-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_1/scaffold_1_19185257-19364555

-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: +)Couldn't classify 55917, 55940
Sorry, prediction pasa_asmbl_2587.p1 fails validation.
(GAG)	 CA	55917-55940	GT	AGG
(GCC)	 AG	56558-56688	GT	AAG
(GTT)	 AG	56850-57027	GT	AGG
(GTG)	 AG	57167-57349	GT	CTG
(ATG)	 AG	57806-57882	GT	TGG
(GAG)	 AG	58089-58169	GT	AGG
(TGA)	 AG	58268-58354	GT	AGG
(TCG)	 AG	58599-58769	GT	GGG
(CAC)	 AG	60000-60477	GA	GAG
-recovered pasa_asmbl_2587.p1, initial, 57806, 57882
-recovered pasa_asmbl_2587.p1, terminal, 60000, 60477
-recovered pasa_asmbl_2587.p1, internal, 56558, 56688
-recovered pasa_asmbl_2587.p1, internal, 56850, 57027
-recovered pasa_asmbl_2587.p1, internal, 57167, 57349
-recovered pasa_asmbl_2587.p1, internal, 57806, 57882
-recovered pasa_asmbl_2587.p1, internal, 58089, 58169
-recovered pasa_asmbl_2587.p1, internal, 58268, 58354
-recovered pasa_asmbl_2587.p1, internal, 58599, 58769
Valid prediction for GlimmerHMM_glimmerT_2596-T1
Valid prediction for snap_scaffold_1-snap.3573-T1
Valid prediction for snap_scaffold_1-snap.3548-T1
Valid prediction for snap_scaffold_1-snap.3558-T1
Valid prediction for Augustus_model.g1875.t1
Valid prediction for snap_scaffold_1-snap.3551-T1
Valid prediction for snap_scaffold_1-snap.3544-T1
Valid prediction for snap_scaffold_1-snap.3568-T1
Valid prediction for GlimmerHMM_glimmerT_2580-T1
Valid prediction for GlimmerHMM_glimmerT_2589-T1
Valid prediction for snap_scaffold_1-snap.3538-T1
Valid prediction for GlimmerHMM_glimmerT_2585-T1
Valid prediction for GlimmerHMM_glimmerT_2595-T1
Valid prediction for GlimmerHMM_glimmerT_2587-T1
Valid prediction for GlimmerHMM_glimmerT_2584-T1
Valid prediction for CodingQuarry_transcript_3013-T1
Valid prediction for CodingQuarry_transcript_3012-T1
Valid prediction for Augustus_model.g1869.t1
Valid prediction for snap_scaffold_1-snap.3572-T1
Valid prediction for pasa_asmbl_2590.p1
Valid prediction for snap_scaffold_1-snap.3540-T1
Valid prediction for Augustus_model.g1870.t1
Valid prediction for Augustus_model.g1864.t1
Valid prediction for Augustus_model.g1873.t1
Valid prediction for snap_scaffold_1-snap.3534-T1
Valid prediction for snap_scaffold_1-snap.3539-T1
Valid prediction for GlimmerHMM_glimmerT_2577-T1
Valid prediction for snap_scaffold_1-snap.3554-T1
Valid prediction for snap_scaffold_1-snap.3561-T1
Valid prediction for snap_scaffold_1-snap.3559-T1
Valid prediction for snap_scaffold_1-snap.3563-T1
Valid prediction for GlimmerHMM_glimmerT_2582-T1
Valid prediction for GlimmerHMM_glimmerT_2593-T1
Valid prediction for Augustus_model.g1866.t1
Valid prediction for GlimmerHMM_glimmerT_2592-T1
Couldn't classify 40867, 40998
Couldn't classify 43420, 43495
Sorry, prediction pasa_asmbl_2583.p1 fails validation.
(CAT)	 AG	40867-40998	GT	AGG
(ATC)	 AG	41164-41376	GT	GGG
(GCC)	 AG	41559-41677	GT	AGG
(CCA)	 AG	43420-43495	TA	ACT
-recovered pasa_asmbl_2583.p1, internal, 40867, 40998
-recovered pasa_asmbl_2583.p1, internal, 41164, 41376
-recovered pasa_asmbl_2583.p1, internal, 41559, 41677
Couldn't classify 53118, 53161
Couldn't classify 54105, 54151
Sorry, prediction pasa_asmbl_2586.p2 fails validation.
(CAG)	 CC	53118-53161	GT	TGG
(GCA)	 AG	53294-53360	GT	AGG
(ATC)	 AG	53546-53867	GT	GGG
(GCA)	 AG	54105-54151	AG	CCA
-recovered pasa_asmbl_2586.p2, internal, 53294, 53360
-recovered pasa_asmbl_2586.p2, internal, 53546, 53867
Couldn't classify 47969, 48574
Sorry, prediction pasa_asmbl_2585.p1 fails validation.
(CCA)	 CC	47969-48574	AA	AAA
Valid prediction for HiQ_model.g1871.t1
Valid prediction for Augustus_model.g1874.t1
Couldn't classify 43932, 43963
Couldn't classify 45083, 45262
Sorry, prediction pasa_asmbl_2584.p1 fails validation.
(AGC)	 AC	43932-43963	GT	AGG
(GGC)	 AG	44352-44557	GT	TGG
(ACC)	 AG	44655-44830	GT	AGG
(CCA)	 AG	45083-45262	TT	CCT
-recovered pasa_asmbl_2584.p1, internal, 44352, 44557
-recovered pasa_asmbl_2584.p1, internal, 44655, 44830
Valid prediction for Augustus_model.g1876.t1
Valid prediction for CodingQuarry_transcript_3011-T1
Valid prediction for GlimmerHMM_glimmerT_2575-T1
Valid prediction for snap_scaffold_1-snap.3553-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_1-snap.3537-T1
Valid prediction for snap_scaffold_1-snap.3550-T1
Valid prediction for GlimmerHMM_glimmerT_2579-T1
Valid prediction for snap_scaffold_1-snap.3546-T1
Valid prediction for snap_scaffold_1-snap.3569-T1
Valid prediction for Augustus_model.g1862.t1
Valid prediction for snap_scaffold_1-snap.3567-T1
Valid prediction for CodingQuarry_transcript_3010-T1
Valid prediction for snap_scaffold_1-snap.3541-T1
Couldn't classify 71828, 71979
Couldn't classify 75980, 76011
Sorry, prediction pasa_asmbl_1147.p1 fails validation.
(AGA)	 AC	71828-71979	GT	ACG
(GGA)	 AG	73849-74019	GT	AGG
(AAA)	 AG	75268-75322	GT	AGG
(GTG)	 AG	75541-75703	GT	AGG
(ATC)	 AG	75980-76011	CT	ACC
-recovered pasa_asmbl_1147.p1, internal, 73849, 74019
-recovered pasa_asmbl_1147.p1, internal, 75268, 75322
-recovered pasa_asmbl_1147.p1, internal, 75541, 75703
Valid prediction for snap_scaffold_1-snap.3545-T1
Valid prediction for Augustus_model.g1861.t1
Valid prediction for snap_scaffold_1-snap.3552-T1
Valid prediction for snap_scaffold_1-snap.3556-T1
Valid prediction for GlimmerHMM_glimmerT_2590-T1
Valid prediction for snap_scaffold_1-snap.3549-T1
Valid prediction for Augustus_model.g1867.t1
Valid prediction for GlimmerHMM_glimmerT_2583-T1
Valid prediction for GlimmerHMM_glimmerT_2581-T1
Valid prediction for snap_scaffold_1-snap.3557-T1
Valid prediction for snap_scaffold_1-snap.3535-T1
Valid prediction for Augustus_model.g1860.t1
Valid prediction for snap_scaffold_1-snap.3562-T1
Valid prediction for GlimmerHMM_glimmerT_2586-T1
Valid prediction for snap_scaffold_1-snap.3564-T1
Valid prediction for snap_scaffold_1-snap.3565-T1
Valid prediction for snap_scaffold_1-snap.3542-T1
Valid prediction for GlimmerHMM_glimmerT_2591-T1
Valid prediction for GlimmerHMM_glimmerT_2572-T1
Valid prediction for snap_scaffold_1-snap.3555-T1
Valid prediction for GlimmerHMM_glimmerT_2588-T1
Valid prediction for GlimmerHMM_glimmerT_2594-T1
Valid prediction for snap_scaffold_1-snap.3560-T1
Valid prediction for GlimmerHMM_glimmerT_2574-T1
Valid prediction for snap_scaffold_1-snap.3571-T1
Valid prediction for pasa_asmbl_1146.p1
Valid prediction for snap_scaffold_1-snap.3536-T1
Valid prediction for GlimmerHMM_glimmerT_2576-T1
Valid prediction for GlimmerHMM_glimmerT_2573-T1
Valid prediction for HiQ_model.g1863.t1
Valid prediction for Augustus_model.g1872.t1
Valid prediction for snap_scaffold_1-snap.3547-T1
Valid prediction for snap_scaffold_1-snap.3543-T1
Valid prediction for snap_scaffold_1-snap.3566-T1
Valid prediction for Augustus_model.g1865.t1
Valid prediction for snap_scaffold_1-snap.3570-T1
Valid prediction for Augustus_model.g1868.t1
Valid prediction for GlimmerHMM_glimmerT_2578-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17504, rend_intergenic: 12010  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29541, rend_intergenic: 21495  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48574, rend_intergenic: 35226  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60857, rend_intergenic: 54602  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72278, rend_intergenic: 65770  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82332, rend_intergenic: 79944  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94892, rend_intergenic: 83235  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100944, rend_intergenic: 97266  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110052, rend_intergenic: 106025  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114700, rend_intergenic: 111665  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116378, rend_intergenic: 115130  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117576, rend_intergenic: 117370  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130796, rend_intergenic: 119691  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150024, rend_intergenic: 131046  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166729, rend_intergenic: 151383  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 179299
-exon list size: 382


building trellis

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14.6    
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18.2    
18.5    
18.8    
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19.3    
19.5    
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20.6    
20.8    
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25.3    
25.5    
25.8    
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27.9    
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28.4    
28.6    
28.9    
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29.7    
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30.7    
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31.8    
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32.3    
32.6    
32.8    
33.1    
33.3    
33.6    
33.9    
34.1    
34.4    
34.6    
34.9    
35.2    
35.4    
35.7    
35.9    
36.2    
36.5    
36.7    
37.0    
37.2    
37.5    
37.8    
38.0    
38.3    
38.5    
38.8    
39.1    
39.3    
39.6    
39.8    
40.1    
40.4    
40.6    
40.9    
41.1    
41.4    
41.7    
41.9    
42.2    
42.4    
42.7    
43.0    
43.2    
43.5    
43.8    
44.0    
44.3    
44.5    
44.8    
45.1    
45.3    
45.6    
45.8    
46.1    
46.4    
46.6    
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47.4    
47.7    
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48.2    
48.4    
48.7    
49.0    
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50.0    
50.3    
50.5    
50.8    
51.0    
51.3    
51.6    
51.8    
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52.3    
52.6    
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53.6    
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56.0    
56.2    
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57.3    
57.6    
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58.3    
58.6    
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59.6    
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70.6    
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73.4    
73.7    
74.0    
74.2    
74.5    
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75.0    
75.3    
75.5    
75.8    
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76.6    
76.8    
77.1    
77.3    
77.6    
77.9    
78.1    
78.4    
78.6    
78.9    
79.2    
79.4    
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80.2    
80.5    
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81.0    
81.2    
81.5    
81.8    
82.0    
82.3    
82.6    
82.8    
83.1    
83.3    
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83.9    
84.1    
84.4    
84.6    
84.9    
85.2    
85.4    
85.7    
85.9    
86.2    
86.5    
86.7    
87.0    
87.2    
87.5    
87.8    
88.0    
88.3    
88.5    
88.8    
89.1    
89.3    
89.6    
89.8    
90.1    
90.4    
90.6    
90.9    
91.1    
91.4    
91.7    
91.9    
92.2    
92.4    
92.7    
93.0    
93.2    
93.5    
93.8    
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94.3    
94.5    
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95.1    
95.3    
95.6    
95.8    
96.1    
96.4    
96.6    
96.9    
97.1    
97.4    
97.7    
97.9    
98.2    
98.4    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 17504, rend_intergenic: 12010  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29541, rend_intergenic: 21495  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48574, rend_intergenic: 35226  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60857, rend_intergenic: 54602  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72278, rend_intergenic: 65770  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82332, rend_intergenic: 79944  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94892, rend_intergenic: 83235  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100944, rend_intergenic: 97266  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110052, rend_intergenic: 106025  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114700, rend_intergenic: 111665  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116378, rend_intergenic: 115130  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117576, rend_intergenic: 117370  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130796, rend_intergenic: 119691  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150024, rend_intergenic: 131046  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166729, rend_intergenic: 151383  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support