-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_15224798-15374638

-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 GlimmerHMM_glimmerT_8019-T1
Valid prediction for GeneMark_model.13067_t
Valid prediction for GeneMark_model.13047_t
Valid prediction for snap_scaffold_3-snap.2939-T1
Valid prediction for GeneMark_model.13055_t
Valid prediction for GlimmerHMM_glimmerT_8016-T1
Valid prediction for snap_scaffold_3-snap.2935-T1
Valid prediction for snap_scaffold_3-snap.2914-T1
Valid prediction for Augustus_model.g5331.t1
Valid prediction for GeneMark_model.13065_t
Valid prediction for GeneMark_model.13074_t
Valid prediction for snap_scaffold_3-snap.2902-T1
Valid prediction for GeneMark_model.13040_t
Valid prediction for GeneMark_model.13078_t
Valid prediction for snap_scaffold_3-snap.2927-T1
Valid prediction for GeneMark_model.13068_t
Valid prediction for GeneMark_model.13058_t
Valid prediction for GeneMark_model.13044_t
Valid prediction for snap_scaffold_3-snap.2911-T1
Valid prediction for GlimmerHMM_glimmerT_8018-T1
Valid prediction for GlimmerHMM_glimmerT_8030-T1
Valid prediction for snap_scaffold_3-snap.2922-T1
Valid prediction for GeneMark_model.13038_t
Valid prediction for GlimmerHMM_glimmerT_8025-T1
Valid prediction for GlimmerHMM_glimmerT_8024-T1
Valid prediction for GeneMark_model.13051_t
Valid prediction for GeneMark_model.13061_t
Valid prediction for GlimmerHMM_glimmerT_8033-T1
Valid prediction for snap_scaffold_3-snap.2921-T1
Valid prediction for Augustus_model.g5328.t1
Valid prediction for GlimmerHMM_glimmerT_8017-T1
Valid prediction for snap_scaffold_3-snap.2928-T1
Valid prediction for GeneMark_model.13042_t
Valid prediction for GlimmerHMM_glimmerT_8021-T1
Valid prediction for GeneMark_model.13081_t
Valid prediction for Augustus_model.g5330.t1
Valid prediction for snap_scaffold_3-snap.2916-T1
Valid prediction for snap_scaffold_3-snap.2918-T1
Valid prediction for GeneMark_model.13070_t
Valid prediction for GeneMark_model.13053_t
Valid prediction for snap_scaffold_3-snap.2925-T1
Valid prediction for GeneMark_model.13049_t
Valid prediction for GeneMark_model.13076_t
Valid prediction for snap_scaffold_3-snap.2909-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_3-snap.2913-T1
Valid prediction for snap_scaffold_3-snap.2940-T1
Valid prediction for snap_scaffold_3-snap.2907-T1
Valid prediction for snap_scaffold_3-snap.2904-T1
Valid prediction for GlimmerHMM_glimmerT_8023-T1
Valid prediction for GeneMark_model.13063_t
Valid prediction for snap_scaffold_3-snap.2931-T1
Valid prediction for GeneMark_model.13079_t
Valid prediction for GeneMark_model.13057_t

-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_3-snap.2912-T1
Valid prediction for Augustus_model.g5337.t1
Valid prediction for Augustus_model.g5338.t1
Valid prediction for snap_scaffold_3-snap.2934-T1
Valid prediction for Augustus_model.g5333.t1
Valid prediction for snap_scaffold_3-snap.2923-T1
Valid prediction for GeneMark_model.13054_t
Valid prediction for GlimmerHMM_glimmerT_8029-T1
Valid prediction for GeneMark_model.13064_t
Valid prediction for Augustus_model.g5336.t1
Valid prediction for GeneMark_model.13075_t
Valid prediction for GeneMark_model.13072_t
Valid prediction for snap_scaffold_3-snap.2906-T1
Valid prediction for snap_scaffold_3-snap.2917-T1
Valid prediction for snap_scaffold_3-snap.2920-T1
Valid prediction for GeneMark_model.13080_t
Valid prediction for snap_scaffold_3-snap.2910-T1
Valid prediction for GeneMark_model.13077_t
Valid prediction for GeneMark_model.13052_t
Valid prediction for GeneMark_model.13046_t
Couldn't classify 48236, 48389
Sorry, prediction pasa_asmbl_39382.p1 fails validation.
(ATG)	 CC	46534-46695	GT	AGG
(GAC)	 AG	47913-48028	GT	AGG
(GCT)	 AG	48236-48389	GC	AGG
-recovered pasa_asmbl_39382.p1, initial, 46534, 46695
-recovered pasa_asmbl_39382.p1, internal, 47913, 48028
-recovered pasa_asmbl_39382.p1, internal, 48236, 48389
Valid prediction for snap_scaffold_3-snap.2915-T1
Valid prediction for Augustus_model.g5327.t1
Valid prediction for Augustus_model.g5334.t1
Valid prediction for GeneMark_model.13060_t
Valid prediction for snap_scaffold_3-snap.2908-T1
Valid prediction for Augustus_model.g5326.t1
Valid prediction for GeneMark_model.13041_t
Valid prediction for GeneMark_model.13036_t
Valid prediction for snap_scaffold_3-snap.2901-T1
Valid prediction for GlimmerHMM_glimmerT_8027-T1
Valid prediction for GeneMark_model.13071_t
Valid prediction for snap_scaffold_3-snap.2930-T1
Couldn't classify 57014, 57059
Sorry, prediction pasa_asmbl_39649.p1 fails validation.
(CAC)	 CA	57014-57059	GT	AGG
(GCA)	 AG	58710-58822	GT	AGG
(GAG)	 AG	59633-59702	GT	AGG
(CGG)	 AG	59987-60135	CC	GAC
-recovered pasa_asmbl_39649.p1, terminal, 59633, 59702
-recovered pasa_asmbl_39649.p1, terminal, 59987, 60135
-recovered pasa_asmbl_39649.p1, internal, 58710, 58822
-recovered pasa_asmbl_39649.p1, internal, 59633, 59702
Couldn't classify 56512, 56571
Sorry, prediction pasa_asmbl_39744.p1 fails validation.
(ATG)	 TG	52508-52657	GT	GGG
(GGG)	 AG	53305-53436	GT	AGG
(GTC)	 AG	53577-53656	GT	AGG
(GCT)	 AG	55271-55378	GT	CAG
(ACC)	 AG	55599-55740	GT	TGG
(TAT)	 AG	56512-56571	AA	TCA
-recovered pasa_asmbl_39744.p1, initial, 52508, 52657
-recovered pasa_asmbl_39744.p1, internal, 53305, 53436
-recovered pasa_asmbl_39744.p1, internal, 53577, 53656
-recovered pasa_asmbl_39744.p1, internal, 55271, 55378
-recovered pasa_asmbl_39744.p1, internal, 55599, 55740
Valid prediction for GeneMark_model.13056_t
Valid prediction for GlimmerHMM_glimmerT_8032-T1
Valid prediction for GlimmerHMM_glimmerT_8022-T1
Valid prediction for GlimmerHMM_glimmerT_8034-T1
Valid prediction for GeneMark_model.13073_t
Valid prediction for GeneMark_model.13066_t
Valid prediction for GeneMark_model.13059_t
Valid prediction for snap_scaffold_3-snap.2932-T1
Valid prediction for GeneMark_model.13043_t
Valid prediction for GlimmerHMM_glimmerT_8020-T1
Valid prediction for snap_scaffold_3-snap.2929-T1
Valid prediction for snap_scaffold_3-snap.2937-T1
Valid prediction for Augustus_model.g5332.t1
Valid prediction for snap_scaffold_3-snap.2905-T1
Valid prediction for GeneMark_model.13035_t
Valid prediction for GeneMark_model.13062_t
Valid prediction for Augustus_model.g5335.t1
Valid prediction for GeneMark_model.13048_t
Valid prediction for snap_scaffold_3-snap.2926-T1
Valid prediction for snap_scaffold_3-snap.2903-T1
Valid prediction for GeneMark_model.13039_t
Valid prediction for GlimmerHMM_glimmerT_8015-T1
Valid prediction for Augustus_model.g5324.t1
Valid prediction for GeneMark_model.13069_t
Valid prediction for snap_scaffold_3-snap.2936-T1
Valid prediction for Augustus_model.g5329.t1
Valid prediction for GlimmerHMM_glimmerT_8013-T1
Valid prediction for GlimmerHMM_glimmerT_8028-T1
Valid prediction for GeneMark_model.13045_t
Valid prediction for Augustus_model.g5325.t1
Valid prediction for snap_scaffold_3-snap.2933-T1
Valid prediction for GeneMark_model.13050_t
Valid prediction for GlimmerHMM_glimmerT_8035-T1
Valid prediction for GlimmerHMM_glimmerT_8014-T1
Valid prediction for snap_scaffold_3-snap.2919-T1
Valid prediction for snap_scaffold_3-snap.2924-T1
Valid prediction for GeneMark_model.13037_t
Valid prediction for GlimmerHMM_glimmerT_8031-T1
Valid prediction for GlimmerHMM_glimmerT_8026-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 4975, rend_intergenic: 2597  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13478, rend_intergenic: 5528  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14655, rend_intergenic: 13576  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22397, rend_intergenic: 19531  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25727, rend_intergenic: 22875  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33949, rend_intergenic: 29876  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35712, rend_intergenic: 34030  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37272, rend_intergenic: 35913  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44136, rend_intergenic: 42590  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47080, rend_intergenic: 44904  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50332, rend_intergenic: 48974  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51884, rend_intergenic: 50445  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54060, rend_intergenic: 52890  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74622, rend_intergenic: 67362  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94741, rend_intergenic: 89707  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114359, rend_intergenic: 111729  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132106, rend_intergenic: 125978  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 149841
-exon list size: 561


building trellis

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19.0    
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24.9    
25.0    
25.2    
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25.8    
25.9    
26.1    
26.3    
26.5    
26.6    
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27.0    
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27.9    
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28.2    
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28.6    
28.8    
29.0    
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29.7    
29.8    
30.0    
30.2    
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31.1    
31.3    
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31.8    
32.0    
32.1    
32.3    
32.5    
32.7    
32.9    
33.0    
33.2    
33.4    
33.6    
33.7    
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34.1    
34.3    
34.5    
34.6    
34.8    
35.0    
35.2    
35.3    
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35.9    
36.1    
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36.9    
37.1    
37.3    
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38.9    
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40.1    
40.3    
40.5    
40.7    
40.9    
41.0    
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68.2    
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73.4    
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84.9    
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85.3    
85.4    
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86.3    
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86.7    
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87.2    
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88.3    
88.5    
88.6    
88.8    
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89.2    
89.3    
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90.1    
90.2    
90.4    
90.6    
90.8    
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91.1    
91.3    
91.5    
91.7    
91.8    
92.0    
92.2    
92.4    
92.5    
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92.9    
93.1    
93.3    
93.4    
93.6    
93.8    
94.0    
94.1    
94.3    
94.5    
94.7    
94.8    
95.0    
95.2    
95.4    
95.6    
95.7    
95.9    
96.1    
96.3    
96.4    
96.6    
96.8    
97.0    
97.2    
97.3    
97.5    
97.7    
97.9    
98.0    
98.2    
98.4    
98.6    
98.8    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 4975, rend_intergenic: 2597  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13478, rend_intergenic: 5528  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14655, rend_intergenic: 13576  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22397, rend_intergenic: 19531  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25727, rend_intergenic: 22875  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33949, rend_intergenic: 29876  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35712, rend_intergenic: 34030  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37272, rend_intergenic: 35913  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44136, rend_intergenic: 42590  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47080, rend_intergenic: 44904  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50332, rend_intergenic: 48974  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51884, rend_intergenic: 50445  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54060, rend_intergenic: 52890  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74622, rend_intergenic: 67362  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94741, rend_intergenic: 89707  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114359, rend_intergenic: 111729  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132106, rend_intergenic: 125978  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support