-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_28/scaffold_28_2777792-2918616

-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_28-snap.709-T1
Valid prediction for GlimmerHMM_glimmerT_58428-T1
Valid prediction for pasa_asmbl_37416.p1
Valid prediction for snap_scaffold_28-snap.695-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_28-snap.703-T1
Valid prediction for snap_scaffold_28-snap.712-T1
Valid prediction for GlimmerHMM_glimmerT_58414-T1
Valid prediction for GlimmerHMM_glimmerT_58429-T1
Valid prediction for snap_scaffold_28-snap.705-T1
Valid prediction for snap_scaffold_28-snap.721-T1
Valid prediction for snap_scaffold_28-snap.711-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_28-snap.702-T1
Valid prediction for snap_scaffold_28-snap.689-T1
Valid prediction for GlimmerHMM_glimmerT_58413-T1
Valid prediction for GlimmerHMM_glimmerT_58426-T1
Valid prediction for snap_scaffold_28-snap.715-T1
Valid prediction for GlimmerHMM_glimmerT_58417-T1
Valid prediction for snap_scaffold_28-snap.700-T1
Valid prediction for snap_scaffold_28-snap.692-T1
Valid prediction for snap_scaffold_28-snap.716-T1
Valid prediction for Augustus_model.g38679.t1
Valid prediction for GlimmerHMM_glimmerT_58415-T1
Valid prediction for Augustus_model.g38693.t1
Valid prediction for snap_scaffold_28-snap.710-T1
Valid prediction for snap_scaffold_28-snap.723-T1
Valid prediction for snap_scaffold_28-snap.701-T1
Valid prediction for snap_scaffold_28-snap.724-T1
Valid prediction for snap_scaffold_28-snap.688-T1
Valid prediction for Augustus_model.g38682.t1
Valid prediction for Augustus_model.g38686.t1
Valid prediction for HiQ_model.g38683.t1
Valid prediction for Augustus_model.g38685.t1
Valid prediction for Augustus_model.g38688.t1
Couldn't classify 121917, 121961
Sorry, prediction pasa_asmbl_37419.p1 fails validation.
(CAG)	 AC	121917-121961	GT	TGG
(GCC)	 AG	122177-122301	GT	TGG
(CTA)	 AG	122778-122885	GT	AGG
(CCT)	 AG	123099-123228	GT	AGG
(CTA)	 AG	123460-123654	GT	CTG
(GAA)	 AG	123747-123861	GT	TCG
(AGA)	 AG	124065-124188	GT	ATG
(CAT)	 AG	124346-124497	GT	AGG
(CCT)	 AG	124813-124874	GT	AGG
(GCG)	 AG	124999-125102	GT	CTG
(TGA)	 AG	126129-126178	GT	AGG
(ACC)	 AG	126323-126422	GT	AGG
(CAA)	 AG	126551-126698	GT	GTG
(AGC)	 AG	126863-126960	GT	CTG
(GGA)	 AG	127074-127167	GT	AGG
(AAT)	 AG	127747-127806	CT	GAC
add_exon() Sorry, pasa_asmbl_37419.p1 124346-124497-terminal-2 is invalid.
-recovered pasa_asmbl_37419.p1, terminal, 124346, 124497
-recovered pasa_asmbl_37419.p1, terminal, 127747, 127806
-recovered pasa_asmbl_37419.p1, internal, 122177, 122301
-recovered pasa_asmbl_37419.p1, internal, 122778, 122885
-recovered pasa_asmbl_37419.p1, internal, 123099, 123228
-recovered pasa_asmbl_37419.p1, internal, 123460, 123654
-recovered pasa_asmbl_37419.p1, internal, 123747, 123861
-recovered pasa_asmbl_37419.p1, internal, 124065, 124188
-recovered pasa_asmbl_37419.p1, internal, 124346, 124497
-recovered pasa_asmbl_37419.p1, internal, 124813, 124874
-recovered pasa_asmbl_37419.p1, internal, 124999, 125102
-recovered pasa_asmbl_37419.p1, internal, 126129, 126178
-recovered pasa_asmbl_37419.p1, internal, 126323, 126422
-recovered pasa_asmbl_37419.p1, internal, 126551, 126698
-recovered pasa_asmbl_37419.p1, internal, 126863, 126960
-recovered pasa_asmbl_37419.p1, internal, 127074, 127167
Valid prediction for snap_scaffold_28-snap.718-T1
Valid prediction for snap_scaffold_28-snap.707-T1
Valid prediction for snap_scaffold_28-snap.717-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 GlimmerHMM_glimmerT_58430-T1
Valid prediction for snap_scaffold_28-snap.720-T1
Valid prediction for snap_scaffold_28-snap.704-T1
Valid prediction for GlimmerHMM_glimmerT_58431-T1
Valid prediction for Augustus_model.g38691.t1
Couldn't classify 83996, 84112
Sorry, prediction pasa_asmbl_38096.p1 fails validation.
(GGT)	 CA	83996-84112	GT	AGG
(GGT)	 AG	84222-84295	GT	GCG
(GTT)	 AG	84544-84655	TG	AGT
-recovered pasa_asmbl_38096.p1, terminal, 84544, 84655
-recovered pasa_asmbl_38096.p1, internal, 84222, 84295
Valid prediction for snap_scaffold_28-snap.714-T1
Valid prediction for snap_scaffold_28-snap.708-T1
Valid prediction for Augustus_model.g38689.t1
Valid prediction for snap_scaffold_28-snap.706-T1
Valid prediction for CodingQuarry_transcript_43582-T1
Valid prediction for snap_scaffold_28-snap.699-T1
Couldn't classify 37000, 37075
Sorry, prediction pasa_asmbl_38102.p1 fails validation.
(GGC)	 AT	37000-37075	GT	CCG
(CCA)	 AG	37474-37539	GT	AGG
(CAA)	 AG	37800-38004	GT	AAG
(GTT)	 AG	38128-38270	GT	CGG
(TCC)	 AG	38482-38622	GT	ATG
(TTG)	 AG	39086-39234	GT	AGG
(GGT)	 AG	39429-39590	GG	GAG
-recovered pasa_asmbl_38102.p1, terminal, 39429, 39590
-recovered pasa_asmbl_38102.p1, internal, 37474, 37539
-recovered pasa_asmbl_38102.p1, internal, 37800, 38004
-recovered pasa_asmbl_38102.p1, internal, 38128, 38270
-recovered pasa_asmbl_38102.p1, internal, 38482, 38622
-recovered pasa_asmbl_38102.p1, internal, 39086, 39234
Valid prediction for GlimmerHMM_glimmerT_58425-T1
Valid prediction for GlimmerHMM_glimmerT_58420-T1
Valid prediction for GlimmerHMM_glimmerT_58416-T1
Valid prediction for CodingQuarry_transcript_43587-T1
Valid prediction for snap_scaffold_28-snap.722-T1
Valid prediction for GlimmerHMM_glimmerT_58411-T1
Valid prediction for HiQ_model.g38684.t1
Valid prediction for HiQ_model.g38680.t1
Couldn't classify 61068, 61189
Couldn't classify 61366, 61570
Sorry, prediction pasa_asmbl_38099.p1 fails validation.
(GTG)	 CG	61068-61189	GT	AGG
(ACT)	 AG	61366-61570	AG	AGA
Valid prediction for snap_scaffold_28-snap.719-T1
Valid prediction for Augustus_model.g38687.t1
Valid prediction for pasa_asmbl_38087.p1
Valid prediction for GlimmerHMM_glimmerT_58412-T1
Valid prediction for GlimmerHMM_glimmerT_58422-T1
Valid prediction for GlimmerHMM_glimmerT_58423-T1
Valid prediction for GlimmerHMM_glimmerT_58424-T1
Valid prediction for GlimmerHMM_glimmerT_58419-T1
Valid prediction for GlimmerHMM_glimmerT_58410-T1
Couldn't classify 54963, 55085
Couldn't classify 56692, 56847
Sorry, prediction pasa_asmbl_38100.p1 fails validation.
(GAA)	 TG	54963-55085	GT	AGG
(CAA)	 AG	55287-55448	GT	AGG
(CTG)	 AG	56223-56336	GT	AGG
(ATT)	 AG	56692-56847	GT	GGG
-recovered pasa_asmbl_38100.p1, internal, 55287, 55448
-recovered pasa_asmbl_38100.p1, internal, 56223, 56336
-recovered pasa_asmbl_38100.p1, internal, 56692, 56847
Valid prediction for snap_scaffold_28-snap.713-T1
Valid prediction for pasa_asmbl_38106.p1
Valid prediction for Augustus_model.g38695.t1
Valid prediction for CodingQuarry_transcript_43583-T1
Valid prediction for GlimmerHMM_glimmerT_58421-T1
Valid prediction for Augustus_model.g38681.t1
Valid prediction for snap_scaffold_28-snap.693-T1
Couldn't classify 10246, 10340
Sorry, prediction pasa_asmbl_38104.p1 fails validation.
(TAC)	 TG	10246-10340	GT	GTG
(GAA)	 AG	10709-10859	GT	CTG
(GCC)	 AG	11023-11080	GT	AGG
(GAG)	 AG	11264-11355	GG	AAG
-recovered pasa_asmbl_38104.p1, terminal, 11264, 11355
-recovered pasa_asmbl_38104.p1, internal, 10709, 10859
-recovered pasa_asmbl_38104.p1, internal, 11023, 11080
Valid prediction for Augustus_model.g38692.t1
Valid prediction for snap_scaffold_28-snap.696-T1
Valid prediction for CodingQuarry_transcript_43584-T1
Valid prediction for snap_scaffold_28-snap.690-T1
Couldn't classify 52588, 52795
Sorry, prediction Augustus_model.g38690.t1 fails validation.
(CTG)	 AG	52588-52795	GT	AGG
(CTG)	 AG	53175-53219	GT	AGG
(CTG)	 AG	54817-55085	GT	AGG
(CAA)	 AG	55287-55448	GT	AGG
(CTG)	 AG	56223-56336	GT	AGG
(ATT)	 AG	56692-56865	GT	AGG
(GTG)	 AG	57123-57320	GT	AGG
(GGA)	 AG	57479-57679	GT	AGG
(TTG)	 AG	58073-58225	GT	AGG
(GTG)	 AG	58315-58437	GT	AGG
(ATA)	 AG	59183-59320	GT	AGG
(GTG)	 AG	59486-59650	GT	AGG
(TGG)	 AG	59824-60011	GT	TGG
(GAT)	 AG	60329-60448	GT	AGG
(GAA)	 AG	60752-60815	GT	TGG
(GTG)	 AG	61047-61189	GT	AGG
(ACT)	 AG	61366-61600	GT	AGG
(GTG)	 AG	61928-62050	GT	AGG
(GTG)	 AG	62299-62444	GT	CGG
(AAA)	 AG	62559-62742	GT	AGG
(GTA)	 AG	62842-63034	GT	CGG
(ATA)	 AG	63192-63349	GT	AGG
(GTG)	 AG	63522-63686	GT	AGG
(GTG)	 AG	63963-64238	GT	AGG
(GTC)	 AG	65308-65457	GT	AGG
(GTG)	 AG	65642-65773	GT	AGG
(ATG)	 AG	66014-66124	GT	AGG
(GGC)	 AG	66539-66709	GT	AGG
(GAC)	 AG	66820-67041	GT	AGG
(GTG)	 AG	67274-67294	GT	AGG
(CCG)	 AG	67569-67619	CC	AGC
-recovered Augustus_model.g38690.t1, initial, 66014, 66124
add_exon() Sorry, Augustus_model.g38690.t1 53175-53219-terminal-1 is invalid.
-recovered Augustus_model.g38690.t1, terminal, 53175, 53219
-recovered Augustus_model.g38690.t1, terminal, 67569, 67619
-recovered Augustus_model.g38690.t1, internal, 52588, 52795
-recovered Augustus_model.g38690.t1, internal, 53175, 53219
-recovered Augustus_model.g38690.t1, internal, 54817, 55085
-recovered Augustus_model.g38690.t1, internal, 55287, 55448
-recovered Augustus_model.g38690.t1, internal, 56223, 56336
-recovered Augustus_model.g38690.t1, internal, 56692, 56865
-recovered Augustus_model.g38690.t1, internal, 57123, 57320
-recovered Augustus_model.g38690.t1, internal, 57479, 57679
-recovered Augustus_model.g38690.t1, internal, 58073, 58225
-recovered Augustus_model.g38690.t1, internal, 58315, 58437
-recovered Augustus_model.g38690.t1, internal, 59183, 59320
-recovered Augustus_model.g38690.t1, internal, 59486, 59650
-recovered Augustus_model.g38690.t1, internal, 59824, 60011
-recovered Augustus_model.g38690.t1, internal, 60329, 60448
-recovered Augustus_model.g38690.t1, internal, 60752, 60815
-recovered Augustus_model.g38690.t1, internal, 61047, 61189
-recovered Augustus_model.g38690.t1, internal, 61366, 61600
-recovered Augustus_model.g38690.t1, internal, 61928, 62050
-recovered Augustus_model.g38690.t1, internal, 62299, 62444
-recovered Augustus_model.g38690.t1, internal, 62559, 62742
-recovered Augustus_model.g38690.t1, internal, 62842, 63034
-recovered Augustus_model.g38690.t1, internal, 63192, 63349
-recovered Augustus_model.g38690.t1, internal, 63522, 63686
-recovered Augustus_model.g38690.t1, internal, 63963, 64238
-recovered Augustus_model.g38690.t1, internal, 65308, 65457
-recovered Augustus_model.g38690.t1, internal, 65642, 65773
-recovered Augustus_model.g38690.t1, internal, 66014, 66124
-recovered Augustus_model.g38690.t1, internal, 66539, 66709
-recovered Augustus_model.g38690.t1, internal, 66820, 67041
-recovered Augustus_model.g38690.t1, internal, 67274, 67294
Valid prediction for GlimmerHMM_glimmerT_58427-T1
Valid prediction for HiQ_model.g38694.t1
Valid prediction for snap_scaffold_28-snap.697-T1
Valid prediction for CodingQuarry_transcript_43581-T1
Valid prediction for snap_scaffold_28-snap.691-T1
Valid prediction for GlimmerHMM_glimmerT_58418-T1
Valid prediction for snap_scaffold_28-snap.698-T1
Couldn't classify 61934, 62050
Couldn't classify 66820, 66969
Sorry, prediction pasa_asmbl_38098.p1 fails validation.
(AAC)	 GC	61934-62050	GT	AGG
(GTG)	 AG	62299-62444	GT	CGG
(AAA)	 AG	62559-62742	GT	AGG
(GTA)	 AG	62842-63034	GT	CGG
(ATA)	 AG	63192-63349	GT	AGG
(GTG)	 AG	63522-63686	GT	AGG
(GTG)	 AG	63963-64238	GT	AGG
(GTC)	 AG	65308-65457	GT	AGG
(GTG)	 AG	65642-65773	GT	AGG
(ATG)	 AG	66014-66124	GT	AGG
(GGC)	 AG	66539-66709	GT	AGG
(GAC)	 AG	66820-66969	GC	CGG
-recovered pasa_asmbl_38098.p1, initial, 66014, 66124
-recovered pasa_asmbl_38098.p1, internal, 62299, 62444
-recovered pasa_asmbl_38098.p1, internal, 62559, 62742
-recovered pasa_asmbl_38098.p1, internal, 62842, 63034
-recovered pasa_asmbl_38098.p1, internal, 63192, 63349
-recovered pasa_asmbl_38098.p1, internal, 63522, 63686
-recovered pasa_asmbl_38098.p1, internal, 63963, 64238
-recovered pasa_asmbl_38098.p1, internal, 65308, 65457
-recovered pasa_asmbl_38098.p1, internal, 65642, 65773
-recovered pasa_asmbl_38098.p1, internal, 66014, 66124
-recovered pasa_asmbl_38098.p1, internal, 66539, 66709
-recovered pasa_asmbl_38098.p1, internal, 66820, 66969
Couldn't classify 121194, 121627
Sorry, prediction pasa_asmbl_38085.p1 fails validation.
(CCC)	 TG	121194-121627	GT	AGG
(CTG)	 AG	121770-121937	GT	AGG
(GTG)	 AG	122027-122177	GT	AGG
(GGG)	 AG	122551-122742	GT	AGG
(CTT)	 AG	124086-124260	GT	AGG
(TGT)	 AG	124408-125402	GG	GAG
-recovered pasa_asmbl_38085.p1, terminal, 124408, 125402
-recovered pasa_asmbl_38085.p1, internal, 121770, 121937
-recovered pasa_asmbl_38085.p1, internal, 122027, 122177
-recovered pasa_asmbl_38085.p1, internal, 122551, 122742
-recovered pasa_asmbl_38085.p1, internal, 124086, 124260
Valid prediction for pasa_asmbl_38597.p1
Valid prediction for snap_scaffold_28-snap.694-T1
Valid prediction for CodingQuarry_transcript_43586-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 18389, rend_intergenic: 15453  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22690, rend_intergenic: 18424  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51366, rend_intergenic: 30667  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65845, rend_intergenic: 56171  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73586, rend_intergenic: 70494  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76271, rend_intergenic: 73727  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79831, rend_intergenic: 76504  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90348, rend_intergenic: 80941  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94082, rend_intergenic: 92421  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110981, rend_intergenic: 100802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124598, rend_intergenic: 116696  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127981, rend_intergenic: 124785  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134575, rend_intergenic: 131832  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 140825
-exon list size: 440


building trellis

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63.3    
63.6    
63.8    
64.0    
64.3    
64.5    
64.7    
64.9    
65.2    
65.4    
65.6    
65.8    
66.1    
66.3    
66.5    
66.7    
67.0    
67.2    
67.4    
67.6    
67.9    
68.1    
68.3    
68.6    
68.8    
69.0    
69.2    
69.5    
69.7    
69.9    
70.1    
70.4    
70.6    
70.8    
71.0    
71.3    
71.5    
71.7    
71.9    
72.2    
72.4    
72.6    
72.9    
73.1    
73.3    
73.5    
73.8    
74.0    
74.2    
74.4    
74.7    
74.9    
75.1    
75.3    
75.6    
75.8    
76.0    
76.2    
76.5    
76.7    
76.9    
77.1    
77.4    
77.6    
77.8    
78.1    
78.3    
78.5    
78.7    
79.0    
79.2    
79.4    
79.6    
79.9    
80.1    
80.3    
80.5    
80.8    
81.0    
81.2    
81.4    
81.7    
81.9    
82.1    
82.4    
82.6    
82.8    
83.0    
83.3    
83.5    
83.7    
83.9    
84.2    
84.4    
84.6    
84.8    
85.1    
85.3    
85.5    
85.7    
86.0    
86.2    
86.4    
86.7    
86.9    
87.1    
87.3    
87.6    
87.8    
88.0    
88.2    
88.5    
88.7    
88.9    
89.1    
89.4    
89.6    
89.8    
90.0    
90.3    
90.5    
90.7    
91.0    
91.2    
91.4    
91.6    
91.9    
92.1    
92.3    
92.5    
92.8    
93.0    
93.2    
93.4    
93.7    
93.9    
94.1    
94.3    
94.6    
94.8    
95.0    
95.2    
95.5    
95.7    
95.9    
96.2    
96.4    
96.6    
96.8    
97.1    
97.3    
97.5    
97.7    
98.0    
98.2    
98.4    
98.6    
98.9    
99.1    
99.3    
99.5    
99.8    
-found 20 predictions from path traversal
Error with prediction: snap lend_intergenic: 18389, rend_intergenic: 15453  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22690, rend_intergenic: 18424  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51366, rend_intergenic: 30667  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65845, rend_intergenic: 56171  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73586, rend_intergenic: 70494  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76271, rend_intergenic: 73727  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79831, rend_intergenic: 76504  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90348, rend_intergenic: 80941  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94082, rend_intergenic: 92421  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110981, rend_intergenic: 100802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124598, rend_intergenic: 116696  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127981, rend_intergenic: 124785  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134575, rend_intergenic: 131832  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support