-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_1/scaffold_1_10230107-10648240

-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_1394-T1
Valid prediction for HiQ_model.g1034.t1
Valid prediction for snap_scaffold_1-snap.1782-T1
Valid prediction for Augustus_model.g1036.t1
Valid prediction for Augustus_model.g1017.t1
Valid prediction for CodingQuarry_transcript_2742-T1
Couldn't classify 283510, 284373
Sorry, prediction pasa_asmbl_2012.p1 fails validation.
(GTT)	 AT	283510-284373	GT	AGG
(ACT)	 AG	284537-284620	GT	AGG
(GAG)	 AG	284842-285261	AA	GAA
-recovered pasa_asmbl_2012.p1, terminal, 284842, 285261
-recovered pasa_asmbl_2012.p1, internal, 284537, 284620
Valid prediction for GlimmerHMM_glimmerT_1396-T1
Valid prediction for snap_scaffold_1-snap.1781-T1
Valid prediction for Augustus_model.g1038.t1
Couldn't classify 306157, 306184
Couldn't classify 306546, 306640
Sorry, prediction CodingQuarry_transcript_2750-T1 fails validation.
(ATG)	 TA	306157-306184	AC	AAA
(AAC)	 CC	306546-306640	GT	AGG
(AAT)	 AG	306830-307195	GT	AGG
(GCT)	 AG	307311-307427	GT	AGG
(AAC)	 AG	308242-308357	GT	GGG
(GAC)	 AG	308491-308669	GT	CTG
(TTT)	 AG	308845-308912	GT	AGG
(AAT)	 AG	309584-309750	GT	AGG
(CAC)	 AG	310658-310950	GT	TGG
(TTT)	 AG	311908-312003	GT	AGG
(CGC)	 AG	312102-312211	GT	AGG
(GAG)	 AG	312371-312656	GT	AGG
(CAA)	 AG	312972-313060	CA	AAC
-recovered CodingQuarry_transcript_2750-T1, terminal, 312972, 313060
-recovered CodingQuarry_transcript_2750-T1, internal, 306830, 307195
-recovered CodingQuarry_transcript_2750-T1, internal, 307311, 307427
-recovered CodingQuarry_transcript_2750-T1, internal, 308242, 308357
-recovered CodingQuarry_transcript_2750-T1, internal, 308491, 308669
-recovered CodingQuarry_transcript_2750-T1, internal, 308845, 308912
-recovered CodingQuarry_transcript_2750-T1, internal, 309584, 309750
-recovered CodingQuarry_transcript_2750-T1, internal, 310658, 310950
-recovered CodingQuarry_transcript_2750-T1, internal, 311908, 312003
-recovered CodingQuarry_transcript_2750-T1, internal, 312102, 312211
-recovered CodingQuarry_transcript_2750-T1, internal, 312371, 312656
Valid prediction for pasa_asmbl_2005.p1
Valid prediction for snap_scaffold_1-snap.1801-T1
Valid prediction for GlimmerHMM_glimmerT_1414-T1
Valid prediction for GlimmerHMM_glimmerT_1401-T1
Valid prediction for GlimmerHMM_glimmerT_1409-T1
Valid prediction for snap_scaffold_1-snap.1785-T1
Couldn't classify 294413, 294478
Sorry, prediction pasa_asmbl_2014.p1 fails validation.
(ATG)	 AC	290090-290146	GT	AGG
(TCA)	 AG	290445-290535	GT	AGG
(TCA)	 AG	291250-291347	GT	GGG
(GCC)	 AG	291454-291704	GT	AAG
(TCA)	 AG	291832-291919	GT	GTG
(GCT)	 AG	292013-292222	GT	AGG
(GGT)	 AG	292358-292529	GT	GTG
(ATC)	 AG	292656-292905	GT	CGG
(GTT)	 AG	293113-293227	GT	AGG
(ATT)	 AG	293924-294133	GT	AGG
(GCT)	 AG	294413-294478	CC	GCC
-recovered pasa_asmbl_2014.p1, initial, 290090, 290146
-recovered pasa_asmbl_2014.p1, terminal, 290445, 290535
-recovered pasa_asmbl_2014.p1, internal, 290445, 290535
-recovered pasa_asmbl_2014.p1, internal, 291250, 291347
-recovered pasa_asmbl_2014.p1, internal, 291454, 291704
-recovered pasa_asmbl_2014.p1, internal, 291832, 291919
-recovered pasa_asmbl_2014.p1, internal, 292013, 292222
-recovered pasa_asmbl_2014.p1, internal, 292358, 292529
-recovered pasa_asmbl_2014.p1, internal, 292656, 292905
-recovered pasa_asmbl_2014.p1, internal, 293113, 293227
-recovered pasa_asmbl_2014.p1, internal, 293924, 294133
Valid prediction for GlimmerHMM_glimmerT_1391-T1
Valid prediction for snap_scaffold_1-snap.1793-T1
Valid prediction for snap_scaffold_1-snap.1784-T1
Valid prediction for snap_scaffold_1-snap.1791-T1
Valid prediction for GlimmerHMM_glimmerT_1416-T1
Valid prediction for snap_scaffold_1-snap.1809-T1
Valid prediction for snap_scaffold_1-snap.1802-T1
Valid prediction for snap_scaffold_1-snap.1816-T1
Valid prediction for snap_scaffold_1-snap.1812-T1
Valid prediction for snap_scaffold_1-snap.1778-T1
Valid prediction for GlimmerHMM_glimmerT_1415-T1
Valid prediction for CodingQuarry_transcript_2751-T1
Valid prediction for snap_scaffold_1-snap.1800-T1
Valid prediction for Augustus_model.g1027.t1
Valid prediction for GlimmerHMM_glimmerT_1418-T1
Valid prediction for Augustus_model.g1018.t1
Couldn't classify 288599, 288763
Sorry, prediction pasa_asmbl_2013.p1 fails validation.
(ATG)	 TC	286882-287355	GT	GGG
(GTT)	 AG	288599-288763	AC	CCA
-recovered pasa_asmbl_2013.p1, initial, 286882, 287355
Valid prediction for snap_scaffold_1-snap.1804-T1
Valid prediction for snap_scaffold_1-snap.1819-T1
Valid prediction for Augustus_model.g1031.t1
Valid prediction for GlimmerHMM_glimmerT_1420-T1
Couldn't classify 301953, 301953
Couldn't classify 304489, 304515
Sorry, prediction pasa_asmbl_2783.p1 fails validation.
(AGT)	 CA	301953-301953	GT	AAG
(TGA)	 AG	302049-302163	GT	AGG
(TGC)	 AG	302968-303128	GT	TGG
(GTC)	 AG	303493-303634	GT	AGG
(GAT)	 AG	304125-304311	GT	AGG
(GGA)	 AG	304489-304515	CC	AGC
-recovered pasa_asmbl_2783.p1, internal, 302049, 302163
-recovered pasa_asmbl_2783.p1, internal, 302968, 303128
-recovered pasa_asmbl_2783.p1, internal, 303493, 303634
-recovered pasa_asmbl_2783.p1, internal, 304125, 304311
Valid prediction for GlimmerHMM_glimmerT_1398-T1
Valid prediction for snap_scaffold_1-snap.1780-T1
Valid prediction for snap_scaffold_1-snap.1810-T1
Valid prediction for snap_scaffold_1-snap.1808-T1
Valid prediction for Augustus_model.g1016.t1
Couldn't classify 354888, 355024
Couldn't classify 356141, 356178
Sorry, prediction pasa_asmbl_2018.p1 fails validation.
(GTG)	 AG	354888-355024	GT	TGG
(GAT)	 AG	355324-355404	GT	AGG
(GTG)	 AG	355609-355727	GT	CAG
(TTT)	 AG	356141-356178	GC	TGG
-recovered pasa_asmbl_2018.p1, internal, 354888, 355024
-recovered pasa_asmbl_2018.p1, internal, 355324, 355404
-recovered pasa_asmbl_2018.p1, internal, 355609, 355727
-recovered pasa_asmbl_2018.p1, internal, 356141, 356178
Valid prediction for snap_scaffold_1-snap.1815-T1
Valid prediction for GlimmerHMM_glimmerT_1392-T1
Valid prediction for snap_scaffold_1-snap.1779-T1
Couldn't classify 174400, 174443
Sorry, prediction pasa_asmbl_2004.p1 fails validation.
(GCA)	 CA	174400-174443	GT	GGG
(AAT)	 AG	174529-174660	GT	ATG
(AAA)	 AG	174767-174922	GT	AGG
(CTG)	 AG	175055-175118	GT	AGG
(ATC)	 AG	175211-175271	GT	TGG
(TTC)	 AG	175376-175467	GT	AGG
(GGG)	 AG	175651-175827	GT	TGG
(ATC)	 AG	175911-175970	GT	AGG
(ATT)	 AG	176070-176237	GT	TGG
(GAG)	 AG	176318-176385	GT	AAG
(GAT)	 AG	176623-176665	GT	AGG
(GTG)	 AG	176759-176822	GT	TGG
(CTC)	 AG	176938-177014	GT	AGG
(GGC)	 AG	177131-177172	AG	AAA
-recovered pasa_asmbl_2004.p1, terminal, 177131, 177172
-recovered pasa_asmbl_2004.p1, internal, 174529, 174660
-recovered pasa_asmbl_2004.p1, internal, 174767, 174922
-recovered pasa_asmbl_2004.p1, internal, 175055, 175118
-recovered pasa_asmbl_2004.p1, internal, 175211, 175271
-recovered pasa_asmbl_2004.p1, internal, 175376, 175467
-recovered pasa_asmbl_2004.p1, internal, 175651, 175827
-recovered pasa_asmbl_2004.p1, internal, 175911, 175970
-recovered pasa_asmbl_2004.p1, internal, 176070, 176237
-recovered pasa_asmbl_2004.p1, internal, 176318, 176385
-recovered pasa_asmbl_2004.p1, internal, 176623, 176665
-recovered pasa_asmbl_2004.p1, internal, 176759, 176822
-recovered pasa_asmbl_2004.p1, internal, 176938, 177014
Valid prediction for snap_scaffold_1-snap.1807-T1
Valid prediction for snap_scaffold_1-snap.1813-T1
Valid prediction for HiQ_model.g1021.t1
Valid prediction for CodingQuarry_transcript_2749-T1
Valid prediction for pasa_asmbl_2007.p1
Valid prediction for Augustus_model.g1040.t1
Couldn't classify 305007, 305109
Sorry, prediction pasa_asmbl_2702.p1 fails validation.
(TAC)	 CC	305007-305109	GT	AGG
(GAT)	 AG	306097-306188	GT	AGG
(GCT)	 AG	306551-306640	GT	AGG
(AAT)	 AG	306830-307195	GT	AGG
(GCT)	 AG	307311-307427	GT	AGG
(AAC)	 AG	308242-308357	GT	GGG
(GAC)	 AG	308491-308669	GT	CTG
(TTT)	 AG	308845-308912	GT	AGG
(AAT)	 AG	309584-309750	GT	AGG
(CAC)	 AG	310658-310950	GT	TGG
(TTT)	 AG	311908-312003	GT	AGG
(CGC)	 AG	312102-312211	GT	AGG
(GAG)	 AG	312371-312656	GT	AGG
(CAA)	 AG	312972-313060	CA	AAC
-recovered pasa_asmbl_2702.p1, terminal, 312972, 313060
-recovered pasa_asmbl_2702.p1, internal, 306097, 306188
-recovered pasa_asmbl_2702.p1, internal, 306551, 306640
-recovered pasa_asmbl_2702.p1, internal, 306830, 307195
-recovered pasa_asmbl_2702.p1, internal, 307311, 307427
-recovered pasa_asmbl_2702.p1, internal, 308242, 308357
-recovered pasa_asmbl_2702.p1, internal, 308491, 308669
-recovered pasa_asmbl_2702.p1, internal, 308845, 308912
-recovered pasa_asmbl_2702.p1, internal, 309584, 309750
-recovered pasa_asmbl_2702.p1, internal, 310658, 310950
-recovered pasa_asmbl_2702.p1, internal, 311908, 312003
-recovered pasa_asmbl_2702.p1, internal, 312102, 312211
-recovered pasa_asmbl_2702.p1, internal, 312371, 312656
Valid prediction for pasa_asmbl_2807.p1
Valid prediction for GlimmerHMM_glimmerT_1408-T1
Valid prediction for snap_scaffold_1-snap.1806-T1
Valid prediction for GlimmerHMM_glimmerT_1407-T1
Valid prediction for snap_scaffold_1-snap.1789-T1
Valid prediction for HiQ_model.g1033.t1
Valid prediction for pasa_asmbl_2009.p1
Valid prediction for GlimmerHMM_glimmerT_1413-T1
Valid prediction for snap_scaffold_1-snap.1811-T1
Valid prediction for HiQ_model.g1035.t1
Valid prediction for snap_scaffold_1-snap.1783-T1
Valid prediction for Augustus_model.g1029.t1
Couldn't classify 294539, 294605
Sorry, prediction pasa_asmbl_2015.p1 fails validation.
(CCT)	 CC	294539-294605	GT	TGG
(GAC)	 AG	294897-295035	GT	GGG
(TCG)	 AG	295300-295396	GT	AGG
(AAC)	 AG	296124-296432	AC	AAA
-recovered pasa_asmbl_2015.p1, terminal, 296124, 296432
-recovered pasa_asmbl_2015.p1, internal, 294897, 295035
-recovered pasa_asmbl_2015.p1, internal, 295300, 295396

-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 snap_scaffold_1-snap.1803-T1
Couldn't classify 8744, 8831
Sorry, prediction pasa_asmbl_591.p1 fails validation.
(CGC)	 AA	8744-8831	GT	GGG
(ATA)	 AG	10012-10149	GT	TGG
(ATG)	 AG	10583-10726	GT	CGG
(ATG)	 AG	11048-11176	GT	AGG
(ATG)	 AG	11648-11773	GT	AGG
(ACC)	 AG	12441-12557	GT	AGG
(ATA)	 AG	13192-13320	GT	AGG
(ATA)	 AG	14056-14179	GT	ACG
(GCG)	 AG	15037-15394	GC	AGG
-recovered pasa_asmbl_591.p1, initial, 10583, 10726
-recovered pasa_asmbl_591.p1, initial, 11048, 11176
add_exon() Sorry, pasa_asmbl_591.p1 11648-11773-initial-1 is invalid.
-recovered pasa_asmbl_591.p1, initial, 11648, 11773
-recovered pasa_asmbl_591.p1, terminal, 15037, 15394
-recovered pasa_asmbl_591.p1, internal, 10012, 10149
-recovered pasa_asmbl_591.p1, internal, 10583, 10726
-recovered pasa_asmbl_591.p1, internal, 11048, 11176
-recovered pasa_asmbl_591.p1, internal, 11648, 11773
-recovered pasa_asmbl_591.p1, internal, 12441, 12557
-recovered pasa_asmbl_591.p1, internal, 13192, 13320
-recovered pasa_asmbl_591.p1, internal, 14056, 14179
-recovered pasa_asmbl_591.p1, internal, 15037, 15394
Valid prediction for snap_scaffold_1-snap.1792-T1
Valid prediction for CodingQuarry_transcript_2746-T1
Valid prediction for GlimmerHMM_glimmerT_1393-T1
Valid prediction for snap_scaffold_1-snap.1796-T1
Valid prediction for snap_scaffold_1-snap.1814-T1
Valid prediction for GlimmerHMM_glimmerT_1404-T1
Valid prediction for GlimmerHMM_glimmerT_1419-T1
Valid prediction for snap_scaffold_1-snap.1795-T1
Couldn't classify 216725, 216869
Sorry, prediction pasa_asmbl_587.p1 fails validation.
(GCT)	 TA	216725-216869	GT	TGG
(GTA)	 AG	217010-217201	GT	AGG
(GGG)	 AG	217294-217409	CC	GAC
-recovered pasa_asmbl_587.p1, terminal, 217294, 217409
-recovered pasa_asmbl_587.p1, internal, 217010, 217201
Valid prediction for snap_scaffold_1-snap.1797-T1
Valid prediction for snap_scaffold_1-snap.1794-T1
Valid prediction for Augustus_model.g1039.t1
Valid prediction for snap_scaffold_1-snap.1788-T1
Valid prediction for snap_scaffold_1-snap.1787-T1
Valid prediction for GlimmerHMM_glimmerT_1410-T1
Valid prediction for CodingQuarry_transcript_2745-T1
Valid prediction for CodingQuarry_transcript_2743-T1
Valid prediction for CodingQuarry_transcript_2744-T1
Valid prediction for HiQ_model.g1025.t1
Valid prediction for Augustus_model.g1019.t1
Valid prediction for snap_scaffold_1-snap.1817-T1
Valid prediction for Augustus_model.g1026.t1
Valid prediction for GlimmerHMM_glimmerT_1406-T1
Valid prediction for pasa_asmbl_586.p1
Valid prediction for GlimmerHMM_glimmerT_1395-T1
Valid prediction for snap_scaffold_1-snap.1790-T1
Valid prediction for CodingQuarry_transcript_2747-T1
Valid prediction for CodingQuarry_transcript_2748-T1
Valid prediction for GlimmerHMM_glimmerT_1397-T1
Valid prediction for GlimmerHMM_glimmerT_1412-T1
Valid prediction for GlimmerHMM_glimmerT_1417-T1
Valid prediction for pasa_asmbl_579.p1
Valid prediction for GlimmerHMM_glimmerT_1421-T1
Valid prediction for snap_scaffold_1-snap.1799-T1
Valid prediction for GlimmerHMM_glimmerT_1411-T1
Valid prediction for Augustus_model.g1041.t1
Valid prediction for GlimmerHMM_glimmerT_1403-T1
Valid prediction for HiQ_model.g1022.t1
Valid prediction for GlimmerHMM_glimmerT_1405-T1
Valid prediction for HiQ_model.g1037.t1
Valid prediction for snap_scaffold_1-snap.1805-T1
Valid prediction for pasa_asmbl_578.p1
Valid prediction for snap_scaffold_1-snap.1798-T1
Couldn't classify 292010, 292051
Sorry, prediction pasa_asmbl_576.p1 fails validation.
(ATG)	 AC	290022-290099	GT	AGG
(CAA)	 AG	290680-290757	GT	TGG
(GCA)	 AG	291277-291330	GT	CTG
(GTG)	 AG	291757-291852	GT	AGG
(ACA)	 AG	292010-292051	AT	GGA
-recovered pasa_asmbl_576.p1, initial, 290022, 290099
-recovered pasa_asmbl_576.p1, internal, 290680, 290757
-recovered pasa_asmbl_576.p1, internal, 291277, 291330
-recovered pasa_asmbl_576.p1, internal, 291757, 291852
Valid prediction for GlimmerHMM_glimmerT_1400-T1
Valid prediction for GlimmerHMM_glimmerT_1402-T1
Valid prediction for Augustus_model.g1020.t1
Valid prediction for pasa_asmbl_585.p1
Valid prediction for GlimmerHMM_glimmerT_1399-T1
Valid prediction for Augustus_model.g1024.t1
Valid prediction for Augustus_model.g1032.t1
Valid prediction for HiQ_model.g1023.t1
Valid prediction for Augustus_model.g1028.t1
Valid prediction for CodingQuarry_transcript_2752-T1
Valid prediction for Augustus_model.g1030.t1
Valid prediction for snap_scaffold_1-snap.1786-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 165382, rend_intergenic: 162457  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 418134
-exon list size: 525


building trellis

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49.3    
49.5    
49.7    
49.9    
50.1    
50.3    
50.5    
50.7    
50.9    
51.0    
51.2    
51.4    
51.6    
51.8    
52.0    
52.2    
52.4    
52.6    
52.8    
52.9    
53.1    
53.3    
53.5    
53.7    
53.9    
54.1    
54.3    
54.5    
54.6    
54.8    
55.0    
55.2    
55.4    
55.6    
55.8    
56.0    
56.2    
56.4    
56.5    
56.7    
56.9    
57.1    
57.3    
57.5    
57.7    
57.9    
58.1    
58.3    
58.4    
58.6    
58.8    
59.0    
59.2    
59.4    
59.6    
59.8    
60.0    
60.2    
60.3    
60.5    
60.7    
60.9    
61.1    
61.3    
61.5    
61.7    
61.9    
62.0    
62.2    
62.4    
62.6    
62.8    
63.0    
63.2    
63.4    
63.6    
63.8    
63.9    
64.1    
64.3    
64.5    
64.7    
64.9    
65.1    
65.3    
65.5    
65.7    
65.8    
66.0    
66.2    
66.4    
66.6    
66.8    
67.0    
67.2    
67.4    
67.6    
67.7    
67.9    
68.1    
68.3    
68.5    
68.7    
68.9    
69.1    
69.3    
69.4    
69.6    
69.8    
70.0    
70.2    
70.4    
70.6    
70.8    
71.0    
71.2    
71.3    
71.5    
71.7    
71.9    
72.1    
72.3    
72.5    
72.7    
72.9    
73.1    
73.2    
73.4    
73.6    
73.8    
74.0    
74.2    
74.4    
74.6    
74.8    
75.0    
75.1    
75.3    
75.5    
75.7    
75.9    
76.1    
76.3    
76.5    
76.7    
76.9    
77.0    
77.2    
77.4    
77.6    
77.8    
78.0    
78.2    
78.4    
78.6    
78.7    
78.9    
79.1    
79.3    
79.5    
79.7    
79.9    
80.1    
80.3    
80.5    
80.6    
80.8    
81.0    
81.2    
81.4    
81.6    
81.8    
82.0    
82.2    
82.4    
82.5    
82.7    
82.9    
83.1    
83.3    
83.5    
83.7    
83.9    
84.1    
84.3    
84.4    
84.6    
84.8    
85.0    
85.2    
85.4    
85.6    
85.8    
86.0    
86.1    
86.3    
86.5    
86.7    
86.9    
87.1    
87.3    
87.5    
87.7    
87.9    
88.0    
88.2    
88.4    
88.6    
88.8    
89.0    
89.2    
89.4    
89.6    
89.8    
89.9    
90.1    
90.3    
90.5    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
91.8    
92.0    
92.2    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.5    
93.7    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.4    
95.6    
95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.2    
99.4    
99.6    
99.8    
-found 39 predictions from path traversal
Error with prediction: snap lend_intergenic: 165382, rend_intergenic: 162457  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 32 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 10790
-exon list size: 1


building trellis

33.3    
66.7    
-found 1 predictions from path traversal

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