-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_10/scaffold_10_690501-924735

-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_10-snap.179-T1
Valid prediction for Augustus_model.g16009.t1
Valid prediction for snap_scaffold_10-snap.182-T1
Valid prediction for CodingQuarry_transcript_5258-T1
Valid prediction for snap_scaffold_10-snap.201-T1
Valid prediction for GlimmerHMM_glimmerT_24038-T1
Valid prediction for GlimmerHMM_glimmerT_24039-T1
Valid prediction for Augustus_model.g16012.t1
Valid prediction for pasa_asmbl_2871.p1
Valid prediction for GlimmerHMM_glimmerT_24036-T1
Valid prediction for snap_scaffold_10-snap.167-T1
Valid prediction for snap_scaffold_10-snap.196-T1
Couldn't classify 13261, 13418
Sorry, prediction pasa_asmbl_2863.p1 fails validation.
(CAG)	 TC	13261-13418	GT	AGG
(GTG)	 AG	13566-13791	GA	GAG
-recovered pasa_asmbl_2863.p1, terminal, 13566, 13791
Valid prediction for pasa_asmbl_2867.p1
Valid prediction for GlimmerHMM_glimmerT_24019-T1
Valid prediction for Augustus_model.g16029.t1
Valid prediction for snap_scaffold_10-snap.206-T1
Valid prediction for GlimmerHMM_glimmerT_24037-T1
Valid prediction for GlimmerHMM_glimmerT_24030-T1
Valid prediction for GlimmerHMM_glimmerT_24026-T1
Valid prediction for CodingQuarry_transcript_5263-T1
Valid prediction for GlimmerHMM_glimmerT_24031-T1
Valid prediction for snap_scaffold_10-snap.202-T1
Valid prediction for GlimmerHMM_glimmerT_24016-T1
Valid prediction for GlimmerHMM_glimmerT_24046-T1
Valid prediction for snap_scaffold_10-snap.191-T1
Valid prediction for snap_scaffold_10-snap.186-T1
Valid prediction for snap_scaffold_10-snap.197-T1
Valid prediction for GlimmerHMM_glimmerT_24032-T1
Valid prediction for snap_scaffold_10-snap.162-T1
Couldn't classify 17226, 17636
Sorry, prediction pasa_asmbl_3985.p1 fails validation.
(CAT)	 TC	17226-17636	TC	GAT
Valid prediction for GlimmerHMM_glimmerT_24040-T1
Valid prediction for GlimmerHMM_glimmerT_24034-T1
Valid prediction for GlimmerHMM_glimmerT_24042-T1
Valid prediction for HiQ_model.g16020.t1
Valid prediction for GlimmerHMM_glimmerT_24045-T1
Couldn't classify 7179, 7304
Sorry, prediction pasa_asmbl_3826.p1 fails validation.
(ATG)	 GG	4935-5157	GT	GGG
(CCC)	 AG	5363-5557	GT	GGG
(GCA)	 AG	5802-5954	GT	AGG
(CAA)	 AG	6256-6495	GT	TGG
(CTG)	 AG	6799-6947	GT	AGG
(GAC)	 AG	7179-7304	GT	AGG
-recovered pasa_asmbl_3826.p1, initial, 4935, 5157
-recovered pasa_asmbl_3826.p1, internal, 5363, 5557
-recovered pasa_asmbl_3826.p1, internal, 5802, 5954
-recovered pasa_asmbl_3826.p1, internal, 6256, 6495
-recovered pasa_asmbl_3826.p1, internal, 6799, 6947
-recovered pasa_asmbl_3826.p1, internal, 7179, 7304
Valid prediction for snap_scaffold_10-snap.163-T1
Couldn't classify 224242, 224268
Couldn't classify 229816, 229900
Couldn't classify 230149, 230241
Sorry, prediction pasa_asmbl_2879.p1 fails validation.
(GGC)	 GT	224242-224268	GT	CGG
(AGC)	 AG	225921-226067	GT	CGG
(AGT)	 AG	226792-226884	GT	GAG
(GAG)	 AG	227882-227967	GT	AGG
(AAG)	 AG	228208-228313	GT	AGG
(AAT)	 AG	229281-229356	GT	AGG
(ATC)	 AG	229816-229900	AT	AGA
(GTA)	 AC	230149-230241	GT	TGG
(TCT)	 AG	230566-230751	GT	AGG
(ACC)	 AG	230894-230978	GT	AGG
(ATT)	 AG	231119-231213	GT	TGG
(GGT)	 AG	231403-231481	GT	AGG
(CAC)	 AG	231703-231804	GT	AGG
(GGA)	 AG	232182-232279	GT	CTG
(GGG)	 AG	232419-232547	GT	GTG
(GCA)	 AG	232759-232909	AG	AGA
-recovered pasa_asmbl_2879.p1, terminal, 232759, 232909
-recovered pasa_asmbl_2879.p1, internal, 225921, 226067
-recovered pasa_asmbl_2879.p1, internal, 226792, 226884
-recovered pasa_asmbl_2879.p1, internal, 227882, 227967
-recovered pasa_asmbl_2879.p1, internal, 228208, 228313
-recovered pasa_asmbl_2879.p1, internal, 229281, 229356
-recovered pasa_asmbl_2879.p1, internal, 230566, 230751
-recovered pasa_asmbl_2879.p1, internal, 230894, 230978
-recovered pasa_asmbl_2879.p1, internal, 231119, 231213
-recovered pasa_asmbl_2879.p1, internal, 231403, 231481
-recovered pasa_asmbl_2879.p1, internal, 231703, 231804
-recovered pasa_asmbl_2879.p1, internal, 232182, 232279
-recovered pasa_asmbl_2879.p1, internal, 232419, 232547
Valid prediction for Augustus_model.g16032.t1
Valid prediction for Augustus_model.g16033.t1
Valid prediction for snap_scaffold_10-snap.187-T1
Valid prediction for snap_scaffold_10-snap.176-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_10-snap.199-T1
Valid prediction for Augustus_model.g16019.t1
Valid prediction for snap_scaffold_10-snap.168-T1
Valid prediction for GlimmerHMM_glimmerT_24033-T1
Valid prediction for snap_scaffold_10-snap.192-T1
Valid prediction for GlimmerHMM_glimmerT_24044-T1
Valid prediction for GlimmerHMM_glimmerT_24029-T1
Valid prediction for snap_scaffold_10-snap.177-T1
Valid prediction for Augustus_model.g16010.t1
Valid prediction for CodingQuarry_transcript_5264-T1
Valid prediction for snap_scaffold_10-snap.178-T1
Couldn't classify 220774, 220883
Sorry, prediction pasa_asmbl_2878.p1 fails validation.
(ATG)	 CC	219901-219942	GT	AGG
(CAG)	 AG	220251-220437	GT	GGG
(ACA)	 AG	220774-220883	TC	AGT
-recovered pasa_asmbl_2878.p1, initial, 219901, 219942
-recovered pasa_asmbl_2878.p1, internal, 220251, 220437
Valid prediction for pasa_asmbl_2873.p3
Valid prediction for GlimmerHMM_glimmerT_24015-T1
Valid prediction for snap_scaffold_10-snap.194-T1
Valid prediction for snap_scaffold_10-snap.166-T1
Valid prediction for GlimmerHMM_glimmerT_24022-T1
Valid prediction for GlimmerHMM_glimmerT_24043-T1
Valid prediction for Augustus_model.g16027.t1
Valid prediction for snap_scaffold_10-snap.205-T1
Valid prediction for GlimmerHMM_glimmerT_24018-T1
Valid prediction for GlimmerHMM_glimmerT_24014-T1
Valid prediction for CodingQuarry_transcript_5265-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_10-snap.189-T1
Valid prediction for Augustus_model.g16028.t1
Valid prediction for GlimmerHMM_glimmerT_24020-T1
Valid prediction for snap_scaffold_10-snap.165-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for pasa_asmbl_3988.p1
Valid prediction for pasa_asmbl_4002.p1
Valid prediction for snap_scaffold_10-snap.188-T1
Couldn't classify 129179, 129266
Couldn't classify 129487, 129701
Sorry, prediction pasa_asmbl_5142.p1 fails validation.
(GTG)	 CA	129179-129266	GT	AGG
(ACT)	 AG	129487-129701	AG	AGA
Valid prediction for GlimmerHMM_glimmerT_24035-T1
Valid prediction for Augustus_model.g16024.t1
Valid prediction for pasa_asmbl_4004.p1
Valid prediction for snap_scaffold_10-snap.190-T1
Couldn't classify 202761, 202939
Sorry, prediction pasa_asmbl_3993.p1 fails validation.
(AGC)	 CC	202761-202939	GT	CGG
(TCT)	 AG	203544-203862	AG	AAA
-recovered pasa_asmbl_3993.p1, terminal, 203544, 203862
Couldn't classify 132425, 132590
Sorry, prediction pasa_asmbl_4008.p1 fails validation.
(TGT)	 AC	132425-132590	GT	TGG
(AGT)	 AG	133615-133749	GT	CCG
(CCA)	 AG	134933-135156	TT	GAT
-recovered pasa_asmbl_4008.p1, terminal, 134933, 135156
-recovered pasa_asmbl_4008.p1, internal, 133615, 133749
Valid prediction for Augustus_model.g16022.t1
Valid prediction for Augustus_model.g16031.t1
Valid prediction for snap_scaffold_10-snap.203-T1
Valid prediction for snap_scaffold_10-snap.170-T1
Valid prediction for Augustus_model.g16016.t1
Valid prediction for snap_scaffold_10-snap.207-T1
Valid prediction for snap_scaffold_10-snap.180-T1
Valid prediction for snap_scaffold_10-snap.181-T1
Valid prediction for snap_scaffold_10-snap.175-T1
Valid prediction for CodingQuarry_transcript_5259-T1
Valid prediction for snap_scaffold_10-snap.173-T1
Valid prediction for Augustus_model.g16013.t1
Valid prediction for snap_scaffold_10-snap.185-T1
Valid prediction for Augustus_model.g16021.t1
Valid prediction for snap_scaffold_10-snap.183-T1
Valid prediction for GlimmerHMM_glimmerT_24027-T1
Valid prediction for snap_scaffold_10-snap.174-T1
Valid prediction for snap_scaffold_10-snap.198-T1
Valid prediction for GlimmerHMM_glimmerT_24017-T1
Valid prediction for Augustus_model.g16014.t1
Valid prediction for CodingQuarry_transcript_5261-T1
Valid prediction for HiQ_model.g16017.t1
Valid prediction for snap_scaffold_10-snap.169-T1
Couldn't classify 170956, 171267
Sorry, prediction pasa_asmbl_4000.p1 fails validation.
(ATG)	 AG	170956-171267	GA	AAG
Valid prediction for CodingQuarry_transcript_5266-T1
Valid prediction for snap_scaffold_10-snap.171-T1
Valid prediction for CodingQuarry_transcript_5260-T1
Valid prediction for snap_scaffold_10-snap.184-T1
Valid prediction for snap_scaffold_10-snap.172-T1
Valid prediction for GlimmerHMM_glimmerT_24028-T1
Valid prediction for HiQ_model.g16018.t1
Valid prediction for snap_scaffold_10-snap.208-T1
Valid prediction for Augustus_model.g16011.t1
Valid prediction for snap_scaffold_10-snap.195-T1
Valid prediction for CodingQuarry_transcript_5262-T1
Valid prediction for GlimmerHMM_glimmerT_24021-T1
Valid prediction for Augustus_model.g16026.t1
Valid prediction for GlimmerHMM_glimmerT_24023-T1
Valid prediction for snap_scaffold_10-snap.193-T1
Valid prediction for Augustus_model.g16015.t1
Valid prediction for Augustus_model.g16023.t1
Valid prediction for Augustus_model.g16030.t1
Valid prediction for GlimmerHMM_glimmerT_24024-T1
Valid prediction for Augustus_model.g16025.t1
Valid prediction for snap_scaffold_10-snap.164-T1
Valid prediction for snap_scaffold_10-snap.200-T1
Valid prediction for snap_scaffold_10-snap.204-T1
Valid prediction for GlimmerHMM_glimmerT_24025-T1
Valid prediction for GlimmerHMM_glimmerT_24041-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 107047, rend_intergenic: 104242  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115473, rend_intergenic: 107833  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118113, rend_intergenic: 115856  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126220, rend_intergenic: 122480  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153025, rend_intergenic: 149682  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165390, rend_intergenic: 158603  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188688, rend_intergenic: 183485  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195427, rend_intergenic: 191768  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201842, rend_intergenic: 196498  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 216638, rend_intergenic: 208374  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 232909, rend_intergenic: 219720  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 234235
-exon list size: 428


building trellis

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18.8    
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20.9    
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23.3    
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23.7    
24.0    
24.2    
24.4    
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24.9    
25.1    
25.3    
25.6    
25.8    
26.0    
26.3    
26.5    
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27.0    
27.2    
27.4    
27.7    
27.9    
28.1    
28.4    
28.6    
28.8    
29.1    
29.3    
29.5    
29.8    
30.0    
30.2    
30.5    
30.7    
30.9    
31.2    
31.4    
31.6    
31.9    
32.1    
32.3    
32.6    
32.8    
33.0    
33.3    
33.5    
33.7    
34.0    
34.2    
34.4    
34.7    
34.9    
35.1    
35.3    
35.6    
35.8    
36.0    
36.3    
36.5    
36.7    
37.0    
37.2    
37.4    
37.7    
37.9    
38.1    
38.4    
38.6    
38.8    
39.1    
39.3    
39.5    
39.8    
40.0    
40.2    
40.5    
40.7    
40.9    
41.2    
41.4    
41.6    
41.9    
42.1    
42.3    
42.6    
42.8    
43.0    
43.3    
43.5    
43.7    
44.0    
44.2    
44.4    
44.7    
44.9    
45.1    
45.3    
45.6    
45.8    
46.0    
46.3    
46.5    
46.7    
47.0    
47.2    
47.4    
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47.9    
48.1    
48.4    
48.6    
48.8    
49.1    
49.3    
49.5    
49.8    
50.0    
50.2    
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50.9    
51.2    
51.4    
51.6    
51.9    
52.1    
52.3    
52.6    
52.8    
53.0    
53.3    
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55.3    
55.6    
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56.0    
56.3    
56.5    
56.7    
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75.3    
75.6    
75.8    
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76.5    
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77.0    
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78.6    
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79.1    
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80.0    
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85.1    
85.3    
85.6    
85.8    
86.0    
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87.4    
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88.1    
88.4    
88.6    
88.8    
89.1    
89.3    
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90.0    
90.2    
90.5    
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90.9    
91.2    
91.4    
91.6    
91.9    
92.1    
92.3    
92.6    
92.8    
93.0    
93.3    
93.5    
93.7    
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94.2    
94.4    
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95.1    
95.3    
95.6    
95.8    
96.0    
96.3    
96.5    
96.7    
97.0    
97.2    
97.4    
97.7    
97.9    
98.1    
98.4    
98.6    
98.8    
99.1    
99.3    
99.5    
99.8    
-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 107047, rend_intergenic: 104242  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115473, rend_intergenic: 107833  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118113, rend_intergenic: 115856  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126220, rend_intergenic: 122480  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153025, rend_intergenic: 149682  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165390, rend_intergenic: 158603  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188688, rend_intergenic: 183485  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195427, rend_intergenic: 191768  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201842, rend_intergenic: 196498  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 216638, rend_intergenic: 208374  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 232909, rend_intergenic: 219720  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 27 predictions persist after filtering for low support