-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_11/scaffold_11_10827208-11041297

-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.49139_t
Valid prediction for GeneMark_model.49108_t
Valid prediction for GeneMark_model.49110_t
Valid prediction for GlimmerHMM_glimmerT_28446-T1
Valid prediction for GeneMark_model.49127_t
Valid prediction for snap_scaffold_11-snap.2444-T1
Valid prediction for snap_scaffold_11-snap.2434-T1
Valid prediction for Augustus_model.g18996.t1
Valid prediction for GlimmerHMM_glimmerT_28452-T1
Valid prediction for GeneMark_model.49118_t
Valid prediction for GeneMark_model.49117_t
Valid prediction for GlimmerHMM_glimmerT_28458-T1
Valid prediction for GeneMark_model.49129_t
Valid prediction for snap_scaffold_11-snap.2421-T1
Valid prediction for GlimmerHMM_glimmerT_28449-T1
Valid prediction for snap_scaffold_11-snap.2436-T1
Valid prediction for GeneMark_model.49145_t
Valid prediction for GlimmerHMM_glimmerT_28465-T1
Valid prediction for GeneMark_model.49142_t
Valid prediction for GeneMark_model.49138_t
Valid prediction for GeneMark_model.49131_t
Valid prediction for GeneMark_model.49114_t
Valid prediction for GeneMark_model.49151_t
Valid prediction for GlimmerHMM_glimmerT_28443-T1
Valid prediction for snap_scaffold_11-snap.2420-T1
Valid prediction for snap_scaffold_11-snap.2427-T1
Valid prediction for GlimmerHMM_glimmerT_28450-T1
Valid prediction for GeneMark_model.49125_t
Valid prediction for GlimmerHMM_glimmerT_28462-T1
Valid prediction for Augustus_model.g18994.t1
Valid prediction for snap_scaffold_11-snap.2439-T1
Valid prediction for GeneMark_model.49152_t
Valid prediction for GeneMark_model.49122_t
Valid prediction for GeneMark_model.49112_t
Valid prediction for GeneMark_model.49147_t
Valid prediction for snap_scaffold_11-snap.2429-T1
Valid prediction for GeneMark_model.49124_t
Valid prediction for GeneMark_model.49136_t
Valid prediction for snap_scaffold_11-snap.2428-T1
Valid prediction for snap_scaffold_11-snap.2423-T1
Valid prediction for GlimmerHMM_glimmerT_28464-T1
Valid prediction for GeneMark_model.49123_t
Valid prediction for snap_scaffold_11-snap.2445-T1
Valid prediction for snap_scaffold_11-snap.2418-T1
Valid prediction for GlimmerHMM_glimmerT_28455-T1
Valid prediction for GeneMark_model.49135_t
Valid prediction for snap_scaffold_11-snap.2426-T1
Valid prediction for snap_scaffold_11-snap.2424-T1
Valid prediction for snap_scaffold_11-snap.2448-T1
Valid prediction for GeneMark_model.49149_t
Valid prediction for snap_scaffold_11-snap.2443-T1
Valid prediction for snap_scaffold_11-snap.2416-T1
Valid prediction for GlimmerHMM_glimmerT_28448-T1
Valid prediction for GlimmerHMM_glimmerT_28454-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 GeneMark_model.49144_t
Valid prediction for GeneMark_model.49115_t
Valid prediction for GeneMark_model.49111_t
Valid prediction for Augustus_model.g18999.t1
Valid prediction for GeneMark_model.49121_t
Valid prediction for snap_scaffold_11-snap.2419-T1
Couldn't classify 186039, 186163
Sorry, prediction pasa_asmbl_6979.p1 fails validation.
(CCC)	 TC	186039-186163	GT	AGG
(GAC)	 AG	188201-188666	CT	GAC
-recovered pasa_asmbl_6979.p1, terminal, 188201, 188666
Valid prediction for GeneMark_model.49143_t
Valid prediction for snap_scaffold_11-snap.2446-T1
Valid prediction for GeneMark_model.49120_t
Valid prediction for GeneMark_model.49119_t
Valid prediction for snap_scaffold_11-snap.2413-T1
Valid prediction for GeneMark_model.49105_t
Valid prediction for GeneMark_model.49132_t
Valid prediction for GeneMark_model.49146_t
Valid prediction for GeneMark_model.49109_t
Valid prediction for GeneMark_model.49116_t
Valid prediction for GlimmerHMM_glimmerT_28444-T1
Valid prediction for GeneMark_model.49137_t
Valid prediction for pasa_asmbl_6982.p1
Valid prediction for GlimmerHMM_glimmerT_28466-T1
Valid prediction for GeneMark_model.49134_t
Valid prediction for Augustus_model.g18988.t1
Valid prediction for Augustus_model.g18997.t1
Valid prediction for snap_scaffold_11-snap.2417-T1
Couldn't classify 62572, 62901
Sorry, prediction pasa_asmbl_6984.p1 fails validation.
(ATA)	 AT	62572-62901	GT	AGG
(TTA)	 AG	63211-63318	GT	GGG
(GAG)	 AG	64935-65543	GC	GAG
-recovered pasa_asmbl_6984.p1, terminal, 64935, 65543
-recovered pasa_asmbl_6984.p1, internal, 63211, 63318
-recovered pasa_asmbl_6984.p1, internal, 64935, 65543
Valid prediction for GlimmerHMM_glimmerT_28467-T1
Valid prediction for snap_scaffold_11-snap.2431-T1
Valid prediction for GeneMark_model.49128_t
Valid prediction for GeneMark_model.49150_t
Valid prediction for GlimmerHMM_glimmerT_28463-T1
Valid prediction for Augustus_model.g18992.t1
Valid prediction for GeneMark_model.49130_t
Valid prediction for snap_scaffold_11-snap.2447-T1
Couldn't classify 44572, 44573
Sorry, prediction CodingQuarry_transcript_8207-T1 fails validation.
(ATG)	 GA	44572-44573	GT	ATG
(GGG)	 AG	44884-44966	GT	CGG
(TGG)	 AG	45096-45249	GT	AAG
(AGC)	 AG	46270-46333	GA	AGG
add_exon() Sorry, CodingQuarry_transcript_8207-T1 45096-45249-terminal-3 is invalid.
-recovered CodingQuarry_transcript_8207-T1, terminal, 45096, 45249
-recovered CodingQuarry_transcript_8207-T1, terminal, 46270, 46333
-recovered CodingQuarry_transcript_8207-T1, internal, 44884, 44966
-recovered CodingQuarry_transcript_8207-T1, internal, 45096, 45249
Valid prediction for snap_scaffold_11-snap.2437-T1
Valid prediction for GlimmerHMM_glimmerT_28459-T1
Valid prediction for Augustus_model.g19000.t1
Valid prediction for snap_scaffold_11-snap.2442-T1
Valid prediction for CodingQuarry_transcript_8205-T1
Valid prediction for snap_scaffold_11-snap.2425-T1
Valid prediction for GeneMark_model.49107_t
Valid prediction for snap_scaffold_11-snap.2438-T1
Valid prediction for GeneMark_model.49113_t
Valid prediction for Augustus_model.g18995.t1
Valid prediction for GeneMark_model.49126_t
Valid prediction for GlimmerHMM_glimmerT_28445-T1
Valid prediction for GeneMark_model.49141_t
Valid prediction for snap_scaffold_11-snap.2414-T1
Valid prediction for GlimmerHMM_glimmerT_28461-T1
Valid prediction for snap_scaffold_11-snap.2432-T1
Valid prediction for GeneMark_model.49148_t
Valid prediction for Augustus_model.g18993.t1
Valid prediction for snap_scaffold_11-snap.2433-T1
Valid prediction for GlimmerHMM_glimmerT_28451-T1
Couldn't classify 42116, 42214
Sorry, prediction pasa_asmbl_7333.p1 fails validation.
(GCC)	 GT	42116-42214	GT	AGG
(GTG)	 AG	44503-44573	GT	ATG
(GGG)	 AG	44884-44966	GT	CGG
(TGG)	 AG	45096-45249	GT	AAG
(AGC)	 AG	46270-46333	GA	AGG
add_exon() Sorry, pasa_asmbl_7333.p1 45096-45249-terminal-3 is invalid.
-recovered pasa_asmbl_7333.p1, terminal, 45096, 45249
-recovered pasa_asmbl_7333.p1, terminal, 46270, 46333
-recovered pasa_asmbl_7333.p1, internal, 44503, 44573
-recovered pasa_asmbl_7333.p1, internal, 44884, 44966
-recovered pasa_asmbl_7333.p1, internal, 45096, 45249
Valid prediction for GlimmerHMM_glimmerT_28460-T1
Valid prediction for snap_scaffold_11-snap.2422-T1
Valid prediction for GeneMark_model.49106_t
Valid prediction for Augustus_model.g18989.t1
Valid prediction for GlimmerHMM_glimmerT_28447-T1
Valid prediction for snap_scaffold_11-snap.2435-T1
Valid prediction for snap_scaffold_11-snap.2441-T1
Valid prediction for snap_scaffold_11-snap.2440-T1
Valid prediction for GeneMark_model.49140_t
Valid prediction for snap_scaffold_11-snap.2430-T1
Valid prediction for Augustus_model.g18991.t1
Valid prediction for GlimmerHMM_glimmerT_28457-T1
Valid prediction for GlimmerHMM_glimmerT_28456-T1
Valid prediction for snap_scaffold_11-snap.2412-T1
Valid prediction for Augustus_model.g18998.t1
Valid prediction for Augustus_model.g18990.t1
Valid prediction for GlimmerHMM_glimmerT_28453-T1
Valid prediction for GeneMark_model.49133_t
Valid prediction for snap_scaffold_11-snap.2415-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 29882, rend_intergenic: 27053  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35822, rend_intergenic: 30794  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38982, rend_intergenic: 36979  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41034, rend_intergenic: 39508  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44760, rend_intergenic: 43298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53536, rend_intergenic: 47959  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64980, rend_intergenic: 59509  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72197, rend_intergenic: 70231  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91056, rend_intergenic: 73363  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137011, rend_intergenic: 136000  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139428, rend_intergenic: 137578  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173217, rend_intergenic: 168838  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183220, rend_intergenic: 176003  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 214090
-exon list size: 508


building trellis

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13.9    
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24.9    
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25.9    
26.1    
26.3    
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26.7    
26.9    
27.1    
27.3    
27.5    
27.6    
27.8    
28.0    
28.2    
28.4    
28.6    
28.8    
29.0    
29.2    
29.4    
29.6    
29.8    
30.0    
30.2    
30.4    
30.6    
30.8    
31.0    
31.2    
31.4    
31.6    
31.8    
32.0    
32.2    
32.4    
32.5    
32.7    
32.9    
33.1    
33.3    
33.5    
33.7    
33.9    
34.1    
34.3    
34.5    
34.7    
34.9    
35.1    
35.3    
35.5    
35.7    
35.9    
36.1    
36.3    
36.5    
36.7    
36.9    
37.1    
37.3    
37.5    
37.6    
37.8    
38.0    
38.2    
38.4    
38.6    
38.8    
39.0    
39.2    
39.4    
39.6    
39.8    
40.0    
40.2    
40.4    
40.6    
40.8    
41.0    
41.2    
41.4    
41.6    
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42.0    
42.2    
42.4    
42.5    
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42.9    
43.1    
43.3    
43.5    
43.7    
43.9    
44.1    
44.3    
44.5    
44.7    
44.9    
45.1    
45.3    
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45.7    
45.9    
46.1    
46.3    
46.5    
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47.1    
47.3    
47.5    
47.6    
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48.2    
48.4    
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48.8    
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53.3    
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55.3    
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59.6    
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60.8    
61.0    
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61.4    
61.6    
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62.2    
62.4    
62.5    
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62.9    
63.1    
63.3    
63.5    
63.7    
63.9    
64.1    
64.3    
64.5    
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64.9    
65.1    
65.3    
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66.1    
66.3    
66.5    
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67.1    
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68.0    
68.2    
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68.8    
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73.3    
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74.1    
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75.3    
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76.1    
76.3    
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77.1    
77.3    
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78.0    
78.2    
78.4    
78.6    
78.8    
79.0    
79.2    
79.4    
79.6    
79.8    
80.0    
80.2    
80.4    
80.6    
80.8    
81.0    
81.2    
81.4    
81.6    
81.8    
82.0    
82.2    
82.4    
82.5    
82.7    
82.9    
83.1    
83.3    
83.5    
83.7    
83.9    
84.1    
84.3    
84.5    
84.7    
84.9    
85.1    
85.3    
85.5    
85.7    
85.9    
86.1    
86.3    
86.5    
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86.9    
87.1    
87.3    
87.5    
87.6    
87.8    
88.0    
88.2    
88.4    
88.6    
88.8    
89.0    
89.2    
89.4    
89.6    
89.8    
90.0    
90.2    
90.4    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.8    
92.0    
92.2    
92.4    
92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.7    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.3    
97.5    
97.6    
97.8    
98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 29882, rend_intergenic: 27053  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35822, rend_intergenic: 30794  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38982, rend_intergenic: 36979  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41034, rend_intergenic: 39508  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44760, rend_intergenic: 43298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53536, rend_intergenic: 47959  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64980, rend_intergenic: 59509  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72197, rend_intergenic: 70231  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91056, rend_intergenic: 73363  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137011, rend_intergenic: 136000  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139428, rend_intergenic: 137578  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173217, rend_intergenic: 168838  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183220, rend_intergenic: 176003  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support