-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_835355-1024651

-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: +)Couldn't classify 181551, 181586
Couldn't classify 182660, 182901
Sorry, prediction pasa_asmbl_39775.p1 fails validation.
(GAT)	 GG	181551-181586	GT	TGG
(GTG)	 AG	181807-182052	GT	AGG
(GTG)	 AG	182300-182465	GT	AGG
(GTA)	 AG	182660-182901	AC	ACA
-recovered pasa_asmbl_39775.p1, internal, 181807, 182052
-recovered pasa_asmbl_39775.p1, internal, 182300, 182465
Valid prediction for snap_scaffold_3-snap.248-T1
Valid prediction for snap_scaffold_3-snap.240-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GeneMark_model.9970_t
Valid prediction for HiQ_model.g3988.t1
Valid prediction for GlimmerHMM_glimmerT_6059-T1
Valid prediction for snap_scaffold_3-snap.214-T1
Valid prediction for snap_scaffold_3-snap.235-T1
Valid prediction for GeneMark_model.9957_t
Valid prediction for GeneMark_model.9939_t
Valid prediction for snap_scaffold_3-snap.222-T1
Valid prediction for GlimmerHMM_glimmerT_6086-T1
Couldn't classify 98910, 99174
Sorry, prediction pasa_asmbl_39772.p1 fails validation.
(TCT)	 GT	98910-99174	GT	AGG
(GTT)	 AG	99328-99576	GT	AAG
(TGT)	 AG	99743-100023	GT	CGG
(ACT)	 AG	100139-100351	GT	GGG
(GCT)	 AG	100528-100630	GT	TGG
(AGG)	 AG	100864-101207	AA	AAA
-recovered pasa_asmbl_39772.p1, terminal, 100864, 101207
-recovered pasa_asmbl_39772.p1, internal, 99328, 99576
-recovered pasa_asmbl_39772.p1, internal, 99743, 100023
-recovered pasa_asmbl_39772.p1, internal, 100139, 100351
-recovered pasa_asmbl_39772.p1, internal, 100528, 100630
Valid prediction for snap_scaffold_3-snap.216-T1
Valid prediction for GeneMark_model.9960_t
Valid prediction for snap_scaffold_3-snap.249-T1
Valid prediction for snap_scaffold_3-snap.213-T1
Valid prediction for GlimmerHMM_glimmerT_6069-T1
Valid prediction for Augustus_model.g3996.t1
Valid prediction for GeneMark_model.9979_t
Valid prediction for snap_scaffold_3-snap.231-T1
Valid prediction for GeneMark_model.9988_t
Valid prediction for GeneMark_model.9989_t
Valid prediction for GeneMark_model.9937_t
Valid prediction for GeneMark_model.9951_t
Valid prediction for GlimmerHMM_glimmerT_6060-T1
Valid prediction for snap_scaffold_3-snap.241-T1
Valid prediction for Augustus_model.g3989.t1
Valid prediction for GeneMark_model.9973_t
Valid prediction for GeneMark_model.9964_t
Valid prediction for GeneMark_model.9953_t
Valid prediction for snap_scaffold_3-snap.236-T1
Valid prediction for GeneMark_model.9985_t
Valid prediction for GlimmerHMM_glimmerT_6076-T1
Valid prediction for GeneMark_model.9966_t
Valid prediction for GeneMark_model.9986_t
Valid prediction for GeneMark_model.9971_t
Valid prediction for GeneMark_model.9955_t
Valid prediction for Augustus_model.g3980.t1
Valid prediction for GeneMark_model.9933_t
Valid prediction for GlimmerHMM_glimmerT_6089-T1
Valid prediction for GlimmerHMM_glimmerT_6077-T1
Valid prediction for snap_scaffold_3-snap.225-T1
Valid prediction for GeneMark_model.9968_t
Valid prediction for Augustus_model.g3981.t1
Valid prediction for GeneMark_model.9941_t
Valid prediction for GeneMark_model.9959_t
Valid prediction for GeneMark_model.9977_t
Valid prediction for Augustus_model.g3994.t1
Valid prediction for GlimmerHMM_glimmerT_6075-T1
Valid prediction for snap_scaffold_3-snap.250-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_3-snap.211-T1
Valid prediction for GlimmerHMM_glimmerT_6079-T1
Valid prediction for GeneMark_model.9981_t
Valid prediction for snap_scaffold_3-snap.223-T1
Valid prediction for GeneMark_model.9983_t
Valid prediction for GlimmerHMM_glimmerT_6093-T1
Valid prediction for GlimmerHMM_glimmerT_6081-T1
Valid prediction for GlimmerHMM_glimmerT_6070-T1
Valid prediction for snap_scaffold_3-snap.252-T1
Valid prediction for GeneMark_model.9946_t
Valid prediction for snap_scaffold_3-snap.226-T1
Valid prediction for snap_scaffold_3-snap.220-T1
Valid prediction for GlimmerHMM_glimmerT_6085-T1
Valid prediction for snap_scaffold_3-snap.230-T1
Valid prediction for Augustus_model.g3998.t1
Valid prediction for Augustus_model.g3992.t1
Valid prediction for GeneMark_model.9948_t
Valid prediction for GeneMark_model.9943_t
Valid prediction for snap_scaffold_3-snap.237-T1
Valid prediction for GeneMark_model.9932_t
Valid prediction for GlimmerHMM_glimmerT_6091-T1
Valid prediction for snap_scaffold_3-snap.228-T1
Valid prediction for GeneMark_model.9935_t
Valid prediction for snap_scaffold_3-snap.227-T1
Couldn't classify 104022, 104099
Sorry, prediction pasa_asmbl_39773.p1 fails validation.
(ATG)	 CA	103357-103528	GT	CGG
(GAT)	 AG	103744-103871	GT	AGG
(GGA)	 AG	104022-104099	AC	GGA
-recovered pasa_asmbl_39773.p1, initial, 103357, 103528
-recovered pasa_asmbl_39773.p1, internal, 103744, 103871
Valid prediction for GeneMark_model.9975_t
Valid prediction for GlimmerHMM_glimmerT_6065-T1
Valid prediction for GeneMark_model.9944_t
Valid prediction for GlimmerHMM_glimmerT_6084-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_6061-T1
Valid prediction for snap_scaffold_3-snap.219-T1
Valid prediction for GlimmerHMM_glimmerT_6074-T1
Valid prediction for GlimmerHMM_glimmerT_6082-T1
Couldn't classify 28033, 28789
Sorry, prediction pasa_asmbl_38649.p1 fails validation.
(CTC)	 CC	28033-28789	GT	AGG
(GTC)	 AG	29339-29517	GT	AGG
(GTC)	 AG	30805-30967	GT	GGG
(TGA)	 AG	31120-31418	AC	AGA
-recovered pasa_asmbl_38649.p1, terminal, 31120, 31418
-recovered pasa_asmbl_38649.p1, internal, 29339, 29517
-recovered pasa_asmbl_38649.p1, internal, 30805, 30967
Valid prediction for GeneMark_model.9931_t
Valid prediction for snap_scaffold_3-snap.212-T1
Valid prediction for GeneMark_model.9954_t
Valid prediction for GlimmerHMM_glimmerT_6068-T1
Valid prediction for GeneMark_model.9940_t
Valid prediction for HiQ_model.g3997.t1
Valid prediction for Augustus_model.g3985.t1
Couldn't classify 153140, 153284
Sorry, prediction pasa_asmbl_39726.p1 fails validation.
(ATG)	 AA	152589-152702	GT	TTG
(GTG)	 AG	152856-152908	GT	GCG
(GAT)	 AG	153140-153284	GG	GGG
-recovered pasa_asmbl_39726.p1, initial, 152589, 152702
-recovered pasa_asmbl_39726.p1, internal, 152856, 152908
Valid prediction for GeneMark_model.9945_t
Valid prediction for GeneMark_model.9962_t
Valid prediction for GlimmerHMM_glimmerT_6067-T1
Valid prediction for snap_scaffold_3-snap.217-T1
Valid prediction for GeneMark_model.9936_t
Valid prediction for HiQ_model.g3987.t1
Couldn't classify 22326, 22427
Couldn't classify 27437, 27591
Sorry, prediction pasa_asmbl_38651.p1 fails validation.
(ATC)	 CC	22326-22427	GT	CGG
(GTA)	 AG	25013-25258	GT	AGG
(TCG)	 AG	25464-25631	GT	GGG
(CTC)	 AG	26637-26716	GT	AGG
(GTA)	 AG	27053-27222	GT	AGG
(TCC)	 AG	27437-27591	AC	GCA
-recovered pasa_asmbl_38651.p1, internal, 25013, 25258
-recovered pasa_asmbl_38651.p1, internal, 25464, 25631
-recovered pasa_asmbl_38651.p1, internal, 26637, 26716
-recovered pasa_asmbl_38651.p1, internal, 27053, 27222
Valid prediction for GeneMark_model.9984_t
Valid prediction for GeneMark_model.9961_t
Couldn't classify 99930, 99949
Couldn't classify 101254, 101369
Sorry, prediction pasa_asmbl_38638.p1 fails validation.
(GAT)	 TG	99930-99949	GT	AGG
(ACC)	 AG	100345-100544	GT	AGG
(GAT)	 AG	101254-101369	GA	GGG
-recovered pasa_asmbl_38638.p1, internal, 100345, 100544
Valid prediction for snap_scaffold_3-snap.244-T1
Valid prediction for GlimmerHMM_glimmerT_6066-T1
Valid prediction for GeneMark_model.9952_t
Valid prediction for GlimmerHMM_glimmerT_6064-T1
Valid prediction for GeneMark_model.9972_t
Valid prediction for Augustus_model.g3979.t1
Valid prediction for GeneMark_model.9950_t
Valid prediction for Augustus_model.g3991.t1
Valid prediction for GeneMark_model.9958_t
Valid prediction for GeneMark_model.9965_t
Valid prediction for GeneMark_model.9967_t
Valid prediction for snap_scaffold_3-snap.233-T1
Valid prediction for snap_scaffold_3-snap.246-T1
Valid prediction for GeneMark_model.9976_t
Valid prediction for GeneMark_model.9980_t
Valid prediction for snap_scaffold_3-snap.247-T1
Couldn't classify 95072, 95290
Couldn't classify 96259, 96272
Sorry, prediction pasa_asmbl_38639.p1 fails validation.
(CTG)	 GC	95072-95290	GT	TGG
(GAG)	 AG	95555-95764	GT	AGG
(GCA)	 AG	95937-96039	GT	AGG
(AGC)	 AG	96259-96272	AT	GGA
-recovered pasa_asmbl_38639.p1, internal, 95555, 95764
-recovered pasa_asmbl_38639.p1, internal, 95937, 96039
Valid prediction for HiQ_model.g3990.t1
Valid prediction for snap_scaffold_3-snap.215-T1
Valid prediction for GlimmerHMM_glimmerT_6090-T1
Couldn't classify 19705, 19932
Couldn't classify 21783, 21860
Sorry, prediction pasa_asmbl_38652.p1 fails validation.
(CTC)	 CT	19705-19932	GT	AGG
(TTG)	 AG	21783-21860	AT	AGA
Valid prediction for GlimmerHMM_glimmerT_6073-T1
Valid prediction for GeneMark_model.9969_t
Valid prediction for Augustus_model.g3983.t1
Valid prediction for snap_scaffold_3-snap.239-T1
Valid prediction for GeneMark_model.9990_t
Valid prediction for GlimmerHMM_glimmerT_6071-T1
Valid prediction for snap_scaffold_3-snap.224-T1
Valid prediction for GeneMark_model.9974_t
Valid prediction for GeneMark_model.9938_t
Valid prediction for snap_scaffold_3-snap.221-T1
Valid prediction for snap_scaffold_3-snap.243-T1
Valid prediction for snap_scaffold_3-snap.242-T1
Valid prediction for GeneMark_model.9942_t
Valid prediction for GlimmerHMM_glimmerT_6063-T1
Valid prediction for snap_scaffold_3-snap.229-T1
Valid prediction for snap_scaffold_3-snap.251-T1
Valid prediction for pasa_asmbl_38645.p1
Valid prediction for GeneMark_model.9934_t
Valid prediction for snap_scaffold_3-snap.238-T1
Valid prediction for snap_scaffold_3-snap.218-T1
Valid prediction for Augustus_model.g3986.t1
Valid prediction for Augustus_model.g3984.t1
Valid prediction for snap_scaffold_3-snap.234-T1
Valid prediction for GlimmerHMM_glimmerT_6088-T1
Valid prediction for GeneMark_model.9978_t
Valid prediction for GlimmerHMM_glimmerT_6078-T1
Valid prediction for snap_scaffold_3-snap.232-T1
Valid prediction for GeneMark_model.9987_t
Valid prediction for Augustus_model.g3995.t1
Valid prediction for snap_scaffold_3-snap.245-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_6083-T1
Valid prediction for snap_scaffold_3-snap.210-T1
Valid prediction for Augustus_model.g3982.t1
Valid prediction for GeneMark_model.9956_t
Valid prediction for GlimmerHMM_glimmerT_6092-T1
Valid prediction for Augustus_model.g3993.t1
Valid prediction for GeneMark_model.9982_t
Valid prediction for GeneMark_model.9963_t
Valid prediction for GlimmerHMM_glimmerT_6072-T1
Valid prediction for GlimmerHMM_glimmerT_6062-T1
Valid prediction for GlimmerHMM_glimmerT_6080-T1
Valid prediction for GlimmerHMM_glimmerT_6087-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9442, rend_intergenic: 6663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15993, rend_intergenic: 10683  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17368, rend_intergenic: 16096  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24550, rend_intergenic: 20846  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33766, rend_intergenic: 24641  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46052, rend_intergenic: 38654  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52547, rend_intergenic: 46127  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67403, rend_intergenic: 54466  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87106, rend_intergenic: 69815  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171861, rend_intergenic: 160358  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 189297
-exon list size: 761


building trellis

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68.7    
68.8    
68.9    
69.1    
69.2    
69.3    
69.5    
69.6    
69.7    
69.9    
70.0    
70.1    
70.2    
70.4    
70.5    
70.6    
70.8    
70.9    
71.0    
71.2    
71.3    
71.4    
71.6    
71.7    
71.8    
72.0    
72.1    
72.2    
72.3    
72.5    
72.6    
72.7    
72.9    
73.0    
73.1    
73.3    
73.4    
73.5    
73.7    
73.8    
73.9    
74.0    
74.2    
74.3    
74.4    
74.6    
74.7    
74.8    
75.0    
75.1    
75.2    
75.4    
75.5    
75.6    
75.8    
75.9    
76.0    
76.1    
76.3    
76.4    
76.5    
76.7    
76.8    
76.9    
77.1    
77.2    
77.3    
77.5    
77.6    
77.7    
77.9    
78.0    
78.1    
78.2    
78.4    
78.5    
78.6    
78.8    
78.9    
79.0    
79.2    
79.3    
79.4    
79.6    
79.7    
79.8    
79.9    
80.1    
80.2    
80.3    
80.5    
80.6    
80.7    
80.9    
81.0    
81.1    
81.3    
81.4    
81.5    
81.7    
81.8    
81.9    
82.0    
82.2    
82.3    
82.4    
82.6    
82.7    
82.8    
83.0    
83.1    
83.2    
83.4    
83.5    
83.6    
83.7    
83.9    
84.0    
84.1    
84.3    
84.4    
84.5    
84.7    
84.8    
84.9    
85.1    
85.2    
85.3    
85.5    
85.6    
85.7    
85.8    
86.0    
86.1    
86.2    
86.4    
86.5    
86.6    
86.8    
86.9    
87.0    
87.2    
87.3    
87.4    
87.5    
87.7    
87.8    
87.9    
88.1    
88.2    
88.3    
88.5    
88.6    
88.7    
88.9    
89.0    
89.1    
89.3    
89.4    
89.5    
89.6    
89.8    
89.9    
90.0    
90.2    
90.3    
90.4    
90.6    
90.7    
90.8    
91.0    
91.1    
91.2    
91.3    
91.5    
91.6    
91.7    
91.9    
92.0    
92.1    
92.3    
92.4    
92.5    
92.7    
92.8    
92.9    
93.1    
93.2    
93.3    
93.4    
93.6    
93.7    
93.8    
94.0    
94.1    
94.2    
94.4    
94.5    
94.6    
94.8    
94.9    
95.0    
95.2    
95.3    
95.4    
95.5    
95.7    
95.8    
95.9    
96.1    
96.2    
96.3    
96.5    
96.6    
96.7    
96.9    
97.0    
97.1    
97.2    
97.4    
97.5    
97.6    
97.8    
97.9    
98.0    
98.2    
98.3    
98.4    
98.6    
98.7    
98.8    
99.0    
99.1    
99.2    
99.3    
99.5    
99.6    
99.7    
99.9    
-found 41 predictions from path traversal
Error with prediction: snap lend_intergenic: 9442, rend_intergenic: 6663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15993, rend_intergenic: 10683  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17368, rend_intergenic: 16096  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24550, rend_intergenic: 20846  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33766, rend_intergenic: 24641  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46052, rend_intergenic: 38654  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52547, rend_intergenic: 46127  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67403, rend_intergenic: 54466  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87106, rend_intergenic: 69815  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171861, rend_intergenic: 160358  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support