-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_11/scaffold_11_1-231329

-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_11-snap.21-T1
Valid prediction for GlimmerHMM_glimmerT_26306-T1
Valid prediction for GlimmerHMM_glimmerT_26302-T1
Valid prediction for pasa_asmbl_5251.p1
Valid prediction for snap_scaffold_11-snap.1-T1
Valid prediction for Augustus_model.g17451.t1
Couldn't classify 181686, 181832
Sorry, prediction pasa_asmbl_5270.p1 fails validation.
(ATG)	 CC	180627-180774	GT	AGG
(AGA)	 AG	181172-181299	GT	GGG
(TTC)	 AG	181472-181588	GT	AGG
(GAG)	 AG	181686-181832	GT	CTG
-recovered pasa_asmbl_5270.p1, initial, 180627, 180774
-recovered pasa_asmbl_5270.p1, internal, 181172, 181299
-recovered pasa_asmbl_5270.p1, internal, 181472, 181588
-recovered pasa_asmbl_5270.p1, internal, 181686, 181832
Valid prediction for snap_scaffold_11-snap.33-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_26300-T1
Valid prediction for snap_scaffold_11-snap.19-T1
Valid prediction for snap_scaffold_11-snap.9-T1
Valid prediction for Augustus_model.g17462.t1
Valid prediction for GlimmerHMM_glimmerT_26299-T1
Valid prediction for snap_scaffold_11-snap.11-T1
Valid prediction for HiQ_model.g17463.t1
Valid prediction for snap_scaffold_11-snap.27-T1
Valid prediction for pasa_asmbl_5261.p1
Valid prediction for GlimmerHMM_glimmerT_26318-T1
Valid prediction for pasa_asmbl_5278.p1
Valid prediction for GlimmerHMM_glimmerT_26314-T1
Valid prediction for snap_scaffold_11-snap.36-T1
Valid prediction for snap_scaffold_11-snap.30-T1
Valid prediction for CodingQuarry_transcript_7932-T1
Valid prediction for CodingQuarry_transcript_7935-T1
Valid prediction for GlimmerHMM_glimmerT_26312-T1
Valid prediction for snap_scaffold_11-snap.45-T1
Valid prediction for HiQ_model.g17460.t1
Valid prediction for snap_scaffold_11-snap.10-T1
Valid prediction for CodingQuarry_transcript_7933-T1
Valid prediction for snap_scaffold_11-snap.22-T1
Valid prediction for Augustus_model.g17459.t1
Valid prediction for snap_scaffold_11-snap.35-T1
Valid prediction for snap_scaffold_11-snap.26-T1
Valid prediction for Augustus_model.g17464.t1
Valid prediction for snap_scaffold_11-snap.42-T1
Valid prediction for snap_scaffold_11-snap.13-T1
Valid prediction for pasa_asmbl_5275.p1
Valid prediction for CodingQuarry_transcript_7939-T1
Valid prediction for snap_scaffold_11-snap.41-T1
Valid prediction for snap_scaffold_11-snap.34-T1
Valid prediction for CodingQuarry_transcript_7936-T1
Valid prediction for CodingQuarry_transcript_7934-T1
Valid prediction for pasa_asmbl_5263.p1
Valid prediction for Augustus_model.g17466.t1
Valid prediction for GlimmerHMM_glimmerT_26313-T1
Valid prediction for HiQ_model.g17452.t1
Valid prediction for Augustus_model.g17446.t1
Valid prediction for GlimmerHMM_glimmerT_26310-T1
Valid prediction for snap_scaffold_11-snap.8-T1
Valid prediction for pasa_asmbl_5254.p1
Valid prediction for GlimmerHMM_glimmerT_26320-T1
Valid prediction for snap_scaffold_11-snap.37-T1
Valid prediction for Augustus_model.g17455.t1
Couldn't classify 185545, 185829
Sorry, prediction pasa_asmbl_5273.p2 fails validation.
(AGG)	 TC	185545-185829	GT	ACG
(CCT)	 AG	185903-185979	GT	GCG
(GGA)	 AG	186052-186110	GT	CGG
(CTC)	 AG	186248-186348	CT	GAC
-recovered pasa_asmbl_5273.p2, terminal, 186248, 186348
-recovered pasa_asmbl_5273.p2, internal, 185903, 185979
-recovered pasa_asmbl_5273.p2, internal, 186052, 186110
Valid prediction for GlimmerHMM_glimmerT_26307-T1
Valid prediction for CodingQuarry_transcript_7931-T1
Valid prediction for HiQ_model.g17448.t1
Valid prediction for snap_scaffold_11-snap.31-T1
Valid prediction for GlimmerHMM_glimmerT_26319-T1
Valid prediction for snap_scaffold_11-snap.43-T1
Couldn't classify 218231, 218248
Couldn't classify 219522, 219548
Sorry, prediction pasa_asmbl_5277.p1 fails validation.
(ATC)	 AC	218231-218248	GT	AGG
(ATG)	 AG	219104-219364	GT	AGG
(GCC)	 AG	219522-219548	AC	GGA
-recovered pasa_asmbl_5277.p1, initial, 219104, 219364
-recovered pasa_asmbl_5277.p1, internal, 219104, 219364
Valid prediction for CodingQuarry_transcript_7937-T1
Valid prediction for pasa_asmbl_5257.p1
Valid prediction for snap_scaffold_11-snap.15-T1
Valid prediction for snap_scaffold_11-snap.47-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_11-snap.5-T1
Valid prediction for snap_scaffold_11-snap.6-T1
Valid prediction for Augustus_model.g17458.t1
Valid prediction for Augustus_model.g17456.t1
Valid prediction for snap_scaffold_11-snap.17-T1
Valid prediction for GlimmerHMM_glimmerT_26311-T1
Valid prediction for CodingQuarry_transcript_7930-T1
Valid prediction for snap_scaffold_11-snap.2-T1
Valid prediction for snap_scaffold_11-snap.46-T1
Valid prediction for snap_scaffold_11-snap.28-T1
Valid prediction for GlimmerHMM_glimmerT_26305-T1
Valid prediction for snap_scaffold_11-snap.39-T1
Couldn't classify 25412, 25587
Sorry, prediction pasa_asmbl_6380.p1 fails validation.
(GAT)	 CA	25412-25587	GT	AGG
(GTA)	 AG	25738-25909	TG	GAT
-recovered pasa_asmbl_6380.p1, terminal, 25738, 25909
Valid prediction for GlimmerHMM_glimmerT_26304-T1
Valid prediction for GlimmerHMM_glimmerT_26309-T1
Valid prediction for snap_scaffold_11-snap.7-T1
Couldn't classify 80297, 80845
Sorry, prediction pasa_asmbl_6377.p1 fails validation.
(ATG)	 AG	80297-80845	CC	CTC
Valid prediction for snap_scaffold_11-snap.40-T1
Valid prediction for Augustus_model.g17461.t1
Couldn't classify 16337, 16423
Couldn't classify 19868, 19980
Sorry, prediction pasa_asmbl_6383.p1 fails validation.
(AAG)	 GG	16337-16423	GT	AGG
(GTC)	 AG	18110-18176	GT	TGG
(GTT)	 AG	19613-19732	GT	AGG
(TGG)	 AG	19868-19980	TA	CGT
-recovered pasa_asmbl_6383.p1, internal, 18110, 18176
-recovered pasa_asmbl_6383.p1, internal, 19613, 19732
Valid prediction for snap_scaffold_11-snap.4-T1
Valid prediction for GlimmerHMM_glimmerT_26316-T1
Valid prediction for snap_scaffold_11-snap.38-T1
Valid prediction for GlimmerHMM_glimmerT_26296-T1
Valid prediction for GlimmerHMM_glimmerT_26315-T1
Valid prediction for snap_scaffold_11-snap.12-T1
Valid prediction for Augustus_model.g17449.t1
Couldn't classify 179289, 179439
Couldn't classify 180372, 180398
Sorry, prediction pasa_asmbl_6371.p1 fails validation.
(TCC)	 AC	179289-179439	GT	TGG
(CAA)	 AG	179725-179918	GT	TGG
(GCA)	 AG	180050-180226	GT	TGG
(GTG)	 AG	180372-180398	CC	CCC
-recovered pasa_asmbl_6371.p1, internal, 179725, 179918
-recovered pasa_asmbl_6371.p1, internal, 180050, 180226
Valid prediction for snap_scaffold_11-snap.16-T1
Valid prediction for Augustus_model.g17465.t1
Valid prediction for snap_scaffold_11-snap.20-T1
Valid prediction for GlimmerHMM_glimmerT_26321-T1
Couldn't classify 20556, 20747
Couldn't classify 21620, 21835
Sorry, prediction pasa_asmbl_6382.p1 fails validation.
(CCA)	 CT	20556-20747	GT	AGG
(ATG)	 AG	21620-21835	AG	GCA
Valid prediction for Augustus_model.g17447.t1
Couldn't classify 15542, 16129
Sorry, prediction pasa_asmbl_6384.p1 fails validation.
(TTC)	 AG	15542-16129	CT	GCC
Couldn't classify 184101, 184205
Sorry, prediction pasa_asmbl_6370.p1 fails validation.
(GCA)	 AG	184101-184205	GT	TGG
(ACG)	 AG	184479-184666	GT	AGG
(GAT)	 AG	185008-185236	CG	GAC
-recovered pasa_asmbl_6370.p1, terminal, 185008, 185236
-recovered pasa_asmbl_6370.p1, internal, 184101, 184205
-recovered pasa_asmbl_6370.p1, internal, 184479, 184666
Valid prediction for GlimmerHMM_glimmerT_26303-T1
Valid prediction for Augustus_model.g17445.t1
Valid prediction for snap_scaffold_11-snap.14-T1
Valid prediction for Augustus_model.g17457.t1
Valid prediction for Augustus_model.g17454.t1
Valid prediction for Augustus_model.g17450.t1
Valid prediction for snap_scaffold_11-snap.23-T1
Valid prediction for snap_scaffold_11-snap.29-T1
Valid prediction for pasa_asmbl_6364.p1
Valid prediction for GlimmerHMM_glimmerT_26308-T1
Valid prediction for pasa_asmbl_6365.p1
Valid prediction for GlimmerHMM_glimmerT_26301-T1
Valid prediction for snap_scaffold_11-snap.44-T1
Valid prediction for snap_scaffold_11-snap.18-T1
Valid prediction for snap_scaffold_11-snap.25-T1
Valid prediction for GlimmerHMM_glimmerT_26317-T1
Valid prediction for snap_scaffold_11-snap.24-T1
Couldn't classify 171669, 171886
Couldn't classify 175304, 175463
Sorry, prediction pasa_asmbl_6373.p1 fails validation.
(TGG)	 GC	171669-171886	GT	AGG
(GGC)	 AG	172330-172524	GT	GGG
(GAA)	 AG	175304-175463	AC	AGA
-recovered pasa_asmbl_6373.p1, internal, 172330, 172524
Valid prediction for Augustus_model.g17467.t1
Valid prediction for GlimmerHMM_glimmerT_26297-T1
Valid prediction for snap_scaffold_11-snap.3-T1
Valid prediction for Augustus_model.g17453.t1
Valid prediction for GlimmerHMM_glimmerT_26298-T1
Couldn't classify 26791, 26851
Sorry, prediction pasa_asmbl_6378.p1 fails validation.
(AGG)	 CC	26791-26851	GT	GGG
(ACT)	 AG	26965-27051	GT	TGG
(ACC)	 AG	27155-27408	CT	GAC
-recovered pasa_asmbl_6378.p1, terminal, 27155, 27408
-recovered pasa_asmbl_6378.p1, internal, 26965, 27051
Couldn't classify 81974, 83861
Sorry, prediction pasa_asmbl_6375.p1 fails validation.
(AGC)	 AA	81974-83861	GT	GGG
(GTT)	 AG	83966-84000	GG	GAG
-recovered pasa_asmbl_6375.p1, terminal, 83966, 84000
Valid prediction for snap_scaffold_11-snap.32-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 131574, rend_intergenic: 125319  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162505, rend_intergenic: 158572  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 215935, rend_intergenic: 206892  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 225088, rend_intergenic: 223608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 229658, rend_intergenic: 227256  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 231329
-exon list size: 411


building trellis

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28.6    
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29.3    
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30.8    
31.0    
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32.9    
33.2    
33.4    
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33.9    
34.1    
34.4    
34.6    
34.9    
35.1    
35.4    
35.6    
35.8    
36.1    
36.3    
36.6    
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37.0    
37.3    
37.5    
37.8    
38.0    
38.3    
38.5    
38.7    
39.0    
39.2    
39.5    
39.7    
40.0    
40.2    
40.4    
40.7    
40.9    
41.2    
41.4    
41.6    
41.9    
42.1    
42.4    
42.6    
42.9    
43.1    
43.3    
43.6    
43.8    
44.1    
44.3    
44.6    
44.8    
45.0    
45.3    
45.5    
45.8    
46.0    
46.2    
46.5    
46.7    
47.0    
47.2    
47.5    
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47.9    
48.2    
48.4    
48.7    
48.9    
49.2    
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49.6    
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50.1    
50.4    
50.6    
50.8    
51.1    
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52.1    
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55.0    
55.2    
55.4    
55.7    
55.9    
56.2    
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56.7    
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57.1    
57.4    
57.6    
57.9    
58.1    
58.4    
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58.8    
59.1    
59.3    
59.6    
59.8    
60.0    
60.3    
60.5    
60.8    
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61.3    
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62.0    
62.2    
62.5    
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79.2    
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84.0    
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88.1    
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88.6    
88.9    
89.1    
89.3    
89.6    
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90.3    
90.6    
90.8    
91.0    
91.3    
91.5    
91.8    
92.0    
92.3    
92.5    
92.7    
93.0    
93.2    
93.5    
93.7    
93.9    
94.2    
94.4    
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94.9    
95.2    
95.4    
95.6    
95.9    
96.1    
96.4    
96.6    
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97.6    
97.8    
98.1    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 43 predictions from path traversal
Error with prediction: snap lend_intergenic: 131574, rend_intergenic: 125319  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162505, rend_intergenic: 158572  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 215935, rend_intergenic: 206892  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 225088, rend_intergenic: 223608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 229658, rend_intergenic: 227256  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 37 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 12516
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support