-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_24/scaffold_24_6028567-6269108

-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_53900-T1
Valid prediction for snap_scaffold_24-snap.1230-T1
Valid prediction for GeneMark_model.93956_t
Valid prediction for GeneMark_model.93950_t
Valid prediction for snap_scaffold_24-snap.1231-T1
Valid prediction for snap_scaffold_24-snap.1205-T1
Couldn't classify 223424, 223431
Couldn't classify 226543, 226638
Sorry, prediction pasa_asmbl_32300.p1 fails validation.
(GAG)	 AC	223424-223431	GT	GGG
(GAC)	 AG	223637-223805	GT	CGG
(AAC)	 AG	224640-224820	GT	AGG
(GTG)	 AG	226293-226381	GT	AGG
(GCC)	 AG	226543-226638	GT	GGG
-recovered pasa_asmbl_32300.p1, internal, 223637, 223805
-recovered pasa_asmbl_32300.p1, internal, 224640, 224820
-recovered pasa_asmbl_32300.p1, internal, 226293, 226381
-recovered pasa_asmbl_32300.p1, internal, 226543, 226638
Valid prediction for snap_scaffold_24-snap.1232-T1
Valid prediction for HiQ_model.g36072.t1
Valid prediction for GlimmerHMM_glimmerT_53888-T1
Valid prediction for snap_scaffold_24-snap.1233-T1
Valid prediction for Augustus_model.g36085.t1
Valid prediction for Augustus_model.g36078.t1
Valid prediction for snap_scaffold_24-snap.1200-T1
Valid prediction for GeneMark_model.93985_t
Valid prediction for snap_scaffold_24-snap.1228-T1
Valid prediction for GeneMark_model.93973_t
Valid prediction for snap_scaffold_24-snap.1203-T1
Valid prediction for GlimmerHMM_glimmerT_53895-T1
Valid prediction for Augustus_model.g36083.t1
Couldn't classify 221044, 221104
Couldn't classify 222769, 222886
Sorry, prediction pasa_asmbl_32299.p1 fails validation.
(ACC)	 AC	221044-221104	GT	CGG
(TCA)	 AG	221245-221396	GT	AGG
(GTT)	 AG	221596-221715	GT	AGG
(AAG)	 AG	222306-222451	GT	AGG
(GCG)	 AG	222769-222886	CC	CCC
-recovered pasa_asmbl_32299.p1, internal, 221245, 221396
-recovered pasa_asmbl_32299.p1, internal, 221596, 221715
-recovered pasa_asmbl_32299.p1, internal, 222306, 222451
Valid prediction for GlimmerHMM_glimmerT_53886-T1
Valid prediction for snap_scaffold_24-snap.1218-T1
Valid prediction for snap_scaffold_24-snap.1208-T1
Valid prediction for GeneMark_model.93943_t
Valid prediction for snap_scaffold_24-snap.1199-T1
Valid prediction for snap_scaffold_24-snap.1237-T1
Valid prediction for GlimmerHMM_glimmerT_53913-T1
Valid prediction for snap_scaffold_24-snap.1206-T1
Valid prediction for Augustus_model.g36076.t1
Couldn't classify 154853, 156508
Sorry, prediction pasa_asmbl_32295.p1 fails validation.
(ATG)	 AC	154853-156508	TA	GGT
Valid prediction for Augustus_model.g36080.t1
Couldn't classify 126555, 126642
Couldn't classify 128806, 128898
Sorry, prediction pasa_asmbl_32622.p1 fails validation.
(GTC)	 AG	126555-126642	GT	TCG
(TCG)	 AG	127500-127590	GT	GGG
(GGG)	 AG	128454-128559	GT	TGG
(ATC)	 AG	128806-128898	GG	AAG
-recovered pasa_asmbl_32622.p1, internal, 126555, 126642
-recovered pasa_asmbl_32622.p1, internal, 127500, 127590
-recovered pasa_asmbl_32622.p1, internal, 128454, 128559
Valid prediction for GeneMark_model.93967_t
Valid prediction for GlimmerHMM_glimmerT_53911-T1
Valid prediction for Augustus_model.g36068.t1
Valid prediction for GeneMark_model.93976_t
Valid prediction for GeneMark_model.93947_t
Valid prediction for snap_scaffold_24-snap.1220-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_37254-T1
Valid prediction for GeneMark_model.93960_t
Valid prediction for snap_scaffold_24-snap.1214-T1
Valid prediction for snap_scaffold_24-snap.1201-T1
Valid prediction for snap_scaffold_24-snap.1235-T1
Valid prediction for snap_scaffold_24-snap.1223-T1
Valid prediction for snap_scaffold_24-snap.1202-T1
Valid prediction for Augustus_model.g36074.t1
Valid prediction for snap_scaffold_24-snap.1215-T1
Valid prediction for pasa_asmbl_32296.p1
Valid prediction for GeneMark_model.93969_t
Valid prediction for HiQ_model.g36065.t1
Valid prediction for snap_scaffold_24-snap.1226-T1
Valid prediction for snap_scaffold_24-snap.1224-T1
Valid prediction for GeneMark_model.93982_t
Valid prediction for Augustus_model.g36067.t1
Valid prediction for Augustus_model.g36084.t1
Valid prediction for snap_scaffold_24-snap.1221-T1
Valid prediction for GlimmerHMM_glimmerT_53912-T1
Valid prediction for GeneMark_model.93978_t
Valid prediction for GeneMark_model.93966_t
Valid prediction for GlimmerHMM_glimmerT_53899-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.93948_t
Valid prediction for GlimmerHMM_glimmerT_53898-T1
Valid prediction for GeneMark_model.93944_t
Valid prediction for snap_scaffold_24-snap.1219-T1
Valid prediction for Augustus_model.g36073.t1
Valid prediction for GlimmerHMM_glimmerT_53906-T1
Couldn't classify 134110, 134191
Sorry, prediction pasa_asmbl_32294.p1 fails validation.
(GGG)	 CA	134110-134191	GT	CGG
(CCT)	 AG	135296-135663	CC	GAC
-recovered pasa_asmbl_32294.p1, terminal, 135296, 135663
Valid prediction for GlimmerHMM_glimmerT_53903-T1
Valid prediction for snap_scaffold_24-snap.1196-T1
Valid prediction for GeneMark_model.93954_t
Valid prediction for GeneMark_model.93980_t
Valid prediction for pasa_asmbl_32286.p1
Couldn't classify 20303, 20368
Sorry, prediction pasa_asmbl_32285.p1 fails validation.
(ATG)	 AG	14955-14970	GT	CGG
(CTG)	 AG	15688-15731	GT	AGG
(GAA)	 AG	15895-15968	GT	ATG
(CGA)	 AG	16089-16258	GT	TGG
(CCA)	 AG	16416-16624	GT	CGG
(AAT)	 AG	17000-17143	GT	AGG
(TGC)	 AG	17282-17508	GT	GGG
(CGA)	 AG	17826-17886	GT	TGG
(GAT)	 AG	18007-18132	GT	AGG
(GAT)	 AG	18346-18434	GT	AGG
(AGA)	 AG	18541-18619	GT	AGG
(GGT)	 AG	18756-18929	GT	ATG
(ATT)	 AG	19058-19169	GT	AGG
(GTG)	 AG	19328-19524	GT	AGG
(GAC)	 AG	19801-19896	GT	CTG
(GTC)	 AG	20303-20368	TA	GGT
-recovered pasa_asmbl_32285.p1, initial, 14955, 14970
-recovered pasa_asmbl_32285.p1, internal, 14955, 14970
-recovered pasa_asmbl_32285.p1, internal, 15688, 15731
-recovered pasa_asmbl_32285.p1, internal, 15895, 15968
-recovered pasa_asmbl_32285.p1, internal, 16089, 16258
-recovered pasa_asmbl_32285.p1, internal, 16416, 16624
-recovered pasa_asmbl_32285.p1, internal, 17000, 17143
-recovered pasa_asmbl_32285.p1, internal, 17282, 17508
-recovered pasa_asmbl_32285.p1, internal, 17826, 17886
-recovered pasa_asmbl_32285.p1, internal, 18007, 18132
-recovered pasa_asmbl_32285.p1, internal, 18346, 18434
-recovered pasa_asmbl_32285.p1, internal, 18541, 18619
-recovered pasa_asmbl_32285.p1, internal, 18756, 18929
-recovered pasa_asmbl_32285.p1, internal, 19058, 19169
-recovered pasa_asmbl_32285.p1, internal, 19328, 19524
-recovered pasa_asmbl_32285.p1, internal, 19801, 19896
Valid prediction for GeneMark_model.93986_t
Valid prediction for pasa_asmbl_32284.p1
Valid prediction for snap_scaffold_24-snap.1238-T1
Valid prediction for GeneMark_model.93958_t

-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.g36075.t1
Valid prediction for GeneMark_model.93981_t
Valid prediction for GlimmerHMM_glimmerT_53885-T1
Valid prediction for Augustus_model.g36070.t1
Valid prediction for snap_scaffold_24-snap.1216-T1
Valid prediction for GlimmerHMM_glimmerT_53897-T1
Valid prediction for snap_scaffold_24-snap.1212-T1
Valid prediction for GeneMark_model.93961_t
Valid prediction for GeneMark_model.93964_t
Valid prediction for Augustus_model.g36069.t1
Valid prediction for GlimmerHMM_glimmerT_53890-T1
Valid prediction for GlimmerHMM_glimmerT_53892-T1
Valid prediction for GeneMark_model.93968_t
Valid prediction for GeneMark_model.93951_t
Valid prediction for GlimmerHMM_glimmerT_53893-T1
Valid prediction for GlimmerHMM_glimmerT_53909-T1
Valid prediction for snap_scaffold_24-snap.1227-T1
Valid prediction for GlimmerHMM_glimmerT_53901-T1
Valid prediction for GeneMark_model.93955_t
Valid prediction for snap_scaffold_24-snap.1204-T1
Valid prediction for snap_scaffold_24-snap.1210-T1
Valid prediction for GeneMark_model.93983_t
Valid prediction for Augustus_model.g36071.t1
Valid prediction for GeneMark_model.93957_t
Valid prediction for GeneMark_model.93984_t
Valid prediction for GlimmerHMM_glimmerT_53896-T1
Valid prediction for GlimmerHMM_glimmerT_53902-T1
Valid prediction for GeneMark_model.93953_t
Valid prediction for GeneMark_model.93970_t
Valid prediction for snap_scaffold_24-snap.1209-T1
Valid prediction for GlimmerHMM_glimmerT_53904-T1
Valid prediction for pasa_asmbl_32933.p1
Valid prediction for GeneMark_model.93949_t
Valid prediction for GlimmerHMM_glimmerT_53894-T1
Valid prediction for GeneMark_model.93977_t
Valid prediction for GlimmerHMM_glimmerT_53910-T1
Valid prediction for CodingQuarry_transcript_37255-T1
Valid prediction for GeneMark_model.93979_t
Valid prediction for GlimmerHMM_glimmerT_53887-T1
Valid prediction for snap_scaffold_24-snap.1213-T1
Valid prediction for Augustus_model.g36082.t1
Valid prediction for GeneMark_model.93975_t
Valid prediction for GeneMark_model.93972_t
Valid prediction for snap_scaffold_24-snap.1234-T1
Valid prediction for GeneMark_model.93965_t
Valid prediction for GeneMark_model.93946_t
Valid prediction for Augustus_model.g36077.t1
Valid prediction for GeneMark_model.93962_t
Valid prediction for GlimmerHMM_glimmerT_53891-T1
Valid prediction for GlimmerHMM_glimmerT_53908-T1
Valid prediction for snap_scaffold_24-snap.1222-T1
Valid prediction for GeneMark_model.93974_t
Couldn't classify 161779, 161835
Sorry, prediction pasa_asmbl_32919.p1 fails validation.
(GCC)	 GG	161779-161835	GT	AGG
(CTC)	 AG	163081-163200	GT	AGG
(TCC)	 AG	163763-163816	GT	CGG
(ATT)	 AG	164723-164781	GT	GAG
(GGA)	 AG	165931-166114	GT	AGG
(ATC)	 AG	167691-167735	GT	CGG
(ATG)	 AG	167884-167979	GT	AGG
(TTG)	 AG	170960-171034	GT	AGG
(GCT)	 AG	172286-172297	GT	AGG
(GGG)	 AG	173634-173696	GT	CCG
(GAC)	 AG	175895-176007	GT	AGG
(GCG)	 AG	176779-176830	GT	AGG
(GAT)	 AG	177219-177319	GT	AAG
(GAG)	 AG	177642-177747	GT	AGG
(AAA)	 AG	178041-178249	GT	AGG
(GAG)	 AG	178478-178547	GT	AGG
(TTG)	 AG	178753-178847	GT	AGG
(ACA)	 AG	179043-179245	GT	TGG
(TCA)	 AG	180233-180325	GT	AGG
(ACG)	 AG	180663-180898	GT	GGG
(GGC)	 AG	181021-181130	GT	GGG
(ACA)	 AG	181377-181487	GT	CTG
(GCT)	 AG	181618-181765	GC	AGG
-recovered pasa_asmbl_32919.p1, initial, 167884, 167979
add_exon() Sorry, pasa_asmbl_32919.p1 175895-176007-terminal-2 is invalid.
-recovered pasa_asmbl_32919.p1, terminal, 175895, 176007
-recovered pasa_asmbl_32919.p1, terminal, 181618, 181765
-recovered pasa_asmbl_32919.p1, internal, 163081, 163200
-recovered pasa_asmbl_32919.p1, internal, 163763, 163816
-recovered pasa_asmbl_32919.p1, internal, 164723, 164781
-recovered pasa_asmbl_32919.p1, internal, 165931, 166114
-recovered pasa_asmbl_32919.p1, internal, 167691, 167735
-recovered pasa_asmbl_32919.p1, internal, 167884, 167979
-recovered pasa_asmbl_32919.p1, internal, 170960, 171034
-recovered pasa_asmbl_32919.p1, internal, 172286, 172297
-recovered pasa_asmbl_32919.p1, internal, 173634, 173696
-recovered pasa_asmbl_32919.p1, internal, 175895, 176007
-recovered pasa_asmbl_32919.p1, internal, 176779, 176830
-recovered pasa_asmbl_32919.p1, internal, 177219, 177319
-recovered pasa_asmbl_32919.p1, internal, 177642, 177747
-recovered pasa_asmbl_32919.p1, internal, 178041, 178249
-recovered pasa_asmbl_32919.p1, internal, 178478, 178547
-recovered pasa_asmbl_32919.p1, internal, 178753, 178847
-recovered pasa_asmbl_32919.p1, internal, 179043, 179245
-recovered pasa_asmbl_32919.p1, internal, 180233, 180325
-recovered pasa_asmbl_32919.p1, internal, 180663, 180898
-recovered pasa_asmbl_32919.p1, internal, 181021, 181130
-recovered pasa_asmbl_32919.p1, internal, 181377, 181487
-recovered pasa_asmbl_32919.p1, internal, 181618, 181765
Valid prediction for snap_scaffold_24-snap.1229-T1
Valid prediction for snap_scaffold_24-snap.1225-T1
Valid prediction for GeneMark_model.93942_t
Valid prediction for GeneMark_model.93959_t
Valid prediction for GlimmerHMM_glimmerT_53905-T1
Valid prediction for GeneMark_model.93963_t
Valid prediction for GlimmerHMM_glimmerT_53889-T1
Valid prediction for snap_scaffold_24-snap.1211-T1
Valid prediction for snap_scaffold_24-snap.1207-T1
Valid prediction for CodingQuarry_transcript_37253-T1
Valid prediction for snap_scaffold_24-snap.1197-T1
Valid prediction for Augustus_model.g36079.t1
Valid prediction for snap_scaffold_24-snap.1236-T1
Valid prediction for Augustus_model.g36066.t1
Valid prediction for HiQ_model.g36081.t1
Valid prediction for GlimmerHMM_glimmerT_53907-T1
Valid prediction for snap_scaffold_24-snap.1198-T1
Valid prediction for snap_scaffold_24-snap.1217-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 43061, rend_intergenic: 42544  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70504, rend_intergenic: 59439  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110643, rend_intergenic: 109375  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125854, rend_intergenic: 122418  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 205225, rend_intergenic: 203877  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 214477, rend_intergenic: 205352  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 223958, rend_intergenic: 219910  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 227563, rend_intergenic: 226289  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 240542
-exon list size: 646


building trellis

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58.2    
58.3    
58.5    
58.6    
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    
61.0    
61.1    
61.3    
61.4    
61.6    
61.7    
61.9    
62.0    
62.2    
62.3    
62.5    
62.7    
62.8    
63.0    
63.1    
63.3    
63.4    
63.6    
63.7    
63.9    
64.0    
64.2    
64.4    
64.5    
64.7    
64.8    
65.0    
65.1    
65.3    
65.4    
65.6    
65.7    
65.9    
66.0    
66.2    
66.4    
66.5    
66.7    
66.8    
67.0    
67.1    
67.3    
67.4    
67.6    
67.7    
67.9    
68.1    
68.2    
68.4    
68.5    
68.7    
68.8    
69.0    
69.1    
69.3    
69.4    
69.6    
69.8    
69.9    
70.1    
70.2    
70.4    
70.5    
70.7    
70.8    
71.0    
71.1    
71.3    
71.5    
71.6    
71.8    
71.9    
72.1    
72.2    
72.4    
72.5    
72.7    
72.8    
73.0    
73.1    
73.3    
73.5    
73.6    
73.8    
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    
76.2    
76.4    
76.5    
76.7    
76.9    
77.0    
77.2    
77.3    
77.5    
77.6    
77.8    
77.9    
78.1    
78.2    
78.4    
78.5    
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    
82.3    
82.4    
82.6    
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    
85.0    
85.2    
85.3    
85.5    
85.6    
85.8    
86.0    
86.1    
86.3    
86.4    
86.6    
86.7    
86.9    
87.0    
87.2    
87.3    
87.5    
87.7    
87.8    
88.0    
88.1    
88.3    
88.4    
88.6    
88.7    
88.9    
89.0    
89.2    
89.4    
89.5    
89.7    
89.8    
90.0    
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    
92.4    
92.6    
92.7    
92.9    
93.1    
93.2    
93.4    
93.5    
93.7    
93.8    
94.0    
94.1    
94.3    
94.4    
94.6    
94.8    
94.9    
95.1    
95.2    
95.4    
95.5    
95.7    
95.8    
96.0    
96.1    
96.3    
96.5    
96.6    
96.8    
96.9    
97.1    
97.2    
97.4    
97.5    
97.7    
97.8    
98.0    
98.1    
98.3    
98.5    
98.6    
98.8    
98.9    
99.1    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 43061, rend_intergenic: 42544  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70504, rend_intergenic: 59439  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110643, rend_intergenic: 109375  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125854, rend_intergenic: 122418  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 205225, rend_intergenic: 203877  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 214477, rend_intergenic: 205352  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 223958, rend_intergenic: 219910  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 227563, rend_intergenic: 226289  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 12203
-exon list size: 6


building trellis

12.5    
25.0    
37.5    
50.0    
62.5    
75.0    
87.5    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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