript_10401-T1
Valid prediction for snap_scaffold_12-snap.2198-T1
Valid prediction for GlimmerHMM_glimmerT_30139-T1
Valid prediction for GlimmerHMM_glimmerT_30143-T1
Valid prediction for GlimmerHMM_glimmerT_30132-T1
Valid prediction for GlimmerHMM_glimmerT_30148-T1
Valid prediction for Augustus_model.g19947.t1
Valid prediction for snap_scaffold_12-snap.2222-T1
Valid prediction for snap_scaffold_12-snap.2209-T1
Valid prediction for snap_scaffold_12-snap.2197-T1
Couldn't classify 158351, 158521
Sorry, prediction pasa_asmbl_8850.p1 fails validation.
(ATG)	 CA	157223-157501	GT	AGG
(AAA)	 AG	157932-158027	GT	AGG
(AGG)	 AG	158351-158521	GA	TGG
-recovered pasa_asmbl_8850.p1, initial, 157223, 157501
-recovered pasa_asmbl_8850.p1, internal, 157932, 158027
Valid prediction for GlimmerHMM_glimmerT_30127-T1
Valid prediction for snap_scaffold_12-snap.2216-T1
Valid prediction for snap_scaffold_12-snap.2217-T1
Valid prediction for GlimmerHMM_glimmerT_30129-T1
Valid prediction for snap_scaffold_12-snap.2214-T1
Valid prediction for Augustus_model.g19940.t1
Valid prediction for Augustus_model.g19954.t1
Valid prediction for snap_scaffold_12-snap.2213-T1
Valid prediction for GlimmerHMM_glimmerT_30135-T1
Valid prediction for snap_scaffold_12-snap.2228-T1
Valid prediction for snap_scaffold_12-snap.2224-T1
Valid prediction for Augustus_model.g19952.t1
Valid prediction for snap_scaffold_12-snap.2215-T1
Couldn't classify 158965, 159082
Sorry, prediction pasa_asmbl_9197.p1 fails validation.
(AGA)	 GC	158965-159082	GT	AGG
(GCC)	 AG	159290-159849	CT	AGC
-recovered pasa_asmbl_9197.p1, terminal, 159290, 159849
Valid prediction for Augustus_model.g19950.t1
Valid prediction for Augustus_model.g19948.t1
Couldn't classify 189724, 189753
Couldn't classify 190786, 190855
Sorry, prediction pasa_asmbl_8849.p1 fails validation.
(CGT)	 CA	189724-189753	GT	AGG
(TGT)	 AG	189951-190073	GT	ATG
(GCT)	 AG	190277-190388	GT	GGG
(GAG)	 AG	190555-190654	GT	ATG
(ATA)	 AG	190786-190855	AT	AGA
-recovered pasa_asmbl_8849.p1, internal, 189951, 190073
-recovered pasa_asmbl_8849.p1, internal, 190277, 190388
-recovered pasa_asmbl_8849.p1, internal, 190555, 190654
Couldn't classify 190977, 191098
Sorry, prediction pasa_asmbl_8848.p1 fails validation.
(GGA)	 AT	190977-191098	GT	AGG
(GTA)	 AG	191581-191701	GT	ACG
(GAC)	 AG	191863-191948	GT	AGG
(TCA)	 AG	192181-192403	TC	AGT
-recovered pasa_asmbl_8848.p1, terminal, 192181, 192403
-recovered pasa_asmbl_8848.p1, internal, 191581, 191701
-recovered pasa_asmbl_8848.p1, internal, 191863, 191948

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 27274, rend_intergenic: 23823  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46957, rend_intergenic: 35869  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47733, rend_intergenic: 47155  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55262, rend_intergenic: 49151  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 227062
-exon list size: 290


building trellis

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2.4    
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11.0    
11.3    
11.6    
12.0    
12.3    
12.7    
13.0    
13.4    
13.7    
14.0    
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14.7    
15.1    
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16.1    
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17.1    
17.5    
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19.2    
19.5    
19.9    
20.2    
20.5    
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21.6    
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22.3    
22.6    
22.9    
23.3    
23.6    
24.0    
24.3    
24.7    
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25.3    
25.7    
26.0    
26.4    
26.7    
27.1    
27.4    
27.7    
28.1    
28.4    
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29.1    
29.5    
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30.1    
30.5    
30.8    
31.2    
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32.2    
32.5    
32.9    
33.2    
33.6    
33.9    
34.2    
34.6    
34.9    
35.3    
35.6    
36.0    
36.3    
36.6    
37.0    
37.3    
37.7    
38.0    
38.4    
38.7    
39.0    
39.4    
39.7    
40.1    
40.4    
40.8    
41.1    
41.4    
41.8    
42.1    
42.5    
42.8    
43.2    
43.5    
43.8    
44.2    
44.5    
44.9    
45.2    
45.5    
45.9    
46.2    
46.6    
46.9    
47.3    
47.6    
47.9    
48.3    
48.6    
49.0    
49.3    
49.7    
50.0    
50.3    
50.7    
51.0    
51.4    
51.7    
52.1    
52.4    
52.7    
53.1    
53.4    
53.8    
54.1    
54.5    
54.8    
55.1    
55.5    
55.8    
56.2    
56.5    
56.8    
57.2    
57.5    
57.9    
58.2    
58.6    
58.9    
59.2    
59.6    
59.9    
60.3    
60.6    
61.0    
61.3    
61.6    
62.0    
62.3    
62.7    
63.0    
63.4    
63.7    
64.0    
64.4    
64.7    
65.1    
65.4    
65.8    
66.1    
66.4    
66.8    
67.1    
67.5    
67.8    
68.2    
68.5    
68.8    
69.2    
69.5    
69.9    
70.2    
70.5    
70.9    
71.2    
71.6    
71.9    
72.3    
72.6    
72.9    
73.3    
73.6    
74.0    
74.3    
74.7    
75.0    
75.3    
75.7    
76.0    
76.4    
76.7    
77.1    
77.4    
77.7    
78.1    
78.4    
78.8    
79.1    
79.5    
79.8    
80.1    
80.5    
80.8    
81.2    
81.5    
81.8    
82.2    
82.5    
82.9    
83.2    
83.6    
83.9    
84.2    
84.6    
84.9    
85.3    
85.6    
86.0    
86.3    
86.6    
87.0    
87.3    
87.7    
88.0    
88.4    
88.7    
89.0    
89.4    
89.7    
90.1    
90.4    
90.8    
91.1    
91.4    
91.8    
92.1    
92.5    
92.8    
93.2    
93.5    
93.8    
94.2    
94.5    
94.9    
95.2    
95.5    
95.9    
96.2    
96.6    
96.9    
97.3    
97.6    
97.9    
98.3    
98.6    
99.0    
99.3    
99.7    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 27274, rend_intergenic: 23823  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46957, rend_intergenic: 35869  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47733, rend_intergenic: 47155  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55262, rend_intergenic: 49151  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 214254 - 227062
-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