-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_5/scaffold_5_1-141604

-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 GeneMark_model.19181_t
Valid prediction for GlimmerHMM_glimmerT_11562-T1
Valid prediction for GeneMark_model.19203_t
Valid prediction for GeneMark_model.19186_t
Valid prediction for GeneMark_model.19177_t
Couldn't classify 63119, 63189
Sorry, prediction pasa_asmbl_43730.p1 fails validation.
(ATG)	 GG	58414-58527	GT	AGG
(GTG)	 AG	60221-60313	GT	AGG
(GGC)	 AG	60973-61100	GT	ACG
(GCA)	 AG	61622-61712	GC	AGG
(GTG)	 AG	61932-62049	GT	AGG
(ATG)	 AG	63119-63189	AG	AAA
-recovered pasa_asmbl_43730.p1, initial, 58414, 58527
-recovered pasa_asmbl_43730.p1, internal, 60221, 60313
-recovered pasa_asmbl_43730.p1, internal, 60973, 61100
-recovered pasa_asmbl_43730.p1, internal, 61622, 61712
-recovered pasa_asmbl_43730.p1, internal, 61932, 62049
Valid prediction for snap_scaffold_5-snap.20-T1
Valid prediction for HiQ_model.g7609.t1
Valid prediction for snap_scaffold_5-snap.24-T1
Valid prediction for GlimmerHMM_glimmerT_11557-T1
Valid prediction for HiQ_model.g7608.t1
Valid prediction for GeneMark_model.19183_t
Valid prediction for GlimmerHMM_glimmerT_11556-T1
Valid prediction for GlimmerHMM_glimmerT_11559-T1
Valid prediction for Augustus_model.g7614.t1
Valid prediction for snap_scaffold_5-snap.9-T1
Valid prediction for snap_scaffold_5-snap.14-T1
Valid prediction for snap_scaffold_5-snap.26-T1
Valid prediction for snap_scaffold_5-snap.13-T1
Couldn't classify 136997, 137118
Couldn't classify 138547, 138550
Sorry, prediction CodingQuarry_transcript_51836-T1 fails validation.
(ATG)	 CC	131738-132163	GT	AGG
(GTG)	 AG	134540-134622	GT	AAG
(GTA)	 AG	134802-134958	GT	ACG
(GAA)	 AG	136526-136690	GT	AGG
(ATC)	 AG	136997-137118	AA	AGA
(GTA)	 CT	138547-138550	AA	AGA
-recovered CodingQuarry_transcript_51836-T1, initial, 131738, 132163
-recovered CodingQuarry_transcript_51836-T1, internal, 134540, 134622
-recovered CodingQuarry_transcript_51836-T1, internal, 134802, 134958
-recovered CodingQuarry_transcript_51836-T1, internal, 136526, 136690
Valid prediction for snap_scaffold_5-snap.7-T1
Valid prediction for snap_scaffold_5-snap.11-T1
Valid prediction for snap_scaffold_5-snap.17-T1
Valid prediction for GlimmerHMM_glimmerT_11564-T1
Valid prediction for snap_scaffold_5-snap.8-T1
Valid prediction for GeneMark_model.19199_t
Valid prediction for GeneMark_model.19190_t
Valid prediction for snap_scaffold_5-snap.2-T1
Valid prediction for GeneMark_model.19187_t
Valid prediction for snap_scaffold_5-snap.28-T1
Valid prediction for Augustus_model.g7604.t1
Valid prediction for GlimmerHMM_glimmerT_11567-T1
Valid prediction for CodingQuarry_transcript_51834-T1
Valid prediction for GeneMark_model.19180_t
Valid prediction for snap_scaffold_5-snap.1-T1
Valid prediction for GlimmerHMM_glimmerT_11555-T1
Valid prediction for GeneMark_model.19184_t
Valid prediction for GlimmerHMM_glimmerT_11571-T1
Valid prediction for Augustus_model.g7605.t1
Valid prediction for snap_scaffold_5-snap.5-T1
Valid prediction for GeneMark_model.19201_t
Valid prediction for Augustus_model.g7610.t1
Valid prediction for GlimmerHMM_glimmerT_11563-T1
Valid prediction for GlimmerHMM_glimmerT_11560-T1
Valid prediction for Augustus_model.g7606.t1
Valid prediction for snap_scaffold_5-snap.16-T1
Valid prediction for GeneMark_model.19193_t
Valid prediction for GeneMark_model.19202_t
Valid prediction for GeneMark_model.19189_t
Valid prediction for GeneMark_model.19191_t
Valid prediction for pasa_asmbl_43736.p1
Valid prediction for snap_scaffold_5-snap.30-T1
Valid prediction for GlimmerHMM_glimmerT_11554-T1
add_exon() Sorry, GlimmerHMM_glimmerT_11554-T1 5031-5548-terminal-1 is invalid.
Valid prediction for GlimmerHMM_glimmerT_11570-T1
Couldn't classify 136997, 137118
Couldn't classify 138547, 138550
Sorry, prediction CodingQuarry_transcript_51835-T1 fails validation.
(ATG)	 CC	131738-132163	GT	AGG
(GTG)	 AG	134540-134622	GT	AAG
(GTA)	 AG	136010-136166	GT	ACG
(GAA)	 AG	136526-136690	GT	AGG
(ATC)	 AG	136997-137118	AA	AGA
(GTA)	 CT	138547-138550	AA	AGA
-recovered CodingQuarry_transcript_51835-T1, initial, 131738, 132163
-recovered CodingQuarry_transcript_51835-T1, internal, 134540, 134622
-recovered CodingQuarry_transcript_51835-T1, internal, 136010, 136166
-recovered CodingQuarry_transcript_51835-T1, internal, 136526, 136690
Valid prediction for pasa_asmbl_45087.p1
Valid prediction for GeneMark_model.19194_t
Valid prediction for CodingQuarry_transcript_51837-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_5-snap.22-T1
Valid prediction for GeneMark_model.19179_t
Valid prediction for snap_scaffold_5-snap.6-T1
Valid prediction for GeneMark_model.19195_t
Valid prediction for GeneMark_model.19182_t
Valid prediction for GeneMark_model.19200_t
Valid prediction for snap_scaffold_5-snap.15-T1
Valid prediction for Augustus_model.g7611.t1
Valid prediction for GlimmerHMM_glimmerT_11558-T1
Valid prediction for pasa_asmbl_45138.p1
Valid prediction for GlimmerHMM_glimmerT_11566-T1
Valid prediction for GlimmerHMM_glimmerT_11568-T1
Valid prediction for snap_scaffold_5-snap.10-T1
Valid prediction for GlimmerHMM_glimmerT_11565-T1
Valid prediction for GlimmerHMM_glimmerT_11569-T1
Valid prediction for GeneMark_model.19198_t
Valid prediction for GeneMark_model.19188_t
Valid prediction for snap_scaffold_5-snap.23-T1
Valid prediction for pasa_asmbl_45141.p1
Valid prediction for snap_scaffold_5-snap.19-T1
Valid prediction for snap_scaffold_5-snap.29-T1
Valid prediction for snap_scaffold_5-snap.3-T1
Valid prediction for GeneMark_model.19185_t
Valid prediction for snap_scaffold_5-snap.18-T1
Valid prediction for snap_scaffold_5-snap.21-T1
Valid prediction for snap_scaffold_5-snap.4-T1
Valid prediction for snap_scaffold_5-snap.25-T1
Valid prediction for CodingQuarry_transcript_51833-T1
Valid prediction for HiQ_model.g7607.t1
Valid prediction for GeneMark_model.19197_t
Valid prediction for snap_scaffold_5-snap.12-T1
Valid prediction for Augustus_model.g7613.t1
Valid prediction for GlimmerHMM_glimmerT_11561-T1
Valid prediction for GeneMark_model.19192_t
Valid prediction for GeneMark_model.19196_t
Valid prediction for snap_scaffold_5-snap.31-T1
Valid prediction for Augustus_model.g7612.t1
Valid prediction for snap_scaffold_5-snap.27-T1
Valid prediction for GeneMark_model.19178_t
Couldn't classify 28316, 28783
Sorry, prediction pasa_asmbl_45143.p1 fails validation.
(ATC)	 TC	28316-28783	GT	AGG
(GTG)	 AG	30409-30617	GT	AAG
(GTA)	 AG	31301-31361	GT	AGG
(GAT)	 AG	31514-31609	GT	AGG
(GAG)	 AG	32017-32181	GT	AGG
(TAT)	 AG	32454-32579	GT	AGG
(CGG)	 AG	32961-33181	GT	AGG
(GCT)	 AG	33396-33439	GT	CAG
(CGG)	 AG	33795-34069	GG	GAG
-recovered pasa_asmbl_45143.p1, terminal, 33795, 34069
-recovered pasa_asmbl_45143.p1, internal, 30409, 30617
-recovered pasa_asmbl_45143.p1, internal, 31301, 31361
-recovered pasa_asmbl_45143.p1, internal, 31514, 31609
-recovered pasa_asmbl_45143.p1, internal, 32017, 32181
-recovered pasa_asmbl_45143.p1, internal, 32454, 32579
-recovered pasa_asmbl_45143.p1, internal, 32961, 33181
-recovered pasa_asmbl_45143.p1, internal, 33396, 33439

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 31007, rend_intergenic: 14548  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33089, rend_intergenic: 31084  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42840, rend_intergenic: 34928  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51077, rend_intergenic: 47333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56169, rend_intergenic: 52710  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64884, rend_intergenic: 58414  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72834, rend_intergenic: 69710  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78047, rend_intergenic: 74522  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89916, rend_intergenic: 78180  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100214, rend_intergenic: 96324  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104190, rend_intergenic: 103482  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109155, rend_intergenic: 107536  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120774, rend_intergenic: 109503  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125252, rend_intergenic: 122268  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139326, rend_intergenic: 127466  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 141604
-exon list size: 455


building trellis

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23.9    
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27.6    
27.8    
28.0    
28.2    
28.4    
28.7    
28.9    
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29.8    
30.0    
30.2    
30.4    
30.6    
30.9    
31.1    
31.3    
31.5    
31.7    
31.9    
32.2    
32.4    
32.6    
32.8    
33.0    
33.3    
33.5    
33.7    
33.9    
34.1    
34.4    
34.6    
34.8    
35.0    
35.2    
35.4    
35.7    
35.9    
36.1    
36.3    
36.5    
36.8    
37.0    
37.2    
37.4    
37.6    
37.9    
38.1    
38.3    
38.5    
38.7    
38.9    
39.2    
39.4    
39.6    
39.8    
40.0    
40.3    
40.5    
40.7    
40.9    
41.1    
41.4    
41.6    
41.8    
42.0    
42.2    
42.5    
42.7    
42.9    
43.1    
43.3    
43.5    
43.8    
44.0    
44.2    
44.4    
44.6    
44.9    
45.1    
45.3    
45.5    
45.7    
46.0    
46.2    
46.4    
46.6    
46.8    
47.0    
47.3    
47.5    
47.7    
47.9    
48.1    
48.4    
48.6    
48.8    
49.0    
49.2    
49.5    
49.7    
49.9    
50.1    
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50.8    
51.0    
51.2    
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51.6    
51.9    
52.1    
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52.5    
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53.0    
53.2    
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53.6    
53.8    
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54.3    
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54.9    
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55.8    
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60.0    
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60.6    
60.8    
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61.3    
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62.4    
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62.8    
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63.2    
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65.0    
65.2    
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65.6    
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66.3    
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67.0    
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72.2    
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78.3    
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79.6    
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80.3    
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81.0    
81.2    
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81.6    
81.8    
82.1    
82.3    
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85.3    
85.6    
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86.0    
86.2    
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88.0    
88.2    
88.4    
88.6    
88.8    
89.1    
89.3    
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89.7    
89.9    
90.2    
90.4    
90.6    
90.8    
91.0    
91.2    
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91.9    
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92.3    
92.6    
92.8    
93.0    
93.2    
93.4    
93.7    
93.9    
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95.2    
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95.6    
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97.2    
97.4    
97.6    
97.8    
98.0    
98.2    
98.5    
98.7    
98.9    
99.1    
99.3    
99.6    
99.8    
-found 19 predictions from path traversal
Error with prediction: snap lend_intergenic: 31007, rend_intergenic: 14548  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33089, rend_intergenic: 31084  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42840, rend_intergenic: 34928  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51077, rend_intergenic: 47333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56169, rend_intergenic: 52710  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64884, rend_intergenic: 58414  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72834, rend_intergenic: 69710  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78047, rend_intergenic: 74522  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89916, rend_intergenic: 78180  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100214, rend_intergenic: 96324  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104190, rend_intergenic: 103482  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109155, rend_intergenic: 107536  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120774, rend_intergenic: 109503  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125252, rend_intergenic: 122268  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139326, rend_intergenic: 127466  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 10 predictions persist after filtering for low support