-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_28/scaffold_28_424686-601278

-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.g38394.t1
Valid prediction for GlimmerHMM_glimmerT_58004-T1
Valid prediction for GlimmerHMM_glimmerT_57993-T1
Valid prediction for snap_scaffold_28-snap.98-T1
Valid prediction for snap_scaffold_28-snap.123-T1
Valid prediction for GlimmerHMM_glimmerT_58010-T1
Valid prediction for GlimmerHMM_glimmerT_58009-T1
Valid prediction for GlimmerHMM_glimmerT_57991-T1
Couldn't classify 57610, 57762
Sorry, prediction pasa_asmbl_37844.p1 fails validation.
(ATG)	 AA	56142-56243	GT	AGG
(AGC)	 AG	56359-56500	GT	CGG
(GAA)	 AG	57048-57094	GT	AGG
(ATA)	 AG	57234-57305	GT	AGG
(GGA)	 AG	57408-57494	GT	AGG
(GTT)	 AG	57610-57762	GA	TCG
-recovered pasa_asmbl_37844.p1, initial, 56142, 56243
-recovered pasa_asmbl_37844.p1, internal, 56359, 56500
-recovered pasa_asmbl_37844.p1, internal, 57048, 57094
-recovered pasa_asmbl_37844.p1, internal, 57234, 57305
-recovered pasa_asmbl_37844.p1, internal, 57408, 57494
Valid prediction for GlimmerHMM_glimmerT_57992-T1
Valid prediction for snap_scaffold_28-snap.119-T1
Valid prediction for pasa_asmbl_37284.p1
Valid prediction for CodingQuarry_transcript_43513-T1
Valid prediction for snap_scaffold_28-snap.111-T1
Valid prediction for snap_scaffold_28-snap.92-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_28-snap.96-T1
Valid prediction for Augustus_model.g38387.t1
Valid prediction for GlimmerHMM_glimmerT_57996-T1
Valid prediction for Augustus_model.g38383.t1
Valid prediction for Augustus_model.g38380.t1
Valid prediction for snap_scaffold_28-snap.99-T1
Valid prediction for snap_scaffold_28-snap.100-T1
Valid prediction for GlimmerHMM_glimmerT_58003-T1
Valid prediction for snap_scaffold_28-snap.105-T1
Valid prediction for snap_scaffold_28-snap.108-T1
Valid prediction for GlimmerHMM_glimmerT_57995-T1
Valid prediction for GlimmerHMM_glimmerT_57988-T1
Valid prediction for snap_scaffold_28-snap.109-T1
Valid prediction for snap_scaffold_28-snap.103-T1
Valid prediction for snap_scaffold_28-snap.126-T1
Valid prediction for GlimmerHMM_glimmerT_58000-T1
Valid prediction for Augustus_model.g38389.t1
Valid prediction for snap_scaffold_28-snap.115-T1
Valid prediction for snap_scaffold_28-snap.117-T1
Couldn't classify 126782, 126825
Couldn't classify 137457, 137615
Sorry, prediction pasa_asmbl_37287.p1 fails validation.
(TTC)	 TG	126782-126825	GT	AGG
(GGA)	 AG	127475-127556	GT	GGG
(GCC)	 AG	127741-127774	GT	AGG
(GCT)	 AG	127968-128047	GT	AGG
(GCC)	 AG	128825-128893	GT	AGG
(CTC)	 AG	129112-129192	GT	CGG
(ATC)	 AG	130297-130357	GT	AGG
(AAT)	 AG	131107-131205	GT	GAG
(TGG)	 AG	133922-133991	GT	ATG
(GGC)	 AG	134127-134205	GT	GTG
(TCT)	 AG	134439-134534	GT	TGG
(ATC)	 AG	136198-136239	GT	CGG
(GAC)	 AG	137097-137192	GT	AGG
(GTG)	 AG	137457-137615	CC	CCC
-recovered pasa_asmbl_37287.p1, internal, 127475, 127556
-recovered pasa_asmbl_37287.p1, internal, 127741, 127774
-recovered pasa_asmbl_37287.p1, internal, 127968, 128047
-recovered pasa_asmbl_37287.p1, internal, 128825, 128893
-recovered pasa_asmbl_37287.p1, internal, 129112, 129192
-recovered pasa_asmbl_37287.p1, internal, 130297, 130357
-recovered pasa_asmbl_37287.p1, internal, 131107, 131205
-recovered pasa_asmbl_37287.p1, internal, 133922, 133991
-recovered pasa_asmbl_37287.p1, internal, 134127, 134205
-recovered pasa_asmbl_37287.p1, internal, 134439, 134534
-recovered pasa_asmbl_37287.p1, internal, 136198, 136239
-recovered pasa_asmbl_37287.p1, internal, 137097, 137192
Valid prediction for GlimmerHMM_glimmerT_58001-T1
Valid prediction for HiQ_model.g38386.t1
Valid prediction for Augustus_model.g38395.t1
Valid prediction for snap_scaffold_28-snap.125-T1
Valid prediction for Augustus_model.g38382.t1
Valid prediction for snap_scaffold_28-snap.116-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 GlimmerHMM_glimmerT_58002-T1
Valid prediction for Augustus_model.g38385.t1
Valid prediction for HiQ_model.g38398.t1
Valid prediction for Augustus_model.g38391.t1
Valid prediction for GlimmerHMM_glimmerT_58008-T1
Valid prediction for Augustus_model.g38392.t1
Couldn't classify 16306, 16373
Sorry, prediction pasa_asmbl_37920.p1 fails validation.
(ATC)	 CC	16306-16373	GT	CCG
(TCT)	 AG	16681-16787	GT	TGG
(TAA)	 AG	16885-17020	GT	AGG
(GCA)	 AG	17152-17218	GT	AGG
(ACT)	 AG	17301-17418	GC	AGG
(AAC)	 AG	17506-17569	GT	AGG
(GCC)	 AG	18096-18270	GT	AGG
(GTG)	 AG	18392-18433	GA	AGG
-recovered pasa_asmbl_37920.p1, terminal, 18392, 18433
-recovered pasa_asmbl_37920.p1, internal, 16681, 16787
-recovered pasa_asmbl_37920.p1, internal, 16885, 17020
-recovered pasa_asmbl_37920.p1, internal, 17152, 17218
-recovered pasa_asmbl_37920.p1, internal, 17301, 17418
-recovered pasa_asmbl_37920.p1, internal, 17506, 17569
-recovered pasa_asmbl_37920.p1, internal, 18096, 18270
Valid prediction for HiQ_model.g38396.t1
Valid prediction for CodingQuarry_transcript_43514-T1
Valid prediction for snap_scaffold_28-snap.106-T1
Valid prediction for snap_scaffold_28-snap.120-T1
Valid prediction for GlimmerHMM_glimmerT_57994-T1
Valid prediction for snap_scaffold_28-snap.107-T1
Valid prediction for GlimmerHMM_glimmerT_57987-T1
Valid prediction for CodingQuarry_transcript_43515-T1
Valid prediction for GlimmerHMM_glimmerT_58005-T1
Valid prediction for snap_scaffold_28-snap.101-T1
Valid prediction for GlimmerHMM_glimmerT_57999-T1
Valid prediction for GlimmerHMM_glimmerT_57990-T1
Valid prediction for snap_scaffold_28-snap.104-T1
Valid prediction for snap_scaffold_28-snap.97-T1
Valid prediction for snap_scaffold_28-snap.110-T1
Valid prediction for GlimmerHMM_glimmerT_58012-T1
Valid prediction for snap_scaffold_28-snap.113-T1
Valid prediction for snap_scaffold_28-snap.94-T1
Valid prediction for Augustus_model.g38384.t1
Valid prediction for HiQ_model.g38397.t1
Valid prediction for snap_scaffold_28-snap.122-T1
Valid prediction for snap_scaffold_28-snap.91-T1
Couldn't classify 12816, 13478
Sorry, prediction pasa_asmbl_37923.p1 fails validation.
(GAG)	 CA	12816-13478	CA	GGC
Valid prediction for Augustus_model.g38381.t1
Valid prediction for snap_scaffold_28-snap.121-T1
Valid prediction for snap_scaffold_28-snap.112-T1
Valid prediction for CodingQuarry_transcript_43516-T1
Couldn't classify 77048, 77126
Couldn't classify 80946, 81037
Sorry, prediction pasa_asmbl_37905.p1 fails validation.
(GAC)	 AG	77048-77126	GT	AGG
(GAC)	 AG	77868-77999	GT	TGG
(GCA)	 AG	78197-78314	GT	GGG
(GTG)	 AG	80473-80651	GT	AGG
(GAC)	 AG	80946-81037	AA	GGA
-recovered pasa_asmbl_37905.p1, internal, 77048, 77126
-recovered pasa_asmbl_37905.p1, internal, 77868, 77999
-recovered pasa_asmbl_37905.p1, internal, 78197, 78314
-recovered pasa_asmbl_37905.p1, internal, 80473, 80651
Valid prediction for Augustus_model.g38390.t1
Valid prediction for GlimmerHMM_glimmerT_57998-T1
Valid prediction for GlimmerHMM_glimmerT_57989-T1
Valid prediction for GlimmerHMM_glimmerT_57997-T1
Valid prediction for Augustus_model.g38399.t1
Valid prediction for HiQ_model.g38393.t1
Valid prediction for snap_scaffold_28-snap.95-T1
Valid prediction for snap_scaffold_28-snap.118-T1
Valid prediction for GlimmerHMM_glimmerT_58006-T1
Valid prediction for snap_scaffold_28-snap.102-T1
Valid prediction for pasa_asmbl_37916.p1
Valid prediction for GlimmerHMM_glimmerT_58013-T1
Valid prediction for snap_scaffold_28-snap.93-T1
Couldn't classify 89860, 89875
Sorry, prediction pasa_asmbl_37904.p1 fails validation.
(GCT)	 CC	89860-89875	GT	AGG
(AGA)	 AG	90216-90341	GT	GGG
(CTG)	 AG	91352-91512	GT	ACG
(GTG)	 AG	91647-91827	GT	AGG
(ACA)	 AG	92109-92234	GT	AGG
(CGG)	 AG	92550-92677	GT	TTG
(GCT)	 AG	93096-93309	GT	AGG
(AAT)	 AG	93642-93892	GT	GGG
(CCT)	 AG	95712-95846	CC	GAC
-recovered pasa_asmbl_37904.p1, terminal, 95712, 95846
-recovered pasa_asmbl_37904.p1, internal, 90216, 90341
-recovered pasa_asmbl_37904.p1, internal, 91352, 91512
-recovered pasa_asmbl_37904.p1, internal, 91647, 91827
-recovered pasa_asmbl_37904.p1, internal, 92109, 92234
-recovered pasa_asmbl_37904.p1, internal, 92550, 92677
-recovered pasa_asmbl_37904.p1, internal, 93096, 93309
-recovered pasa_asmbl_37904.p1, internal, 93642, 93892
Valid prediction for Augustus_model.g38388.t1
Valid prediction for GlimmerHMM_glimmerT_58007-T1
Valid prediction for GlimmerHMM_glimmerT_58011-T1
Valid prediction for pasa_asmbl_37909.p1
Couldn't classify 65031, 65232
Sorry, prediction pasa_asmbl_37907.p2 fails validation.
(CTG)	 AA	65031-65232	GT	AGG
(TGA)	 AG	65791-65912	CA	GAC
-recovered pasa_asmbl_37907.p2, terminal, 65791, 65912
Valid prediction for snap_scaffold_28-snap.114-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11120, rend_intergenic: 5232  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30176, rend_intergenic: 12422  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40290, rend_intergenic: 36626  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71144, rend_intergenic: 68574  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83522, rend_intergenic: 81911  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93129, rend_intergenic: 86680  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99766, rend_intergenic: 99394  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101986, rend_intergenic: 100206  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149237, rend_intergenic: 147373  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 176593
-exon list size: 466


building trellis

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23.9    
24.1    
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24.8    
25.0    
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25.4    
25.6    
25.9    
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27.8    
28.0    
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28.4    
28.6    
28.8    
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29.3    
29.5    
29.7    
29.9    
30.1    
30.3    
30.6    
30.8    
31.0    
31.2    
31.4    
31.6    
31.8    
32.1    
32.3    
32.5    
32.7    
32.9    
33.1    
33.3    
33.5    
33.8    
34.0    
34.2    
34.4    
34.6    
34.8    
35.0    
35.3    
35.5    
35.7    
35.9    
36.1    
36.3    
36.5    
36.8    
37.0    
37.2    
37.4    
37.6    
37.8    
38.0    
38.2    
38.5    
38.7    
38.9    
39.1    
39.3    
39.5    
39.7    
40.0    
40.2    
40.4    
40.6    
40.8    
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41.7    
41.9    
42.1    
42.3    
42.5    
42.7    
42.9    
43.2    
43.4    
43.6    
43.8    
44.0    
44.2    
44.4    
44.7    
44.9    
45.1    
45.3    
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45.7    
45.9    
46.2    
46.4    
46.6    
46.8    
47.0    
47.2    
47.4    
47.6    
47.9    
48.1    
48.3    
48.5    
48.7    
48.9    
49.1    
49.4    
49.6    
49.8    
50.0    
50.2    
50.4    
50.6    
50.9    
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51.9    
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52.6    
52.8    
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54.9    
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78.0    
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84.0    
84.2    
84.4    
84.6    
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85.9    
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86.3    
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87.0    
87.2    
87.4    
87.6    
87.8    
88.0    
88.2    
88.5    
88.7    
88.9    
89.1    
89.3    
89.5    
89.7    
90.0    
90.2    
90.4    
90.6    
90.8    
91.0    
91.2    
91.5    
91.7    
91.9    
92.1    
92.3    
92.5    
92.7    
92.9    
93.2    
93.4    
93.6    
93.8    
94.0    
94.2    
94.4    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.9    
96.2    
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 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 11120, rend_intergenic: 5232  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30176, rend_intergenic: 12422  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40290, rend_intergenic: 36626  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71144, rend_intergenic: 68574  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83522, rend_intergenic: 81911  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93129, rend_intergenic: 86680  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99766, rend_intergenic: 99394  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101986, rend_intergenic: 100206  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149237, rend_intergenic: 147373  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 163197 - 176593
-exon list size: 11


building trellis

7.7    
15.4    
23.1    
30.8    
38.5    
46.2    
53.8    
61.5    
69.2    
76.9    
84.6    
92.3    
-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 163948 - 176593
-exon list size: 10


building trellis

8.3    
16.7    
25.0    
33.3    
41.7    
50.0    
58.3    
66.7    
75.0    
83.3    
91.7    
-found 1 predictions from path traversal

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