-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_28/scaffold_28_6365125-6623240

-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_58977-T1
Valid prediction for snap_scaffold_28-snap.1435-T1
Valid prediction for snap_scaffold_28-snap.1439-T1
Valid prediction for snap_scaffold_28-snap.1458-T1
Valid prediction for snap_scaffold_28-snap.1472-T1
Valid prediction for snap_scaffold_28-snap.1448-T1
Valid prediction for snap_scaffold_28-snap.1461-T1
Valid prediction for GlimmerHMM_glimmerT_58978-T1
Valid prediction for GlimmerHMM_glimmerT_58962-T1
Valid prediction for GlimmerHMM_glimmerT_58973-T1
Valid prediction for GlimmerHMM_glimmerT_58951-T1
Valid prediction for snap_scaffold_28-snap.1443-T1
Valid prediction for Augustus_model.g39094.t1
Valid prediction for snap_scaffold_28-snap.1453-T1
Valid prediction for Augustus_model.g39082.t1
Valid prediction for snap_scaffold_28-snap.1451-T1
Valid prediction for snap_scaffold_28-snap.1441-T1
Valid prediction for snap_scaffold_28-snap.1442-T1
Valid prediction for snap_scaffold_28-snap.1434-T1
Valid prediction for GlimmerHMM_glimmerT_58964-T1
Valid prediction for snap_scaffold_28-snap.1463-T1
Valid prediction for snap_scaffold_28-snap.1477-T1
Valid prediction for Augustus_model.g39074.t1
Valid prediction for snap_scaffold_28-snap.1469-T1
Valid prediction for snap_scaffold_28-snap.1474-T1
Valid prediction for snap_scaffold_28-snap.1436-T1
Valid prediction for GlimmerHMM_glimmerT_58976-T1
Valid prediction for snap_scaffold_28-snap.1447-T1
Valid prediction for snap_scaffold_28-snap.1467-T1
Valid prediction for GlimmerHMM_glimmerT_58961-T1
Valid prediction for snap_scaffold_28-snap.1460-T1
Couldn't classify 250612, 251142
Sorry, prediction pasa_asmbl_37628.p2 fails validation.
(GAG)	 AG	250612-251142	GT	AGG
(ATC)	 AG	251347-251442	CT	AAC
-recovered pasa_asmbl_37628.p2, terminal, 251347, 251442
-recovered pasa_asmbl_37628.p2, internal, 250612, 251142
Valid prediction for snap_scaffold_28-snap.1438-T1
Valid prediction for GlimmerHMM_glimmerT_58965-T1
Couldn't classify 250118, 250518
Sorry, prediction pasa_asmbl_37848.p1 fails validation.
(ATG)	 TT	249725-249776	GT	AGG
(GTT)	 AG	250118-250518	CA	AGC
-recovered pasa_asmbl_37848.p1, initial, 249725, 249776
Valid prediction for Augustus_model.g39096.t1
Valid prediction for Augustus_model.g39083.t1
Couldn't classify 211062, 211189
Sorry, prediction pasa_asmbl_37626.p1 fails validation.
(ATG)	 AA	210609-210743	GT	AGG
(CAA)	 AG	210877-210949	GT	AGG
(CAC)	 AG	211062-211189	GT	CGG
-recovered pasa_asmbl_37626.p1, initial, 210609, 210743
-recovered pasa_asmbl_37626.p1, internal, 210877, 210949
-recovered pasa_asmbl_37626.p1, internal, 211062, 211189
Valid prediction for GlimmerHMM_glimmerT_58954-T1
Valid prediction for snap_scaffold_28-snap.1454-T1
Valid prediction for snap_scaffold_28-snap.1476-T1
Valid prediction for GlimmerHMM_glimmerT_58974-T1
Valid prediction for HiQ_model.g39097.t1
Valid prediction for snap_scaffold_28-snap.1466-T1
Valid prediction for Augustus_model.g39075.t1
Couldn't classify 239581, 239728
Sorry, prediction pasa_asmbl_37627.p1 fails validation.
(CCC)	 CT	239581-239728	GT	AGG
(GGA)	 AG	239831-239933	GT	CAG
(ACA)	 AG	240211-240294	GT	AGG
(CCT)	 AG	242812-242955	GT	TCG
(CAG)	 AG	243334-243496	GT	GGG
(TGG)	 AG	244001-244108	GT	ATG
(GGA)	 AG	244352-244403	GT	GGG
(ACT)	 AG	245066-245544	AG	AAA
-recovered pasa_asmbl_37627.p1, terminal, 245066, 245544
-recovered pasa_asmbl_37627.p1, internal, 239831, 239933
-recovered pasa_asmbl_37627.p1, internal, 240211, 240294
-recovered pasa_asmbl_37627.p1, internal, 242812, 242955
-recovered pasa_asmbl_37627.p1, internal, 243334, 243496
-recovered pasa_asmbl_37627.p1, internal, 244001, 244108
-recovered pasa_asmbl_37627.p1, internal, 244352, 244403
Valid prediction for snap_scaffold_28-snap.1468-T1
Valid prediction for GlimmerHMM_glimmerT_58963-T1
Valid prediction for Augustus_model.g39079.t1
Valid prediction for Augustus_model.g39092.t1
Valid prediction for snap_scaffold_28-snap.1428-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: -)Valid prediction for snap_scaffold_28-snap.1452-T1
Valid prediction for Augustus_model.g39078.t1
Valid prediction for GlimmerHMM_glimmerT_58959-T1
Valid prediction for GlimmerHMM_glimmerT_58967-T1
Valid prediction for snap_scaffold_28-snap.1450-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for snap_scaffold_28-snap.1449-T1
Valid prediction for Augustus_model.g39095.t1
Valid prediction for Augustus_model.g39081.t1
Couldn't classify 207278, 207401
Couldn't classify 208039, 208106
Sorry, prediction pasa_asmbl_38555.p1 fails validation.
(GGC)	 CC	207278-207401	GT	GGG
(ACG)	 AG	207821-207940	GT	CGG
(ACA)	 AG	208039-208106	GG	GGG
-recovered pasa_asmbl_38555.p1, internal, 207821, 207940
Valid prediction for GlimmerHMM_glimmerT_58955-T1
Valid prediction for GlimmerHMM_glimmerT_58968-T1
Valid prediction for GlimmerHMM_glimmerT_58960-T1
Valid prediction for GlimmerHMM_glimmerT_58969-T1
Valid prediction for pasa_asmbl_38354.p2
Valid prediction for snap_scaffold_28-snap.1462-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_58956-T1
Valid prediction for snap_scaffold_28-snap.1427-T1
Valid prediction for GlimmerHMM_glimmerT_58957-T1
Valid prediction for HiQ_model.g39084.t1
Valid prediction for snap_scaffold_28-snap.1430-T1
Valid prediction for snap_scaffold_28-snap.1432-T1
Valid prediction for Augustus_model.g39089.t1
Valid prediction for HiQ_model.g39088.t1
Valid prediction for HiQ_model.g39085.t1
Valid prediction for snap_scaffold_28-snap.1475-T1
Valid prediction for snap_scaffold_28-snap.1444-T1
Valid prediction for Augustus_model.g39080.t1
Couldn't classify 159372, 159422
Sorry, prediction pasa_asmbl_38341.p1 fails validation.
(GAT)	 GA	159372-159422	GT	AGG
(GAC)	 AG	160359-160437	GT	ATG
(GGG)	 AG	160536-160624	GT	TGG
(GGA)	 AG	160741-160818	GT	AGG
(AAT)	 AG	161820-161918	AG	AGA
-recovered pasa_asmbl_38341.p1, terminal, 161820, 161918
-recovered pasa_asmbl_38341.p1, internal, 160359, 160437
-recovered pasa_asmbl_38341.p1, internal, 160536, 160624
-recovered pasa_asmbl_38341.p1, internal, 160741, 160818
Valid prediction for Augustus_model.g39086.t1
Valid prediction for snap_scaffold_28-snap.1456-T1
Valid prediction for Augustus_model.g39076.t1
Couldn't classify 205088, 205220
Couldn't classify 205910, 205968
Sorry, prediction pasa_asmbl_38593.p1 fails validation.
(ATT)	 AT	205088-205220	GT	AGG
(ATG)	 AG	205337-205456	GT	GGG
(ATG)	 AG	205910-205968	GG	AGG
-recovered pasa_asmbl_38593.p1, initial, 205337, 205456
-recovered pasa_asmbl_38593.p1, internal, 205337, 205456
Valid prediction for pasa_asmbl_38342.p1
Valid prediction for CodingQuarry_transcript_43691-T1
Valid prediction for Augustus_model.g39091.t1
Valid prediction for Augustus_model.g39077.t1
Valid prediction for snap_scaffold_28-snap.1445-T1
Valid prediction for CodingQuarry_transcript_43690-T1
Valid prediction for snap_scaffold_28-snap.1429-T1
Valid prediction for snap_scaffold_28-snap.1426-T1
Valid prediction for GlimmerHMM_glimmerT_58952-T1
Valid prediction for snap_scaffold_28-snap.1433-T1
Valid prediction for Augustus_model.g39093.t1
Valid prediction for snap_scaffold_28-snap.1457-T1
Valid prediction for CodingQuarry_transcript_43689-T1
Valid prediction for GlimmerHMM_glimmerT_58979-T1
Valid prediction for GlimmerHMM_glimmerT_58972-T1
Couldn't classify 231454, 231724
Sorry, prediction pasa_asmbl_38334.p1 fails validation.
(CAA)	 AG	231454-231724	GT	AGG
(GTA)	 AG	232009-232208	CT	AGC
-recovered pasa_asmbl_38334.p1, terminal, 232009, 232208
-recovered pasa_asmbl_38334.p1, internal, 231454, 231724
Valid prediction for snap_scaffold_28-snap.1471-T1
Valid prediction for snap_scaffold_28-snap.1470-T1
Couldn't classify 225056, 225982
Sorry, prediction pasa_asmbl_38335.p1 fails validation.
(CCC)	 AC	225056-225982	GG	CGG
Valid prediction for snap_scaffold_28-snap.1446-T1
Valid prediction for GlimmerHMM_glimmerT_58975-T1
Valid prediction for snap_scaffold_28-snap.1440-T1
Valid prediction for snap_scaffold_28-snap.1473-T1
Valid prediction for snap_scaffold_28-snap.1459-T1
Valid prediction for GlimmerHMM_glimmerT_58958-T1
Valid prediction for GlimmerHMM_glimmerT_58966-T1
Valid prediction for GlimmerHMM_glimmerT_58950-T1
Valid prediction for GlimmerHMM_glimmerT_58953-T1
Valid prediction for snap_scaffold_28-snap.1437-T1
Valid prediction for Augustus_model.g39087.t1
Couldn't classify 105775, 105834
Sorry, prediction pasa_asmbl_38349.p1 fails validation.
(CTG)	 AC	105775-105834	GT	AGG
(TGC)	 AG	106023-106175	GT	AGG
(TGT)	 AG	106378-106554	GT	AGG
(TGC)	 AG	106637-106783	GT	AGG
(TGC)	 AG	107056-107206	GT	AGG
(GTC)	 AG	107536-107651	CA	AAC
-recovered pasa_asmbl_38349.p1, terminal, 107536, 107651
-recovered pasa_asmbl_38349.p1, internal, 106023, 106175
-recovered pasa_asmbl_38349.p1, internal, 106378, 106554
-recovered pasa_asmbl_38349.p1, internal, 106637, 106783
-recovered pasa_asmbl_38349.p1, internal, 107056, 107206
Valid prediction for CodingQuarry_transcript_43692-T1
Valid prediction for snap_scaffold_28-snap.1464-T1
Valid prediction for GlimmerHMM_glimmerT_58970-T1
Couldn't classify 129096, 129586
Sorry, prediction pasa_asmbl_38345.p1 fails validation.
(ATG)	 GG	127805-127911	GT	AGG
(TAA)	 AG	128058-128233	GT	AGG
(ACC)	 AG	128335-128441	GT	GGG
(ATT)	 AG	128587-128695	GT	TGG
(GGA)	 AG	128784-128870	GT	AGG
(GTG)	 AG	129096-129586	GC	ACG
-recovered pasa_asmbl_38345.p1, initial, 127805, 127911
-recovered pasa_asmbl_38345.p1, internal, 128058, 128233
-recovered pasa_asmbl_38345.p1, internal, 128335, 128441
-recovered pasa_asmbl_38345.p1, internal, 128587, 128695
-recovered pasa_asmbl_38345.p1, internal, 128784, 128870
-recovered pasa_asmbl_38345.p1, internal, 129096, 129586
Valid prediction for snap_scaffold_28-snap.1465-T1
Valid prediction for CodingQuarry_transcript_43694-T1
Valid prediction for snap_scaffold_28-snap.1455-T1
Valid prediction for CodingQuarry_transcript_43693-T1
Valid prediction for GlimmerHMM_glimmerT_58971-T1
Valid prediction for Augustus_model.g39090.t1
Valid prediction for snap_scaffold_28-snap.1431-T1
Couldn't classify 104644, 105498
Sorry, prediction pasa_asmbl_38351.p1 fails validation.
(ATG)	 CC	98049-98129	GT	TGG
(GTG)	 AG	98408-98491	GT	AGG
(AAA)	 AG	98883-99007	GC	AGG
(GAA)	 AG	99318-99467	GT	AGG
(CTT)	 AG	99751-99894	GT	GAG
(TCG)	 AG	100102-100246	GT	ATG
(AAT)	 AG	100353-100445	GT	AGG
(TGG)	 AG	100631-100776	GT	AAG
(ACC)	 AG	101063-101232	GT	AGG
(TGA)	 AG	101508-101641	GT	AGG
(GAG)	 AG	102021-102141	GT	CGG
(GCT)	 AG	103387-103631	GT	AGG
(TTG)	 AG	103804-103945	GT	AGG
(GTG)	 AG	104071-104197	GT	AGG
(GTG)	 AG	104339-104549	GT	CAG
(TGC)	 AG	104644-105498	GT	GGG
-recovered pasa_asmbl_38351.p1, initial, 98049, 98129
add_exon() Sorry, pasa_asmbl_38351.p1 103804-103945-terminal-3 is invalid.
-recovered pasa_asmbl_38351.p1, terminal, 103804, 103945
-recovered pasa_asmbl_38351.p1, internal, 98408, 98491
-recovered pasa_asmbl_38351.p1, internal, 98883, 99007
-recovered pasa_asmbl_38351.p1, internal, 99318, 99467
-recovered pasa_asmbl_38351.p1, internal, 99751, 99894
-recovered pasa_asmbl_38351.p1, internal, 100102, 100246
-recovered pasa_asmbl_38351.p1, internal, 100353, 100445
-recovered pasa_asmbl_38351.p1, internal, 100631, 100776
-recovered pasa_asmbl_38351.p1, internal, 101063, 101232
-recovered pasa_asmbl_38351.p1, internal, 101508, 101641
-recovered pasa_asmbl_38351.p1, internal, 102021, 102141
-recovered pasa_asmbl_38351.p1, internal, 103387, 103631
-recovered pasa_asmbl_38351.p1, internal, 103804, 103945
-recovered pasa_asmbl_38351.p1, internal, 104071, 104197
-recovered pasa_asmbl_38351.p1, internal, 104339, 104549
-recovered pasa_asmbl_38351.p1, internal, 104644, 105498

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 62620, rend_intergenic: 50130  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74542, rend_intergenic: 65450  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78194, rend_intergenic: 74576  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86886, rend_intergenic: 80516  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92227, rend_intergenic: 87842  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96975, rend_intergenic: 95078  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98455, rend_intergenic: 97038  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136802, rend_intergenic: 135675  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147600, rend_intergenic: 136935  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165430, rend_intergenic: 149932  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183372, rend_intergenic: 180711  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 227931, rend_intergenic: 222772  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 237274, rend_intergenic: 230587  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 244587, rend_intergenic: 242840  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 258116
-exon list size: 651


building trellis

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55.6    
55.7    
55.9    
56.0    
56.2    
56.4    
56.5    
56.7    
56.8    
57.0    
57.1    
57.3    
57.4    
57.6    
57.7    
57.9    
58.0    
58.2    
58.3    
58.5    
58.7    
58.8    
59.0    
59.1    
59.3    
59.4    
59.6    
59.7    
59.9    
60.0    
60.2    
60.3    
60.5    
60.6    
60.8    
60.9    
61.1    
61.3    
61.4    
61.6    
61.7    
61.9    
62.0    
62.2    
62.3    
62.5    
62.6    
62.8    
62.9    
63.1    
63.2    
63.4    
63.6    
63.7    
63.9    
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    
68.1    
68.3    
68.5    
68.6    
68.8    
68.9    
69.1    
69.2    
69.4    
69.5    
69.7    
69.8    
70.0    
70.1    
70.3    
70.4    
70.6    
70.8    
70.9    
71.1    
71.2    
71.4    
71.5    
71.7    
71.8    
72.0    
72.1    
72.3    
72.4    
72.6    
72.7    
72.9    
73.0    
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    
75.2    
75.3    
75.5    
75.7    
75.8    
76.0    
76.1    
76.3    
76.4    
76.6    
76.7    
76.9    
77.0    
77.2    
77.3    
77.5    
77.6    
77.8    
77.9    
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    
80.6    
80.7    
80.9    
81.0    
81.2    
81.3    
81.5    
81.6    
81.8    
81.9    
82.1    
82.2    
82.4    
82.5    
82.7    
82.8    
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    
85.5    
85.6    
85.8    
85.9    
86.1    
86.2    
86.4    
86.5    
86.7    
86.8    
87.0    
87.1    
87.3    
87.4    
87.6    
87.7    
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    
90.4    
90.5    
90.7    
90.8    
91.0    
91.1    
91.3    
91.4    
91.6    
91.7    
91.9    
92.0    
92.2    
92.3    
92.5    
92.6    
92.8    
93.0    
93.1    
93.3    
93.4    
93.6    
93.7    
93.9    
94.0    
94.2    
94.3    
94.5    
94.6    
94.8    
94.9    
95.1    
95.3    
95.4    
95.6    
95.7    
95.9    
96.0    
96.2    
96.3    
96.5    
96.6    
96.8    
96.9    
97.1    
97.2    
97.4    
97.5    
97.7    
97.9    
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 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 62620, rend_intergenic: 50130  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74542, rend_intergenic: 65450  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78194, rend_intergenic: 74576  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86886, rend_intergenic: 80516  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92227, rend_intergenic: 87842  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96975, rend_intergenic: 95078  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98455, rend_intergenic: 97038  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136802, rend_intergenic: 135675  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147600, rend_intergenic: 136935  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165430, rend_intergenic: 149932  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183372, rend_intergenic: 180711  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 227931, rend_intergenic: 222772  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 237274, rend_intergenic: 230587  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 244587, rend_intergenic: 242840  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 29 predictions persist after filtering for low support