-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_5/scaffold_5_9332893-9620371

-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_12416-T1
Valid prediction for snap_scaffold_5-snap.1760-T1
Valid prediction for snap_scaffold_5-snap.1783-T1
Valid prediction for GlimmerHMM_glimmerT_12407-T1
Valid prediction for GlimmerHMM_glimmerT_12414-T1
Valid prediction for GlimmerHMM_glimmerT_12405-T1
Valid prediction for snap_scaffold_5-snap.1752-T1
Valid prediction for GlimmerHMM_glimmerT_12419-T1
Valid prediction for GlimmerHMM_glimmerT_12421-T1
Valid prediction for snap_scaffold_5-snap.1770-T1
Valid prediction for snap_scaffold_5-snap.1761-T1
Valid prediction for Augustus_model.g8180.t1
Valid prediction for GlimmerHMM_glimmerT_12410-T1
Valid prediction for snap_scaffold_5-snap.1788-T1
Valid prediction for HiQ_model.g8191.t1
Valid prediction for Augustus_model.g8178.t1
Couldn't classify 33889, 33928
Sorry, prediction pasa_asmbl_45619.p1 fails validation.
(TAT)	 GA	33889-33928	GT	AGG
(GAC)	 AG	34347-34475	GT	AGG
(AGG)	 AG	34665-34861	GT	AGG
(CAG)	 AG	35043-35240	GT	AGG
(GTT)	 AG	35392-35565	GA	GAG
-recovered pasa_asmbl_45619.p1, terminal, 35392, 35565
-recovered pasa_asmbl_45619.p1, internal, 34347, 34475
-recovered pasa_asmbl_45619.p1, internal, 34665, 34861
-recovered pasa_asmbl_45619.p1, internal, 35043, 35240
Valid prediction for Augustus_model.g8194.t1
Valid prediction for snap_scaffold_5-snap.1754-T1
Valid prediction for snap_scaffold_5-snap.1789-T1
Valid prediction for Augustus_model.g8171.t1
Valid prediction for snap_scaffold_5-snap.1749-T1
Valid prediction for snap_scaffold_5-snap.1750-T1
Valid prediction for snap_scaffold_5-snap.1785-T1
Valid prediction for snap_scaffold_5-snap.1781-T1
Valid prediction for snap_scaffold_5-snap.1769-T1
Valid prediction for GlimmerHMM_glimmerT_12435-T1
Valid prediction for GlimmerHMM_glimmerT_12432-T1
Valid prediction for snap_scaffold_5-snap.1767-T1
Valid prediction for Augustus_model.g8193.t1
Valid prediction for snap_scaffold_5-snap.1758-T1
Valid prediction for snap_scaffold_5-snap.1777-T1
Valid prediction for snap_scaffold_5-snap.1772-T1
Valid prediction for Augustus_model.g8176.t1
Valid prediction for GlimmerHMM_glimmerT_12408-T1
Valid prediction for Augustus_model.g8181.t1
Valid prediction for GlimmerHMM_glimmerT_12425-T1
Valid prediction for HiQ_model.g8170.t1
Valid prediction for CodingQuarry_transcript_52180-T1
Valid prediction for Augustus_model.g8182.t1
Valid prediction for GlimmerHMM_glimmerT_12422-T1
Valid prediction for snap_scaffold_5-snap.1756-T1
Couldn't classify 247497, 247555
Sorry, prediction pasa_asmbl_45621.p1 fails validation.
(GTA)	 CG	247497-247555	GT	AGG
(CCC)	 AG	247713-247787	GT	ATG
(AGA)	 AG	247914-247987	GT	AGG
(ACG)	 AG	248068-248179	GT	TGG
(TGG)	 AG	248302-248402	GT	GGG
(CTG)	 AG	248549-248722	GT	AGG
(GGA)	 AG	248823-248880	GT	AGG
(AGG)	 AG	248986-249136	GC	GAG
-recovered pasa_asmbl_45621.p1, terminal, 248986, 249136
-recovered pasa_asmbl_45621.p1, internal, 247713, 247787
-recovered pasa_asmbl_45621.p1, internal, 247914, 247987
-recovered pasa_asmbl_45621.p1, internal, 248068, 248179
-recovered pasa_asmbl_45621.p1, internal, 248302, 248402
-recovered pasa_asmbl_45621.p1, internal, 248549, 248722
-recovered pasa_asmbl_45621.p1, internal, 248823, 248880
-recovered pasa_asmbl_45621.p1, internal, 248986, 249136
Valid prediction for snap_scaffold_5-snap.1787-T1
Valid prediction for Augustus_model.g8179.t1
Valid prediction for snap_scaffold_5-snap.1771-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.g8184.t1
Valid prediction for snap_scaffold_5-snap.1745-T1
Valid prediction for CodingQuarry_transcript_52174-T1
Couldn't classify 286604, 287020
Sorry, prediction pasa_asmbl_44272.p1 fails validation.
(ACA)	 CT	286604-287020	AG	GAA
Valid prediction for snap_scaffold_5-snap.1763-T1
Sorry, intron length (3) is less than minimum required (10)
Couldn't classify 277473, 277528
Sorry, prediction CodingQuarry_transcript_52176-T1 fails validation.
(ATG)	 AA	277262-277392	GT	GGG
(TCT)	 GG	277473-277528	GT	AGG
(GTG)	 AG	277775-277906	GT	AGG
(TCC)	 AG	278101-278241	GT	AGG
(CTA)	 AG	278335-278580	GT	AGG
(GAG)	 AG	278810-278981	GT	CTG
(GGC)	 AG	279099-279384	GT	AGG
(TAC)	 AG	279496-279633	GT	TGG
(TTC)	 AG	279794-279947	GC	AGG
(AAA)	 AG	280091-280266	CT	AAC
-recovered CodingQuarry_transcript_52176-T1, initial, 277262, 277392
-recovered CodingQuarry_transcript_52176-T1, terminal, 280091, 280266
-recovered CodingQuarry_transcript_52176-T1, internal, 277775, 277906
-recovered CodingQuarry_transcript_52176-T1, internal, 278101, 278241
-recovered CodingQuarry_transcript_52176-T1, internal, 278335, 278580
-recovered CodingQuarry_transcript_52176-T1, internal, 278810, 278981
-recovered CodingQuarry_transcript_52176-T1, internal, 279099, 279384
-recovered CodingQuarry_transcript_52176-T1, internal, 279496, 279633
-recovered CodingQuarry_transcript_52176-T1, internal, 279794, 279947
Couldn't classify 283074, 283175
Couldn't classify 284204, 284299
Sorry, prediction pasa_asmbl_44276.p1 fails validation.
(CTG)	 AC	283074-283175	GT	AGG
(TTT)	 AG	283328-283420	GT	AGG
(CTC)	 AG	283513-283585	GT	GGG
(GTG)	 AG	283967-284058	GT	GGG
(GGG)	 AG	284204-284299	AC	TCA
-recovered pasa_asmbl_44276.p1, internal, 283328, 283420
-recovered pasa_asmbl_44276.p1, internal, 283513, 283585
-recovered pasa_asmbl_44276.p1, internal, 283967, 284058
Valid prediction for CodingQuarry_transcript_52177-T1
Valid prediction for snap_scaffold_5-snap.1751-T1
Valid prediction for snap_scaffold_5-snap.1768-T1
Valid prediction for snap_scaffold_5-snap.1782-T1
Valid prediction for GlimmerHMM_glimmerT_12404-T1
Valid prediction for GlimmerHMM_glimmerT_12415-T1
Valid prediction for GlimmerHMM_glimmerT_12403-T1
Valid prediction for GlimmerHMM_glimmerT_12424-T1
Valid prediction for GlimmerHMM_glimmerT_12411-T1
Valid prediction for GlimmerHMM_glimmerT_12423-T1
Valid prediction for GlimmerHMM_glimmerT_12420-T1
Valid prediction for Augustus_model.g8189.t1
Valid prediction for Augustus_model.g8177.t1
Valid prediction for snap_scaffold_5-snap.1790-T1
Valid prediction for snap_scaffold_5-snap.1766-T1
Valid prediction for Augustus_model.g8183.t1
Valid prediction for snap_scaffold_5-snap.1786-T1
Valid prediction for pasa_asmbl_44291.p1
Valid prediction for GlimmerHMM_glimmerT_12412-T1
Valid prediction for snap_scaffold_5-snap.1759-T1
Valid prediction for Augustus_model.g8188.t1
Valid prediction for pasa_asmbl_44281.p1
Valid prediction for HiQ_model.g8192.t1
Couldn't classify 170642, 171475
Sorry, prediction pasa_asmbl_44280.p1 fails validation.
(ATG)	 TA	169709-169735	GT	AGG
(ACG)	 AG	170056-170080	GT	AGG
(TCT)	 AG	170452-170546	GT	AGG
(AAC)	 AG	170642-171475	CC	CTC
-recovered pasa_asmbl_44280.p1, initial, 169709, 169735
-recovered pasa_asmbl_44280.p1, internal, 170056, 170080
-recovered pasa_asmbl_44280.p1, internal, 170452, 170546
Valid prediction for GlimmerHMM_glimmerT_12428-T1
Valid prediction for GlimmerHMM_glimmerT_12434-T1
Valid prediction for CodingQuarry_transcript_52178-T1
Couldn't classify 286130, 286495
Sorry, prediction pasa_asmbl_44274.p1 fails validation.
(ACT)	 TC	286130-286495	CC	GGC
Valid prediction for Augustus_model.g8167.t1
Valid prediction for snap_scaffold_5-snap.1778-T1
Couldn't classify 73324, 73329
Sorry, prediction pasa_asmbl_44286.p1 fails validation.
(GAA)	 AG	73324-73329	GT	TAG
(CTC)	 AG	73594-73749	GT	GTG
(GAT)	 AG	73835-73933	GT	GGG
(GTG)	 AG	74037-74133	GT	TGG
(ATG)	 AG	75253-75266	AC	AGA
-recovered pasa_asmbl_44286.p1, terminal, 75253, 75266
-recovered pasa_asmbl_44286.p1, internal, 73324, 73329
-recovered pasa_asmbl_44286.p1, internal, 73594, 73749
-recovered pasa_asmbl_44286.p1, internal, 73835, 73933
-recovered pasa_asmbl_44286.p1, internal, 74037, 74133
Valid prediction for GlimmerHMM_glimmerT_12402-T1
Couldn't classify 277473, 277528
Sorry, prediction CodingQuarry_transcript_52175-T1 fails validation.
(ATG)	 AA	277262-277392	GT	GGG
(TCT)	 GG	277473-277528	GT	AGG
(GTG)	 AG	277775-277906	GT	AGG
(CTT)	 AG	278083-278241	GT	AGG
(CTA)	 AG	278335-278580	GT	AGG
(GAG)	 AG	278810-278981	GT	CTG
(GGC)	 AG	279099-279633	GT	TGG
(TTC)	 AG	279794-279947	GC	AGG
(AAA)	 AG	280091-280266	CT	AAC
-recovered CodingQuarry_transcript_52175-T1, initial, 277262, 277392
-recovered CodingQuarry_transcript_52175-T1, terminal, 280091, 280266
-recovered CodingQuarry_transcript_52175-T1, internal, 277775, 277906
-recovered CodingQuarry_transcript_52175-T1, internal, 278083, 278241
-recovered CodingQuarry_transcript_52175-T1, internal, 278335, 278580
-recovered CodingQuarry_transcript_52175-T1, internal, 278810, 278981
-recovered CodingQuarry_transcript_52175-T1, internal, 279099, 279633
-recovered CodingQuarry_transcript_52175-T1, internal, 279794, 279947
Valid prediction for GlimmerHMM_glimmerT_12430-T1
Valid prediction for GlimmerHMM_glimmerT_12409-T1
Valid prediction for snap_scaffold_5-snap.1748-T1
Valid prediction for snap_scaffold_5-snap.1775-T1
Valid prediction for Augustus_model.g8185.t1
Valid prediction for GlimmerHMM_glimmerT_12400-T1
Valid prediction for GlimmerHMM_glimmerT_12433-T1
Couldn't classify 280947, 281312
Sorry, prediction pasa_asmbl_44277.p1 fails validation.
(CGG)	 GG	280947-281312	CA	GAC
Valid prediction for GlimmerHMM_glimmerT_12426-T1
Valid prediction for Augustus_model.g8172.t1
Valid prediction for GlimmerHMM_glimmerT_12413-T1
Valid prediction for HiQ_model.g8174.t1
Valid prediction for GlimmerHMM_glimmerT_12401-T1
Valid prediction for snap_scaffold_5-snap.1780-T1
Valid prediction for snap_scaffold_5-snap.1764-T1
Valid prediction for snap_scaffold_5-snap.1746-T1
Valid prediction for snap_scaffold_5-snap.1755-T1
Valid prediction for GlimmerHMM_glimmerT_12406-T1
Valid prediction for Augustus_model.g8169.t1
Couldn't classify 93844, 94176
Sorry, prediction pasa_asmbl_44285.p1 fails validation.
(CCT)	 TG	93844-94176	AT	GCA
Valid prediction for snap_scaffold_5-snap.1765-T1
Valid prediction for pasa_asmbl_44290.p1
Couldn't classify 277762, 277906
Sorry, prediction pasa_asmbl_45036.p1 fails validation.
(CCT)	 CC	277762-277906	GT	AGG
(CTT)	 AG	278083-278241	GT	AGG
(CTA)	 AG	278335-278580	GT	AGG
(GAG)	 AG	278810-278981	GT	CTG
(GGC)	 AG	279099-279384	GT	AGG
(TAC)	 AG	279496-279633	GT	TGG
(TTC)	 AG	279794-279947	GC	AGG
(AAA)	 AG	280091-280266	CT	AAC
-recovered pasa_asmbl_45036.p1, terminal, 280091, 280266
-recovered pasa_asmbl_45036.p1, internal, 278083, 278241
-recovered pasa_asmbl_45036.p1, internal, 278335, 278580
-recovered pasa_asmbl_45036.p1, internal, 278810, 278981
-recovered pasa_asmbl_45036.p1, internal, 279099, 279384
-recovered pasa_asmbl_45036.p1, internal, 279496, 279633
-recovered pasa_asmbl_45036.p1, internal, 279794, 279947
Valid prediction for snap_scaffold_5-snap.1784-T1
Valid prediction for snap_scaffold_5-snap.1776-T1
Valid prediction for snap_scaffold_5-snap.1791-T1
Valid prediction for CodingQuarry_transcript_52179-T1
Valid prediction for GlimmerHMM_glimmerT_12431-T1
Valid prediction for GlimmerHMM_glimmerT_12418-T1
Valid prediction for snap_scaffold_5-snap.1773-T1
Valid prediction for Augustus_model.g8168.t1
Valid prediction for GlimmerHMM_glimmerT_12429-T1
Valid prediction for snap_scaffold_5-snap.1757-T1
Valid prediction for Augustus_model.g8173.t1
Valid prediction for GlimmerHMM_glimmerT_12417-T1
Couldn't classify 171671, 172282
Sorry, prediction pasa_asmbl_44279.p1 fails validation.
(GTG)	 GT	171671-172282	GT	AGG
(AAC)	 AG	172429-172473	GT	AGG
(GAG)	 AG	173217-173243	AA	AGA
-recovered pasa_asmbl_44279.p1, terminal, 173217, 173243
-recovered pasa_asmbl_44279.p1, internal, 172429, 172473
Valid prediction for snap_scaffold_5-snap.1774-T1
Valid prediction for Augustus_model.g8187.t1
Valid prediction for GlimmerHMM_glimmerT_12427-T1
Valid prediction for snap_scaffold_5-snap.1779-T1
Valid prediction for snap_scaffold_5-snap.1753-T1
Valid prediction for HiQ_model.g8186.t1
Valid prediction for Augustus_model.g8175.t1
Valid prediction for snap_scaffold_5-snap.1747-T1
Valid prediction for snap_scaffold_5-snap.1762-T1
Valid prediction for Augustus_model.g8190.t1
Couldn't classify 284774, 284807
Couldn't classify 286191, 286495
Sorry, prediction pasa_asmbl_44275.p1 fails validation.
(AAT)	 TC	284774-284807	GT	AGG
(TGA)	 AG	284960-285065	GT	CTG
(ATC)	 AG	285266-285369	GT	AGG
(TGC)	 AG	285589-285698	GT	TGG
(GTG)	 AG	285819-285891	GT	TGG
(AGC)	 AG	286011-286085	GT	CAG
(CCT)	 AG	286191-286495	CC	GGC
-recovered pasa_asmbl_44275.p1, internal, 284960, 285065
-recovered pasa_asmbl_44275.p1, internal, 285266, 285369
-recovered pasa_asmbl_44275.p1, internal, 285589, 285698
-recovered pasa_asmbl_44275.p1, internal, 285819, 285891
-recovered pasa_asmbl_44275.p1, internal, 286011, 286085

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 51684, rend_intergenic: 50081  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65110, rend_intergenic: 55779  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77741, rend_intergenic: 74230  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99280, rend_intergenic: 83435  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 207593, rend_intergenic: 202478  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 243698, rend_intergenic: 239249  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 274089, rend_intergenic: 267463  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 283142, rend_intergenic: 278109  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 192751, rend_intergenic: 192748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 287479
-exon list size: 613


building trellis

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54.0    
54.1    
54.3    
54.5    
54.6    
54.8    
55.0    
55.1    
55.3    
55.4    
55.6    
55.8    
55.9    
56.1    
56.3    
56.4    
56.6    
56.7    
56.9    
57.1    
57.2    
57.4    
57.6    
57.7    
57.9    
58.0    
58.2    
58.4    
58.5    
58.7    
58.9    
59.0    
59.2    
59.3    
59.5    
59.7    
59.8    
60.0    
60.2    
60.3    
60.5    
60.7    
60.8    
61.0    
61.1    
61.3    
61.5    
61.6    
61.8    
62.0    
62.1    
62.3    
62.4    
62.6    
62.8    
62.9    
63.1    
63.3    
63.4    
63.6    
63.7    
63.9    
64.1    
64.2    
64.4    
64.6    
64.7    
64.9    
65.0    
65.2    
65.4    
65.5    
65.7    
65.9    
66.0    
66.2    
66.3    
66.5    
66.7    
66.8    
67.0    
67.2    
67.3    
67.5    
67.6    
67.8    
68.0    
68.1    
68.3    
68.5    
68.6    
68.8    
68.9    
69.1    
69.3    
69.4    
69.6    
69.8    
69.9    
70.1    
70.2    
70.4    
70.6    
70.7    
70.9    
71.1    
71.2    
71.4    
71.5    
71.7    
71.9    
72.0    
72.2    
72.4    
72.5    
72.7    
72.8    
73.0    
73.2    
73.3    
73.5    
73.7    
73.8    
74.0    
74.1    
74.3    
74.5    
74.6    
74.8    
75.0    
75.1    
75.3    
75.4    
75.6    
75.8    
75.9    
76.1    
76.3    
76.4    
76.6    
76.7    
76.9    
77.1    
77.2    
77.4    
77.6    
77.7    
77.9    
78.0    
78.2    
78.4    
78.5    
78.7    
78.9    
79.0    
79.2    
79.3    
79.5    
79.7    
79.8    
80.0    
80.2    
80.3    
80.5    
80.7    
80.8    
81.0    
81.1    
81.3    
81.5    
81.6    
81.8    
82.0    
82.1    
82.3    
82.4    
82.6    
82.8    
82.9    
83.1    
83.3    
83.4    
83.6    
83.7    
83.9    
84.1    
84.2    
84.4    
84.6    
84.7    
84.9    
85.0    
85.2    
85.4    
85.5    
85.7    
85.9    
86.0    
86.2    
86.3    
86.5    
86.7    
86.8    
87.0    
87.2    
87.3    
87.5    
87.6    
87.8    
88.0    
88.1    
88.3    
88.5    
88.6    
88.8    
88.9    
89.1    
89.3    
89.4    
89.6    
89.8    
89.9    
90.1    
90.2    
90.4    
90.6    
90.7    
90.9    
91.1    
91.2    
91.4    
91.5    
91.7    
91.9    
92.0    
92.2    
92.4    
92.5    
92.7    
92.8    
93.0    
93.2    
93.3    
93.5    
93.7    
93.8    
94.0    
94.1    
94.3    
94.5    
94.6    
94.8    
95.0    
95.1    
95.3    
95.4    
95.6    
95.8    
95.9    
96.1    
96.3    
96.4    
96.6    
96.7    
96.9    
97.1    
97.2    
97.4    
97.6    
97.7    
97.9    
98.0    
98.2    
98.4    
98.5    
98.7    
98.9    
99.0    
99.2    
99.3    
99.5    
99.7    
99.8    
-found 38 predictions from path traversal
Error with prediction: snap lend_intergenic: 51684, rend_intergenic: 50081  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65110, rend_intergenic: 55779  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77741, rend_intergenic: 74230  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99280, rend_intergenic: 83435  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 207593, rend_intergenic: 202478  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 243698, rend_intergenic: 239249  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 274089, rend_intergenic: 267463  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 283142, rend_intergenic: 278109  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 192751, rend_intergenic: 192748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 30 predictions persist after filtering for low support