-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_10/scaffold_10_9053337-9285483

-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 Augustus_model.g17225.t1
Valid prediction for pasa_asmbl_4643.p1
Valid prediction for Augustus_model.g17239.t1
Valid prediction for GeneMark_model.43897_t
Valid prediction for GlimmerHMM_glimmerT_25671-T1
Valid prediction for GeneMark_model.43890_t
Valid prediction for CodingQuarry_transcript_5508-T1
Valid prediction for GlimmerHMM_glimmerT_25662-T1
Valid prediction for GeneMark_model.43868_t
Valid prediction for Augustus_model.g17233.t1
Valid prediction for snap_scaffold_10-snap.1799-T1
Valid prediction for GeneMark_model.43859_t
Valid prediction for snap_scaffold_10-snap.1778-T1
Valid prediction for GeneMark_model.43854_t
Valid prediction for snap_scaffold_10-snap.1788-T1
Valid prediction for snap_scaffold_10-snap.1766-T1
Valid prediction for GeneMark_model.43907_t
Valid prediction for GlimmerHMM_glimmerT_25668-T1
Valid prediction for Augustus_model.g17235.t1
Valid prediction for snap_scaffold_10-snap.1776-T1
Valid prediction for GlimmerHMM_glimmerT_25675-T1
Valid prediction for GeneMark_model.43886_t
Valid prediction for GlimmerHMM_glimmerT_25660-T1
Valid prediction for GeneMark_model.43894_t
Valid prediction for GeneMark_model.43870_t
Valid prediction for GlimmerHMM_glimmerT_25678-T1
Valid prediction for GeneMark_model.43903_t
Valid prediction for snap_scaffold_10-snap.1767-T1
Valid prediction for HiQ_model.g17227.t1
Valid prediction for GlimmerHMM_glimmerT_25670-T1
Valid prediction for GeneMark_model.43853_t
Valid prediction for snap_scaffold_10-snap.1760-T1
Valid prediction for GeneMark_model.43866_t
Valid prediction for GlimmerHMM_glimmerT_25676-T1
Valid prediction for GeneMark_model.43881_t
Valid prediction for GeneMark_model.43875_t
Valid prediction for snap_scaffold_10-snap.1768-T1
Valid prediction for snap_scaffold_10-snap.1800-T1
Valid prediction for GlimmerHMM_glimmerT_25677-T1
Valid prediction for GeneMark_model.43872_t
Valid prediction for GeneMark_model.43863_t
Valid prediction for snap_scaffold_10-snap.1764-T1
Valid prediction for Augustus_model.g17240.t1
Valid prediction for snap_scaffold_10-snap.1781-T1
Valid prediction for CodingQuarry_transcript_5506-T1
Valid prediction for GeneMark_model.43856_t
Valid prediction for snap_scaffold_10-snap.1793-T1
Valid prediction for GeneMark_model.43916_t
Valid prediction for GeneMark_model.43914_t
Valid prediction for GeneMark_model.43884_t
Valid prediction for snap_scaffold_10-snap.1785-T1
Valid prediction for GlimmerHMM_glimmerT_25664-T1
Valid prediction for Augustus_model.g17229.t1
Valid prediction for snap_scaffold_10-snap.1795-T1
Valid prediction for GeneMark_model.43892_t
Valid prediction for GeneMark_model.43902_t
Valid prediction for snap_scaffold_10-snap.1771-T1
Valid prediction for snap_scaffold_10-snap.1786-T1
Valid prediction for snap_scaffold_10-snap.1792-T1
Valid prediction for snap_scaffold_10-snap.1780-T1
Valid prediction for snap_scaffold_10-snap.1755-T1
Valid prediction for snap_scaffold_10-snap.1791-T1
Valid prediction for snap_scaffold_10-snap.1762-T1
Valid prediction for pasa_asmbl_4644.p1
Valid prediction for snap_scaffold_10-snap.1756-T1
Couldn't classify 40776, 40837
Sorry, prediction pasa_asmbl_4645.p1 fails validation.
(CGA)	 AT	40776-40837	GT	AGG
(TGT)	 AG	41051-41115	GT	TGG
(GTC)	 AG	41318-41423	GT	AGG
(TTA)	 AG	41549-41637	GT	CAG
(CAT)	 AG	41718-41765	GT	AGG
(CGG)	 AG	41847-41989	GT	AGG
(CCT)	 AG	42099-42197	CC	GAC
-recovered pasa_asmbl_4645.p1, terminal, 42099, 42197
-recovered pasa_asmbl_4645.p1, internal, 41051, 41115
-recovered pasa_asmbl_4645.p1, internal, 41318, 41423
-recovered pasa_asmbl_4645.p1, internal, 41549, 41637
-recovered pasa_asmbl_4645.p1, internal, 41718, 41765
-recovered pasa_asmbl_4645.p1, internal, 41847, 41989
Valid prediction for GeneMark_model.43889_t
Valid prediction for GeneMark_model.43905_t
Valid prediction for GeneMark_model.43879_t
Valid prediction for snap_scaffold_10-snap.1757-T1
Valid prediction for GeneMark_model.43895_t
Valid prediction for snap_scaffold_10-snap.1783-T1
Valid prediction for snap_scaffold_10-snap.1794-T1
Valid prediction for GeneMark_model.43910_t
Valid prediction for GeneMark_model.43861_t
Valid prediction for GeneMark_model.43909_t
Valid prediction for GeneMark_model.43877_t
Valid prediction for GeneMark_model.43899_t

-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: -)Couldn't classify 197807, 197839
Sorry, prediction pasa_asmbl_3581.p1 fails validation.
(CGC)	 CT	197807-197839	GT	AGG
(GTA)	 AG	198325-198494	GT	TGG
(GTT)	 AG	198698-198815	GC	GAG
-recovered pasa_asmbl_3581.p1, terminal, 198698, 198815
-recovered pasa_asmbl_3581.p1, internal, 198325, 198494
-recovered pasa_asmbl_3581.p1, internal, 198698, 198815
Valid prediction for Augustus_model.g17230.t1
Valid prediction for CodingQuarry_transcript_5509-T1
Valid prediction for snap_scaffold_10-snap.1774-T1
Valid prediction for GeneMark_model.43896_t
Valid prediction for snap_scaffold_10-snap.1763-T1
Valid prediction for snap_scaffold_10-snap.1752-T1
Valid prediction for GeneMark_model.43912_t
Valid prediction for GlimmerHMM_glimmerT_25672-T1
Valid prediction for Augustus_model.g17238.t1
Valid prediction for GeneMark_model.43882_t
Couldn't classify 63343, 63550
Sorry, prediction pasa_asmbl_3588.p1 fails validation.
(ATG)	 CC	61656-61669	GT	AGG
(TAC)	 AG	62626-62981	GT	GGG
(TCA)	 AG	63068-63176	GT	CGG
(GTA)	 AG	63343-63550	AT	ACA
-recovered pasa_asmbl_3588.p1, initial, 61656, 61669
-recovered pasa_asmbl_3588.p1, internal, 62626, 62981
-recovered pasa_asmbl_3588.p1, internal, 63068, 63176
Valid prediction for GeneMark_model.43906_t
Valid prediction for GeneMark_model.43908_t
Valid prediction for GeneMark_model.43871_t
Couldn't classify 196416, 196606
Sorry, prediction pasa_asmbl_3583.p1 fails validation.
(ATG)	 AA	192492-192553	GT	GGG
(AAA)	 AG	193520-193868	GT	AGG
(ATC)	 AG	194155-194348	GT	AAG
(GTA)	 AG	194543-194702	GT	AGG
(GTC)	 AG	194962-195180	GT	AGG
(GAA)	 AG	195416-195583	GT	AGG
(GTT)	 AG	195718-195804	GT	AGG
(GTG)	 AG	195920-196069	GT	AGG
(GAC)	 AG	196211-196319	GT	AGG
(CCC)	 AG	196416-196606	GG	CAG
-recovered pasa_asmbl_3583.p1, initial, 192492, 192553
-recovered pasa_asmbl_3583.p1, internal, 193520, 193868
-recovered pasa_asmbl_3583.p1, internal, 194155, 194348
-recovered pasa_asmbl_3583.p1, internal, 194543, 194702
-recovered pasa_asmbl_3583.p1, internal, 194962, 195180
-recovered pasa_asmbl_3583.p1, internal, 195416, 195583
-recovered pasa_asmbl_3583.p1, internal, 195718, 195804
-recovered pasa_asmbl_3583.p1, internal, 195920, 196069
-recovered pasa_asmbl_3583.p1, internal, 196211, 196319
Valid prediction for GeneMark_model.43885_t
Valid prediction for snap_scaffold_10-snap.1753-T1
Valid prediction for snap_scaffold_10-snap.1754-T1
Valid prediction for GeneMark_model.43913_t
Valid prediction for GeneMark_model.43851_t
Valid prediction for GlimmerHMM_glimmerT_25659-T1
Valid prediction for GeneMark_model.43893_t
Valid prediction for snap_scaffold_10-snap.1797-T1
Valid prediction for GeneMark_model.43901_t
Valid prediction for snap_scaffold_10-snap.1751-T1
Valid prediction for GeneMark_model.43874_t
Valid prediction for GlimmerHMM_glimmerT_25663-T1
Valid prediction for GeneMark_model.43864_t
Valid prediction for snap_scaffold_10-snap.1761-T1
Valid prediction for GeneMark_model.43878_t
Valid prediction for Augustus_model.g17232.t1
Valid prediction for GeneMark_model.43891_t
Valid prediction for GlimmerHMM_glimmerT_25661-T1
Valid prediction for GeneMark_model.43887_t
Valid prediction for snap_scaffold_10-snap.1750-T1
Valid prediction for Augustus_model.g17237.t1
Valid prediction for CodingQuarry_transcript_5507-T1
Valid prediction for Augustus_model.g17234.t1
Valid prediction for Augustus_model.g17231.t1
Couldn't classify 214299, 214323
Sorry, prediction pasa_asmbl_3579.p1 fails validation.
(GGC)	 CT	214299-214323	GT	ACG
(GGC)	 AG	215397-217864	TT	AGT
-recovered pasa_asmbl_3579.p1, terminal, 215397, 217864
Couldn't classify 187062, 187154
Sorry, prediction pasa_asmbl_3584.p1 fails validation.
(GAT)	 CA	187062-187154	GT	AGG
(ACC)	 AG	187596-187703	GT	AGG
(GCC)	 AG	187849-188031	GT	AGG
(GCT)	 AG	188284-188377	GT	AGG
(AAT)	 AG	188490-188605	GT	TGG
(CTA)	 AG	188725-188844	CC	GAC
-recovered pasa_asmbl_3584.p1, terminal, 188725, 188844
-recovered pasa_asmbl_3584.p1, internal, 187596, 187703
-recovered pasa_asmbl_3584.p1, internal, 187849, 188031
-recovered pasa_asmbl_3584.p1, internal, 188284, 188377
-recovered pasa_asmbl_3584.p1, internal, 188490, 188605
Valid prediction for snap_scaffold_10-snap.1789-T1
Valid prediction for GlimmerHMM_glimmerT_25673-T1
Valid prediction for CodingQuarry_transcript_5504-T1
Valid prediction for Augustus_model.g17228.t1
Valid prediction for GeneMark_model.43900_t
Valid prediction for snap_scaffold_10-snap.1773-T1
Couldn't classify 63730, 63937
Sorry, prediction pasa_asmbl_3587.p1 fails validation.
(CAG)	 GT	63730-63937	GT	CAG
(GCA)	 AG	64845-65012	GT	GGG
(GTT)	 AG	65298-65477	GT	AGG
(GTG)	 AG	65600-65746	GT	AAG
(CTC)	 AG	65890-66095	CT	AGC
-recovered pasa_asmbl_3587.p1, terminal, 65890, 66095
-recovered pasa_asmbl_3587.p1, internal, 64845, 65012
-recovered pasa_asmbl_3587.p1, internal, 65298, 65477
-recovered pasa_asmbl_3587.p1, internal, 65600, 65746
Valid prediction for GlimmerHMM_glimmerT_25669-T1
Valid prediction for snap_scaffold_10-snap.1801-T1
Valid prediction for GeneMark_model.43883_t
Valid prediction for snap_scaffold_10-snap.1777-T1
Valid prediction for GeneMark_model.43915_t
Valid prediction for snap_scaffold_10-snap.1796-T1
Valid prediction for snap_scaffold_10-snap.1772-T1
Valid prediction for CodingQuarry_transcript_5503-T1
Valid prediction for snap_scaffold_10-snap.1769-T1
Valid prediction for Augustus_model.g17223.t1
Valid prediction for Augustus_model.g17236.t1
Valid prediction for GeneMark_model.43880_t
Valid prediction for Augustus_model.g17224.t1
Valid prediction for GeneMark_model.43911_t
Valid prediction for snap_scaffold_10-snap.1790-T1
Valid prediction for GeneMark_model.43873_t
Valid prediction for GeneMark_model.43849_t
Valid prediction for snap_scaffold_10-snap.1770-T1
Valid prediction for pasa_asmbl_3570.p1
Valid prediction for GlimmerHMM_glimmerT_25674-T1
Valid prediction for snap_scaffold_10-snap.1798-T1
Valid prediction for GeneMark_model.43862_t
Valid prediction for GeneMark_model.43858_t
Valid prediction for HiQ_model.g17226.t1
Valid prediction for GeneMark_model.43860_t
Valid prediction for GeneMark_model.43888_t
Valid prediction for snap_scaffold_10-snap.1758-T1
Valid prediction for snap_scaffold_10-snap.1787-T1
Valid prediction for snap_scaffold_10-snap.1782-T1
Valid prediction for GeneMark_model.43876_t
Valid prediction for GeneMark_model.43850_t
Valid prediction for GeneMark_model.43855_t
Valid prediction for snap_scaffold_10-snap.1775-T1
Valid prediction for GeneMark_model.43867_t
Valid prediction for GeneMark_model.43904_t
Valid prediction for GeneMark_model.43898_t
Valid prediction for GlimmerHMM_glimmerT_25667-T1
Valid prediction for GeneMark_model.43869_t
Valid prediction for GlimmerHMM_glimmerT_25665-T1
Valid prediction for GlimmerHMM_glimmerT_25666-T1
Valid prediction for snap_scaffold_10-snap.1784-T1
Valid prediction for snap_scaffold_10-snap.1759-T1
Valid prediction for GeneMark_model.43857_t
Valid prediction for snap_scaffold_10-snap.1779-T1
Valid prediction for GeneMark_model.43852_t
Valid prediction for snap_scaffold_10-snap.1765-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 48722, rend_intergenic: 44022  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56626, rend_intergenic: 49732  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87816, rend_intergenic: 67904  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104463, rend_intergenic: 92546  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121456, rend_intergenic: 104915  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127619, rend_intergenic: 123863  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135939, rend_intergenic: 132179  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149089, rend_intergenic: 143351  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159485, rend_intergenic: 153878  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175604, rend_intergenic: 169534  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 219893, rend_intergenic: 208264  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 229845, rend_intergenic: 223716  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 232147
-exon list size: 770


building trellis

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60.4    
60.5    
60.6    
60.8    
60.9    
61.0    
61.1    
61.3    
61.4    
61.5    
61.7    
61.8    
61.9    
62.0    
62.2    
62.3    
62.4    
62.6    
62.7    
62.8    
63.0    
63.1    
63.2    
63.3    
63.5    
63.6    
63.7    
63.9    
64.0    
64.1    
64.2    
64.4    
64.5    
64.6    
64.8    
64.9    
65.0    
65.2    
65.3    
65.4    
65.5    
65.7    
65.8    
65.9    
66.1    
66.2    
66.3    
66.5    
66.6    
66.7    
66.8    
67.0    
67.1    
67.2    
67.4    
67.5    
67.6    
67.7    
67.9    
68.0    
68.1    
68.3    
68.4    
68.5    
68.7    
68.8    
68.9    
69.0    
69.2    
69.3    
69.4    
69.6    
69.7    
69.8    
69.9    
70.1    
70.2    
70.3    
70.5    
70.6    
70.7    
70.9    
71.0    
71.1    
71.2    
71.4    
71.5    
71.6    
71.8    
71.9    
72.0    
72.2    
72.3    
72.4    
72.5    
72.7    
72.8    
72.9    
73.1    
73.2    
73.3    
73.4    
73.6    
73.7    
73.8    
74.0    
74.1    
74.2    
74.4    
74.5    
74.6    
74.7    
74.9    
75.0    
75.1    
75.3    
75.4    
75.5    
75.6    
75.8    
75.9    
76.0    
76.2    
76.3    
76.4    
76.6    
76.7    
76.8    
76.9    
77.1    
77.2    
77.3    
77.5    
77.6    
77.7    
77.8    
78.0    
78.1    
78.2    
78.4    
78.5    
78.6    
78.8    
78.9    
79.0    
79.1    
79.3    
79.4    
79.5    
79.7    
79.8    
79.9    
80.1    
80.2    
80.3    
80.4    
80.6    
80.7    
80.8    
81.0    
81.1    
81.2    
81.3    
81.5    
81.6    
81.7    
81.9    
82.0    
82.1    
82.3    
82.4    
82.5    
82.6    
82.8    
82.9    
83.0    
83.2    
83.3    
83.4    
83.5    
83.7    
83.8    
83.9    
84.1    
84.2    
84.3    
84.5    
84.6    
84.7    
84.8    
85.0    
85.1    
85.2    
85.4    
85.5    
85.6    
85.8    
85.9    
86.0    
86.1    
86.3    
86.4    
86.5    
86.7    
86.8    
86.9    
87.0    
87.2    
87.3    
87.4    
87.6    
87.7    
87.8    
88.0    
88.1    
88.2    
88.3    
88.5    
88.6    
88.7    
88.9    
89.0    
89.1    
89.2    
89.4    
89.5    
89.6    
89.8    
89.9    
90.0    
90.2    
90.3    
90.4    
90.5    
90.7    
90.8    
90.9    
91.1    
91.2    
91.3    
91.5    
91.6    
91.7    
91.8    
92.0    
92.1    
92.2    
92.4    
92.5    
92.6    
92.7    
92.9    
93.0    
93.1    
93.3    
93.4    
93.5    
93.7    
93.8    
93.9    
94.0    
94.2    
94.3    
94.4    
94.6    
94.7    
94.8    
94.9    
95.1    
95.2    
95.3    
95.5    
95.6    
95.7    
95.9    
96.0    
96.1    
96.2    
96.4    
96.5    
96.6    
96.8    
96.9    
97.0    
97.2    
97.3    
97.4    
97.5    
97.7    
97.8    
97.9    
98.1    
98.2    
98.3    
98.4    
98.6    
98.7    
98.8    
99.0    
99.1    
99.2    
99.4    
99.5    
99.6    
99.7    
99.9    
-found 44 predictions from path traversal
Error with prediction: snap lend_intergenic: 48722, rend_intergenic: 44022  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56626, rend_intergenic: 49732  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87816, rend_intergenic: 67904  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104463, rend_intergenic: 92546  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121456, rend_intergenic: 104915  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127619, rend_intergenic: 123863  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135939, rend_intergenic: 132179  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149089, rend_intergenic: 143351  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159485, rend_intergenic: 153878  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175604, rend_intergenic: 169534  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 219893, rend_intergenic: 208264  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 229845, rend_intergenic: 223716  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 28 predictions persist after filtering for low support