-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_19/scaffold_19_2170608-2363773

-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: +)Couldn't classify 103224, 103259
Couldn't classify 107002, 107120
Sorry, prediction pasa_asmbl_21258.p1 fails validation.
(AAG)	 CC	103224-103259	GT	ATG
(CTG)	 AG	103784-103889	GT	GGG
(ACC)	 AG	104374-104579	GT	GGG
(GAG)	 AG	105045-105106	GT	AGG
(CAC)	 AG	105280-105354	GT	AAG
(ATG)	 AG	105727-105875	GT	AGG
(GTC)	 AG	106108-106222	GT	AAG
(GAA)	 AG	106576-106763	GT	TGG
(CTC)	 AG	107002-107120	CA	ACC
add_exon() Sorry, pasa_asmbl_21258.p1 105727-105875-initial-1 is invalid.
-recovered pasa_asmbl_21258.p1, initial, 105727, 105875
-recovered pasa_asmbl_21258.p1, internal, 103784, 103889
-recovered pasa_asmbl_21258.p1, internal, 104374, 104579
-recovered pasa_asmbl_21258.p1, internal, 105045, 105106
-recovered pasa_asmbl_21258.p1, internal, 105280, 105354
-recovered pasa_asmbl_21258.p1, internal, 105727, 105875
-recovered pasa_asmbl_21258.p1, internal, 106108, 106222
-recovered pasa_asmbl_21258.p1, internal, 106576, 106763
Valid prediction for snap_scaffold_19-snap.474-T1
Valid prediction for snap_scaffold_19-snap.472-T1
Valid prediction for snap_scaffold_19-snap.488-T1
Valid prediction for snap_scaffold_19-snap.467-T1
Valid prediction for Augustus_model.g29021.t1
Valid prediction for Augustus_model.g29013.t1
Valid prediction for snap_scaffold_19-snap.492-T1
Couldn't classify 109551, 109973
Sorry, prediction pasa_asmbl_21259.p1 fails validation.
(CCA)	 CT	109551-109973	CC	AGC
Valid prediction for snap_scaffold_19-snap.476-T1
Valid prediction for snap_scaffold_19-snap.468-T1
Valid prediction for GlimmerHMM_glimmerT_43724-T1
Valid prediction for Augustus_model.g29026.t1
Valid prediction for snap_scaffold_19-snap.502-T1
Valid prediction for snap_scaffold_19-snap.460-T1
Valid prediction for snap_scaffold_19-snap.473-T1
Valid prediction for snap_scaffold_19-snap.478-T1
Valid prediction for snap_scaffold_19-snap.495-T1
Couldn't classify 179474, 179591
Sorry, prediction pasa_asmbl_21261.p1 fails validation.
(ATG)	 CC	177074-177258	GT	AGG
(AGC)	 AG	177463-177826	GT	AGG
(ACG)	 AG	178519-178789	GT	CAG
(TCC)	 AG	179092-179317	GT	AGG
(GTC)	 AG	179474-179591	AG	GCA
-recovered pasa_asmbl_21261.p1, initial, 177074, 177258
-recovered pasa_asmbl_21261.p1, internal, 177463, 177826
-recovered pasa_asmbl_21261.p1, internal, 178519, 178789
-recovered pasa_asmbl_21261.p1, internal, 179092, 179317
Valid prediction for GlimmerHMM_glimmerT_43719-T1
Valid prediction for snap_scaffold_19-snap.469-T1
Valid prediction for GlimmerHMM_glimmerT_43713-T1
Valid prediction for snap_scaffold_19-snap.501-T1
Valid prediction for snap_scaffold_19-snap.494-T1
Valid prediction for snap_scaffold_19-snap.463-T1
Valid prediction for Augustus_model.g29016.t1
Couldn't classify 49476, 50060
Sorry, prediction pasa_asmbl_21256.p1 fails validation.
(ATG)	 CG	49476-50060	AG	CCA
Valid prediction for Augustus_model.g29020.t1
Valid prediction for GlimmerHMM_glimmerT_43712-T1
Valid prediction for snap_scaffold_19-snap.462-T1
Valid prediction for snap_scaffold_19-snap.500-T1
Valid prediction for snap_scaffold_19-snap.491-T1
Valid prediction for snap_scaffold_19-snap.464-T1
Valid prediction for GlimmerHMM_glimmerT_43718-T1
Valid prediction for snap_scaffold_19-snap.487-T1
Valid prediction for GlimmerHMM_glimmerT_43717-T1
Valid prediction for snap_scaffold_19-snap.484-T1
Valid prediction for snap_scaffold_19-snap.489-T1
Valid prediction for snap_scaffold_19-snap.499-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_19-snap.470-T1
Valid prediction for GlimmerHMM_glimmerT_43709-T1
Valid prediction for Augustus_model.g29023.t1
Valid prediction for snap_scaffold_19-snap.485-T1
Valid prediction for snap_scaffold_19-snap.477-T1
Valid prediction for snap_scaffold_19-snap.504-T1
Valid prediction for snap_scaffold_19-snap.480-T1
Valid prediction for GlimmerHMM_glimmerT_43715-T1
Valid prediction for snap_scaffold_19-snap.461-T1
Valid prediction for CodingQuarry_transcript_25602-T1
Valid prediction for snap_scaffold_19-snap.471-T1
Valid prediction for snap_scaffold_19-snap.466-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for snap_scaffold_19-snap.496-T1
Valid prediction for Augustus_model.g29025.t1
Valid prediction for GlimmerHMM_glimmerT_43721-T1
Valid prediction for GlimmerHMM_glimmerT_43714-T1
Valid prediction for snap_scaffold_19-snap.490-T1
Valid prediction for snap_scaffold_19-snap.465-T1
Valid prediction for snap_scaffold_19-snap.483-T1
Valid prediction for GlimmerHMM_glimmerT_43711-T1
Valid prediction for GlimmerHMM_glimmerT_43722-T1
Valid prediction for snap_scaffold_19-snap.481-T1
Valid prediction for snap_scaffold_19-snap.497-T1
Valid prediction for snap_scaffold_19-snap.503-T1
Valid prediction for Augustus_model.g29024.t1
Valid prediction for pasa_asmbl_22053.p2
Valid prediction for CodingQuarry_transcript_25601-T1
Couldn't classify 57948, 57983
Sorry, prediction pasa_asmbl_22056.p2 fails validation.
(TCA)	 CT	57948-57983	GT	AGG
(CTT)	 AG	58461-58545	GT	CAG
(GTA)	 AG	58667-58808	GT	AGG
(GCC)	 AG	59113-59152	GT	AGG
-recovered pasa_asmbl_22056.p2, terminal, 59113, 59152
-recovered pasa_asmbl_22056.p2, internal, 58461, 58545
-recovered pasa_asmbl_22056.p2, internal, 58667, 58808
-recovered pasa_asmbl_22056.p2, internal, 59113, 59152
Valid prediction for GlimmerHMM_glimmerT_43710-T1
Valid prediction for GlimmerHMM_glimmerT_43723-T1
Valid prediction for Augustus_model.g29018.t1
Valid prediction for snap_scaffold_19-snap.479-T1
Valid prediction for Augustus_model.g29022.t1
Valid prediction for snap_scaffold_19-snap.486-T1
Valid prediction for Augustus_model.g29015.t1
Valid prediction for Augustus_model.g29017.t1
Valid prediction for snap_scaffold_19-snap.493-T1
Couldn't classify 163117, 163268
Sorry, prediction pasa_asmbl_22050.p1 fails validation.
(CTT)	 AT	163117-163268	GT	TGG
(GAG)	 AG	163682-163797	GT	AGG
(TTT)	 AG	165733-165813	GT	GGG
(GAG)	 AG	166298-166378	GT	TCG
(ACA)	 AG	166624-166826	GT	AGG
(GCT)	 AG	168975-169049	AT	GAA
-recovered pasa_asmbl_22050.p1, terminal, 168975, 169049
-recovered pasa_asmbl_22050.p1, internal, 163682, 163797
-recovered pasa_asmbl_22050.p1, internal, 165733, 165813
-recovered pasa_asmbl_22050.p1, internal, 166298, 166378
-recovered pasa_asmbl_22050.p1, internal, 166624, 166826
Valid prediction for HiQ_model.g29019.t1
Valid prediction for snap_scaffold_19-snap.498-T1
Valid prediction for snap_scaffold_19-snap.475-T1
Valid prediction for snap_scaffold_19-snap.482-T1
Valid prediction for GlimmerHMM_glimmerT_43716-T1
Valid prediction for Augustus_model.g29014.t1
Valid prediction for GlimmerHMM_glimmerT_43720-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 37007, rend_intergenic: 25329  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39435, rend_intergenic: 37203  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49748, rend_intergenic: 40901  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62224, rend_intergenic: 49802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68851, rend_intergenic: 63502  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110182, rend_intergenic: 85482  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117613, rend_intergenic: 112177  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129419, rend_intergenic: 118292  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137241, rend_intergenic: 134015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139881, rend_intergenic: 137309  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143098, rend_intergenic: 140674  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147626, rend_intergenic: 143213  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156663, rend_intergenic: 148205  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173276, rend_intergenic: 156820  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180951, rend_intergenic: 177650  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 50824, rend_intergenic: 50821  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 193166
-exon list size: 352


building trellis

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31.4    
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33.6    
33.9    
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35.6    
35.9    
36.2    
36.4    
36.7    
37.0    
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37.6    
37.9    
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38.4    
38.7    
39.0    
39.3    
39.5    
39.8    
40.1    
40.4    
40.7    
41.0    
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41.5    
41.8    
42.1    
42.4    
42.7    
42.9    
43.2    
43.5    
43.8    
44.1    
44.4    
44.6    
44.9    
45.2    
45.5    
45.8    
46.0    
46.3    
46.6    
46.9    
47.2    
47.5    
47.7    
48.0    
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    
52.0    
52.3    
52.5    
52.8    
53.1    
53.4    
53.7    
54.0    
54.2    
54.5    
54.8    
55.1    
55.4    
55.6    
55.9    
56.2    
56.5    
56.8    
57.1    
57.3    
57.6    
57.9    
58.2    
58.5    
58.8    
59.0    
59.3    
59.6    
59.9    
60.2    
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60.7    
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61.3    
61.6    
61.9    
62.1    
62.4    
62.7    
63.0    
63.3    
63.6    
63.8    
64.1    
64.4    
64.7    
65.0    
65.3    
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65.8    
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66.7    
66.9    
67.2    
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68.1    
68.4    
68.6    
68.9    
69.2    
69.5    
69.8    
70.1    
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70.6    
70.9    
71.2    
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72.0    
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75.4    
75.7    
76.0    
76.3    
76.6    
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78.8    
79.1    
79.4    
79.7    
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80.2    
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80.8    
81.1    
81.4    
81.6    
81.9    
82.2    
82.5    
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83.3    
83.6    
83.9    
84.2    
84.5    
84.7    
85.0    
85.3    
85.6    
85.9    
86.2    
86.4    
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87.0    
87.3    
87.6    
87.9    
88.1    
88.4    
88.7    
89.0    
89.3    
89.5    
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90.1    
90.4    
90.7    
91.0    
91.2    
91.5    
91.8    
92.1    
92.4    
92.7    
92.9    
93.2    
93.5    
93.8    
94.1    
94.4    
94.6    
94.9    
95.2    
95.5    
95.8    
96.0    
96.3    
96.6    
96.9    
97.2    
97.5    
97.7    
98.0    
98.3    
98.6    
98.9    
99.2    
99.4    
99.7    
-found 21 predictions from path traversal
Error with prediction: snap lend_intergenic: 37007, rend_intergenic: 25329  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39435, rend_intergenic: 37203  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49748, rend_intergenic: 40901  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62224, rend_intergenic: 49802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68851, rend_intergenic: 63502  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110182, rend_intergenic: 85482  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117613, rend_intergenic: 112177  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129419, rend_intergenic: 118292  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137241, rend_intergenic: 134015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139881, rend_intergenic: 137309  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143098, rend_intergenic: 140674  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147626, rend_intergenic: 143213  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156663, rend_intergenic: 148205  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173276, rend_intergenic: 156820  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180951, rend_intergenic: 177650  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 50824, rend_intergenic: 50821  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 11 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 180305 - 193166
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-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
	-no exons in range 180952 - 193166