-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_12/scaffold_12_4914780-5065637

-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_12-snap.1006-T1
Valid prediction for GlimmerHMM_glimmerT_29304-T1
Valid prediction for GlimmerHMM_glimmerT_29305-T1
Valid prediction for Augustus_model.g19342.t1
Valid prediction for snap_scaffold_12-snap.1023-T1
Valid prediction for snap_scaffold_12-snap.1019-T1
Valid prediction for snap_scaffold_12-snap.1002-T1
Valid prediction for GlimmerHMM_glimmerT_29319-T1
Valid prediction for GlimmerHMM_glimmerT_29313-T1
Valid prediction for CodingQuarry_transcript_10211-T1
Valid prediction for CodingQuarry_transcript_10212-T1
Valid prediction for snap_scaffold_12-snap.1016-T1
Valid prediction for HiQ_model.g19338.t1
Valid prediction for GlimmerHMM_glimmerT_29315-T1
Valid prediction for pasa_asmbl_7638.p1
Valid prediction for snap_scaffold_12-snap.1012-T1
Valid prediction for snap_scaffold_12-snap.993-T1
Valid prediction for Augustus_model.g19348.t1
Valid prediction for GlimmerHMM_glimmerT_29323-T1
Valid prediction for GlimmerHMM_glimmerT_29318-T1
Valid prediction for Augustus_model.g19333.t1
Valid prediction for GlimmerHMM_glimmerT_29310-T1
Valid prediction for snap_scaffold_12-snap.1005-T1
Valid prediction for snap_scaffold_12-snap.1029-T1
Valid prediction for snap_scaffold_12-snap.1022-T1
Couldn't classify 84149, 84433
Couldn't classify 85260, 85385
Sorry, prediction pasa_asmbl_8248.p1 fails validation.
(ACC)	 GA	84149-84433	GT	AGG
(GCC)	 AG	85260-85385	CA	GCC
Valid prediction for Augustus_model.g19332.t1
Valid prediction for snap_scaffold_12-snap.1032-T1
Valid prediction for Augustus_model.g19335.t1
Valid prediction for snap_scaffold_12-snap.995-T1
Valid prediction for GlimmerHMM_glimmerT_29307-T1
Valid prediction for HiQ_model.g19340.t1
Valid prediction for GlimmerHMM_glimmerT_29298-T1
Valid prediction for Augustus_model.g19327.t1
Valid prediction for Augustus_model.g19345.t1
Valid prediction for GlimmerHMM_glimmerT_29314-T1
Couldn't classify 89195, 89379
Sorry, prediction pasa_asmbl_8226.p1 fails validation.
(TCT)	 CC	89195-89379	GT	GCG
(GTT)	 AG	89495-89597	GT	AGG
(TCC)	 AG	89689-89808	CG	AGC
-recovered pasa_asmbl_8226.p1, terminal, 89689, 89808
-recovered pasa_asmbl_8226.p1, internal, 89495, 89597
Valid prediction for GlimmerHMM_glimmerT_29296-T1
Valid prediction for snap_scaffold_12-snap.1008-T1
Valid prediction for Augustus_model.g19341.t1
Valid prediction for snap_scaffold_12-snap.1004-T1
Valid prediction for GlimmerHMM_glimmerT_29325-T1
Valid prediction for GlimmerHMM_glimmerT_29322-T1
Valid prediction for Augustus_model.g19349.t1
Valid prediction for snap_scaffold_12-snap.1018-T1
Valid prediction for snap_scaffold_12-snap.1010-T1
Valid prediction for GlimmerHMM_glimmerT_29312-T1
Valid prediction for snap_scaffold_12-snap.997-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_29299-T1
Valid prediction for snap_scaffold_12-snap.999-T1
Valid prediction for pasa_asmbl_7624.p1
Valid prediction for snap_scaffold_12-snap.1014-T1
Valid prediction for snap_scaffold_12-snap.1011-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_12-snap.1017-T1
Valid prediction for Augustus_model.g19334.t1
Valid prediction for Augustus_model.g19346.t1
Valid prediction for GlimmerHMM_glimmerT_29301-T1
Valid prediction for snap_scaffold_12-snap.996-T1
Valid prediction for GlimmerHMM_glimmerT_29297-T1
Valid prediction for snap_scaffold_12-snap.1024-T1
Valid prediction for snap_scaffold_12-snap.1031-T1
Valid prediction for snap_scaffold_12-snap.998-T1
Valid prediction for snap_scaffold_12-snap.1028-T1
Valid prediction for snap_scaffold_12-snap.1001-T1
Valid prediction for snap_scaffold_12-snap.1025-T1
Valid prediction for GlimmerHMM_glimmerT_29321-T1
Valid prediction for Augustus_model.g19331.t1
Valid prediction for Augustus_model.g19326.t1
Valid prediction for snap_scaffold_12-snap.1015-T1
Valid prediction for GlimmerHMM_glimmerT_29316-T1
Valid prediction for Augustus_model.g19336.t1
Valid prediction for CodingQuarry_transcript_10214-T1
Valid prediction for snap_scaffold_12-snap.1007-T1
Couldn't classify 33698, 33903
Couldn't classify 34558, 34586
Sorry, prediction pasa_asmbl_9228.p2 fails validation.
(CCA)	 CT	33698-33903	GT	AGG
(GTA)	 AG	34164-34279	GT	TCG
(AGC)	 AG	34558-34586	AA	AGA
-recovered pasa_asmbl_9228.p2, internal, 34164, 34279
Valid prediction for GlimmerHMM_glimmerT_29311-T1
Valid prediction for GlimmerHMM_glimmerT_29320-T1
Valid prediction for GlimmerHMM_glimmerT_29306-T1
Valid prediction for Augustus_model.g19343.t1
Valid prediction for snap_scaffold_12-snap.1027-T1
Valid prediction for snap_scaffold_12-snap.992-T1
Couldn't classify 49090, 49113
Sorry, prediction pasa_asmbl_8471.p3 fails validation.
(CCA)	 CT	49090-49113	GT	AGG
(GAC)	 AG	49426-49524	GT	AGG
(GGA)	 AG	49759-49956	TG	AGT
-recovered pasa_asmbl_8471.p3, terminal, 49759, 49956
-recovered pasa_asmbl_8471.p3, internal, 49426, 49524
Valid prediction for snap_scaffold_12-snap.1026-T1
Valid prediction for GlimmerHMM_glimmerT_29317-T1
Valid prediction for GlimmerHMM_glimmerT_29302-T1
Valid prediction for snap_scaffold_12-snap.1030-T1
Valid prediction for GlimmerHMM_glimmerT_29303-T1
Valid prediction for snap_scaffold_12-snap.1020-T1
Valid prediction for pasa_asmbl_8473.p1
Valid prediction for Augustus_model.g19328.t1
Valid prediction for snap_scaffold_12-snap.1013-T1
Valid prediction for GlimmerHMM_glimmerT_29324-T1
Valid prediction for GlimmerHMM_glimmerT_29308-T1
Valid prediction for HiQ_model.g19347.t1
Valid prediction for HiQ_model.g19339.t1
Valid prediction for snap_scaffold_12-snap.1009-T1
Valid prediction for CodingQuarry_transcript_10209-T1
Valid prediction for GlimmerHMM_glimmerT_29309-T1
Valid prediction for Augustus_model.g19329.t1
Valid prediction for snap_scaffold_12-snap.994-T1
Valid prediction for snap_scaffold_12-snap.1021-T1
Valid prediction for HiQ_model.g19330.t1
Valid prediction for CodingQuarry_transcript_10210-T1
Couldn't classify 108700, 108781
Sorry, prediction pasa_asmbl_8470.p1 fails validation.
(AGT)	 AG	108700-108781	GT	AGG
(GTA)	 AG	109167-109225	GT	GGG
(GAG)	 AG	109354-109447	GT	GGG
(GGC)	 AG	110122-110402	GC	AAG
-recovered pasa_asmbl_8470.p1, terminal, 110122, 110402
-recovered pasa_asmbl_8470.p1, internal, 108700, 108781
-recovered pasa_asmbl_8470.p1, internal, 109167, 109225
-recovered pasa_asmbl_8470.p1, internal, 109354, 109447
-recovered pasa_asmbl_8470.p1, internal, 110122, 110402
Valid prediction for snap_scaffold_12-snap.1003-T1
Valid prediction for Augustus_model.g19337.t1
Valid prediction for pasa_asmbl_9239.p1
Valid prediction for snap_scaffold_12-snap.1000-T1
Valid prediction for GlimmerHMM_glimmerT_29300-T1
Valid prediction for HiQ_model.g19344.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7426, rend_intergenic: 3109  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14298, rend_intergenic: 10379  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19436, rend_intergenic: 18378  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21216, rend_intergenic: 20157  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28908, rend_intergenic: 21299  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37116, rend_intergenic: 31585  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46239, rend_intergenic: 37331  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56539, rend_intergenic: 52692  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68699, rend_intergenic: 60022  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83384, rend_intergenic: 79568  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84330, rend_intergenic: 83879  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89808, rend_intergenic: 84331  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108280, rend_intergenic: 105572  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142054, rend_intergenic: 134536  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148630, rend_intergenic: 144863  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 98759, rend_intergenic: 98756  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 150858
-exon list size: 447


building trellis

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18.9    
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22.9    
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23.6    
23.8    
24.1    
24.3    
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24.7    
24.9    
25.2    
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25.8    
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26.3    
26.5    
26.7    
26.9    
27.2    
27.4    
27.6    
27.8    
28.1    
28.3    
28.5    
28.7    
29.0    
29.2    
29.4    
29.6    
29.8    
30.1    
30.3    
30.5    
30.7    
31.0    
31.2    
31.4    
31.6    
31.8    
32.1    
32.3    
32.5    
32.7    
33.0    
33.2    
33.4    
33.6    
33.9    
34.1    
34.3    
34.5    
34.7    
35.0    
35.2    
35.4    
35.6    
35.9    
36.1    
36.3    
36.5    
36.7    
37.0    
37.2    
37.4    
37.6    
37.9    
38.1    
38.3    
38.5    
38.8    
39.0    
39.2    
39.4    
39.6    
39.9    
40.1    
40.3    
40.5    
40.8    
41.0    
41.2    
41.4    
41.6    
41.9    
42.1    
42.3    
42.5    
42.8    
43.0    
43.2    
43.4    
43.7    
43.9    
44.1    
44.3    
44.5    
44.8    
45.0    
45.2    
45.4    
45.7    
45.9    
46.1    
46.3    
46.5    
46.8    
47.0    
47.2    
47.4    
47.7    
47.9    
48.1    
48.3    
48.6    
48.8    
49.0    
49.2    
49.4    
49.7    
49.9    
50.1    
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50.6    
50.8    
51.0    
51.2    
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51.9    
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52.3    
52.6    
52.8    
53.0    
53.2    
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53.7    
53.9    
54.1    
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55.0    
55.2    
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57.9    
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58.4    
58.6    
58.8    
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59.2    
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60.1    
60.4    
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60.8    
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61.9    
62.1    
62.4    
62.6    
62.8    
63.0    
63.3    
63.5    
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63.9    
64.1    
64.4    
64.6    
64.8    
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66.1    
66.4    
66.6    
66.8    
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68.8    
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78.0    
78.2    
78.4    
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78.8    
79.1    
79.3    
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80.0    
80.2    
80.4    
80.6    
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81.1    
81.3    
81.5    
81.7    
82.0    
82.2    
82.4    
82.6    
82.9    
83.1    
83.3    
83.5    
83.7    
84.0    
84.2    
84.4    
84.6    
84.9    
85.1    
85.3    
85.5    
85.7    
86.0    
86.2    
86.4    
86.6    
86.9    
87.1    
87.3    
87.5    
87.8    
88.0    
88.2    
88.4    
88.6    
88.9    
89.1    
89.3    
89.5    
89.8    
90.0    
90.2    
90.4    
90.6    
90.9    
91.1    
91.3    
91.5    
91.8    
92.0    
92.2    
92.4    
92.7    
92.9    
93.1    
93.3    
93.5    
93.8    
94.0    
94.2    
94.4    
94.7    
94.9    
95.1    
95.3    
95.5    
95.8    
96.0    
96.2    
96.4    
96.7    
96.9    
97.1    
97.3    
97.6    
97.8    
98.0    
98.2    
98.4    
98.7    
98.9    
99.1    
99.3    
99.6    
99.8    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 7426, rend_intergenic: 3109  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14298, rend_intergenic: 10379  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19436, rend_intergenic: 18378  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21216, rend_intergenic: 20157  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28908, rend_intergenic: 21299  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37116, rend_intergenic: 31585  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46239, rend_intergenic: 37331  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56539, rend_intergenic: 52692  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68699, rend_intergenic: 60022  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83384, rend_intergenic: 79568  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84330, rend_intergenic: 83879  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89808, rend_intergenic: 84331  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108280, rend_intergenic: 105572  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142054, rend_intergenic: 134536  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148630, rend_intergenic: 144863  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 98759, rend_intergenic: 98756  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support