-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_15/scaffold_15_6010314-6219848

-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_37069-T1
Valid prediction for CodingQuarry_transcript_17982-T1
Valid prediction for snap_scaffold_15-snap.1305-T1
Valid prediction for GeneMark_model.63741_t
Valid prediction for GlimmerHMM_glimmerT_37053-T1
Valid prediction for GlimmerHMM_glimmerT_37070-T1
Valid prediction for snap_scaffold_15-snap.1329-T1
Valid prediction for GlimmerHMM_glimmerT_37065-T1
Valid prediction for GlimmerHMM_glimmerT_37071-T1
Valid prediction for Augustus_model.g24868.t1
Valid prediction for GlimmerHMM_glimmerT_37050-T1
Valid prediction for GeneMark_model.63763_t
Couldn't classify 150029, 150397
Sorry, prediction pasa_asmbl_14181.p1 fails validation.
(GAG)	 GA	150029-150397	GT	GAG
Valid prediction for GlimmerHMM_glimmerT_37055-T1
Valid prediction for GeneMark_model.63769_t
Valid prediction for GeneMark_model.63758_t
Valid prediction for snap_scaffold_15-snap.1314-T1
Valid prediction for CodingQuarry_transcript_17977-T1
Valid prediction for GeneMark_model.63751_t
Valid prediction for snap_scaffold_15-snap.1334-T1
Valid prediction for HiQ_model.g24859.t1
Valid prediction for Augustus_model.g24865.t1
Valid prediction for GeneMark_model.63733_t
Couldn't classify 77193, 77282
Couldn't classify 77410, 77474
Couldn't classify 78189, 78300
Sorry, prediction pasa_asmbl_14177.p1 fails validation.
(ATG)	 TA	75767-75902	GT	TGG
(AGA)	 AG	76003-76093	GT	CAG
(GCT)	 AG	76237-76364	GT	AGG
(GGA)	 AG	76458-76537	GT	AGG
(AGT)	 AG	76901-76997	GT	AGG
(AAT)	 AG	77193-77282	AT	AGA
(GTC)	 AC	77410-77474	GT	AGG
(GCA)	 AG	77611-77650	GT	TGG
(TGC)	 AG	77891-78017	GT	AGG
(TGC)	 AG	78189-78300	TC	ACT
-recovered pasa_asmbl_14177.p1, initial, 75767, 75902
-recovered pasa_asmbl_14177.p1, internal, 76003, 76093
-recovered pasa_asmbl_14177.p1, internal, 76237, 76364
-recovered pasa_asmbl_14177.p1, internal, 76458, 76537
-recovered pasa_asmbl_14177.p1, internal, 76901, 76997
-recovered pasa_asmbl_14177.p1, internal, 77611, 77650
-recovered pasa_asmbl_14177.p1, internal, 77891, 78017
Valid prediction for GeneMark_model.63737_t
Valid prediction for CodingQuarry_transcript_17980-T1
Valid prediction for snap_scaffold_15-snap.1303-T1
Valid prediction for Augustus_model.g24867.t1
Valid prediction for GeneMark_model.63765_t
Valid prediction for GeneMark_model.63770_t
Valid prediction for GeneMark_model.63767_t
Valid prediction for CodingQuarry_transcript_17978-T1
Valid prediction for GeneMark_model.63780_t
Valid prediction for GeneMark_model.63753_t
Valid prediction for GeneMark_model.63739_t
Valid prediction for snap_scaffold_15-snap.1331-T1
Valid prediction for snap_scaffold_15-snap.1324-T1
Valid prediction for GlimmerHMM_glimmerT_37054-T1
Valid prediction for GlimmerHMM_glimmerT_37067-T1
Couldn't classify 162066, 162201
Couldn't classify 163242, 163795
Sorry, prediction pasa_asmbl_14185.p1 fails validation.
(TCT)	 AT	162066-162201	GT	AAG
(TCA)	 AG	163242-163795	GT	AGG
-recovered pasa_asmbl_14185.p1, internal, 163242, 163795
Valid prediction for snap_scaffold_15-snap.1335-T1
Valid prediction for Augustus_model.g24866.t1
Valid prediction for GeneMark_model.63748_t
Couldn't classify 186803, 186858
Couldn't classify 187755, 187895
Sorry, prediction CodingQuarry_transcript_17983-T1 fails validation.
(ATG)	 TA	183480-183509	GT	TGG
(CCT)	 AG	185088-185189	GT	CGG
(CTG)	 AG	185777-185927	GT	AGG
(CAC)	 AG	186249-186313	GT	TGG
(AGT)	 AG	186632-186707	GT	AGG
(GTC)	 AG	186803-186858	CA	CCC
(CAG)	 CA	187755-187895	GT	AGG
(GAG)	 AG	188047-188136	GT	AGG
(ATC)	 AG	188327-188434	AG	AGA
-recovered CodingQuarry_transcript_17983-T1, initial, 183480, 183509
-recovered CodingQuarry_transcript_17983-T1, terminal, 188327, 188434
-recovered CodingQuarry_transcript_17983-T1, internal, 185088, 185189
-recovered CodingQuarry_transcript_17983-T1, internal, 185777, 185927
-recovered CodingQuarry_transcript_17983-T1, internal, 186249, 186313
-recovered CodingQuarry_transcript_17983-T1, internal, 186632, 186707
-recovered CodingQuarry_transcript_17983-T1, internal, 188047, 188136
Valid prediction for CodingQuarry_transcript_17981-T1
Valid prediction for snap_scaffold_15-snap.1309-T1
Valid prediction for snap_scaffold_15-snap.1316-T1
Valid prediction for GeneMark_model.63743_t
Valid prediction for GeneMark_model.63740_t
Valid prediction for GeneMark_model.63759_t
Valid prediction for pasa_asmbl_14190.p1
Valid prediction for snap_scaffold_15-snap.1307-T1
Valid prediction for GeneMark_model.63773_t
Valid prediction for snap_scaffold_15-snap.1315-T1
Valid prediction for GeneMark_model.63775_t
Valid prediction for GeneMark_model.63734_t
Valid prediction for snap_scaffold_15-snap.1327-T1
Couldn't classify 170249, 170632
Sorry, prediction pasa_asmbl_14186.p3 fails validation.
(ATG)	 CC	170249-170632	AC	CAA
Valid prediction for GeneMark_model.63777_t
Couldn't classify 53830, 53952
Sorry, prediction pasa_asmbl_14175.p1 fails validation.
(CCC)	 AG	53830-53952	GT	AGG
(AGT)	 AG	54305-54502	GT	CTG
(TCT)	 AG	54666-54732	GT	AGG
(CCT)	 AG	54962-55059	GT	AGG
(AAG)	 AG	55359-55568	CC	AAC
-recovered pasa_asmbl_14175.p1, terminal, 55359, 55568
-recovered pasa_asmbl_14175.p1, internal, 53830, 53952
-recovered pasa_asmbl_14175.p1, internal, 54305, 54502
-recovered pasa_asmbl_14175.p1, internal, 54666, 54732
-recovered pasa_asmbl_14175.p1, internal, 54962, 55059
Valid prediction for GeneMark_model.63745_t
Valid prediction for HiQ_model.g24870.t1
Valid prediction for GeneMark_model.63729_t
Valid prediction for GlimmerHMM_glimmerT_37062-T1
Valid prediction for GlimmerHMM_glimmerT_37057-T1
Valid prediction for HiQ_model.g24856.t1
Valid prediction for GeneMark_model.63756_t
Valid prediction for HiQ_model.g24869.t1
Valid prediction for GlimmerHMM_glimmerT_37048-T1
Valid prediction for GlimmerHMM_glimmerT_37066-T1
Valid prediction for GeneMark_model.63761_t
Valid prediction for snap_scaffold_15-snap.1312-T1
Valid prediction for snap_scaffold_15-snap.1311-T1
Valid prediction for snap_scaffold_15-snap.1300-T1
Valid prediction for HiQ_model.g24858.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 112053, 112083
Couldn't classify 115565, 115753
Sorry, prediction pasa_asmbl_15259.p1 fails validation.
(GCC)	 AG	112053-112083	GT	AGG
(AGT)	 AG	112664-112807	GT	CGG
(GCA)	 AG	115172-115278	GT	AGG
(GAT)	 AG	115565-115753	GC	GTG
-recovered pasa_asmbl_15259.p1, internal, 112053, 112083
-recovered pasa_asmbl_15259.p1, internal, 112664, 112807
-recovered pasa_asmbl_15259.p1, internal, 115172, 115278
-recovered pasa_asmbl_15259.p1, internal, 115565, 115753
Valid prediction for GlimmerHMM_glimmerT_37060-T1
Valid prediction for Augustus_model.g24861.t1
Valid prediction for GeneMark_model.63760_t
Valid prediction for GlimmerHMM_glimmerT_37052-T1
Valid prediction for snap_scaffold_15-snap.1337-T1
Valid prediction for CodingQuarry_transcript_17979-T1
Valid prediction for snap_scaffold_15-snap.1323-T1
Valid prediction for snap_scaffold_15-snap.1304-T1
Valid prediction for GlimmerHMM_glimmerT_37051-T1
Valid prediction for GeneMark_model.63768_t
Valid prediction for GeneMark_model.63757_t
Valid prediction for snap_scaffold_15-snap.1302-T1
Valid prediction for GeneMark_model.63744_t
Valid prediction for snap_scaffold_15-snap.1336-T1
Valid prediction for GeneMark_model.63755_t
Valid prediction for snap_scaffold_15-snap.1333-T1
Valid prediction for GeneMark_model.63742_t
Valid prediction for GeneMark_model.63762_t
Valid prediction for GeneMark_model.63774_t
Valid prediction for HiQ_model.g24862.t1
Valid prediction for GeneMark_model.63749_t
Valid prediction for GeneMark_model.63776_t
Valid prediction for GlimmerHMM_glimmerT_37072-T1
Valid prediction for snap_scaffold_15-snap.1321-T1
Valid prediction for GeneMark_model.63747_t
Valid prediction for snap_scaffold_15-snap.1320-T1
Valid prediction for GlimmerHMM_glimmerT_37061-T1
Valid prediction for GeneMark_model.63778_t
Valid prediction for snap_scaffold_15-snap.1322-T1
Valid prediction for GlimmerHMM_glimmerT_37075-T1
Valid prediction for snap_scaffold_15-snap.1326-T1
Valid prediction for pasa_asmbl_15252.p1
Valid prediction for snap_scaffold_15-snap.1318-T1
Valid prediction for GeneMark_model.63750_t
Valid prediction for snap_scaffold_15-snap.1319-T1
Valid prediction for GeneMark_model.63752_t
Valid prediction for snap_scaffold_15-snap.1338-T1
Valid prediction for GlimmerHMM_glimmerT_37063-T1
Valid prediction for snap_scaffold_15-snap.1313-T1
Valid prediction for snap_scaffold_15-snap.1301-T1
Valid prediction for snap_scaffold_15-snap.1332-T1
Valid prediction for GeneMark_model.63766_t
Valid prediction for Augustus_model.g24854.t1
Valid prediction for snap_scaffold_15-snap.1306-T1
Valid prediction for GeneMark_model.63736_t
Valid prediction for GeneMark_model.63730_t
Valid prediction for snap_scaffold_15-snap.1308-T1
Valid prediction for snap_scaffold_15-snap.1328-T1
Valid prediction for GlimmerHMM_glimmerT_37059-T1
Valid prediction for snap_scaffold_15-snap.1330-T1
Valid prediction for GlimmerHMM_glimmerT_37049-T1
Valid prediction for Augustus_model.g24855.t1
Valid prediction for snap_scaffold_15-snap.1339-T1
Valid prediction for Augustus_model.g24863.t1
Valid prediction for HiQ_model.g24857.t1
Valid prediction for GlimmerHMM_glimmerT_37068-T1
Valid prediction for GeneMark_model.63754_t
Valid prediction for GlimmerHMM_glimmerT_37058-T1
Valid prediction for Augustus_model.g24871.t1
Valid prediction for Augustus_model.g24860.t1
Valid prediction for GeneMark_model.63728_t
Valid prediction for snap_scaffold_15-snap.1317-T1
Valid prediction for GeneMark_model.63731_t
Valid prediction for GeneMark_model.63732_t
Valid prediction for GeneMark_model.63771_t
Valid prediction for GlimmerHMM_glimmerT_37074-T1
Valid prediction for GlimmerHMM_glimmerT_37073-T1
Valid prediction for GeneMark_model.63735_t
Couldn't classify 99304, 99330
Sorry, prediction pasa_asmbl_15261.p1 fails validation.
(CGT)	 GA	99304-99330	GT	TGG
(GGT)	 AG	99849-99902	GT	AGG
(GAC)	 AG	100101-100197	GT	AGG
(TCA)	 AG	100524-100648	GT	AGG
(GAG)	 AG	100885-101070	GT	AGG
(GTC)	 AG	101188-101316	GT	AGG
(GAG)	 AG	101452-101548	GT	AGG
(GTA)	 AG	101982-102171	GT	AGG
(ATA)	 AG	102961-103112	GT	TGG
(GGA)	 AG	103338-103492	GT	AGG
(GCT)	 AG	104597-104731	CC	GAC
-recovered pasa_asmbl_15261.p1, terminal, 100101, 100197
-recovered pasa_asmbl_15261.p1, terminal, 104597, 104731
-recovered pasa_asmbl_15261.p1, internal, 99849, 99902
-recovered pasa_asmbl_15261.p1, internal, 100101, 100197
-recovered pasa_asmbl_15261.p1, internal, 100524, 100648
-recovered pasa_asmbl_15261.p1, internal, 100885, 101070
-recovered pasa_asmbl_15261.p1, internal, 101188, 101316
-recovered pasa_asmbl_15261.p1, internal, 101452, 101548
-recovered pasa_asmbl_15261.p1, internal, 101982, 102171
-recovered pasa_asmbl_15261.p1, internal, 102961, 103112
-recovered pasa_asmbl_15261.p1, internal, 103338, 103492
Valid prediction for Augustus_model.g24864.t1
Valid prediction for GeneMark_model.63779_t
Valid prediction for GeneMark_model.63746_t
Valid prediction for GeneMark_model.63764_t
Valid prediction for GlimmerHMM_glimmerT_37064-T1
Valid prediction for snap_scaffold_15-snap.1310-T1
Valid prediction for GeneMark_model.63772_t
Valid prediction for GeneMark_model.63738_t
Valid prediction for GlimmerHMM_glimmerT_37056-T1
Valid prediction for snap_scaffold_15-snap.1325-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 28871, rend_intergenic: 26599  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31406, rend_intergenic: 30683  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33745, rend_intergenic: 32251  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50838, rend_intergenic: 47444  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91855, rend_intergenic: 80571  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130684, rend_intergenic: 127855  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142771, rend_intergenic: 133861  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147149, rend_intergenic: 144103  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153046, rend_intergenic: 147772  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161786, rend_intergenic: 153130  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173465, rend_intergenic: 164453  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176130, rend_intergenic: 173779  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189090, rend_intergenic: 185654  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 209535
-exon list size: 670


building trellis

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67.0    
67.1    
67.3    
67.4    
67.6    
67.7    
67.9    
68.0    
68.2    
68.3    
68.5    
68.6    
68.8    
68.9    
69.0    
69.2    
69.3    
69.5    
69.6    
69.8    
69.9    
70.1    
70.2    
70.4    
70.5    
70.7    
70.8    
71.0    
71.1    
71.3    
71.4    
71.6    
71.7    
71.9    
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    
74.1    
74.3    
74.4    
74.6    
74.7    
74.9    
75.0    
75.1    
75.3    
75.4    
75.6    
75.7    
75.9    
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    
78.1    
78.3    
78.4    
78.6    
78.7    
78.9    
79.0    
79.2    
79.3    
79.5    
79.6    
79.8    
79.9    
80.1    
80.2    
80.4    
80.5    
80.7    
80.8    
81.0    
81.1    
81.2    
81.4    
81.5    
81.7    
81.8    
82.0    
82.1    
82.3    
82.4    
82.6    
82.7    
82.9    
83.0    
83.2    
83.3    
83.5    
83.6    
83.8    
83.9    
84.1    
84.2    
84.4    
84.5    
84.7    
84.8    
85.0    
85.1    
85.3    
85.4    
85.6    
85.7    
85.9    
86.0    
86.2    
86.3    
86.5    
86.6    
86.8    
86.9    
87.1    
87.2    
87.4    
87.5    
87.6    
87.8    
87.9    
88.1    
88.2    
88.4    
88.5    
88.7    
88.8    
89.0    
89.1    
89.3    
89.4    
89.6    
89.7    
89.9    
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    
92.1    
92.3    
92.4    
92.6    
92.7    
92.9    
93.0    
93.2    
93.3    
93.5    
93.6    
93.8    
93.9    
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    
96.1    
96.3    
96.4    
96.6    
96.7    
96.9    
97.0    
97.2    
97.3    
97.5    
97.6    
97.8    
97.9    
98.1    
98.2    
98.4    
98.5    
98.7    
98.8    
99.0    
99.1    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 38 predictions from path traversal
Error with prediction: snap lend_intergenic: 28871, rend_intergenic: 26599  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31406, rend_intergenic: 30683  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33745, rend_intergenic: 32251  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50838, rend_intergenic: 47444  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91855, rend_intergenic: 80571  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130684, rend_intergenic: 127855  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142771, rend_intergenic: 133861  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147149, rend_intergenic: 144103  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153046, rend_intergenic: 147772  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161786, rend_intergenic: 153130  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173465, rend_intergenic: 164453  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176130, rend_intergenic: 173779  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189090, rend_intergenic: 185654  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 14983
-exon list size: 20


building trellis

4.5    
9.1    
13.6    
18.2    
22.7    
27.3    
31.8    
36.4    
40.9    
45.5    
50.0    
54.5    
59.1    
63.6    
68.2    
72.7    
77.3    
81.8    
86.4    
90.9    
95.5    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 14779
-exon list size: 16


building trellis

5.6    
11.1    
16.7    
22.2    
27.8    
33.3    
38.9    
44.4    
50.0    
55.6    
61.1    
66.7    
72.2    
77.8    
83.3    
88.9    
94.4    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 4505 - 14779
-exon list size: 13


building trellis

6.7    
13.3    
20.0    
26.7    
33.3    
40.0    
46.7    
53.3    
60.0    
66.7    
73.3    
80.0    
86.7    
93.3    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support