-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_20/scaffold_20_9225808-9405495

-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_20-snap.2037-T1
Valid prediction for GlimmerHMM_glimmerT_46587-T1
Valid prediction for Augustus_model.g30949.t1
Valid prediction for snap_scaffold_20-snap.2044-T1
Valid prediction for snap_scaffold_20-snap.2021-T1
Valid prediction for snap_scaffold_20-snap.2030-T1
Valid prediction for GlimmerHMM_glimmerT_46598-T1
Valid prediction for snap_scaffold_20-snap.2010-T1
Valid prediction for snap_scaffold_20-snap.2013-T1
Couldn't classify 58154, 58267
Couldn't classify 59304, 59445
Sorry, prediction pasa_asmbl_27226.p1 fails validation.
(ATC)	 AG	58154-58267	GT	TGG
(AGT)	 AG	58970-59097	GT	AGG
(CTG)	 AG	59304-59445	GT	TGG
-recovered pasa_asmbl_27226.p1, internal, 58154, 58267
-recovered pasa_asmbl_27226.p1, internal, 58970, 59097
-recovered pasa_asmbl_27226.p1, internal, 59304, 59445
Valid prediction for snap_scaffold_20-snap.2014-T1
Valid prediction for snap_scaffold_20-snap.2033-T1
Valid prediction for snap_scaffold_20-snap.2038-T1
Valid prediction for CodingQuarry_transcript_30595-T1
Couldn't classify 55385, 55392
Couldn't classify 57777, 57869
Sorry, prediction pasa_asmbl_26847.p1 fails validation.
(GCT)	 CT	55385-55392	GT	AGG
(CTG)	 AG	55587-55728	GT	TGG
(CCC)	 AG	56062-56145	GT	AGG
(GTT)	 AG	56760-56870	GT	CTG
(GTG)	 AG	57067-57168	GT	AGG
(ACC)	 AG	57777-57869	CA	AGC
-recovered pasa_asmbl_26847.p1, internal, 55587, 55728
-recovered pasa_asmbl_26847.p1, internal, 56062, 56145
-recovered pasa_asmbl_26847.p1, internal, 56760, 56870
-recovered pasa_asmbl_26847.p1, internal, 57067, 57168
Valid prediction for Augustus_model.g30945.t1
Valid prediction for snap_scaffold_20-snap.2016-T1
Valid prediction for snap_scaffold_20-snap.2046-T1
Valid prediction for GlimmerHMM_glimmerT_46597-T1
Valid prediction for GlimmerHMM_glimmerT_46591-T1
Valid prediction for Augustus_model.g30948.t1
Valid prediction for GlimmerHMM_glimmerT_46599-T1
Valid prediction for snap_scaffold_20-snap.2041-T1
Valid prediction for snap_scaffold_20-snap.2019-T1
Valid prediction for GlimmerHMM_glimmerT_46602-T1
Valid prediction for GlimmerHMM_glimmerT_46600-T1
Valid prediction for GlimmerHMM_glimmerT_46585-T1
Valid prediction for snap_scaffold_20-snap.2048-T1
Valid prediction for snap_scaffold_20-snap.2028-T1
Couldn't classify 50380, 50421
Couldn't classify 51084, 51214
Sorry, prediction pasa_asmbl_26845.p1 fails validation.
(GCC)	 GC	50380-50421	GT	AGG
(ATC)	 AG	50634-50775	GT	GGG
(CAT)	 AG	51084-51214	GG	AAG
-recovered pasa_asmbl_26845.p1, internal, 50634, 50775
Valid prediction for snap_scaffold_20-snap.2017-T1
Valid prediction for GlimmerHMM_glimmerT_46589-T1
Valid prediction for snap_scaffold_20-snap.2039-T1
Couldn't classify 51620, 51742
Couldn't classify 55265, 55393
Sorry, prediction pasa_asmbl_26846.p1 fails validation.
(GAG)	 AC	51620-51742	GT	TGG
(GAG)	 AG	51953-52040	GT	CGG
(GTG)	 AG	52273-52336	GT	ACG
(GTC)	 AG	52434-52529	GT	AAG
(GTC)	 AG	53051-53257	GT	AGG
(GGC)	 AG	53507-53589	GT	AGG
(AGT)	 AG	53709-53868	GT	AGG
(CGT)	 AG	54007-54133	GT	AGG
(ATC)	 AG	54449-54562	GT	TGG
(AGT)	 AG	55265-55393	TG	GGT
-recovered pasa_asmbl_26846.p1, internal, 51953, 52040
-recovered pasa_asmbl_26846.p1, internal, 52273, 52336
-recovered pasa_asmbl_26846.p1, internal, 52434, 52529
-recovered pasa_asmbl_26846.p1, internal, 53051, 53257
-recovered pasa_asmbl_26846.p1, internal, 53507, 53589
-recovered pasa_asmbl_26846.p1, internal, 53709, 53868
-recovered pasa_asmbl_26846.p1, internal, 54007, 54133
-recovered pasa_asmbl_26846.p1, internal, 54449, 54562
Valid prediction for GlimmerHMM_glimmerT_46596-T1
Valid prediction for snap_scaffold_20-snap.2024-T1
Valid prediction for snap_scaffold_20-snap.2025-T1
Couldn't classify 60489, 60590
Sorry, prediction pasa_asmbl_27135.p1 fails validation.
(AAC)	 CA	60489-60590	GT	CTG
(GTG)	 AG	60787-60888	GT	AGG
(ACC)	 AG	61453-61572	GT	ATG
(CGT)	 AG	61679-61771	GT	AGG
(GTG)	 AG	62115-62246	GA	AGG
-recovered pasa_asmbl_27135.p1, terminal, 62115, 62246
-recovered pasa_asmbl_27135.p1, internal, 60787, 60888
-recovered pasa_asmbl_27135.p1, internal, 61453, 61572
-recovered pasa_asmbl_27135.p1, internal, 61679, 61771
Valid prediction for snap_scaffold_20-snap.2036-T1
Couldn't classify 48880, 48903
Sorry, prediction pasa_asmbl_27128.p1 fails validation.
(ATG)	 AA	46654-46839	GT	AGG
(ATA)	 AG	47493-47582	GT	AGG
(GGG)	 AG	47676-47721	GT	TGG
(AGC)	 AG	47843-47943	GT	CGG
(GTT)	 AG	48059-48162	GT	AGG
(GTA)	 AG	48314-48386	GT	AGG
(AGC)	 AG	48494-48646	GT	AGG
(GAT)	 AG	48880-48903	CC	CCC
-recovered pasa_asmbl_27128.p1, initial, 46654, 46839
-recovered pasa_asmbl_27128.p1, internal, 47493, 47582
-recovered pasa_asmbl_27128.p1, internal, 47676, 47721
-recovered pasa_asmbl_27128.p1, internal, 47843, 47943
-recovered pasa_asmbl_27128.p1, internal, 48059, 48162
-recovered pasa_asmbl_27128.p1, internal, 48314, 48386
-recovered pasa_asmbl_27128.p1, internal, 48494, 48646
Valid prediction for GlimmerHMM_glimmerT_46603-T1
Valid prediction for GlimmerHMM_glimmerT_46593-T1
Valid prediction for snap_scaffold_20-snap.2031-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_20-snap.2027-T1
Valid prediction for snap_scaffold_20-snap.2045-T1
Valid prediction for snap_scaffold_20-snap.2043-T1
Valid prediction for GlimmerHMM_glimmerT_46592-T1
Valid prediction for GlimmerHMM_glimmerT_46594-T1
Valid prediction for snap_scaffold_20-snap.2026-T1
Valid prediction for GlimmerHMM_glimmerT_46584-T1
Valid prediction for GlimmerHMM_glimmerT_46586-T1
Valid prediction for GlimmerHMM_glimmerT_46590-T1
Valid prediction for snap_scaffold_20-snap.2035-T1
Valid prediction for snap_scaffold_20-snap.2023-T1
Valid prediction for GlimmerHMM_glimmerT_46601-T1
Valid prediction for snap_scaffold_20-snap.2011-T1
Valid prediction for Augustus_model.g30947.t1
Valid prediction for snap_scaffold_20-snap.2029-T1
Valid prediction for snap_scaffold_20-snap.2015-T1
Valid prediction for snap_scaffold_20-snap.2042-T1
Valid prediction for Augustus_model.g30943.t1
Valid prediction for snap_scaffold_20-snap.2032-T1
Valid prediction for snap_scaffold_20-snap.2047-T1
Valid prediction for snap_scaffold_20-snap.2020-T1
Valid prediction for Augustus_model.g30946.t1
Valid prediction for snap_scaffold_20-snap.2012-T1
Valid prediction for Augustus_model.g30942.t1
Valid prediction for snap_scaffold_20-snap.2049-T1
Valid prediction for GlimmerHMM_glimmerT_46588-T1
Valid prediction for Augustus_model.g30944.t1
Valid prediction for snap_scaffold_20-snap.2022-T1
Valid prediction for snap_scaffold_20-snap.2040-T1
Valid prediction for GlimmerHMM_glimmerT_46583-T1
Valid prediction for snap_scaffold_20-snap.2018-T1
Valid prediction for GlimmerHMM_glimmerT_46595-T1
Valid prediction for snap_scaffold_20-snap.2034-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 89875, rend_intergenic: 89872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70796, rend_intergenic: 68315  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84358, rend_intergenic: 81957  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102245, rend_intergenic: 99300  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108149, rend_intergenic: 103915  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119388, rend_intergenic: 116917  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130885, rend_intergenic: 123049  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136183, rend_intergenic: 131439  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149147, rend_intergenic: 144397  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158665, rend_intergenic: 155146  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168305, rend_intergenic: 161096  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170493, rend_intergenic: 169260  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175878, rend_intergenic: 172917  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 179688
-exon list size: 279


building trellis

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38.1    
38.4    
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39.1    
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43.4    
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45.2    
45.6    
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53.4    
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54.4    
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56.6    
56.9    
57.3    
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58.0    
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59.4    
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60.1    
60.5    
60.9    
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63.3    
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64.1    
64.4    
64.8    
65.1    
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66.2    
66.5    
66.9    
67.3    
67.6    
68.0    
68.3    
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69.0    
69.4    
69.8    
70.1    
70.5    
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71.2    
71.5    
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72.6    
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74.4    
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78.3    
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80.8    
81.1    
81.5    
81.9    
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82.9    
83.3    
83.6    
84.0    
84.3    
84.7    
85.1    
85.4    
85.8    
86.1    
86.5    
86.8    
87.2    
87.5    
87.9    
88.3    
88.6    
89.0    
89.3    
89.7    
90.0    
90.4    
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91.1    
91.5    
91.8    
92.2    
92.5    
92.9    
93.2    
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94.3    
94.7    
95.0    
95.4    
95.7    
96.1    
96.4    
96.8    
97.2    
97.5    
97.9    
98.2    
98.6    
98.9    
99.3    
99.6    
-found 23 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 89875, rend_intergenic: 89872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70796, rend_intergenic: 68315  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84358, rend_intergenic: 81957  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102245, rend_intergenic: 99300  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108149, rend_intergenic: 103915  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119388, rend_intergenic: 116917  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130885, rend_intergenic: 123049  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136183, rend_intergenic: 131439  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149147, rend_intergenic: 144397  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158665, rend_intergenic: 155146  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168305, rend_intergenic: 161096  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170493, rend_intergenic: 169260  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175878, rend_intergenic: 172917  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 12 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 10682
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support