-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_8/scaffold_8_8712202-8928352

-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 GlimmerHMM_glimmerT_20636-T1
Valid prediction for snap_scaffold_8-snap.1732-T1
Couldn't classify 31956, 32078
Sorry, prediction pasa_asmbl_52016.p1 fails validation.
(AAT)	 AG	31956-32078	GT	AGG
(GAC)	 AG	32656-32709	GT	GGG
(GGG)	 AG	32900-33018	GT	CGG
(GAT)	 AG	33419-33513	GT	GGG
(GAG)	 AG	33611-33734	GT	CGG
(TGA)	 AG	34235-34392	GT	TGG
(GGC)	 AG	35142-35264	GT	AGG
(GAT)	 AG	35548-35690	CC	AAC
-recovered pasa_asmbl_52016.p1, terminal, 35548, 35690
-recovered pasa_asmbl_52016.p1, internal, 31956, 32078
-recovered pasa_asmbl_52016.p1, internal, 32656, 32709
-recovered pasa_asmbl_52016.p1, internal, 32900, 33018
-recovered pasa_asmbl_52016.p1, internal, 33419, 33513
-recovered pasa_asmbl_52016.p1, internal, 33611, 33734
-recovered pasa_asmbl_52016.p1, internal, 34235, 34392
-recovered pasa_asmbl_52016.p1, internal, 35142, 35264
Valid prediction for GlimmerHMM_glimmerT_20645-T1
Couldn't classify 26747, 26790
Couldn't classify 29650, 29721
Sorry, prediction pasa_asmbl_52014.p1 fails validation.
(CTC)	 TG	26747-26790	GT	CTG
(CAA)	 AG	27115-27252	GT	AGG
(GTC)	 AG	27401-27520	GT	AAG
(GCT)	 AG	27805-27927	GT	AGG
(GGT)	 AG	28824-29010	GT	GTG
(GAG)	 AG	29650-29721	AA	CCA
-recovered pasa_asmbl_52014.p1, internal, 27115, 27252
-recovered pasa_asmbl_52014.p1, internal, 27401, 27520
-recovered pasa_asmbl_52014.p1, internal, 27805, 27927
-recovered pasa_asmbl_52014.p1, internal, 28824, 29010
Valid prediction for snap_scaffold_8-snap.1728-T1
Valid prediction for GeneMark_model.35265_t
Valid prediction for CodingQuarry_transcript_59567-T1
Valid prediction for GlimmerHMM_glimmerT_20651-T1
Valid prediction for GlimmerHMM_glimmerT_20654-T1
Valid prediction for GeneMark_model.35277_t
Valid prediction for snap_scaffold_8-snap.1734-T1
Valid prediction for snap_scaffold_8-snap.1706-T1
Valid prediction for GeneMark_model.35267_t
Valid prediction for GeneMark_model.35291_t
Valid prediction for snap_scaffold_8-snap.1727-T1
Couldn't classify 8278, 8368
Couldn't classify 15382, 15484
Sorry, prediction pasa_asmbl_52008.p1 fails validation.
(AGG)	 AC	8278-8368	GT	AGG
(GAG)	 AG	10284-10456	GT	AGG
(GGC)	 AG	12656-12868	GT	TTG
(GTG)	 AG	14841-14941	GT	AAG
(TCC)	 AG	15382-15484	GG	AAG
-recovered pasa_asmbl_52008.p1, internal, 10284, 10456
-recovered pasa_asmbl_52008.p1, internal, 12656, 12868
-recovered pasa_asmbl_52008.p1, internal, 14841, 14941
Valid prediction for snap_scaffold_8-snap.1725-T1
Valid prediction for Augustus_model.g13801.t1
Valid prediction for GlimmerHMM_glimmerT_20640-T1
Valid prediction for GeneMark_model.35298_t
Valid prediction for snap_scaffold_8-snap.1733-T1
Valid prediction for GlimmerHMM_glimmerT_20658-T1
Valid prediction for GeneMark_model.35293_t
Valid prediction for snap_scaffold_8-snap.1720-T1
Valid prediction for snap_scaffold_8-snap.1709-T1
Couldn't classify 17778, 17949
Sorry, prediction pasa_asmbl_52011.p1 fails validation.
(CTC)	 AT	17778-17949	GT	TGG
(AAT)	 AG	19078-19697	CG	AAC
-recovered pasa_asmbl_52011.p1, terminal, 19078, 19697
Valid prediction for Augustus_model.g13806.t1
Valid prediction for GeneMark_model.35289_t
Valid prediction for snap_scaffold_8-snap.1705-T1
Valid prediction for snap_scaffold_8-snap.1710-T1
Valid prediction for snap_scaffold_8-snap.1736-T1
Valid prediction for CodingQuarry_transcript_59571-T1
Valid prediction for GeneMark_model.35295_t
Valid prediction for GlimmerHMM_glimmerT_20637-T1
Valid prediction for GeneMark_model.35270_t
Valid prediction for HiQ_model.g13811.t1
Valid prediction for snap_scaffold_8-snap.1712-T1
Valid prediction for pasa_asmbl_52026.p1
Valid prediction for snap_scaffold_8-snap.1711-T1
Valid prediction for GlimmerHMM_glimmerT_20657-T1
Valid prediction for Augustus_model.g13815.t1
Valid prediction for HiQ_model.g13809.t1
Valid prediction for Augustus_model.g13808.t1
Valid prediction for GeneMark_model.35259_t
Valid prediction for GlimmerHMM_glimmerT_20652-T1
Valid prediction for Augustus_model.g13802.t1
Couldn't classify 171378, 171416
Sorry, prediction pasa_asmbl_52025.p1 fails validation.
(CTC)	 TC	171378-171416	GT	TGG
(GTC)	 AG	171748-171903	GT	TGG
(GAT)	 AG	172340-172435	GT	GGG
(ATC)	 AG	172582-172677	AG	GAA
-recovered pasa_asmbl_52025.p1, terminal, 172582, 172677
-recovered pasa_asmbl_52025.p1, internal, 171748, 171903
-recovered pasa_asmbl_52025.p1, internal, 172340, 172435
Valid prediction for GlimmerHMM_glimmerT_20633-T1
Valid prediction for CodingQuarry_transcript_59568-T1
Valid prediction for GeneMark_model.35257_t
Valid prediction for HiQ_model.g13812.t1
Valid prediction for HiQ_model.g13807.t1
Valid prediction for GeneMark_model.35287_t
Valid prediction for snap_scaffold_8-snap.1722-T1
Valid prediction for snap_scaffold_8-snap.1714-T1
Valid prediction for GeneMark_model.35282_t
Valid prediction for GeneMark_model.35263_t
Valid prediction for GeneMark_model.35253_t
Valid prediction for snap_scaffold_8-snap.1738-T1
Valid prediction for GeneMark_model.35279_t
Valid prediction for GlimmerHMM_glimmerT_20649-T1
Valid prediction for pasa_asmbl_52021.p1
Valid prediction for HiQ_model.g13803.t1
Valid prediction for snap_scaffold_8-snap.1730-T1
Valid prediction for GeneMark_model.35274_t
Valid prediction for GeneMark_model.35284_t
Valid prediction for GlimmerHMM_glimmerT_20634-T1
Valid prediction for GeneMark_model.35261_t
Valid prediction for GeneMark_model.35268_t
Valid prediction for GlimmerHMM_glimmerT_20647-T1
Valid prediction for GeneMark_model.35297_t
Valid prediction for CodingQuarry_transcript_59572-T1
Valid prediction for pasa_asmbl_52022.p1
Valid prediction for CodingQuarry_transcript_59569-T1
Valid prediction for snap_scaffold_8-snap.1716-T1
Valid prediction for GeneMark_model.35255_t
Valid prediction for pasa_asmbl_52023.p1

-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.35252_t
Valid prediction for Augustus_model.g13813.t1
Valid prediction for Augustus_model.g13805.t1
Valid prediction for GlimmerHMM_glimmerT_20646-T1
Valid prediction for snap_scaffold_8-snap.1735-T1
Valid prediction for GlimmerHMM_glimmerT_20641-T1
Valid prediction for GlimmerHMM_glimmerT_20656-T1
Valid prediction for GeneMark_model.35280_t
Valid prediction for GlimmerHMM_glimmerT_20655-T1
Valid prediction for GeneMark_model.35264_t
Valid prediction for GeneMark_model.35281_t
Valid prediction for GlimmerHMM_glimmerT_20635-T1
Valid prediction for GeneMark_model.35271_t
Valid prediction for GlimmerHMM_glimmerT_20643-T1
Couldn't classify 18994, 19112
Sorry, prediction pasa_asmbl_52974.p1 fails validation.
(TCT)	 CC	18994-19112	GC	TGG
(GAC)	 AG	19784-19857	GT	TGG
(GAG)	 AG	20078-20194	GT	TGG
(ACC)	 AG	20611-20841	GT	GAG
(TGG)	 AG	23169-23335	GT	AGG
(TGT)	 AG	24444-24537	GT	GTG
(ATG)	 AG	24849-24984	GT	ATG
(TCC)	 AG	25098-25209	GT	AGG
(CTG)	 AG	25319-25378	GT	AGG
(TCT)	 AG	25612-25656	GT	CAG
(GAA)	 AG	25777-25891	GT	GGG
(GAG)	 AG	26121-26255	GT	AGG
(AAG)	 AG	27032-27048	TG	GAT
add_exon() Sorry, pasa_asmbl_52974.p1 24849-24984-initial-1 is invalid.
-recovered pasa_asmbl_52974.p1, initial, 24849, 24984
-recovered pasa_asmbl_52974.p1, terminal, 27032, 27048
-recovered pasa_asmbl_52974.p1, internal, 19784, 19857
-recovered pasa_asmbl_52974.p1, internal, 20078, 20194
-recovered pasa_asmbl_52974.p1, internal, 20611, 20841
-recovered pasa_asmbl_52974.p1, internal, 23169, 23335
-recovered pasa_asmbl_52974.p1, internal, 24444, 24537
-recovered pasa_asmbl_52974.p1, internal, 24849, 24984
-recovered pasa_asmbl_52974.p1, internal, 25098, 25209
-recovered pasa_asmbl_52974.p1, internal, 25319, 25378
-recovered pasa_asmbl_52974.p1, internal, 25612, 25656
-recovered pasa_asmbl_52974.p1, internal, 25777, 25891
-recovered pasa_asmbl_52974.p1, internal, 26121, 26255
Valid prediction for GeneMark_model.35258_t
Valid prediction for snap_scaffold_8-snap.1715-T1
Valid prediction for snap_scaffold_8-snap.1707-T1
Couldn't classify 45399, 45585
Sorry, prediction pasa_asmbl_52969.p1 fails validation.
(ACT)	 CA	45399-45585	GT	AAG
(GGA)	 AG	45913-45950	GT	TGG
(ATT)	 AG	46167-46241	GT	AGG
(GTG)	 AG	46328-46381	GT	TGG
(AGG)	 AG	46512-46601	GT	TAG
(TCA)	 AG	46764-46837	GT	AGG
(TGG)	 AG	47041-47129	GT	TGG
(TGT)	 AG	47328-47407	GT	TGG
(GAA)	 AG	47612-47692	GT	TGG
(GTC)	 AG	47816-47902	GG	GAG
-recovered pasa_asmbl_52969.p1, terminal, 47816, 47902
-recovered pasa_asmbl_52969.p1, internal, 45913, 45950
-recovered pasa_asmbl_52969.p1, internal, 46167, 46241
-recovered pasa_asmbl_52969.p1, internal, 46328, 46381
-recovered pasa_asmbl_52969.p1, internal, 46512, 46601
-recovered pasa_asmbl_52969.p1, internal, 46764, 46837
-recovered pasa_asmbl_52969.p1, internal, 47041, 47129
-recovered pasa_asmbl_52969.p1, internal, 47328, 47407
-recovered pasa_asmbl_52969.p1, internal, 47612, 47692
Couldn't classify 34573, 34749
Sorry, prediction pasa_asmbl_52971.p1 fails validation.
(GTC)	 AG	34573-34749	GT	CGG
(GAC)	 AG	35491-35589	GT	TGG
(ATC)	 AG	36436-36600	GG	GAG
-recovered pasa_asmbl_52971.p1, terminal, 36436, 36600
-recovered pasa_asmbl_52971.p1, internal, 34573, 34749
-recovered pasa_asmbl_52971.p1, internal, 35491, 35589
Valid prediction for snap_scaffold_8-snap.1704-T1
Couldn't classify 128523, 128660
Couldn't classify 129790, 129802
Sorry, prediction pasa_asmbl_52968.p1 fails validation.
(GTG)	 GG	128523-128660	GT	AGG
(GAG)	 AG	128854-129015	GT	AGG
(AGT)	 AG	129095-129247	GT	AGG
(GCC)	 AG	129463-129605	GT	AAG
(ACA)	 AG	129790-129802	AC	AGA
-recovered pasa_asmbl_52968.p1, internal, 128854, 129015
-recovered pasa_asmbl_52968.p1, internal, 129095, 129247
-recovered pasa_asmbl_52968.p1, internal, 129463, 129605
Valid prediction for snap_scaffold_8-snap.1717-T1
Valid prediction for GeneMark_model.35254_t
Valid prediction for snap_scaffold_8-snap.1721-T1
Valid prediction for GeneMark_model.35283_t
Valid prediction for snap_scaffold_8-snap.1729-T1
Valid prediction for Augustus_model.g13804.t1
Valid prediction for GlimmerHMM_glimmerT_20650-T1
Valid prediction for GeneMark_model.35276_t
Valid prediction for snap_scaffold_8-snap.1737-T1
Valid prediction for GeneMark_model.35275_t
Valid prediction for CodingQuarry_transcript_59570-T1
Valid prediction for snap_scaffold_8-snap.1723-T1
Valid prediction for HiQ_model.g13814.t1
Valid prediction for GeneMark_model.35296_t
Valid prediction for snap_scaffold_8-snap.1731-T1
Valid prediction for snap_scaffold_8-snap.1718-T1
Valid prediction for GeneMark_model.35294_t
Valid prediction for GeneMark_model.35285_t
Valid prediction for GeneMark_model.35278_t
Valid prediction for GlimmerHMM_glimmerT_20639-T1
Valid prediction for GeneMark_model.35272_t
Valid prediction for GeneMark_model.35288_t
Valid prediction for snap_scaffold_8-snap.1726-T1
Valid prediction for GlimmerHMM_glimmerT_20644-T1
Valid prediction for GlimmerHMM_glimmerT_20648-T1
Valid prediction for GlimmerHMM_glimmerT_20642-T1
Valid prediction for GeneMark_model.35260_t
Valid prediction for snap_scaffold_8-snap.1739-T1
Valid prediction for GlimmerHMM_glimmerT_20653-T1
Valid prediction for GeneMark_model.35269_t
Valid prediction for snap_scaffold_8-snap.1713-T1
Valid prediction for GeneMark_model.35256_t
Valid prediction for HiQ_model.g13810.t1
Couldn't classify 133269, 133524
Sorry, prediction pasa_asmbl_52966.p1 fails validation.
(TCA)	 CG	133269-133524	GT	AGG
(AGC)	 AG	134640-134801	GT	AGG
(TGC)	 AG	135303-135694	CA	AAC
-recovered pasa_asmbl_52966.p1, terminal, 135303, 135694
-recovered pasa_asmbl_52966.p1, internal, 134640, 134801
Valid prediction for GeneMark_model.35273_t
Valid prediction for GlimmerHMM_glimmerT_20638-T1
Valid prediction for snap_scaffold_8-snap.1724-T1
Valid prediction for snap_scaffold_8-snap.1719-T1
Valid prediction for GeneMark_model.35266_t
Valid prediction for GeneMark_model.35292_t
Valid prediction for GeneMark_model.35290_t
Valid prediction for GeneMark_model.35286_t
Valid prediction for snap_scaffold_8-snap.1708-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17470, rend_intergenic: 8012  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22723, rend_intergenic: 17699  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35702, rend_intergenic: 24174  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56328, rend_intergenic: 49083  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89930, rend_intergenic: 80483  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111666, rend_intergenic: 111400  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127925, rend_intergenic: 122359  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140874, rend_intergenic: 138041  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161075, rend_intergenic: 159070  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182066, rend_intergenic: 179552  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192960, rend_intergenic: 189013  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 210878, rend_intergenic: 203948  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 216151
-exon list size: 648


building trellis

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59.5    
59.7    
59.8    
60.0    
60.2    
60.3    
60.5    
60.6    
60.8    
60.9    
61.1    
61.2    
61.4    
61.5    
61.7    
61.8    
62.0    
62.2    
62.3    
62.5    
62.6    
62.8    
62.9    
63.1    
63.2    
63.4    
63.5    
63.7    
63.8    
64.0    
64.2    
64.3    
64.5    
64.6    
64.8    
64.9    
65.1    
65.2    
65.4    
65.5    
65.7    
65.8    
66.0    
66.2    
66.3    
66.5    
66.6    
66.8    
66.9    
67.1    
67.2    
67.4    
67.5    
67.7    
67.8    
68.0    
68.2    
68.3    
68.5    
68.6    
68.8    
68.9    
69.1    
69.2    
69.4    
69.5    
69.7    
69.8    
70.0    
70.2    
70.3    
70.5    
70.6    
70.8    
70.9    
71.1    
71.2    
71.4    
71.5    
71.7    
71.8    
72.0    
72.2    
72.3    
72.5    
72.6    
72.8    
72.9    
73.1    
73.2    
73.4    
73.5    
73.7    
73.8    
74.0    
74.2    
74.3    
74.5    
74.6    
74.8    
74.9    
75.1    
75.2    
75.4    
75.5    
75.7    
75.8    
76.0    
76.2    
76.3    
76.5    
76.6    
76.8    
76.9    
77.1    
77.2    
77.4    
77.5    
77.7    
77.8    
78.0    
78.2    
78.3    
78.5    
78.6    
78.8    
78.9    
79.1    
79.2    
79.4    
79.5    
79.7    
79.8    
80.0    
80.2    
80.3    
80.5    
80.6    
80.8    
80.9    
81.1    
81.2    
81.4    
81.5    
81.7    
81.8    
82.0    
82.2    
82.3    
82.5    
82.6    
82.8    
82.9    
83.1    
83.2    
83.4    
83.5    
83.7    
83.8    
84.0    
84.2    
84.3    
84.5    
84.6    
84.8    
84.9    
85.1    
85.2    
85.4    
85.5    
85.7    
85.8    
86.0    
86.2    
86.3    
86.5    
86.6    
86.8    
86.9    
87.1    
87.2    
87.4    
87.5    
87.7    
87.8    
88.0    
88.2    
88.3    
88.5    
88.6    
88.8    
88.9    
89.1    
89.2    
89.4    
89.5    
89.7    
89.8    
90.0    
90.2    
90.3    
90.5    
90.6    
90.8    
90.9    
91.1    
91.2    
91.4    
91.5    
91.7    
91.8    
92.0    
92.2    
92.3    
92.5    
92.6    
92.8    
92.9    
93.1    
93.2    
93.4    
93.5    
93.7    
93.8    
94.0    
94.2    
94.3    
94.5    
94.6    
94.8    
94.9    
95.1    
95.2    
95.4    
95.5    
95.7    
95.8    
96.0    
96.2    
96.3    
96.5    
96.6    
96.8    
96.9    
97.1    
97.2    
97.4    
97.5    
97.7    
97.8    
98.0    
98.2    
98.3    
98.5    
98.6    
98.8    
98.9    
99.1    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 17470, rend_intergenic: 8012  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22723, rend_intergenic: 17699  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35702, rend_intergenic: 24174  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56328, rend_intergenic: 49083  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89930, rend_intergenic: 80483  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111666, rend_intergenic: 111400  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127925, rend_intergenic: 122359  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140874, rend_intergenic: 138041  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161075, rend_intergenic: 159070  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182066, rend_intergenic: 179552  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192960, rend_intergenic: 189013  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 210878, rend_intergenic: 203948  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