-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_12/scaffold_12_11101280-11437899

-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_12-snap.2098-T1
Valid prediction for snap_scaffold_12-snap.2069-T1
Valid prediction for Augustus_model.g19889.t1
Valid prediction for snap_scaffold_12-snap.2103-T1
Valid prediction for snap_scaffold_12-snap.2104-T1
Valid prediction for Augustus_model.g19883.t1
Valid prediction for snap_scaffold_12-snap.2118-T1
Valid prediction for snap_scaffold_12-snap.2111-T1
Valid prediction for snap_scaffold_12-snap.2122-T1
Valid prediction for CodingQuarry_transcript_10389-T1
Valid prediction for GlimmerHMM_glimmerT_30055-T1
Valid prediction for snap_scaffold_12-snap.2090-T1
Valid prediction for snap_scaffold_12-snap.2080-T1
Valid prediction for snap_scaffold_12-snap.2101-T1
Valid prediction for snap_scaffold_12-snap.2082-T1
Couldn't classify 229323, 229467
Sorry, prediction pasa_asmbl_7963.p1 fails validation.
(AGA)	 CC	229323-229467	GT	AGG
(GTA)	 AG	229548-229882	GT	AGG
(GTG)	 AG	230066-231259	AC	AAA
-recovered pasa_asmbl_7963.p1, terminal, 230066, 231259
-recovered pasa_asmbl_7963.p1, internal, 229548, 229882
Valid prediction for GlimmerHMM_glimmerT_30056-T1
Valid prediction for GlimmerHMM_glimmerT_30049-T1
Valid prediction for snap_scaffold_12-snap.2100-T1
Valid prediction for GlimmerHMM_glimmerT_30058-T1
Valid prediction for GlimmerHMM_glimmerT_30048-T1
Valid prediction for Augustus_model.g19897.t1
Valid prediction for Augustus_model.g19893.t1
Valid prediction for Augustus_model.g19884.t1
Valid prediction for snap_scaffold_12-snap.2106-T1
Valid prediction for GlimmerHMM_glimmerT_30050-T1
Valid prediction for snap_scaffold_12-snap.2117-T1
Valid prediction for snap_scaffold_12-snap.2108-T1
Valid prediction for GlimmerHMM_glimmerT_30064-T1
Valid prediction for HiQ_model.g19887.t1
Valid prediction for snap_scaffold_12-snap.2097-T1
Valid prediction for snap_scaffold_12-snap.2094-T1
Valid prediction for snap_scaffold_12-snap.2115-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for Augustus_model.g19886.t1
Valid prediction for CodingQuarry_transcript_10390-T1
Valid prediction for GlimmerHMM_glimmerT_30051-T1
Valid prediction for GlimmerHMM_glimmerT_30044-T1
Valid prediction for snap_scaffold_12-snap.2091-T1
Valid prediction for Augustus_model.g19882.t1
Valid prediction for GlimmerHMM_glimmerT_30047-T1
Valid prediction for snap_scaffold_12-snap.2113-T1
Valid prediction for GlimmerHMM_glimmerT_30053-T1
Couldn't classify 222588, 222689
Sorry, prediction pasa_asmbl_7959.p1 fails validation.
(TTG)	 GT	222588-222689	GT	TGG
(GCA)	 AG	222828-222892	GT	AGG
(GTA)	 AG	222986-223104	GT	TGG
(GAG)	 AG	223194-223351	GT	AGG
(AAG)	 AG	223452-223523	GT	AAG
-recovered pasa_asmbl_7959.p1, terminal, 223452, 223523
-recovered pasa_asmbl_7959.p1, internal, 222828, 222892
-recovered pasa_asmbl_7959.p1, internal, 222986, 223104
-recovered pasa_asmbl_7959.p1, internal, 223194, 223351
-recovered pasa_asmbl_7959.p1, internal, 223452, 223523
Valid prediction for snap_scaffold_12-snap.2121-T1
Couldn't classify 219093, 219101
Couldn't classify 221500, 221572
Sorry, prediction pasa_asmbl_7958.p1 fails validation.
(CCA)	 AC	219093-219101	GT	AGG
(ATA)	 AG	219379-219460	GT	TGG
(TAG)	 AG	219677-219805	GT	AGG
(GAT)	 AG	219938-219996	GT	AAG
(GAG)	 AG	220148-220332	GT	GGG
(CAA)	 AG	220580-220642	GT	GAG
(CTG)	 AG	220845-220899	GT	AGG
(AAC)	 AG	220993-221072	GT	GGG
(GGA)	 AG	221500-221572	CA	AGC
-recovered pasa_asmbl_7958.p1, terminal, 220580, 220642
-recovered pasa_asmbl_7958.p1, internal, 219379, 219460
-recovered pasa_asmbl_7958.p1, internal, 219677, 219805
-recovered pasa_asmbl_7958.p1, internal, 219938, 219996
-recovered pasa_asmbl_7958.p1, internal, 220148, 220332
-recovered pasa_asmbl_7958.p1, internal, 220580, 220642
-recovered pasa_asmbl_7958.p1, internal, 220845, 220899
-recovered pasa_asmbl_7958.p1, internal, 220993, 221072
Valid prediction for snap_scaffold_12-snap.2076-T1
Valid prediction for snap_scaffold_12-snap.2079-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: -)Couldn't classify 308330, 308400
Couldn't classify 311720, 311828
Sorry, prediction pasa_asmbl_8786.p1 fails validation.
(GTG)	 GG	308330-308400	GT	CAG
(ACA)	 AG	308518-308587	GT	AGG
(TAT)	 AG	309362-309498	GT	ATG
(CTT)	 AG	311720-311828	GT	AGG
-recovered pasa_asmbl_8786.p1, internal, 308518, 308587
-recovered pasa_asmbl_8786.p1, internal, 309362, 309498
-recovered pasa_asmbl_8786.p1, internal, 311720, 311828
Couldn't classify 89280, 89357
Sorry, prediction pasa_asmbl_8802.p1 fails validation.
(ATG)	 GG	86594-86695	GT	AGG
(GAT)	 AG	87688-87792	GT	AGG
(ATC)	 AG	87892-88083	GT	AGG
(GTG)	 AG	88395-88554	GT	AGG
(AAT)	 AG	88790-88965	GT	AGG
(GAT)	 AG	89280-89357	CT	AGC
-recovered pasa_asmbl_8802.p1, initial, 86594, 86695
add_exon() Sorry, pasa_asmbl_8802.p1 88395-88554-terminal-3 is invalid.
-recovered pasa_asmbl_8802.p1, terminal, 88395, 88554
-recovered pasa_asmbl_8802.p1, internal, 87688, 87792
-recovered pasa_asmbl_8802.p1, internal, 87892, 88083
-recovered pasa_asmbl_8802.p1, internal, 88395, 88554
-recovered pasa_asmbl_8802.p1, internal, 88790, 88965
Valid prediction for snap_scaffold_12-snap.2116-T1
Valid prediction for Augustus_model.g19888.t1
Valid prediction for GlimmerHMM_glimmerT_30057-T1
Couldn't classify 41698, 41854
Couldn't classify 48929, 49035
Sorry, prediction pasa_asmbl_8816.p2 fails validation.
(GAT)	 CA	41698-41854	GT	CAG
(ACC)	 AG	43094-43300	GT	TGG
(GCT)	 AG	44732-44965	GT	AGG
(ACG)	 AG	46179-46391	GT	ATG
(TTG)	 AG	48929-49035	GT	AGG
-recovered pasa_asmbl_8816.p2, internal, 43094, 43300
-recovered pasa_asmbl_8816.p2, internal, 44732, 44965
-recovered pasa_asmbl_8816.p2, internal, 46179, 46391
-recovered pasa_asmbl_8816.p2, internal, 48929, 49035
Valid prediction for snap_scaffold_12-snap.2083-T1
Valid prediction for snap_scaffold_12-snap.2093-T1
Valid prediction for snap_scaffold_12-snap.2077-T1
Valid prediction for snap_scaffold_12-snap.2102-T1
Valid prediction for snap_scaffold_12-snap.2112-T1
Valid prediction for snap_scaffold_12-snap.2088-T1
Valid prediction for GlimmerHMM_glimmerT_30054-T1
Valid prediction for CodingQuarry_transcript_10385-T1
Valid prediction for snap_scaffold_12-snap.2072-T1
Valid prediction for CodingQuarry_transcript_10386-T1
Valid prediction for snap_scaffold_12-snap.2099-T1
Valid prediction for snap_scaffold_12-snap.2105-T1
Valid prediction for Augustus_model.g19877.t1
Valid prediction for Augustus_model.g19890.t1
Valid prediction for GlimmerHMM_glimmerT_30060-T1
Valid prediction for GlimmerHMM_glimmerT_30052-T1
Valid prediction for GlimmerHMM_glimmerT_30065-T1
Valid prediction for GlimmerHMM_glimmerT_30059-T1
Valid prediction for snap_scaffold_12-snap.2070-T1
Valid prediction for snap_scaffold_12-snap.2109-T1
Valid prediction for Augustus_model.g19876.t1
Valid prediction for GlimmerHMM_glimmerT_30043-T1
Valid prediction for snap_scaffold_12-snap.2075-T1
Valid prediction for snap_scaffold_12-snap.2092-T1
Valid prediction for HiQ_model.g19885.t1
Valid prediction for Augustus_model.g19878.t1
Valid prediction for GlimmerHMM_glimmerT_30067-T1
Couldn't classify 109791, 110441
Sorry, prediction pasa_asmbl_8795.p1 fails validation.
(GTA)	 TC	109791-110441	AG	GAA
Valid prediction for GlimmerHMM_glimmerT_30045-T1
Couldn't classify 54312, 54502
Sorry, prediction pasa_asmbl_8814.p2 fails validation.
(ATG)	 AC	52361-52469	GT	AGG
(GAG)	 AG	54312-54502	GT	AGG
-recovered pasa_asmbl_8814.p2, initial, 52361, 52469
-recovered pasa_asmbl_8814.p2, internal, 54312, 54502
Valid prediction for pasa_asmbl_8799.p1
Valid prediction for Augustus_model.g19880.t1
Valid prediction for snap_scaffold_12-snap.2078-T1
Valid prediction for GlimmerHMM_glimmerT_30041-T1
Valid prediction for GlimmerHMM_glimmerT_30061-T1
Valid prediction for snap_scaffold_12-snap.2087-T1
Valid prediction for CodingQuarry_transcript_10388-T1
Valid prediction for snap_scaffold_12-snap.2081-T1
Valid prediction for snap_scaffold_12-snap.2107-T1
Couldn't classify 323720, 323840
Sorry, prediction pasa_asmbl_8784.p1 fails validation.
(AGG)	 CT	323720-323840	GT	CGG
(ATC)	 AG	324871-324935	GT	AGG
(TTC)	 AG	325741-325845	GT	AGG
(GCT)	 AG	326000-326110	TT	AAT
-recovered pasa_asmbl_8784.p1, terminal, 326000, 326110
-recovered pasa_asmbl_8784.p1, internal, 324871, 324935
-recovered pasa_asmbl_8784.p1, internal, 325741, 325845
Valid prediction for GlimmerHMM_glimmerT_30066-T1
Couldn't classify 90423, 90522
Couldn't classify 94262, 94327
Sorry, prediction pasa_asmbl_8801.p1 fails validation.
(GTC)	 AG	90423-90522	GT	TGG
(GTT)	 AG	90643-90779	GT	AGG
(ATG)	 AG	91145-91276	GT	AGG
(CGC)	 AG	91737-91863	GT	CAG
(CGG)	 AG	92270-92499	GC	AGG
(GAC)	 AG	92630-92689	GC	AGG
(ATG)	 AG	92797-92967	GT	AGG
(GAG)	 AG	93147-93291	GT	AGG
(GAG)	 AG	94015-94133	GT	AGG
(GTG)	 AG	94262-94327	GT	TGG
-recovered pasa_asmbl_8801.p1, initial, 91145, 91276
-recovered pasa_asmbl_8801.p1, initial, 92797, 92967
-recovered pasa_asmbl_8801.p1, internal, 90423, 90522
-recovered pasa_asmbl_8801.p1, internal, 90643, 90779
-recovered pasa_asmbl_8801.p1, internal, 91145, 91276
-recovered pasa_asmbl_8801.p1, internal, 91737, 91863
-recovered pasa_asmbl_8801.p1, internal, 92270, 92499
-recovered pasa_asmbl_8801.p1, internal, 92630, 92689
-recovered pasa_asmbl_8801.p1, internal, 92797, 92967
-recovered pasa_asmbl_8801.p1, internal, 93147, 93291
-recovered pasa_asmbl_8801.p1, internal, 94015, 94133
-recovered pasa_asmbl_8801.p1, internal, 94262, 94327
Valid prediction for snap_scaffold_12-snap.2114-T1
Valid prediction for GlimmerHMM_glimmerT_30046-T1
Valid prediction for snap_scaffold_12-snap.2086-T1
Valid prediction for GlimmerHMM_glimmerT_30042-T1
Valid prediction for Augustus_model.g19895.t1
Valid prediction for HiQ_model.g19891.t1
Valid prediction for Augustus_model.g19879.t1
Valid prediction for snap_scaffold_12-snap.2096-T1
Valid prediction for snap_scaffold_12-snap.2084-T1
Valid prediction for Augustus_model.g19896.t1
Valid prediction for CodingQuarry_transcript_10392-T1
Valid prediction for GlimmerHMM_glimmerT_30062-T1
Valid prediction for snap_scaffold_12-snap.2071-T1
Valid prediction for snap_scaffold_12-snap.2089-T1
Valid prediction for GlimmerHMM_glimmerT_30063-T1
Valid prediction for snap_scaffold_12-snap.2110-T1
Valid prediction for snap_scaffold_12-snap.2074-T1
Valid prediction for snap_scaffold_12-snap.2085-T1
Valid prediction for snap_scaffold_12-snap.2073-T1
Valid prediction for snap_scaffold_12-snap.2120-T1
Valid prediction for Augustus_model.g19894.t1
Valid prediction for snap_scaffold_12-snap.2119-T1
Valid prediction for Augustus_model.g19881.t1
Couldn't classify 77158, 77229
Sorry, prediction pasa_asmbl_8808.p1 fails validation.
(ATG)	 AC	69620-69798	GT	AAG
(GCA)	 AG	70321-70476	GT	AGG
(ATT)	 AG	72382-72529	GT	CTG
(GCC)	 AG	73642-73875	GT	AGG
(TTG)	 AG	74175-74348	GT	TGG
(ATG)	 AG	74876-75023	GT	CAG
(AGG)	 AG	76250-76398	GT	AGG
(GCC)	 AG	76492-76599	GT	AGG
(AGG)	 AG	76711-77070	GT	GGG
(GGT)	 AG	77158-77229	GT	AGG
-recovered pasa_asmbl_8808.p1, initial, 69620, 69798
-recovered pasa_asmbl_8808.p1, initial, 74876, 75023
-recovered pasa_asmbl_8808.p1, internal, 70321, 70476
-recovered pasa_asmbl_8808.p1, internal, 72382, 72529
-recovered pasa_asmbl_8808.p1, internal, 73642, 73875
-recovered pasa_asmbl_8808.p1, internal, 74175, 74348
-recovered pasa_asmbl_8808.p1, internal, 74876, 75023
-recovered pasa_asmbl_8808.p1, internal, 76250, 76398
-recovered pasa_asmbl_8808.p1, internal, 76492, 76599
-recovered pasa_asmbl_8808.p1, internal, 76711, 77070
-recovered pasa_asmbl_8808.p1, internal, 77158, 77229
Valid prediction for snap_scaffold_12-snap.2095-T1
Valid prediction for pasa_asmbl_8794.p1
Valid prediction for Augustus_model.g19892.t1
Valid prediction for pasa_asmbl_8806.p1
Couldn't classify 56501, 56557
Sorry, prediction pasa_asmbl_8809.p3 fails validation.
(CTG)	 AG	56501-56557	GT	GTG
(GAT)	 AG	57690-57795	GT	TGG
(GGA)	 AG	58607-58692	GT	AGG
(ATC)	 AG	60378-60509	AG	AGA
-recovered pasa_asmbl_8809.p3, terminal, 60378, 60509
-recovered pasa_asmbl_8809.p3, internal, 56501, 56557
-recovered pasa_asmbl_8809.p3, internal, 57690, 57795
-recovered pasa_asmbl_8809.p3, internal, 58607, 58692

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 52753, rend_intergenic: 48536  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53892, rend_intergenic: 52784  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63669, rend_intergenic: 59932  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71452, rend_intergenic: 66936  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196139, rend_intergenic: 192272  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 243824, rend_intergenic: 232878  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 265213, rend_intergenic: 255332  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 287268, rend_intergenic: 276112  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 294899, rend_intergenic: 290241  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 306707, rend_intergenic: 296450  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 326695, rend_intergenic: 319402  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 336620
-exon list size: 485


building trellis

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69.6    
69.8    
70.0    
70.2    
70.4    
70.6    
70.8    
71.0    
71.3    
71.5    
71.7    
71.9    
72.1    
72.3    
72.5    
72.7    
72.9    
73.1    
73.3    
73.5    
73.7    
73.9    
74.1    
74.3    
74.5    
74.7    
74.9    
75.2    
75.4    
75.6    
75.8    
76.0    
76.2    
76.4    
76.6    
76.8    
77.0    
77.2    
77.4    
77.6    
77.8    
78.0    
78.2    
78.4    
78.6    
78.9    
79.1    
79.3    
79.5    
79.7    
79.9    
80.1    
80.3    
80.5    
80.7    
80.9    
81.1    
81.3    
81.5    
81.7    
81.9    
82.1    
82.3    
82.5    
82.8    
83.0    
83.2    
83.4    
83.6    
83.8    
84.0    
84.2    
84.4    
84.6    
84.8    
85.0    
85.2    
85.4    
85.6    
85.8    
86.0    
86.2    
86.4    
86.7    
86.9    
87.1    
87.3    
87.5    
87.7    
87.9    
88.1    
88.3    
88.5    
88.7    
88.9    
89.1    
89.3    
89.5    
89.7    
89.9    
90.1    
90.3    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.8    
92.0    
92.2    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
94.0    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.3    
97.5    
97.7    
97.9    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 43 predictions from path traversal
Error with prediction: snap lend_intergenic: 52753, rend_intergenic: 48536  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53892, rend_intergenic: 52784  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63669, rend_intergenic: 59932  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71452, rend_intergenic: 66936  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196139, rend_intergenic: 192272  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 243824, rend_intergenic: 232878  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 265213, rend_intergenic: 255332  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 287268, rend_intergenic: 276112  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 294899, rend_intergenic: 290241  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 306707, rend_intergenic: 296450  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 326695, rend_intergenic: 319402  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 30 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 324229 - 336620
-exon list size: 10


building trellis

8.3    
16.7    
25.0    
33.3    
41.7    
50.0    
58.3    
66.7    
75.0    
83.3    
91.7    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support