-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_11/scaffold_11_4729437-4868659

-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 GeneMark_model.47655_t
Couldn't classify 108110, 108167
Sorry, prediction pasa_asmbl_5489.p1 fails validation.
(AGC)	 CA	108110-108167	GT	CAG
(GCT)	 AG	110820-110960	GT	AGG
(CGG)	 AG	112000-112202	GT	TGG
(GGT)	 AG	112775-112996	TC	GAT
-recovered pasa_asmbl_5489.p1, terminal, 112775, 112996
-recovered pasa_asmbl_5489.p1, internal, 110820, 110960
-recovered pasa_asmbl_5489.p1, internal, 112000, 112202
Valid prediction for GlimmerHMM_glimmerT_27584-T1
Couldn't classify 130059, 130131
Couldn't classify 133411, 133422
Sorry, prediction pasa_asmbl_5490.p1 fails validation.
(TGC)	 CA	130059-130131	GT	AGG
(AGC)	 AG	131349-131457	GT	AGG
(ACT)	 AG	131775-131966	GT	CGG
(TCA)	 AG	132431-132580	GT	AGG
(GTA)	 AG	132755-133232	GT	AGG
(GAT)	 AG	133411-133422	GA	GGG
-recovered pasa_asmbl_5490.p1, internal, 131349, 131457
-recovered pasa_asmbl_5490.p1, internal, 131775, 131966
-recovered pasa_asmbl_5490.p1, internal, 132431, 132580
-recovered pasa_asmbl_5490.p1, internal, 132755, 133232
Valid prediction for GeneMark_model.47673_t
Valid prediction for CodingQuarry_transcript_8022-T1
Valid prediction for GeneMark_model.47658_t
Valid prediction for CodingQuarry_transcript_8020-T1
Valid prediction for HiQ_model.g18398.t1
Valid prediction for GeneMark_model.47652_t
Couldn't classify 18516, 18769
Couldn't classify 19160, 19292
Sorry, prediction pasa_asmbl_5475.p2 fails validation.
(CGG)	 CC	18516-18769	GT	AGG
(TCT)	 AG	18902-18949	GT	AGG
(GGG)	 AG	19160-19292	GT	AGG
-recovered pasa_asmbl_5475.p2, internal, 18902, 18949
-recovered pasa_asmbl_5475.p2, internal, 19160, 19292
Valid prediction for snap_scaffold_11-snap.1163-T1
Valid prediction for GlimmerHMM_glimmerT_27590-T1
Valid prediction for CodingQuarry_transcript_8025-T1
Couldn't classify 90842, 91028
Couldn't classify 91140, 91204
Sorry, prediction pasa_asmbl_5484.p1 fails validation.
(ATG)	 AA	89712-89850	GT	AGG
(AGA)	 AG	89969-90059	GT	CAG
(GCT)	 AG	90154-90281	GT	AGG
(GGA)	 AG	90411-90490	GT	AGG
(AGT)	 AG	90842-91028	AT	TGA
(GTC)	 AC	91140-91204	GT	AGG
(GCA)	 AG	91373-91409	GT	AGG
(CTC)	 AG	91609-91738	GT	AGG
(TGC)	 AG	91963-92080	AA	GAA
-recovered pasa_asmbl_5484.p1, initial, 89712, 89850
-recovered pasa_asmbl_5484.p1, terminal, 91963, 92080
-recovered pasa_asmbl_5484.p1, internal, 89969, 90059
-recovered pasa_asmbl_5484.p1, internal, 90154, 90281
-recovered pasa_asmbl_5484.p1, internal, 90411, 90490
-recovered pasa_asmbl_5484.p1, internal, 91373, 91409
-recovered pasa_asmbl_5484.p1, internal, 91609, 91738
Valid prediction for snap_scaffold_11-snap.1178-T1
Valid prediction for GeneMark_model.47669_t
Couldn't classify 102161, 102244
Couldn't classify 107931, 108031
Sorry, prediction pasa_asmbl_5486.p1 fails validation.
(TGT)	 AG	102161-102244	GT	AGG
(TCT)	 AG	102403-102507	GT	GGG
(TTA)	 AG	102847-102964	GT	TGG
(CAT)	 AG	103148-103205	GT	AGG
(GGC)	 AG	103303-103375	GT	AGG
(ATC)	 AG	103583-103743	GT	ATG
(TCT)	 AG	104627-104743	GT	AGG
(TGA)	 AG	106878-106975	GT	AGG
(CCT)	 AG	107931-108031	CA	CCC
-recovered pasa_asmbl_5486.p1, internal, 102161, 102244
-recovered pasa_asmbl_5486.p1, internal, 102403, 102507
-recovered pasa_asmbl_5486.p1, internal, 102847, 102964
-recovered pasa_asmbl_5486.p1, internal, 103148, 103205
-recovered pasa_asmbl_5486.p1, internal, 103303, 103375
-recovered pasa_asmbl_5486.p1, internal, 103583, 103743
-recovered pasa_asmbl_5486.p1, internal, 104627, 104743
-recovered pasa_asmbl_5486.p1, internal, 106878, 106975
Valid prediction for Augustus_model.g18403.t1
Valid prediction for snap_scaffold_11-snap.1168-T1
Valid prediction for snap_scaffold_11-snap.1160-T1
Valid prediction for Augustus_model.g18394.t1
Valid prediction for GlimmerHMM_glimmerT_27597-T1
Valid prediction for GeneMark_model.47646_t
Valid prediction for HiQ_model.g18392.t1
Valid prediction for HiQ_model.g18399.t1
Valid prediction for GeneMark_model.47653_t
Valid prediction for HiQ_model.g18390.t1
Valid prediction for GeneMark_model.47680_t
Valid prediction for GlimmerHMM_glimmerT_27594-T1
Couldn't classify 133714, 133819
Sorry, prediction pasa_asmbl_5492.p1 fails validation.
(AAG)	 CA	133714-133819	GT	GGG
(ACA)	 AG	135279-135412	GT	AGG
(GTG)	 AG	135822-135942	GT	AGG
(ATG)	 AG	136023-136198	GT	AGG
(GTT)	 AG	136294-136695	GT	AGG
(GTG)	 AG	136801-137837	GT	AGG
(GTC)	 AG	138232-138373	GT	TGG
(GTG)	 AG	138533-138604	GT	AGG
(GGA)	 AG	138712-138837	CC	GAC
add_exon() Sorry, pasa_asmbl_5492.p1 136023-136198-initial-1 is invalid.
-recovered pasa_asmbl_5492.p1, initial, 136023, 136198
-recovered pasa_asmbl_5492.p1, terminal, 138712, 138837
-recovered pasa_asmbl_5492.p1, internal, 135279, 135412
-recovered pasa_asmbl_5492.p1, internal, 135822, 135942
-recovered pasa_asmbl_5492.p1, internal, 136023, 136198
-recovered pasa_asmbl_5492.p1, internal, 136294, 136695
-recovered pasa_asmbl_5492.p1, internal, 136801, 137837
-recovered pasa_asmbl_5492.p1, internal, 138232, 138373
-recovered pasa_asmbl_5492.p1, internal, 138533, 138604
Couldn't classify 93325, 93463
Couldn't classify 100984, 101127
Sorry, prediction pasa_asmbl_5485.p1 fails validation.
(TGG)	 TG	93325-93463	GT	CGG
(ATG)	 AG	94387-94541	GT	AGG
(CCA)	 AG	94663-94831	GT	AGG
(GTC)	 AG	97536-97669	GT	AGG
(GCC)	 AG	98792-98913	GT	GGG
(CAA)	 AG	100659-100737	GT	TGG
(ACC)	 AG	100984-101127	AG	TCA
add_exon() Sorry, pasa_asmbl_5485.p1 94387-94541-initial-1 is invalid.
-recovered pasa_asmbl_5485.p1, initial, 94387, 94541
-recovered pasa_asmbl_5485.p1, internal, 94387, 94541
-recovered pasa_asmbl_5485.p1, internal, 94663, 94831
-recovered pasa_asmbl_5485.p1, internal, 97536, 97669
-recovered pasa_asmbl_5485.p1, internal, 98792, 98913
-recovered pasa_asmbl_5485.p1, internal, 100659, 100737
Valid prediction for HiQ_model.g18388.t1
Valid prediction for GeneMark_model.47662_t
Valid prediction for snap_scaffold_11-snap.1177-T1
Valid prediction for snap_scaffold_11-snap.1172-T1
Valid prediction for pasa_asmbl_5480.p1
Valid prediction for snap_scaffold_11-snap.1165-T1
Valid prediction for GeneMark_model.47643_t
Valid prediction for snap_scaffold_11-snap.1184-T1
Valid prediction for pasa_asmbl_5476.p1
Valid prediction for Augustus_model.g18400.t1
Valid prediction for GeneMark_model.47678_t
Valid prediction for GeneMark_model.47671_t
Couldn't classify 17787, 18296
Sorry, prediction pasa_asmbl_5473.p1 fails validation.
(ATG)	 AT	17787-18296	AC	GTA
Couldn't classify 90842, 91028
Couldn't classify 91140, 91204
Sorry, prediction CodingQuarry_transcript_8027-T1 fails validation.
(ATG)	 AA	89712-89850	GT	AGG
(AGA)	 AG	89969-90059	GT	CAG
(GCT)	 AG	90154-90281	GT	AGG
(GGA)	 AG	90411-90490	GT	AGG
(AGT)	 AG	90842-91028	AT	TGA
(GTC)	 AC	91140-91204	GT	AGG
(GCA)	 AG	91373-91409	GT	AGG
(CTC)	 AG	91609-91738	GT	AGG
(TGC)	 AG	91963-92080	AA	GAA
-recovered CodingQuarry_transcript_8027-T1, initial, 89712, 89850
-recovered CodingQuarry_transcript_8027-T1, terminal, 91963, 92080
-recovered CodingQuarry_transcript_8027-T1, internal, 89969, 90059
-recovered CodingQuarry_transcript_8027-T1, internal, 90154, 90281
-recovered CodingQuarry_transcript_8027-T1, internal, 90411, 90490
-recovered CodingQuarry_transcript_8027-T1, internal, 91373, 91409
-recovered CodingQuarry_transcript_8027-T1, internal, 91609, 91738
Valid prediction for snap_scaffold_11-snap.1162-T1
Valid prediction for GeneMark_model.47644_t
Valid prediction for GlimmerHMM_glimmerT_27588-T1
Valid prediction for GlimmerHMM_glimmerT_27586-T1
Valid prediction for snap_scaffold_11-snap.1176-T1
Valid prediction for GlimmerHMM_glimmerT_27595-T1
Valid prediction for CodingQuarry_transcript_8023-T1
Valid prediction for snap_scaffold_11-snap.1169-T1
Valid prediction for GeneMark_model.47675_t
Valid prediction for HiQ_model.g18391.t1
Valid prediction for GeneMark_model.47667_t
Valid prediction for GeneMark_model.47664_t
Valid prediction for GeneMark_model.47648_t
Valid prediction for GeneMark_model.47660_t
Valid prediction for snap_scaffold_11-snap.1174-T1
Valid prediction for GeneMark_model.47665_t
Valid prediction for GlimmerHMM_glimmerT_27591-T1
Valid prediction for GlimmerHMM_glimmerT_27596-T1
Valid prediction for snap_scaffold_11-snap.1173-T1
Valid prediction for pasa_asmbl_5472.p1
Valid prediction for GlimmerHMM_glimmerT_27601-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 Augustus_model.g18397.t1
Valid prediction for snap_scaffold_11-snap.1179-T1
Valid prediction for GeneMark_model.47677_t
Valid prediction for snap_scaffold_11-snap.1185-T1
Valid prediction for GlimmerHMM_glimmerT_27589-T1
Valid prediction for GeneMark_model.47659_t
Valid prediction for snap_scaffold_11-snap.1170-T1
Valid prediction for CodingQuarry_transcript_8021-T1
Valid prediction for snap_scaffold_11-snap.1164-T1
Valid prediction for GeneMark_model.47654_t
Valid prediction for pasa_asmbl_6605.p1
Valid prediction for snap_scaffold_11-snap.1182-T1
Valid prediction for snap_scaffold_11-snap.1159-T1
Valid prediction for GeneMark_model.47683_t
Valid prediction for CodingQuarry_transcript_8024-T1
Valid prediction for GlimmerHMM_glimmerT_27585-T1
Valid prediction for snap_scaffold_11-snap.1175-T1
Valid prediction for snap_scaffold_11-snap.1181-T1
Valid prediction for HiQ_model.g18389.t1
Valid prediction for GlimmerHMM_glimmerT_27598-T1
Couldn't classify 130131, 130272
Sorry, prediction pasa_asmbl_6597.p1 fails validation.
(ATG)	 CC	128546-128958	GT	AGG
(GAA)	 AG	129808-129918	GT	GAG
(GAT)	 AG	130131-130272	TC	GCT
-recovered pasa_asmbl_6597.p1, initial, 128546, 128958
-recovered pasa_asmbl_6597.p1, internal, 129808, 129918
Valid prediction for GeneMark_model.47666_t
Valid prediction for snap_scaffold_11-snap.1166-T1
Valid prediction for GeneMark_model.47668_t
Valid prediction for GlimmerHMM_glimmerT_27593-T1
Valid prediction for GeneMark_model.47682_t
Valid prediction for GlimmerHMM_glimmerT_27599-T1
Valid prediction for Augustus_model.g18387.t1
Couldn't classify 130363, 130816
Sorry, prediction pasa_asmbl_6596.p1 fails validation.
(GGC)	 TC	130363-130816	GT	TGG
(GCT)	 AG	131149-131414	GC	AGG
-recovered pasa_asmbl_6596.p1, terminal, 131149, 131414
-recovered pasa_asmbl_6596.p1, internal, 131149, 131414
Valid prediction for GeneMark_model.47674_t
Valid prediction for snap_scaffold_11-snap.1171-T1
Valid prediction for GeneMark_model.47670_t
Valid prediction for Augustus_model.g18401.t1
Valid prediction for GeneMark_model.47676_t
Couldn't classify 15367, 15397
Sorry, prediction pasa_asmbl_6615.p1 fails validation.
(GCT)	 AG	15367-15397	GT	TGG
(AGT)	 AG	15829-15972	GT	CGG
(GCA)	 AG	16396-16502	GT	AGG
(GAC)	 AG	16588-16723	GT	AGG
(AGT)	 AG	17295-17323	AT	GAA
-recovered pasa_asmbl_6615.p1, terminal, 17295, 17323
-recovered pasa_asmbl_6615.p1, internal, 15367, 15397
-recovered pasa_asmbl_6615.p1, internal, 15829, 15972
-recovered pasa_asmbl_6615.p1, internal, 16396, 16502
-recovered pasa_asmbl_6615.p1, internal, 16588, 16723
Valid prediction for snap_scaffold_11-snap.1161-T1
Valid prediction for GeneMark_model.47672_t
Valid prediction for Augustus_model.g18402.t1
Valid prediction for pasa_asmbl_6598.p1
Valid prediction for Augustus_model.g18396.t1
Valid prediction for GlimmerHMM_glimmerT_27592-T1
Valid prediction for GeneMark_model.47656_t
Couldn't classify 78702, 78748
Couldn't classify 82824, 82949
Sorry, prediction pasa_asmbl_6612.p1 fails validation.
(AAC)	 AG	78702-78748	GT	TGG
(CCG)	 AG	78966-79089	GT	AGG
(GTG)	 AG	79387-79542	GT	AGG
(CTG)	 AG	82488-82646	GT	AGG
(GTG)	 AG	82824-82949	TT	ACT
-recovered pasa_asmbl_6612.p1, internal, 78702, 78748
-recovered pasa_asmbl_6612.p1, internal, 78966, 79089
-recovered pasa_asmbl_6612.p1, internal, 79387, 79542
-recovered pasa_asmbl_6612.p1, internal, 82488, 82646
Valid prediction for GlimmerHMM_glimmerT_27600-T1
Valid prediction for snap_scaffold_11-snap.1183-T1
Valid prediction for GeneMark_model.47657_t
Couldn't classify 65418, 65538
Couldn't classify 72763, 72789
Sorry, prediction pasa_asmbl_6614.p1 fails validation.
(GGG)	 GA	65418-65538	GT	AGG
(GGT)	 AG	66054-66206	GT	GGG
(AAA)	 AG	66594-66787	GT	AGG
(ATC)	 AG	67049-67147	GT	AGG
(GCC)	 AG	67324-67479	GT	AGG
(GAC)	 AG	67599-67727	GT	ATG
(GCT)	 AG	67950-68075	GT	AGG
(GAG)	 AG	68481-68539	GT	CGG
(GTG)	 AG	70434-70542	GT	AGG
(TAT)	 AG	72097-72207	GT	AGG
(ATC)	 AG	72763-72789	CT	TGC
-recovered pasa_asmbl_6614.p1, internal, 66054, 66206
-recovered pasa_asmbl_6614.p1, internal, 66594, 66787
-recovered pasa_asmbl_6614.p1, internal, 67049, 67147
-recovered pasa_asmbl_6614.p1, internal, 67324, 67479
-recovered pasa_asmbl_6614.p1, internal, 67599, 67727
-recovered pasa_asmbl_6614.p1, internal, 67950, 68075
-recovered pasa_asmbl_6614.p1, internal, 68481, 68539
-recovered pasa_asmbl_6614.p1, internal, 70434, 70542
-recovered pasa_asmbl_6614.p1, internal, 72097, 72207
Valid prediction for GeneMark_model.47645_t
Valid prediction for HiQ_model.g18393.t1
Couldn't classify 76096, 76488
Sorry, prediction pasa_asmbl_6613.p1 fails validation.
(ATG)	 CC	74209-74335	GT	GGG
(TTC)	 AG	75705-75823	GT	AGG
(GTG)	 AG	76096-76488	GA	AAG
-recovered pasa_asmbl_6613.p1, initial, 74209, 74335
-recovered pasa_asmbl_6613.p1, internal, 75705, 75823
Valid prediction for Augustus_model.g18395.t1
Valid prediction for GeneMark_model.47647_t
Valid prediction for snap_scaffold_11-snap.1180-T1
Valid prediction for GlimmerHMM_glimmerT_27587-T1
Valid prediction for GeneMark_model.47663_t
Valid prediction for GeneMark_model.47681_t
Valid prediction for GeneMark_model.47651_t
Valid prediction for GeneMark_model.47649_t
Valid prediction for snap_scaffold_11-snap.1167-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 57514, rend_intergenic: 46498  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62354, rend_intergenic: 57522  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82545, rend_intergenic: 62368  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87680, rend_intergenic: 82953  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120476, rend_intergenic: 94268  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138837, rend_intergenic: 133377  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 139223
-exon list size: 518


building trellis

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53.1    
53.3    
53.5    
53.7    
53.8    
54.0    
54.2    
54.4    
54.6    
54.8    
55.0    
55.2    
55.4    
55.6    
55.8    
56.0    
56.2    
56.3    
56.5    
56.7    
56.9    
57.1    
57.3    
57.5    
57.7    
57.9    
58.1    
58.3    
58.5    
58.7    
58.8    
59.0    
59.2    
59.4    
59.6    
59.8    
60.0    
60.2    
60.4    
60.6    
60.8    
61.0    
61.2    
61.3    
61.5    
61.7    
61.9    
62.1    
62.3    
62.5    
62.7    
62.9    
63.1    
63.3    
63.5    
63.7    
63.8    
64.0    
64.2    
64.4    
64.6    
64.8    
65.0    
65.2    
65.4    
65.6    
65.8    
66.0    
66.2    
66.3    
66.5    
66.7    
66.9    
67.1    
67.3    
67.5    
67.7    
67.9    
68.1    
68.3    
68.5    
68.7    
68.8    
69.0    
69.2    
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    
73.3    
73.5    
73.7    
73.8    
74.0    
74.2    
74.4    
74.6    
74.8    
75.0    
75.2    
75.4    
75.6    
75.8    
76.0    
76.2    
76.3    
76.5    
76.7    
76.9    
77.1    
77.3    
77.5    
77.7    
77.9    
78.1    
78.3    
78.5    
78.7    
78.8    
79.0    
79.2    
79.4    
79.6    
79.8    
80.0    
80.2    
80.4    
80.6    
80.8    
81.0    
81.2    
81.3    
81.5    
81.7    
81.9    
82.1    
82.3    
82.5    
82.7    
82.9    
83.1    
83.3    
83.5    
83.7    
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    
86.3    
86.5    
86.7    
86.9    
87.1    
87.3    
87.5    
87.7    
87.9    
88.1    
88.3    
88.5    
88.7    
88.8    
89.0    
89.2    
89.4    
89.6    
89.8    
90.0    
90.2    
90.4    
90.6    
90.8    
91.0    
91.2    
91.3    
91.5    
91.7    
91.9    
92.1    
92.3    
92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.7    
93.8    
94.0    
94.2    
94.4    
94.6    
94.8    
95.0    
95.2    
95.4    
95.6    
95.8    
96.0    
96.2    
96.3    
96.5    
96.7    
96.9    
97.1    
97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 57514, rend_intergenic: 46498  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62354, rend_intergenic: 57522  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82545, rend_intergenic: 62368  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87680, rend_intergenic: 82953  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120476, rend_intergenic: 94268  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138837, rend_intergenic: 133377  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support