-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_5/scaffold_5_13612391-13779236

-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_5-snap.2524-T1
Valid prediction for Augustus_model.g8608.t1
Valid prediction for snap_scaffold_5-snap.2530-T1
Valid prediction for GlimmerHMM_glimmerT_12984-T1
Valid prediction for Augustus_model.g8624.t1
Valid prediction for GlimmerHMM_glimmerT_12990-T1
Valid prediction for GlimmerHMM_glimmerT_12981-T1
Valid prediction for snap_scaffold_5-snap.2525-T1
Valid prediction for snap_scaffold_5-snap.2520-T1
Valid prediction for Augustus_model.g8605.t1
Valid prediction for snap_scaffold_5-snap.2537-T1
Valid prediction for GlimmerHMM_glimmerT_12959-T1
Valid prediction for snap_scaffold_5-snap.2512-T1
Valid prediction for snap_scaffold_5-snap.2533-T1
Valid prediction for Augustus_model.g8627.t1
Valid prediction for snap_scaffold_5-snap.2517-T1
Valid prediction for GlimmerHMM_glimmerT_12965-T1
Valid prediction for CodingQuarry_transcript_52330-T1
Valid prediction for GlimmerHMM_glimmerT_12961-T1
Couldn't classify 62841, 62985
Sorry, prediction pasa_asmbl_45885.p1 fails validation.
(CCT)	 GG	62841-62985	GT	TGG
(GTG)	 AG	63127-63207	GT	AGG
(AGA)	 AG	63432-63509	GT	AGG
(GCA)	 AG	63590-63661	GT	AGG
(CTC)	 AG	63737-63858	GT	AGG
(AGC)	 AG	64026-64053	GT	AGG
(CAG)	 AG	64233-64334	GT	AGG
(TTG)	 AG	64463-64531	GT	AGG
(GTC)	 AG	64739-64866	GT	AGG
(AGT)	 AG	65023-65050	GT	AGG
(AAC)	 AG	65391-65453	GT	TCG
(CTG)	 AG	65706-65797	GT	AGG
(AGT)	 AG	65942-65972	GT	GTG
(CAA)	 AG	66065-66145	GT	TGG
(GAT)	 AG	66263-66324	GA	AAG
-recovered pasa_asmbl_45885.p1, terminal, 66263, 66324
-recovered pasa_asmbl_45885.p1, internal, 63127, 63207
-recovered pasa_asmbl_45885.p1, internal, 63432, 63509
-recovered pasa_asmbl_45885.p1, internal, 63590, 63661
-recovered pasa_asmbl_45885.p1, internal, 63737, 63858
-recovered pasa_asmbl_45885.p1, internal, 64026, 64053
-recovered pasa_asmbl_45885.p1, internal, 64233, 64334
-recovered pasa_asmbl_45885.p1, internal, 64463, 64531
-recovered pasa_asmbl_45885.p1, internal, 64739, 64866
-recovered pasa_asmbl_45885.p1, internal, 65023, 65050
-recovered pasa_asmbl_45885.p1, internal, 65391, 65453
-recovered pasa_asmbl_45885.p1, internal, 65706, 65797
-recovered pasa_asmbl_45885.p1, internal, 65942, 65972
-recovered pasa_asmbl_45885.p1, internal, 66065, 66145
Valid prediction for Augustus_model.g8609.t1
Valid prediction for snap_scaffold_5-snap.2526-T1
Valid prediction for snap_scaffold_5-snap.2544-T1
Valid prediction for Augustus_model.g8612.t1
Valid prediction for GlimmerHMM_glimmerT_12970-T1
Valid prediction for GlimmerHMM_glimmerT_12988-T1
Valid prediction for snap_scaffold_5-snap.2545-T1
Valid prediction for GlimmerHMM_glimmerT_12985-T1
Valid prediction for GlimmerHMM_glimmerT_12973-T1
Valid prediction for snap_scaffold_5-snap.2514-T1
Valid prediction for snap_scaffold_5-snap.2528-T1
Valid prediction for GlimmerHMM_glimmerT_12963-T1
Valid prediction for GlimmerHMM_glimmerT_12986-T1
Couldn't classify 60394, 60491
Couldn't classify 62543, 62741
Sorry, prediction pasa_asmbl_45884.p1 fails validation.
(CAC)	 AC	60394-60491	GT	AGG
(CGC)	 AG	61434-61500	GT	AGG
(CGG)	 AG	61588-61665	GT	AGG
(GAA)	 AG	61918-61983	GT	AGG
(GTG)	 AG	62286-62404	GT	AGG
(CTA)	 AG	62543-62741	AG	GGA
-recovered pasa_asmbl_45884.p1, internal, 61434, 61500
-recovered pasa_asmbl_45884.p1, internal, 61588, 61665
-recovered pasa_asmbl_45884.p1, internal, 61918, 61983
-recovered pasa_asmbl_45884.p1, internal, 62286, 62404
Valid prediction for GlimmerHMM_glimmerT_12983-T1
Valid prediction for snap_scaffold_5-snap.2542-T1
Valid prediction for snap_scaffold_5-snap.2536-T1
Valid prediction for GlimmerHMM_glimmerT_12964-T1
Valid prediction for GlimmerHMM_glimmerT_12978-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 Augustus_model.g8620.t1
Valid prediction for snap_scaffold_5-snap.2527-T1
Valid prediction for Augustus_model.g8626.t1
Valid prediction for Augustus_model.g8607.t1
Valid prediction for snap_scaffold_5-snap.2543-T1
Couldn't classify 86975, 86984
Sorry, prediction pasa_asmbl_44552.p1 fails validation.
(CCC)	 TC	86975-86984	GT	TGG
(AGA)	 AG	87206-87302	GT	AGG
(AAA)	 AG	88271-88373	GT	AGG
(GGG)	 AG	88616-88753	GT	AGG
(GTG)	 AG	88948-89086	GT	CAG
(GTA)	 AG	90298-91358	CG	GAC
-recovered pasa_asmbl_44552.p1, terminal, 90298, 91358
-recovered pasa_asmbl_44552.p1, internal, 87206, 87302
-recovered pasa_asmbl_44552.p1, internal, 88271, 88373
-recovered pasa_asmbl_44552.p1, internal, 88616, 88753
-recovered pasa_asmbl_44552.p1, internal, 88948, 89086
Valid prediction for Augustus_model.g8622.t1
Valid prediction for snap_scaffold_5-snap.2522-T1
Valid prediction for Augustus_model.g8610.t1
Valid prediction for GlimmerHMM_glimmerT_12972-T1
Valid prediction for GlimmerHMM_glimmerT_12977-T1
Valid prediction for GlimmerHMM_glimmerT_12969-T1
Valid prediction for snap_scaffold_5-snap.2529-T1
Valid prediction for CodingQuarry_transcript_52329-T1
Valid prediction for snap_scaffold_5-snap.2532-T1
Couldn't classify 84518, 84671
Couldn't classify 86799, 86836
Sorry, prediction pasa_asmbl_44554.p1 fails validation.
(GAG)	 AG	84518-84671	GT	GCG
(CCC)	 AG	84779-84873	GT	CTG
(GTC)	 AG	84971-85163	GT	TGG
(AGG)	 AG	85977-86171	GT	AGG
(TCA)	 AG	86799-86836	CC	GCC
-recovered pasa_asmbl_44554.p1, internal, 84518, 84671
-recovered pasa_asmbl_44554.p1, internal, 84779, 84873
-recovered pasa_asmbl_44554.p1, internal, 84971, 85163
-recovered pasa_asmbl_44554.p1, internal, 85977, 86171
Valid prediction for GlimmerHMM_glimmerT_12982-T1
Valid prediction for Augustus_model.g8613.t1
Valid prediction for Augustus_model.g8606.t1
Valid prediction for GlimmerHMM_glimmerT_12987-T1
Valid prediction for Augustus_model.g8619.t1
Valid prediction for Augustus_model.g8614.t1
Valid prediction for GlimmerHMM_glimmerT_12971-T1
Valid prediction for snap_scaffold_5-snap.2523-T1
Valid prediction for GlimmerHMM_glimmerT_12976-T1
Valid prediction for snap_scaffold_5-snap.2538-T1
Valid prediction for GlimmerHMM_glimmerT_12989-T1
Valid prediction for GlimmerHMM_glimmerT_12968-T1
Valid prediction for snap_scaffold_5-snap.2516-T1
Valid prediction for snap_scaffold_5-snap.2540-T1
Valid prediction for snap_scaffold_5-snap.2541-T1
Valid prediction for GlimmerHMM_glimmerT_12979-T1
Valid prediction for Augustus_model.g8616.t1
Couldn't classify 97562, 98110
Sorry, prediction pasa_asmbl_44551.p1 fails validation.
(GAT)	 AT	97562-98110	GC	GAG
Valid prediction for GlimmerHMM_glimmerT_12974-T1
Valid prediction for Augustus_model.g8617.t1
Valid prediction for Augustus_model.g8625.t1
Valid prediction for Augustus_model.g8611.t1
Valid prediction for GlimmerHMM_glimmerT_12991-T1
Valid prediction for snap_scaffold_5-snap.2535-T1
Valid prediction for Augustus_model.g8621.t1
Valid prediction for snap_scaffold_5-snap.2531-T1
Valid prediction for snap_scaffold_5-snap.2515-T1
Valid prediction for snap_scaffold_5-snap.2539-T1
Valid prediction for Augustus_model.g8628.t1
Valid prediction for snap_scaffold_5-snap.2547-T1
Valid prediction for GlimmerHMM_glimmerT_12966-T1
Valid prediction for snap_scaffold_5-snap.2521-T1
Valid prediction for GlimmerHMM_glimmerT_12962-T1
Valid prediction for GlimmerHMM_glimmerT_12967-T1
Valid prediction for snap_scaffold_5-snap.2511-T1
Valid prediction for Augustus_model.g8618.t1
Valid prediction for Augustus_model.g8604.t1
Valid prediction for snap_scaffold_5-snap.2519-T1
Valid prediction for GlimmerHMM_glimmerT_12975-T1
Valid prediction for snap_scaffold_5-snap.2534-T1
Valid prediction for GlimmerHMM_glimmerT_12960-T1
Valid prediction for snap_scaffold_5-snap.2548-T1
Valid prediction for snap_scaffold_5-snap.2549-T1
Valid prediction for GlimmerHMM_glimmerT_12980-T1
Valid prediction for Augustus_model.g8615.t1
Valid prediction for snap_scaffold_5-snap.2518-T1
Valid prediction for snap_scaffold_5-snap.2513-T1
Valid prediction for snap_scaffold_5-snap.2546-T1
Valid prediction for pasa_asmbl_44545.p1
Valid prediction for Augustus_model.g8623.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9615, rend_intergenic: 4894  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11506, rend_intergenic: 10533  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14956, rend_intergenic: 11837  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24050, rend_intergenic: 20118  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34265, rend_intergenic: 28702  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78612, rend_intergenic: 75489  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90847, rend_intergenic: 86489  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105725, rend_intergenic: 91159  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114856, rend_intergenic: 111830  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119852, rend_intergenic: 115065  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135776, rend_intergenic: 131654  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149713, rend_intergenic: 138239  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162721, rend_intergenic: 150065  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 166846
-exon list size: 429


building trellis

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20.9    
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23.2    
23.4    
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23.9    
24.1    
24.4    
24.6    
24.8    
25.1    
25.3    
25.5    
25.8    
26.0    
26.2    
26.5    
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26.9    
27.1    
27.4    
27.6    
27.8    
28.1    
28.3    
28.5    
28.8    
29.0    
29.2    
29.5    
29.7    
29.9    
30.2    
30.4    
30.6    
30.9    
31.1    
31.3    
31.6    
31.8    
32.0    
32.3    
32.5    
32.7    
32.9    
33.2    
33.4    
33.6    
33.9    
34.1    
34.3    
34.6    
34.8    
35.0    
35.3    
35.5    
35.7    
36.0    
36.2    
36.4    
36.7    
36.9    
37.1    
37.4    
37.6    
37.8    
38.1    
38.3    
38.5    
38.7    
39.0    
39.2    
39.4    
39.7    
39.9    
40.1    
40.4    
40.6    
40.8    
41.1    
41.3    
41.5    
41.8    
42.0    
42.2    
42.5    
42.7    
42.9    
43.2    
43.4    
43.6    
43.9    
44.1    
44.3    
44.5    
44.8    
45.0    
45.2    
45.5    
45.7    
45.9    
46.2    
46.4    
46.6    
46.9    
47.1    
47.3    
47.6    
47.8    
48.0    
48.3    
48.5    
48.7    
49.0    
49.2    
49.4    
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49.9    
50.1    
50.3    
50.6    
50.8    
51.0    
51.3    
51.5    
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52.2    
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54.5    
54.8    
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55.5    
55.7    
55.9    
56.1    
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56.6    
56.8    
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57.5    
57.8    
58.0    
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66.6    
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68.9    
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71.0    
71.2    
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73.1    
73.3    
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74.0    
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74.9    
75.2    
75.4    
75.6    
75.9    
76.1    
76.3    
76.6    
76.8    
77.0    
77.3    
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78.0    
78.2    
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79.1    
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79.6    
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80.0    
80.3    
80.5    
80.7    
81.0    
81.2    
81.4    
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81.9    
82.1    
82.4    
82.6    
82.8    
83.1    
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85.2    
85.4    
85.6    
85.8    
86.1    
86.3    
86.5    
86.8    
87.0    
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87.5    
87.7    
87.9    
88.2    
88.4    
88.6    
88.9    
89.1    
89.3    
89.6    
89.8    
90.0    
90.3    
90.5    
90.7    
91.0    
91.2    
91.4    
91.6    
91.9    
92.1    
92.3    
92.6    
92.8    
93.0    
93.3    
93.5    
93.7    
94.0    
94.2    
94.4    
94.7    
94.9    
95.1    
95.4    
95.6    
95.8    
96.1    
96.3    
96.5    
96.8    
97.0    
97.2    
97.4    
97.7    
97.9    
98.1    
98.4    
98.6    
98.8    
99.1    
99.3    
99.5    
99.8    
-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 9615, rend_intergenic: 4894  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11506, rend_intergenic: 10533  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14956, rend_intergenic: 11837  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24050, rend_intergenic: 20118  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34265, rend_intergenic: 28702  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78612, rend_intergenic: 75489  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90847, rend_intergenic: 86489  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105725, rend_intergenic: 91159  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114856, rend_intergenic: 111830  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119852, rend_intergenic: 115065  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135776, rend_intergenic: 131654  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149713, rend_intergenic: 138239  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162721, rend_intergenic: 150065  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support