-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_24/scaffold_24_6429044-6557489

-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 CodingQuarry_transcript_37266-T1
Valid prediction for GeneMark_model.94043_t
Valid prediction for GeneMark_model.94071_t
Valid prediction for GeneMark_model.94040_t
Valid prediction for GeneMark_model.94055_t
Valid prediction for GeneMark_model.94077_t
Valid prediction for pasa_asmbl_32316.p1
Valid prediction for snap_scaffold_24-snap.1280-T1
Valid prediction for HiQ_model.g36116.t1
Valid prediction for snap_scaffold_24-snap.1302-T1
Valid prediction for Augustus_model.g36120.t1
Valid prediction for snap_scaffold_24-snap.1299-T1
Valid prediction for snap_scaffold_24-snap.1289-T1
Valid prediction for GeneMark_model.94065_t
Valid prediction for GeneMark_model.94048_t
Valid prediction for GlimmerHMM_glimmerT_53947-T1
Valid prediction for GeneMark_model.94046_t
Valid prediction for pasa_asmbl_32325.p1
Valid prediction for GeneMark_model.94057_t
Valid prediction for Augustus_model.g36128.t1
Couldn't classify 85412, 85615
Couldn't classify 87106, 87231
Sorry, prediction pasa_asmbl_32617.p1 fails validation.
(CTC)	 AT	85412-85615	GT	AGG
(CTG)	 AG	87106-87231	GT	ACG
-recovered pasa_asmbl_32617.p1, internal, 87106, 87231
Valid prediction for pasa_asmbl_32336.p1
Valid prediction for CodingQuarry_transcript_37262-T1
Valid prediction for snap_scaffold_24-snap.1284-T1
Valid prediction for snap_scaffold_24-snap.1295-T1
Valid prediction for snap_scaffold_24-snap.1307-T1
Valid prediction for Augustus_model.g36123.t1
Valid prediction for GlimmerHMM_glimmerT_53962-T1
Valid prediction for snap_scaffold_24-snap.1306-T1
Valid prediction for CodingQuarry_transcript_37264-T1
Valid prediction for GlimmerHMM_glimmerT_53946-T1
Valid prediction for GlimmerHMM_glimmerT_53960-T1
Valid prediction for GlimmerHMM_glimmerT_53954-T1
Valid prediction for GlimmerHMM_glimmerT_53953-T1
Valid prediction for Augustus_model.g36117.t1
Valid prediction for GeneMark_model.94064_t
Valid prediction for pasa_asmbl_32319.p1
Valid prediction for GeneMark_model.94037_t
Valid prediction for Augustus_model.g36131.t1
Valid prediction for GeneMark_model.94060_t
Valid prediction for GeneMark_model.94051_t
Valid prediction for GeneMark_model.94073_t
Valid prediction for HiQ_model.g36114.t1
Valid prediction for snap_scaffold_24-snap.1298-T1
Valid prediction for Augustus_model.g36121.t1
Valid prediction for GeneMark_model.94044_t
Valid prediction for CodingQuarry_transcript_37263-T1
Valid prediction for GlimmerHMM_glimmerT_53952-T1
Valid prediction for Augustus_model.g36127.t1
Valid prediction for GlimmerHMM_glimmerT_53966-T1
Valid prediction for snap_scaffold_24-snap.1282-T1
Valid prediction for snap_scaffold_24-snap.1293-T1
Valid prediction for snap_scaffold_24-snap.1292-T1
Valid prediction for GeneMark_model.94067_t
Valid prediction for CodingQuarry_transcript_37265-T1
Valid prediction for Augustus_model.g36115.t1
Valid prediction for GlimmerHMM_glimmerT_53963-T1
Valid prediction for HiQ_model.g36118.t1
Valid prediction for GeneMark_model.94041_t
Valid prediction for GlimmerHMM_glimmerT_53964-T1
Couldn't classify 41218, 41265
Couldn't classify 42351, 42403
Sorry, prediction pasa_asmbl_32330.p2 fails validation.
(TCC)	 CC	41218-41265	GT	CGG
(GTG)	 AG	41689-41868	GT	AGG
(GAG)	 AG	42028-42139	GT	AGG
(GTC)	 AG	42351-42403	AG	TGA
-recovered pasa_asmbl_32330.p2, internal, 41689, 41868
-recovered pasa_asmbl_32330.p2, internal, 42028, 42139
Valid prediction for GlimmerHMM_glimmerT_53949-T1
Valid prediction for snap_scaffold_24-snap.1304-T1
Valid prediction for snap_scaffold_24-snap.1303-T1
Valid prediction for GeneMark_model.94050_t
Valid prediction for GeneMark_model.94075_t
Valid prediction for GlimmerHMM_glimmerT_53967-T1
Valid prediction for GeneMark_model.94053_t
Valid prediction for GeneMark_model.94062_t
Valid prediction for GeneMark_model.94069_t
Valid prediction for HiQ_model.g36130.t1
Valid prediction for GeneMark_model.94039_t
Couldn't classify 97871, 98004
Sorry, prediction pasa_asmbl_32333.p2 fails validation.
(GCT)	 AG	97871-98004	GT	AGG
(AGG)	 AG	98097-98214	GT	AGG
(GTG)	 AG	98560-98630	GT	CTG
(GAA)	 AG	98877-98952	GT	AGG
(TAC)	 AG	99636-99698	GT	AGG
(GCG)	 AG	100034-100103	GT	AGG
(AAA)	 AG	101777-101859	GG	AAG
-recovered pasa_asmbl_32333.p2, terminal, 101777, 101859
-recovered pasa_asmbl_32333.p2, internal, 97871, 98004
-recovered pasa_asmbl_32333.p2, internal, 98097, 98214
-recovered pasa_asmbl_32333.p2, internal, 98560, 98630
-recovered pasa_asmbl_32333.p2, internal, 98877, 98952
-recovered pasa_asmbl_32333.p2, internal, 99636, 99698
-recovered pasa_asmbl_32333.p2, internal, 100034, 100103
Valid prediction for snap_scaffold_24-snap.1281-T1
Valid prediction for snap_scaffold_24-snap.1286-T1
Couldn't classify 42844, 43087
Sorry, prediction pasa_asmbl_32331.p1 fails validation.
(GCC)	 CA	42844-43087	GT	AGG
(TCT)	 AG	43317-43437	GT	CTG
(AAA)	 AG	43702-43917	GT	AAG
(GAT)	 AG	44106-44198	GT	AGG
(GAT)	 AG	44302-44323	CT	AAC
-recovered pasa_asmbl_32331.p1, terminal, 44302, 44323
-recovered pasa_asmbl_32331.p1, internal, 43317, 43437
-recovered pasa_asmbl_32331.p1, internal, 43702, 43917
-recovered pasa_asmbl_32331.p1, internal, 44106, 44198

-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.94066_t
Valid prediction for GeneMark_model.94070_t
Valid prediction for GeneMark_model.94042_t
Valid prediction for GlimmerHMM_glimmerT_53958-T1
Valid prediction for CodingQuarry_transcript_37261-T1
Valid prediction for snap_scaffold_24-snap.1290-T1
Valid prediction for Augustus_model.g36133.t1
Valid prediction for GeneMark_model.94045_t
Valid prediction for GlimmerHMM_glimmerT_53961-T1
Valid prediction for Augustus_model.g36119.t1
Valid prediction for Augustus_model.g36122.t1
Valid prediction for GlimmerHMM_glimmerT_53955-T1
Valid prediction for snap_scaffold_24-snap.1305-T1
Valid prediction for pasa_asmbl_32947.p1
Valid prediction for GlimmerHMM_glimmerT_53948-T1
Valid prediction for snap_scaffold_24-snap.1287-T1
Valid prediction for GeneMark_model.94074_t
Valid prediction for snap_scaffold_24-snap.1279-T1
Valid prediction for GeneMark_model.94052_t
Valid prediction for GeneMark_model.94063_t
Valid prediction for GlimmerHMM_glimmerT_53950-T1
Valid prediction for GlimmerHMM_glimmerT_53945-T1
Valid prediction for GeneMark_model.94068_t
Valid prediction for GeneMark_model.94059_t
Valid prediction for GlimmerHMM_glimmerT_53957-T1
Couldn't classify 23777, 23974
Couldn't classify 25066, 25181
Sorry, prediction pasa_asmbl_32951.p1 fails validation.
(CGG)	 AA	23777-23974	GT	CGG
(CTG)	 AG	24430-24538	GT	AGG
(GCT)	 AG	25066-25181	TA	AGT
-recovered pasa_asmbl_32951.p1, internal, 24430, 24538
Valid prediction for GlimmerHMM_glimmerT_53951-T1
Valid prediction for Augustus_model.g36124.t1
Valid prediction for snap_scaffold_24-snap.1296-T1
Valid prediction for snap_scaffold_24-snap.1297-T1
Valid prediction for GeneMark_model.94056_t
Valid prediction for GeneMark_model.94058_t
Valid prediction for snap_scaffold_24-snap.1291-T1
Valid prediction for CodingQuarry_transcript_37260-T1
Valid prediction for snap_scaffold_24-snap.1288-T1
Valid prediction for Augustus_model.g36125.t1
Valid prediction for Augustus_model.g36126.t1
Valid prediction for snap_scaffold_24-snap.1301-T1
Valid prediction for GeneMark_model.94038_t
Valid prediction for GlimmerHMM_glimmerT_53968-T1
Valid prediction for GlimmerHMM_glimmerT_53965-T1
Valid prediction for snap_scaffold_24-snap.1283-T1
Valid prediction for GeneMark_model.94076_t
Valid prediction for GeneMark_model.94061_t
Valid prediction for GeneMark_model.94047_t
Valid prediction for HiQ_model.g36113.t1
Valid prediction for GlimmerHMM_glimmerT_53959-T1
Valid prediction for snap_scaffold_24-snap.1285-T1
Valid prediction for Augustus_model.g36132.t1
Valid prediction for GeneMark_model.94054_t
Valid prediction for GeneMark_model.94072_t
Valid prediction for snap_scaffold_24-snap.1294-T1
Valid prediction for GeneMark_model.94036_t
Valid prediction for GeneMark_model.94049_t
Valid prediction for GlimmerHMM_glimmerT_53956-T1
Valid prediction for snap_scaffold_24-snap.1300-T1
Valid prediction for Augustus_model.g36129.t1
Valid prediction for GlimmerHMM_glimmerT_53944-T1
Valid prediction for snap_scaffold_24-snap.1278-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 43872, rend_intergenic: 41197  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54379, rend_intergenic: 51644  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74960, rend_intergenic: 68582  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82016, rend_intergenic: 75769  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85741, rend_intergenic: 84265  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89796, rend_intergenic: 87061  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101859, rend_intergenic: 91608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123508, rend_intergenic: 118429  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 128446
-exon list size: 562


building trellis

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32.3    
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34.0    
34.2    
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34.8    
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35.1    
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44.5    
44.7    
44.9    
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45.2    
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46.1    
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46.8    
47.0    
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48.0    
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48.4    
48.6    
48.8    
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49.1    
49.3    
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49.6    
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50.0    
50.2    
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51.1    
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51.6    
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54.3    
54.4    
54.6    
54.8    
55.0    
55.1    
55.3    
55.5    
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55.9    
56.0    
56.2    
56.4    
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56.7    
56.9    
57.1    
57.3    
57.4    
57.6    
57.8    
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58.2    
58.3    
58.5    
58.7    
58.9    
59.0    
59.2    
59.4    
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59.8    
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60.1    
60.3    
60.5    
60.6    
60.8    
61.0    
61.2    
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63.3    
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65.1    
65.2    
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65.6    
65.8    
66.0    
66.1    
66.3    
66.5    
66.7    
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67.0    
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68.1    
68.3    
68.4    
68.6    
68.8    
69.0    
69.1    
69.3    
69.5    
69.7    
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70.9    
71.1    
71.3    
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72.0    
72.2    
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73.2    
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73.8    
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76.1    
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76.6    
76.8    
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77.1    
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78.0    
78.2    
78.4    
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79.1    
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80.1    
80.3    
80.5    
80.7    
80.9    
81.0    
81.2    
81.4    
81.6    
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81.9    
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82.3    
82.4    
82.6    
82.8    
83.0    
83.2    
83.3    
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84.9    
85.1    
85.3    
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86.2    
86.3    
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86.9    
87.1    
87.2    
87.4    
87.6    
87.8    
87.9    
88.1    
88.3    
88.5    
88.7    
88.8    
89.0    
89.2    
89.4    
89.5    
89.7    
89.9    
90.1    
90.2    
90.4    
90.6    
90.8    
91.0    
91.1    
91.3    
91.5    
91.7    
91.8    
92.0    
92.2    
92.4    
92.6    
92.7    
92.9    
93.1    
93.3    
93.4    
93.6    
93.8    
94.0    
94.1    
94.3    
94.5    
94.7    
94.9    
95.0    
95.2    
95.4    
95.6    
95.7    
95.9    
96.1    
96.3    
96.5    
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 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 43872, rend_intergenic: 41197  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54379, rend_intergenic: 51644  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74960, rend_intergenic: 68582  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82016, rend_intergenic: 75769  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85741, rend_intergenic: 84265  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89796, rend_intergenic: 87061  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101859, rend_intergenic: 91608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123508, rend_intergenic: 118429  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support