-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_527654-699916

-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_24013-T1
Valid prediction for Augustus_model.g16006.t1
Valid prediction for GlimmerHMM_glimmerT_23983-T1
Valid prediction for snap_scaffold_10-snap.133-T1
Couldn't classify 170026, 170151
Sorry, prediction pasa_asmbl_3826.p1 fails validation.
(ATG)	 GG	167782-168004	GT	GGG
(CCC)	 AG	168210-168404	GT	GGG
(GCA)	 AG	168649-168801	GT	AGG
(CAA)	 AG	169103-169342	GT	TGG
(CTG)	 AG	169646-169794	GT	AGG
(GAC)	 AG	170026-170151	GT	AGG
-recovered pasa_asmbl_3826.p1, initial, 167782, 168004
-recovered pasa_asmbl_3826.p1, internal, 168210, 168404
-recovered pasa_asmbl_3826.p1, internal, 168649, 168801
-recovered pasa_asmbl_3826.p1, internal, 169103, 169342
-recovered pasa_asmbl_3826.p1, internal, 169646, 169794
-recovered pasa_asmbl_3826.p1, internal, 170026, 170151
Valid prediction for snap_scaffold_10-snap.125-T1
Valid prediction for GlimmerHMM_glimmerT_23978-T1
Valid prediction for Augustus_model.g15988.t1
Valid prediction for snap_scaffold_10-snap.159-T1
Valid prediction for GlimmerHMM_glimmerT_23987-T1
Valid prediction for CodingQuarry_transcript_5257-T1
Valid prediction for Augustus_model.g16003.t1
Couldn't classify 155656, 155733
Sorry, prediction pasa_asmbl_2861.p1 fails validation.
(GAT)	 AG	155656-155733	GT	AGG
(AAA)	 AG	155844-155954	GT	AGG
(CAA)	 AG	156052-156174	GT	AGG
(ATG)	 AG	156352-156399	AC	AGA
-recovered pasa_asmbl_2861.p1, terminal, 156352, 156399
-recovered pasa_asmbl_2861.p1, internal, 155656, 155733
-recovered pasa_asmbl_2861.p1, internal, 155844, 155954
-recovered pasa_asmbl_2861.p1, internal, 156052, 156174
Valid prediction for Augustus_model.g15979.t1
Valid prediction for GlimmerHMM_glimmerT_23992-T1
Valid prediction for GlimmerHMM_glimmerT_23997-T1
Valid prediction for snap_scaffold_10-snap.141-T1
Valid prediction for snap_scaffold_10-snap.146-T1
Valid prediction for snap_scaffold_10-snap.145-T1
Valid prediction for Augustus_model.g15996.t1
Valid prediction for snap_scaffold_10-snap.134-T1
Valid prediction for GlimmerHMM_glimmerT_24014-T1
Valid prediction for snap_scaffold_10-snap.137-T1
Valid prediction for GlimmerHMM_glimmerT_23999-T1
Valid prediction for snap_scaffold_10-snap.160-T1
Valid prediction for Augustus_model.g16007.t1
Valid prediction for CodingQuarry_transcript_5255-T1
Valid prediction for snap_scaffold_10-snap.129-T1
Valid prediction for pasa_asmbl_2859.p1
Valid prediction for GlimmerHMM_glimmerT_24007-T1
Valid prediction for Augustus_model.g15984.t1
Valid prediction for GlimmerHMM_glimmerT_23993-T1
Valid prediction for GlimmerHMM_glimmerT_24008-T1
Valid prediction for snap_scaffold_10-snap.163-T1
Valid prediction for Augustus_model.g15989.t1
Valid prediction for snap_scaffold_10-snap.158-T1
Valid prediction for GlimmerHMM_glimmerT_24001-T1
Valid prediction for snap_scaffold_10-snap.136-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_10-snap.138-T1
Valid prediction for Augustus_model.g15991.t1
Valid prediction for snap_scaffold_10-snap.128-T1
Couldn't classify 149747, 149843
Couldn't classify 150263, 150265
Sorry, prediction CodingQuarry_transcript_5256-T1 fails validation.
(ATG)	 AG	146744-146763	GT	TAG
(TCG)	 AG	148565-148595	GT	AGG
(TAC)	 AG	149479-149624	GT	AGG
(TAA)	 AG	149747-149843	TT	AGT
(TAG)	 AA	150263-150265	GT	AGG
-recovered CodingQuarry_transcript_5256-T1, initial, 146744, 146763
-recovered CodingQuarry_transcript_5256-T1, internal, 146744, 146763
-recovered CodingQuarry_transcript_5256-T1, internal, 148565, 148595
-recovered CodingQuarry_transcript_5256-T1, internal, 149479, 149624
Valid prediction for GlimmerHMM_glimmerT_23994-T1
Valid prediction for Augustus_model.g15994.t1
Valid prediction for snap_scaffold_10-snap.155-T1
Valid prediction for snap_scaffold_10-snap.162-T1
Valid prediction for snap_scaffold_10-snap.157-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for Augustus_model.g16002.t1
Valid prediction for Augustus_model.g15992.t1
Valid prediction for Augustus_model.g15981.t1
Valid prediction for GlimmerHMM_glimmerT_23990-T1
Couldn't classify 133548, 134396
Sorry, prediction pasa_asmbl_2858.p1 fails validation.
(GCC)	 AA	133548-134396	AT	ACA
Valid prediction for GlimmerHMM_glimmerT_23996-T1
Valid prediction for GlimmerHMM_glimmerT_23982-T1
Valid prediction for GlimmerHMM_glimmerT_23986-T1
Valid prediction for snap_scaffold_10-snap.147-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g16005.t1
Valid prediction for GlimmerHMM_glimmerT_24011-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_23980-T1
Valid prediction for Augustus_model.g16000.t1
Valid prediction for GlimmerHMM_glimmerT_24009-T1
Valid prediction for GlimmerHMM_glimmerT_24003-T1
Valid prediction for snap_scaffold_10-snap.148-T1
Valid prediction for GlimmerHMM_glimmerT_23995-T1
Valid prediction for GlimmerHMM_glimmerT_23991-T1
Valid prediction for pasa_asmbl_3962.p1
Valid prediction for Augustus_model.g15980.t1
Valid prediction for snap_scaffold_10-snap.153-T1
Valid prediction for snap_scaffold_10-snap.149-T1
Valid prediction for snap_scaffold_10-snap.139-T1
Valid prediction for snap_scaffold_10-snap.122-T1
Couldn't classify 152313, 152744
Sorry, prediction pasa_asmbl_3961.p1 fails validation.
(CCC)	 CT	152313-152744	AC	GAA
Valid prediction for Augustus_model.g15978.t1
Valid prediction for snap_scaffold_10-snap.150-T1
Valid prediction for GlimmerHMM_glimmerT_24002-T1
Valid prediction for GlimmerHMM_glimmerT_23989-T1
Valid prediction for snap_scaffold_10-snap.142-T1
Valid prediction for snap_scaffold_10-snap.154-T1
Valid prediction for Augustus_model.g15982.t1
Valid prediction for snap_scaffold_10-snap.144-T1
Valid prediction for GlimmerHMM_glimmerT_23984-T1
Valid prediction for snap_scaffold_10-snap.152-T1
Valid prediction for snap_scaffold_10-snap.130-T1
Valid prediction for Augustus_model.g15998.t1
Valid prediction for Augustus_model.g16008.t1
Valid prediction for Augustus_model.g15987.t1
Valid prediction for GlimmerHMM_glimmerT_24006-T1
Valid prediction for GlimmerHMM_glimmerT_23988-T1
Valid prediction for HiQ_model.g15999.t1
Valid prediction for GlimmerHMM_glimmerT_23981-T1
Valid prediction for Augustus_model.g15995.t1
Valid prediction for snap_scaffold_10-snap.127-T1
Valid prediction for snap_scaffold_10-snap.123-T1
Valid prediction for snap_scaffold_10-snap.126-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g15993.t1
Valid prediction for snap_scaffold_10-snap.143-T1
Valid prediction for snap_scaffold_10-snap.140-T1
Valid prediction for Augustus_model.g16004.t1
Valid prediction for CodingQuarry_transcript_5249-T1
Valid prediction for snap_scaffold_10-snap.131-T1
Valid prediction for snap_scaffold_10-snap.151-T1
Couldn't classify 66215, 66322
Sorry, prediction pasa_asmbl_3974.p1 fails validation.
(ATG)	 AG	64696-64839	GT	TGG
(CTG)	 AG	65098-65173	GT	AGG
(ACA)	 AG	65479-65553	GT	AGG
(AAG)	 AG	65726-65771	GT	AGG
(TGT)	 AG	65946-66063	GT	AGG
(GGG)	 AG	66215-66322	AC	CTA
-recovered pasa_asmbl_3974.p1, initial, 64696, 64839
-recovered pasa_asmbl_3974.p1, internal, 64696, 64839
-recovered pasa_asmbl_3974.p1, internal, 65098, 65173
-recovered pasa_asmbl_3974.p1, internal, 65479, 65553
-recovered pasa_asmbl_3974.p1, internal, 65726, 65771
-recovered pasa_asmbl_3974.p1, internal, 65946, 66063
Valid prediction for GlimmerHMM_glimmerT_23985-T1
Valid prediction for Augustus_model.g15983.t1
Valid prediction for snap_scaffold_10-snap.161-T1
Valid prediction for snap_scaffold_10-snap.132-T1
Valid prediction for Augustus_model.g15997.t1
Valid prediction for Augustus_model.g16001.t1
Couldn't classify 159456, 159764
Sorry, prediction pasa_asmbl_3959.p1 fails validation.
(CAG)	 TC	159456-159764	GT	CAG
(GTT)	 AG	159940-160098	AA	AGA
-recovered pasa_asmbl_3959.p1, terminal, 159940, 160098
Valid prediction for GlimmerHMM_glimmerT_24004-T1
Valid prediction for Augustus_model.g15985.t1
Valid prediction for snap_scaffold_10-snap.135-T1
Valid prediction for CodingQuarry_transcript_5254-T1
Valid prediction for GlimmerHMM_glimmerT_23998-T1
Valid prediction for snap_scaffold_10-snap.124-T1
Couldn't classify 168289, 168583
Sorry, prediction pasa_asmbl_3955.p1 fails validation.
(ACT)	 AC	168289-168583	GT	AGG
(CTC)	 AG	170214-170339	GT	GCG
(ACA)	 AG	170453-170643	GT	AGG
(GTG)	 AG	170776-170966	GT	ATG
(GCT)	 AG	171138-171354	AA	AAA
-recovered pasa_asmbl_3955.p1, terminal, 171138, 171354
-recovered pasa_asmbl_3955.p1, internal, 170214, 170339
-recovered pasa_asmbl_3955.p1, internal, 170453, 170643
-recovered pasa_asmbl_3955.p1, internal, 170776, 170966
Valid prediction for GlimmerHMM_glimmerT_24000-T1
Valid prediction for CodingQuarry_transcript_5252-T1
Valid prediction for snap_scaffold_10-snap.156-T1
Valid prediction for GlimmerHMM_glimmerT_23979-T1
Valid prediction for Augustus_model.g15986.t1
Valid prediction for GlimmerHMM_glimmerT_24005-T1
Valid prediction for Augustus_model.g15990.t1
Valid prediction for CodingQuarry_transcript_5251-T1
Valid prediction for GlimmerHMM_glimmerT_24012-T1
Valid prediction for pasa_asmbl_3979.p1
Valid prediction for GlimmerHMM_glimmerT_24010-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 29094, rend_intergenic: 29091  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 172263
-exon list size: 358


building trellis

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30.0    
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33.6    
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35.6    
35.8    
36.1    
36.4    
36.7    
36.9    
37.2    
37.5    
37.8    
38.1    
38.3    
38.6    
38.9    
39.2    
39.4    
39.7    
40.0    
40.3    
40.6    
40.8    
41.1    
41.4    
41.7    
41.9    
42.2    
42.5    
42.8    
43.1    
43.3    
43.6    
43.9    
44.2    
44.4    
44.7    
45.0    
45.3    
45.6    
45.8    
46.1    
46.4    
46.7    
46.9    
47.2    
47.5    
47.8    
48.1    
48.3    
48.6    
48.9    
49.2    
49.4    
49.7    
50.0    
50.3    
50.6    
50.8    
51.1    
51.4    
51.7    
51.9    
52.2    
52.5    
52.8    
53.1    
53.3    
53.6    
53.9    
54.2    
54.4    
54.7    
55.0    
55.3    
55.6    
55.8    
56.1    
56.4    
56.7    
56.9    
57.2    
57.5    
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58.1    
58.3    
58.6    
58.9    
59.2    
59.4    
59.7    
60.0    
60.3    
60.6    
60.8    
61.1    
61.4    
61.7    
61.9    
62.2    
62.5    
62.8    
63.1    
63.3    
63.6    
63.9    
64.2    
64.4    
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65.0    
65.3    
65.6    
65.8    
66.1    
66.4    
66.7    
66.9    
67.2    
67.5    
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68.1    
68.3    
68.6    
68.9    
69.2    
69.4    
69.7    
70.0    
70.3    
70.6    
70.8    
71.1    
71.4    
71.7    
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72.2    
72.5    
72.8    
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73.3    
73.6    
73.9    
74.2    
74.4    
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75.0    
75.3    
75.6    
75.8    
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76.4    
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76.9    
77.2    
77.5    
77.8    
78.1    
78.3    
78.6    
78.9    
79.2    
79.4    
79.7    
80.0    
80.3    
80.6    
80.8    
81.1    
81.4    
81.7    
81.9    
82.2    
82.5    
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83.1    
83.3    
83.6    
83.9    
84.2    
84.4    
84.7    
85.0    
85.3    
85.6    
85.8    
86.1    
86.4    
86.7    
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87.2    
87.5    
87.8    
88.1    
88.3    
88.6    
88.9    
89.2    
89.4    
89.7    
90.0    
90.3    
90.6    
90.8    
91.1    
91.4    
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91.9    
92.2    
92.5    
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93.1    
93.3    
93.6    
93.9    
94.2    
94.4    
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95.3    
95.6    
95.8    
96.1    
96.4    
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97.2    
97.5    
97.8    
98.1    
98.3    
98.6    
98.9    
99.2    
99.4    
99.7    
-found 43 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 29094, rend_intergenic: 29091  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 42 predictions persist after filtering for low support