-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_6/scaffold_6_7653853-7839767

-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_6-snap.1714-T1
Valid prediction for snap_scaffold_6-snap.1728-T1
Valid prediction for snap_scaffold_6-snap.1707-T1
Valid prediction for GlimmerHMM_glimmerT_15333-T1
Valid prediction for GeneMark_model.25871_t
Valid prediction for GlimmerHMM_glimmerT_15351-T1
Valid prediction for Augustus_model.g10230.t1
Valid prediction for GeneMark_model.25877_t
Valid prediction for GeneMark_model.25904_t
Valid prediction for GlimmerHMM_glimmerT_15327-T1
Valid prediction for GlimmerHMM_glimmerT_15350-T1
Valid prediction for GeneMark_model.25891_t
Valid prediction for Augustus_model.g10228.t1
Valid prediction for snap_scaffold_6-snap.1738-T1
Valid prediction for GeneMark_model.25873_t
Valid prediction for GlimmerHMM_glimmerT_15339-T1
Valid prediction for GeneMark_model.25875_t
Valid prediction for Augustus_model.g10219.t1
Valid prediction for snap_scaffold_6-snap.1736-T1
Valid prediction for GeneMark_model.25885_t
Valid prediction for GeneMark_model.25900_t
Valid prediction for Augustus_model.g10218.t1
Valid prediction for GlimmerHMM_glimmerT_15340-T1
Valid prediction for snap_scaffold_6-snap.1737-T1
Valid prediction for GlimmerHMM_glimmerT_15336-T1
Valid prediction for GeneMark_model.25869_t
Valid prediction for GeneMark_model.25903_t
Valid prediction for GeneMark_model.25893_t
Valid prediction for GlimmerHMM_glimmerT_15353-T1
Valid prediction for GlimmerHMM_glimmerT_15349-T1
Valid prediction for GlimmerHMM_glimmerT_15343-T1
Valid prediction for Augustus_model.g10223.t1
Valid prediction for GeneMark_model.25896_t
Valid prediction for GeneMark_model.25898_t
Valid prediction for GlimmerHMM_glimmerT_15347-T1
Valid prediction for GlimmerHMM_glimmerT_15354-T1
Valid prediction for snap_scaffold_6-snap.1739-T1
Valid prediction for GlimmerHMM_glimmerT_15329-T1
Valid prediction for GeneMark_model.25886_t
Valid prediction for Augustus_model.g10216.t1
Valid prediction for GlimmerHMM_glimmerT_15352-T1
Valid prediction for snap_scaffold_6-snap.1730-T1
Valid prediction for GeneMark_model.25882_t
Valid prediction for snap_scaffold_6-snap.1735-T1
Valid prediction for GeneMark_model.25890_t
Valid prediction for Augustus_model.g10214.t1
Valid prediction for GeneMark_model.25894_t
Valid prediction for GlimmerHMM_glimmerT_15337-T1
Valid prediction for snap_scaffold_6-snap.1710-T1
Couldn't classify 152437, 152493
Sorry, prediction Augustus_model.g10229.t1 fails validation.
(ATG)	 GG	131566-131582	GT	AGG
(AGT)	 AG	131934-132152	GT	AGG
(GTG)	 AG	132817-132995	GT	AGG
(TGG)	 AG	133500-133613	GT	AGG
(TGG)	 AG	135285-135447	GT	AGG
(GTA)	 AG	136982-137088	GT	CTG
(ATA)	 AG	137640-137787	GT	ATG
(AGC)	 AG	139264-139397	GT	GGG
(ATG)	 AG	140553-140664	GT	AGG
(GCC)	 AG	141148-141338	GT	CGG
(AGC)	 AG	141457-141540	GT	AGG
(GAG)	 AG	141657-141851	GT	CAG
(GTA)	 AG	142275-142391	GT	AGG
(GTG)	 AG	142539-142706	GT	GGG
(CCA)	 AG	142887-142989	GT	AGG
(GCA)	 AG	143587-143763	GT	AGG
(GCA)	 AG	144149-144285	GT	CAG
(ATG)	 AG	144645-144792	GT	CGG
(ACT)	 AG	146013-146153	GT	AGG
(GTA)	 AG	146911-147092	GT	AGG
(TGC)	 AG	147363-147478	GT	AGG
(CTG)	 AG	147627-147822	GT	CAG
(AAC)	 AG	147959-148057	GT	AGG
(GCT)	 AG	148173-148364	GT	AGG
(AGA)	 AG	148628-148749	GT	AGG
(GTT)	 AG	148838-148947	GT	AGG
(GTT)	 AG	149067-149217	GT	TGG
(CCT)	 AG	149453-149690	GT	TGG
(TGC)	 AG	149825-149940	GT	AGG
(GTG)	 AG	150117-150306	GT	CGG
(TGC)	 AG	150511-150609	GT	GGG
(CCT)	 AG	150747-150941	GT	AGG
(CGA)	 AG	151067-151268	GT	AGG
(GCT)	 AG	151370-151473	GT	CGG
(CCC)	 AG	151771-151841	GT	AGG
(CCT)	 AG	152017-152152	GT	CGG
(CCC)	 AG	152437-152493	GT	CAG
-recovered Augustus_model.g10229.t1, initial, 131566, 131582
add_exon() Sorry, Augustus_model.g10229.t1 140553-140664-initial-1 is invalid.
-recovered Augustus_model.g10229.t1, initial, 140553, 140664
add_exon() Sorry, Augustus_model.g10229.t1 144645-144792-initial-1 is invalid.
-recovered Augustus_model.g10229.t1, initial, 144645, 144792
add_exon() Sorry, Augustus_model.g10229.t1 133500-133613-terminal-1 is invalid.
-recovered Augustus_model.g10229.t1, terminal, 133500, 133613
-recovered Augustus_model.g10229.t1, internal, 131934, 132152
-recovered Augustus_model.g10229.t1, internal, 132817, 132995
-recovered Augustus_model.g10229.t1, internal, 133500, 133613
-recovered Augustus_model.g10229.t1, internal, 135285, 135447
-recovered Augustus_model.g10229.t1, internal, 136982, 137088
-recovered Augustus_model.g10229.t1, internal, 137640, 137787
-recovered Augustus_model.g10229.t1, internal, 139264, 139397
-recovered Augustus_model.g10229.t1, internal, 140553, 140664
-recovered Augustus_model.g10229.t1, internal, 141148, 141338
-recovered Augustus_model.g10229.t1, internal, 141457, 141540
-recovered Augustus_model.g10229.t1, internal, 141657, 141851
-recovered Augustus_model.g10229.t1, internal, 142275, 142391
-recovered Augustus_model.g10229.t1, internal, 142539, 142706
-recovered Augustus_model.g10229.t1, internal, 142887, 142989
-recovered Augustus_model.g10229.t1, internal, 143587, 143763
-recovered Augustus_model.g10229.t1, internal, 144149, 144285
-recovered Augustus_model.g10229.t1, internal, 144645, 144792
-recovered Augustus_model.g10229.t1, internal, 146013, 146153
-recovered Augustus_model.g10229.t1, internal, 146911, 147092
-recovered Augustus_model.g10229.t1, internal, 147363, 147478
-recovered Augustus_model.g10229.t1, internal, 147627, 147822
-recovered Augustus_model.g10229.t1, internal, 147959, 148057
-recovered Augustus_model.g10229.t1, internal, 148173, 148364
-recovered Augustus_model.g10229.t1, internal, 148628, 148749
-recovered Augustus_model.g10229.t1, internal, 148838, 148947
-recovered Augustus_model.g10229.t1, internal, 149067, 149217
-recovered Augustus_model.g10229.t1, internal, 149453, 149690
-recovered Augustus_model.g10229.t1, internal, 149825, 149940
-recovered Augustus_model.g10229.t1, internal, 150117, 150306
-recovered Augustus_model.g10229.t1, internal, 150511, 150609
-recovered Augustus_model.g10229.t1, internal, 150747, 150941
-recovered Augustus_model.g10229.t1, internal, 151067, 151268
-recovered Augustus_model.g10229.t1, internal, 151370, 151473
-recovered Augustus_model.g10229.t1, internal, 151771, 151841
-recovered Augustus_model.g10229.t1, internal, 152017, 152152
-recovered Augustus_model.g10229.t1, internal, 152437, 152493
Valid prediction for snap_scaffold_6-snap.1721-T1
Valid prediction for snap_scaffold_6-snap.1724-T1
Valid prediction for GeneMark_model.25880_t
Valid prediction for snap_scaffold_6-snap.1708-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 GeneMark_model.25905_t
Valid prediction for snap_scaffold_6-snap.1720-T1
Valid prediction for GlimmerHMM_glimmerT_15326-T1
Valid prediction for GlimmerHMM_glimmerT_15334-T1
Valid prediction for snap_scaffold_6-snap.1734-T1
Valid prediction for snap_scaffold_6-snap.1723-T1
Valid prediction for GeneMark_model.25872_t
Valid prediction for GlimmerHMM_glimmerT_15341-T1
Valid prediction for HiQ_model.g10221.t1
Valid prediction for snap_scaffold_6-snap.1729-T1
Valid prediction for Augustus_model.g10224.t1
Valid prediction for GeneMark_model.25874_t
Valid prediction for GeneMark_model.25876_t
Valid prediction for GeneMark_model.25888_t
Valid prediction for CodingQuarry_transcript_54964-T1
Valid prediction for snap_scaffold_6-snap.1731-T1
Valid prediction for Augustus_model.g10226.t1
Valid prediction for GlimmerHMM_glimmerT_15345-T1
Valid prediction for Augustus_model.g10215.t1
Valid prediction for snap_scaffold_6-snap.1732-T1
Valid prediction for Augustus_model.g10225.t1
Valid prediction for GlimmerHMM_glimmerT_15348-T1
Valid prediction for snap_scaffold_6-snap.1709-T1
Valid prediction for GeneMark_model.25901_t
Valid prediction for snap_scaffold_6-snap.1719-T1
Valid prediction for Augustus_model.g10213.t1
Couldn't classify 131520, 131557
Couldn't classify 136357, 136438
Sorry, prediction pasa_asmbl_49325.p1 fails validation.
(CTG)	 GT	131520-131557	GT	ACG
(GAT)	 AG	132591-132663	GT	TGG
(GGC)	 AG	134627-134696	GT	AGG
(ATG)	 AG	134859-134914	GT	AGG
(TCG)	 AG	135653-135745	GT	AGG
(AGA)	 AG	135869-135961	GT	AGG
(GAC)	 AG	136065-136207	GT	AGG
(GGA)	 AG	136357-136438	CA	CTC
add_exon() Sorry, pasa_asmbl_49325.p1 134859-134914-initial-1 is invalid.
-recovered pasa_asmbl_49325.p1, initial, 134859, 134914
-recovered pasa_asmbl_49325.p1, internal, 132591, 132663
-recovered pasa_asmbl_49325.p1, internal, 134627, 134696
-recovered pasa_asmbl_49325.p1, internal, 134859, 134914
-recovered pasa_asmbl_49325.p1, internal, 135653, 135745
-recovered pasa_asmbl_49325.p1, internal, 135869, 135961
-recovered pasa_asmbl_49325.p1, internal, 136065, 136207
Valid prediction for snap_scaffold_6-snap.1716-T1
Valid prediction for GlimmerHMM_glimmerT_15328-T1
Valid prediction for Augustus_model.g10217.t1
Valid prediction for snap_scaffold_6-snap.1715-T1
Valid prediction for snap_scaffold_6-snap.1718-T1
Valid prediction for GlimmerHMM_glimmerT_15338-T1
Valid prediction for GeneMark_model.25902_t
Couldn't classify 141503, 141516
Sorry, prediction CodingQuarry_transcript_54963-T1 fails validation.
(ATG)	 AG	141503-141516	TA	AGT
(GAA)	 AG	141710-141797	GT	TGG
(GTT)	 AG	141944-142030	GT	AGG
(GTC)	 AG	142499-142564	GT	GGG
(CAA)	 AG	142660-142740	GT	AGG
(GGA)	 AG	142867-142936	GT	AGG
(AGA)	 AG	143148-143197	AG	AGA
-recovered CodingQuarry_transcript_54963-T1, terminal, 143148, 143197
-recovered CodingQuarry_transcript_54963-T1, internal, 141710, 141797
-recovered CodingQuarry_transcript_54963-T1, internal, 141944, 142030
-recovered CodingQuarry_transcript_54963-T1, internal, 142499, 142564
-recovered CodingQuarry_transcript_54963-T1, internal, 142660, 142740
-recovered CodingQuarry_transcript_54963-T1, internal, 142867, 142936
Valid prediction for snap_scaffold_6-snap.1733-T1
Valid prediction for GlimmerHMM_glimmerT_15344-T1
Valid prediction for snap_scaffold_6-snap.1712-T1
Valid prediction for GeneMark_model.25906_t
Valid prediction for GeneMark_model.25887_t
Valid prediction for GeneMark_model.25897_t
Valid prediction for GlimmerHMM_glimmerT_15346-T1
Valid prediction for GeneMark_model.25908_t
Valid prediction for Augustus_model.g10222.t1
Valid prediction for GlimmerHMM_glimmerT_15330-T1
Valid prediction for GeneMark_model.25895_t
Valid prediction for GlimmerHMM_glimmerT_15342-T1
Valid prediction for snap_scaffold_6-snap.1717-T1
Valid prediction for Augustus_model.g10220.t1
Valid prediction for snap_scaffold_6-snap.1713-T1
Valid prediction for GeneMark_model.25899_t
Valid prediction for GlimmerHMM_glimmerT_15332-T1
Valid prediction for GlimmerHMM_glimmerT_15335-T1
Valid prediction for GeneMark_model.25881_t
Valid prediction for GeneMark_model.25883_t
Valid prediction for GeneMark_model.25892_t
Valid prediction for snap_scaffold_6-snap.1706-T1
Valid prediction for GeneMark_model.25870_t
Valid prediction for snap_scaffold_6-snap.1711-T1
Valid prediction for snap_scaffold_6-snap.1725-T1
Valid prediction for snap_scaffold_6-snap.1722-T1
Valid prediction for GlimmerHMM_glimmerT_15355-T1
Valid prediction for pasa_asmbl_48443.p1
Valid prediction for snap_scaffold_6-snap.1727-T1
Valid prediction for snap_scaffold_6-snap.1726-T1
Valid prediction for GeneMark_model.25889_t
Valid prediction for Augustus_model.g10227.t1
Valid prediction for GeneMark_model.25879_t
Valid prediction for GeneMark_model.25878_t
Valid prediction for GlimmerHMM_glimmerT_15331-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 23050, rend_intergenic: 12827  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35880, rend_intergenic: 25200  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61223, rend_intergenic: 59917  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63525, rend_intergenic: 61629  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124102, rend_intergenic: 107106  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129715, rend_intergenic: 129619  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132620, rend_intergenic: 130228  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163102, rend_intergenic: 137587  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 185915
-exon list size: 634


building trellis

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73.0    
73.1    
73.3    
73.4    
73.6    
73.7    
73.9    
74.1    
74.2    
74.4    
74.5    
74.7    
74.8    
75.0    
75.2    
75.3    
75.5    
75.6    
75.8    
75.9    
76.1    
76.3    
76.4    
76.6    
76.7    
76.9    
77.0    
77.2    
77.4    
77.5    
77.7    
77.8    
78.0    
78.1    
78.3    
78.5    
78.6    
78.8    
78.9    
79.1    
79.2    
79.4    
79.6    
79.7    
79.9    
80.0    
80.2    
80.3    
80.5    
80.7    
80.8    
81.0    
81.1    
81.3    
81.4    
81.6    
81.8    
81.9    
82.1    
82.2    
82.4    
82.5    
82.7    
82.9    
83.0    
83.2    
83.3    
83.5    
83.6    
83.8    
84.0    
84.1    
84.3    
84.4    
84.6    
84.7    
84.9    
85.1    
85.2    
85.4    
85.5    
85.7    
85.8    
86.0    
86.2    
86.3    
86.5    
86.6    
86.8    
86.9    
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    
89.2    
89.3    
89.5    
89.6    
89.8    
89.9    
90.1    
90.3    
90.4    
90.6    
90.7    
90.9    
91.0    
91.2    
91.4    
91.5    
91.7    
91.8    
92.0    
92.1    
92.3    
92.5    
92.6    
92.8    
92.9    
93.1    
93.2    
93.4    
93.6    
93.7    
93.9    
94.0    
94.2    
94.3    
94.5    
94.7    
94.8    
95.0    
95.1    
95.3    
95.4    
95.6    
95.8    
95.9    
96.1    
96.2    
96.4    
96.5    
96.7    
96.9    
97.0    
97.2    
97.3    
97.5    
97.6    
97.8    
98.0    
98.1    
98.3    
98.4    
98.6    
98.7    
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: 23050, rend_intergenic: 12827  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35880, rend_intergenic: 25200  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61223, rend_intergenic: 59917  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63525, rend_intergenic: 61629  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124102, rend_intergenic: 107106  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129715, rend_intergenic: 129619  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132620, rend_intergenic: 130228  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163102, rend_intergenic: 137587  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support