-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_3232454-3389039

-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_28-snap.824-T1
Valid prediction for GlimmerHMM_glimmerT_58519-T1
Valid prediction for Augustus_model.g38746.t1
Valid prediction for snap_scaffold_28-snap.845-T1
Valid prediction for snap_scaffold_28-snap.848-T1
Couldn't classify 85522, 85682
Couldn't classify 85976, 86153
Sorry, prediction pasa_asmbl_37471.p2 fails validation.
(CTT)	 CT	85522-85682	GT	AGG
(TTC)	 AG	85976-86153	AA	GGA
Valid prediction for snap_scaffold_28-snap.807-T1
Couldn't classify 86299, 86410
Couldn't classify 90403, 90529
Sorry, prediction pasa_asmbl_37474.p1 fails validation.
(GAT)	 AG	86299-86410	GT	AGG
(AGC)	 AG	88009-88051	GT	AGG
(GGT)	 AG	88951-89040	GT	GAG
(GAT)	 AG	90403-90529	AG	TGA
-recovered pasa_asmbl_37474.p1, internal, 86299, 86410
-recovered pasa_asmbl_37474.p1, internal, 88009, 88051
-recovered pasa_asmbl_37474.p1, internal, 88951, 89040
Valid prediction for Augustus_model.g38759.t1
Couldn't classify 91587, 91702
Couldn't classify 92578, 92807
Sorry, prediction pasa_asmbl_37825.p1 fails validation.
(AGA)	 TG	91587-91702	GT	AGG
(GCG)	 AG	91819-91934	GT	GGG
(AAC)	 AG	92128-92268	GT	TGG
(AGC)	 AG	92578-92807	GA	GAG
-recovered pasa_asmbl_37825.p1, internal, 91819, 91934
-recovered pasa_asmbl_37825.p1, internal, 92128, 92268
Valid prediction for snap_scaffold_28-snap.826-T1
Valid prediction for snap_scaffold_28-snap.834-T1
Valid prediction for Augustus_model.g38758.t1
Valid prediction for Augustus_model.g38760.t1
Valid prediction for HiQ_model.g38767.t1
Valid prediction for Augustus_model.g38762.t1
Valid prediction for GlimmerHMM_glimmerT_58509-T1
Valid prediction for CodingQuarry_transcript_43604-T1
Valid prediction for snap_scaffold_28-snap.809-T1
Valid prediction for snap_scaffold_28-snap.830-T1
Valid prediction for GlimmerHMM_glimmerT_58517-T1
Valid prediction for GlimmerHMM_glimmerT_58510-T1
Valid prediction for snap_scaffold_28-snap.840-T1
Valid prediction for snap_scaffold_28-snap.846-T1
Valid prediction for GlimmerHMM_glimmerT_58495-T1
Valid prediction for GlimmerHMM_glimmerT_58516-T1
Couldn't classify 148252, 148779
Sorry, prediction pasa_asmbl_37479.p2 fails validation.
(ATG)	 AA	145887-145931	GT	TGG
(CAG)	 AG	148252-148779	GT	AGG
-recovered pasa_asmbl_37479.p2, initial, 145887, 145931
-recovered pasa_asmbl_37479.p2, internal, 148252, 148779
Valid prediction for snap_scaffold_28-snap.813-T1
Valid prediction for pasa_asmbl_37475.p1
Valid prediction for GlimmerHMM_glimmerT_58514-T1
Valid prediction for snap_scaffold_28-snap.818-T1
Valid prediction for snap_scaffold_28-snap.843-T1
Valid prediction for pasa_asmbl_37470.p1
Couldn't classify 8140, 8157
Sorry, prediction pasa_asmbl_37461.p1 fails validation.
(ACC)	 AC	8140-8157	GT	TGG
(GAG)	 AG	10508-10552	GT	AGG
(GAG)	 AG	11414-11462	GT	AGG
(GGA)	 AG	12954-13043	GT	CTG
(CCA)	 AG	13813-13953	GT	GAG
(TGT)	 AG	14229-14411	GT	GAG
(CAC)	 AG	15637-15712	GT	GCG
(GAA)	 AG	16807-16901	GT	CTG
(TCC)	 AG	17036-17268	GG	GAG
-recovered pasa_asmbl_37461.p1, terminal, 17036, 17268
-recovered pasa_asmbl_37461.p1, internal, 10508, 10552
-recovered pasa_asmbl_37461.p1, internal, 11414, 11462
-recovered pasa_asmbl_37461.p1, internal, 12954, 13043
-recovered pasa_asmbl_37461.p1, internal, 13813, 13953
-recovered pasa_asmbl_37461.p1, internal, 14229, 14411
-recovered pasa_asmbl_37461.p1, internal, 15637, 15712
-recovered pasa_asmbl_37461.p1, internal, 16807, 16901
Valid prediction for CodingQuarry_transcript_43606-T1
Valid prediction for HiQ_model.g38757.t1
Valid prediction for GlimmerHMM_glimmerT_58515-T1
Valid prediction for GlimmerHMM_glimmerT_58518-T1
Valid prediction for snap_scaffold_28-snap.841-T1
Valid prediction for GlimmerHMM_glimmerT_58513-T1
Valid prediction for Augustus_model.g38764.t1
Valid prediction for snap_scaffold_28-snap.838-T1
Valid prediction for snap_scaffold_28-snap.837-T1
Valid prediction for snap_scaffold_28-snap.831-T1
Valid prediction for Augustus_model.g38763.t1
Valid prediction for snap_scaffold_28-snap.827-T1
Valid prediction for GlimmerHMM_glimmerT_58511-T1
Valid prediction for snap_scaffold_28-snap.821-T1
Valid prediction for GlimmerHMM_glimmerT_58499-T1
Valid prediction for GlimmerHMM_glimmerT_58512-T1
Valid prediction for snap_scaffold_28-snap.815-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_28-snap.849-T1
Valid prediction for GlimmerHMM_glimmerT_58500-T1
Valid prediction for GlimmerHMM_glimmerT_58501-T1
Valid prediction for GlimmerHMM_glimmerT_58507-T1
Valid prediction for snap_scaffold_28-snap.817-T1
Valid prediction for snap_scaffold_28-snap.832-T1
Valid prediction for GlimmerHMM_glimmerT_58496-T1
Valid prediction for Augustus_model.g38748.t1
Valid prediction for Augustus_model.g38761.t1
Valid prediction for snap_scaffold_28-snap.825-T1
Valid prediction for snap_scaffold_28-snap.823-T1
Valid prediction for snap_scaffold_28-snap.810-T1
Valid prediction for pasa_asmbl_38141.p1
Valid prediction for GlimmerHMM_glimmerT_58502-T1
Valid prediction for Augustus_model.g38753.t1
Valid prediction for GlimmerHMM_glimmerT_58504-T1
Valid prediction for Augustus_model.g38749.t1
Valid prediction for GlimmerHMM_glimmerT_58520-T1
Valid prediction for snap_scaffold_28-snap.820-T1
Valid prediction for snap_scaffold_28-snap.811-T1
Valid prediction for Augustus_model.g38745.t1
Valid prediction for snap_scaffold_28-snap.844-T1
Valid prediction for GlimmerHMM_glimmerT_58503-T1
Valid prediction for snap_scaffold_28-snap.816-T1
Valid prediction for GlimmerHMM_glimmerT_58497-T1
Valid prediction for GlimmerHMM_glimmerT_58505-T1
Couldn't classify 24149, 24184
Sorry, prediction pasa_asmbl_38147.p1 fails validation.
(GAG)	 CG	24149-24184	GT	AGG
(TGG)	 AG	25618-25684	GT	CAG
(GTC)	 AG	26623-26771	GT	AGG
(GTG)	 AG	26893-27038	GT	AGG
(GAT)	 AG	27384-27458	GT	AGG
(ACT)	 AG	27568-27657	GT	AAG
(AGA)	 AG	27803-27896	GT	TGG
(GTG)	 AG	28025-28140	GT	AGG
(GCT)	 AG	28683-28738	GT	GGG
(GAA)	 AG	28871-28956	GT	AGG
(TAC)	 AG	29218-29346	GT	AGG
(GAG)	 AG	29449-29528	GT	TGG
(GGA)	 AG	29896-30001	CA	GAC
-recovered pasa_asmbl_38147.p1, terminal, 29896, 30001
-recovered pasa_asmbl_38147.p1, internal, 25618, 25684
-recovered pasa_asmbl_38147.p1, internal, 26623, 26771
-recovered pasa_asmbl_38147.p1, internal, 26893, 27038
-recovered pasa_asmbl_38147.p1, internal, 27384, 27458
-recovered pasa_asmbl_38147.p1, internal, 27568, 27657
-recovered pasa_asmbl_38147.p1, internal, 27803, 27896
-recovered pasa_asmbl_38147.p1, internal, 28025, 28140
-recovered pasa_asmbl_38147.p1, internal, 28683, 28738
-recovered pasa_asmbl_38147.p1, internal, 28871, 28956
-recovered pasa_asmbl_38147.p1, internal, 29218, 29346
-recovered pasa_asmbl_38147.p1, internal, 29449, 29528
Valid prediction for GlimmerHMM_glimmerT_58508-T1
Valid prediction for snap_scaffold_28-snap.828-T1
Valid prediction for snap_scaffold_28-snap.835-T1
Valid prediction for snap_scaffold_28-snap.839-T1
Valid prediction for GlimmerHMM_glimmerT_58506-T1
Valid prediction for Augustus_model.g38752.t1
Valid prediction for snap_scaffold_28-snap.829-T1
Valid prediction for snap_scaffold_28-snap.836-T1
Valid prediction for snap_scaffold_28-snap.833-T1
Valid prediction for GlimmerHMM_glimmerT_58521-T1
Valid prediction for pasa_asmbl_38144.p2
Valid prediction for GlimmerHMM_glimmerT_58498-T1
Valid prediction for pasa_asmbl_38148.p1
Valid prediction for snap_scaffold_28-snap.814-T1
Valid prediction for Augustus_model.g38751.t1
Valid prediction for HiQ_model.g38766.t1
Valid prediction for CodingQuarry_transcript_43605-T1
Valid prediction for GlimmerHMM_glimmerT_58522-T1
Valid prediction for snap_scaffold_28-snap.812-T1
Valid prediction for Augustus_model.g38750.t1
Valid prediction for HiQ_model.g38754.t1
Valid prediction for snap_scaffold_28-snap.822-T1
Valid prediction for snap_scaffold_28-snap.847-T1
Valid prediction for Augustus_model.g38755.t1
Valid prediction for snap_scaffold_28-snap.808-T1
Valid prediction for snap_scaffold_28-snap.842-T1
Valid prediction for snap_scaffold_28-snap.819-T1
Valid prediction for HiQ_model.g38765.t1
Valid prediction for CodingQuarry_transcript_43607-T1
Valid prediction for HiQ_model.g38756.t1
Valid prediction for Augustus_model.g38747.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 5379, rend_intergenic: 2350  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17268, rend_intergenic: 8272  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20487, rend_intergenic: 17281  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24337, rend_intergenic: 21610  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29924, rend_intergenic: 27396  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34922, rend_intergenic: 33882  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54865, rend_intergenic: 52219  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73405, rend_intergenic: 67880  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81579, rend_intergenic: 73965  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88058, rend_intergenic: 82630  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97506, rend_intergenic: 88858  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125941, rend_intergenic: 125825  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132531, rend_intergenic: 126217  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138487, rend_intergenic: 135216  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144278, rend_intergenic: 140960  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155684, rend_intergenic: 148204  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 156586
-exon list size: 463


building trellis

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19.6    
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20.9    
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21.3    
21.5    
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21.9    
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22.4    
22.6    
22.8    
23.0    
23.2    
23.4    
23.7    
23.9    
24.1    
24.3    
24.5    
24.7    
24.9    
25.2    
25.4    
25.6    
25.8    
26.0    
26.2    
26.5    
26.7    
26.9    
27.1    
27.3    
27.5    
27.7    
28.0    
28.2    
28.4    
28.6    
28.8    
29.0    
29.2    
29.5    
29.7    
29.9    
30.1    
30.3    
30.5    
30.8    
31.0    
31.2    
31.4    
31.6    
31.8    
32.0    
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    
35.1    
35.3    
35.5    
35.7    
35.9    
36.1    
36.3    
36.6    
36.8    
37.0    
37.2    
37.4    
37.6    
37.8    
38.1    
38.3    
38.5    
38.7    
38.9    
39.1    
39.4    
39.6    
39.8    
40.0    
40.2    
40.4    
40.6    
40.9    
41.1    
41.3    
41.5    
41.7    
41.9    
42.2    
42.4    
42.6    
42.8    
43.0    
43.2    
43.4    
43.7    
43.9    
44.1    
44.3    
44.5    
44.7    
44.9    
45.2    
45.4    
45.6    
45.8    
46.0    
46.2    
46.5    
46.7    
46.9    
47.1    
47.3    
47.5    
47.7    
48.0    
48.2    
48.4    
48.6    
48.8    
49.0    
49.2    
49.5    
49.7    
49.9    
50.1    
50.3    
50.5    
50.8    
51.0    
51.2    
51.4    
51.6    
51.8    
52.0    
52.3    
52.5    
52.7    
52.9    
53.1    
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53.5    
53.8    
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54.6    
54.8    
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55.3    
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59.6    
59.8    
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60.2    
60.4    
60.6    
60.9    
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62.2    
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62.6    
62.8    
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63.4    
63.7    
63.9    
64.1    
64.3    
64.5    
64.7    
64.9    
65.2    
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65.6    
65.8    
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66.2    
66.5    
66.7    
66.9    
67.1    
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68.0    
68.2    
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68.8    
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69.9    
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70.8    
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71.8    
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78.7    
78.9    
79.1    
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79.6    
79.8    
80.0    
80.2    
80.4    
80.6    
80.9    
81.1    
81.3    
81.5    
81.7    
81.9    
82.2    
82.4    
82.6    
82.8    
83.0    
83.2    
83.4    
83.7    
83.9    
84.1    
84.3    
84.5    
84.7    
84.9    
85.2    
85.4    
85.6    
85.8    
86.0    
86.2    
86.5    
86.7    
86.9    
87.1    
87.3    
87.5    
87.7    
88.0    
88.2    
88.4    
88.6    
88.8    
89.0    
89.2    
89.5    
89.7    
89.9    
90.1    
90.3    
90.5    
90.8    
91.0    
91.2    
91.4    
91.6    
91.8    
92.0    
92.3    
92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.8    
94.0    
94.2    
94.4    
94.6    
94.8    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.8    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.4    
99.6    
99.8    
-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 5379, rend_intergenic: 2350  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17268, rend_intergenic: 8272  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20487, rend_intergenic: 17281  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24337, rend_intergenic: 21610  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29924, rend_intergenic: 27396  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34922, rend_intergenic: 33882  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54865, rend_intergenic: 52219  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73405, rend_intergenic: 67880  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81579, rend_intergenic: 73965  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88058, rend_intergenic: 82630  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97506, rend_intergenic: 88858  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125941, rend_intergenic: 125825  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132531, rend_intergenic: 126217  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138487, rend_intergenic: 135216  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144278, rend_intergenic: 140960  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155684, rend_intergenic: 148204  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

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