-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_7/scaffold_7_11714865-11997768

-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_18184-T1
Valid prediction for snap_scaffold_7-snap.2227-T1
Valid prediction for Augustus_model.g12224.t1
Couldn't classify 162024, 162075
Couldn't classify 163850, 163867
Sorry, prediction pasa_asmbl_50608.p1 fails validation.
(CAG)	 CT	162024-162075	GT	AGG
(AGG)	 AG	162838-162925	GT	GGG
(GCC)	 AG	163534-163699	GT	ACG
(TTT)	 AG	163850-163867	TA	ACT
-recovered pasa_asmbl_50608.p1, internal, 162838, 162925
-recovered pasa_asmbl_50608.p1, internal, 163534, 163699
Valid prediction for snap_scaffold_7-snap.2221-T1
Valid prediction for Augustus_model.g12220.t1
Valid prediction for snap_scaffold_7-snap.2244-T1
Valid prediction for GlimmerHMM_glimmerT_18185-T1
Valid prediction for snap_scaffold_7-snap.2234-T1
Couldn't classify 238460, 238645
Sorry, prediction pasa_asmbl_50201.p1 fails validation.
(GTC)	 TT	238460-238645	GT	AGG
(GTG)	 AG	239397-239450	GT	AGG
(TGT)	 AG	239555-239635	GT	AGG
(GAT)	 AG	239732-239782	GA	AAG
-recovered pasa_asmbl_50201.p1, terminal, 239732, 239782
-recovered pasa_asmbl_50201.p1, internal, 239397, 239450
-recovered pasa_asmbl_50201.p1, internal, 239555, 239635
Valid prediction for snap_scaffold_7-snap.2255-T1
Valid prediction for snap_scaffold_7-snap.2248-T1
Couldn't classify 165339, 165359
Sorry, prediction pasa_asmbl_50195.p1 fails validation.
(TAC)	 TC	165339-165359	GT	CAG
(GGT)	 AG	165440-165497	GT	AAG
(GTG)	 AG	165584-165666	GT	AGG
(ATG)	 AG	166198-166299	GT	TGG
(GTA)	 AG	166412-166471	GT	AAG
(GTG)	 AG	167022-167162	GT	GAG
-recovered pasa_asmbl_50195.p1, initial, 166198, 166299
add_exon() Sorry, pasa_asmbl_50195.p1 165440-165497-terminal-3 is invalid.
-recovered pasa_asmbl_50195.p1, terminal, 165440, 165497
-recovered pasa_asmbl_50195.p1, terminal, 167022, 167162
-recovered pasa_asmbl_50195.p1, internal, 165440, 165497
-recovered pasa_asmbl_50195.p1, internal, 165584, 165666
-recovered pasa_asmbl_50195.p1, internal, 166198, 166299
-recovered pasa_asmbl_50195.p1, internal, 166412, 166471
-recovered pasa_asmbl_50195.p1, internal, 167022, 167162
Valid prediction for Augustus_model.g12246.t1
Couldn't classify 222651, 223016
Sorry, prediction pasa_asmbl_50199.p1 fails validation.
(ACC)	 AG	222651-223016	GG	AAG
Valid prediction for snap_scaffold_7-snap.2262-T1
Couldn't classify 229815, 229970
Couldn't classify 231523, 231587
Sorry, prediction pasa_asmbl_50644.p1 fails validation.
(GAG)	 CG	229815-229970	GT	AGG
(TTT)	 AG	230099-230201	GT	TGG
(GGA)	 AG	231523-231587	GT	ATG
-recovered pasa_asmbl_50644.p1, internal, 230099, 230201
-recovered pasa_asmbl_50644.p1, internal, 231523, 231587
Valid prediction for snap_scaffold_7-snap.2224-T1
Couldn't classify 84491, 84586
Sorry, prediction pasa_asmbl_50190.p1 fails validation.
(GGT)	 AG	84491-84586	GT	AGG
(AAT)	 AG	85052-85193	GT	AGG
(GTG)	 AG	85325-85455	GT	AGG
(GTT)	 AG	85575-85694	GT	AGG
(GCC)	 AG	85811-85963	GT	AGG
(CTG)	 AG	86156-86367	GT	AGG
(GTT)	 AG	86507-86666	GT	AGG
(AAA)	 AG	86836-87006	GT	AGG
(GAT)	 AG	87105-87251	CC	AAC
-recovered pasa_asmbl_50190.p1, terminal, 87105, 87251
-recovered pasa_asmbl_50190.p1, internal, 84491, 84586
-recovered pasa_asmbl_50190.p1, internal, 85052, 85193
-recovered pasa_asmbl_50190.p1, internal, 85325, 85455
-recovered pasa_asmbl_50190.p1, internal, 85575, 85694
-recovered pasa_asmbl_50190.p1, internal, 85811, 85963
-recovered pasa_asmbl_50190.p1, internal, 86156, 86367
-recovered pasa_asmbl_50190.p1, internal, 86507, 86666
-recovered pasa_asmbl_50190.p1, internal, 86836, 87006
Valid prediction for snap_scaffold_7-snap.2246-T1
Valid prediction for Augustus_model.g12231.t1
Valid prediction for Augustus_model.g12240.t1
Valid prediction for snap_scaffold_7-snap.2229-T1
Valid prediction for CodingQuarry_transcript_57641-T1
Valid prediction for GlimmerHMM_glimmerT_18194-T1
Valid prediction for pasa_asmbl_50185.p1
Valid prediction for snap_scaffold_7-snap.2257-T1
Valid prediction for GlimmerHMM_glimmerT_18188-T1
Valid prediction for Augustus_model.g12232.t1
Valid prediction for Augustus_model.g12238.t1
Couldn't classify 278299, 278817
Sorry, prediction pasa_asmbl_50204.p1 fails validation.
(GAC)	 TC	278299-278817	TC	AAT
Valid prediction for CodingQuarry_transcript_57639-T1
Valid prediction for snap_scaffold_7-snap.2242-T1
Valid prediction for Augustus_model.g12226.t1
Valid prediction for Augustus_model.g12234.t1
Valid prediction for Augustus_model.g12222.t1
Valid prediction for snap_scaffold_7-snap.2225-T1
Valid prediction for GlimmerHMM_glimmerT_18175-T1
Valid prediction for snap_scaffold_7-snap.2259-T1
Valid prediction for GlimmerHMM_glimmerT_18181-T1
Valid prediction for snap_scaffold_7-snap.2219-T1
Valid prediction for snap_scaffold_7-snap.2243-T1
Valid prediction for GlimmerHMM_glimmerT_18190-T1
Valid prediction for Augustus_model.g12239.t1
Valid prediction for Augustus_model.g12242.t1
Valid prediction for CodingQuarry_transcript_57643-T1
Valid prediction for snap_scaffold_7-snap.2226-T1
Valid prediction for GlimmerHMM_glimmerT_18170-T1
Valid prediction for GlimmerHMM_glimmerT_18195-T1
Valid prediction for snap_scaffold_7-snap.2254-T1
Valid prediction for snap_scaffold_7-snap.2218-T1
Valid prediction for snap_scaffold_7-snap.2233-T1
Valid prediction for snap_scaffold_7-snap.2241-T1
Valid prediction for snap_scaffold_7-snap.2249-T1
Valid prediction for GlimmerHMM_glimmerT_18177-T1
Couldn't classify 134941, 135072
Sorry, prediction pasa_asmbl_50194.p2 fails validation.
(GGT)	 CA	134941-135072	GT	AGG
(GTG)	 AG	135217-135400	GT	AGG
(GCA)	 AG	136001-136167	GT	TTG
(GGA)	 AG	136933-137049	GG	GAG
-recovered pasa_asmbl_50194.p2, terminal, 136933, 137049
-recovered pasa_asmbl_50194.p2, internal, 135217, 135400
-recovered pasa_asmbl_50194.p2, internal, 136001, 136167
Valid prediction for snap_scaffold_7-snap.2239-T1
Valid prediction for snap_scaffold_7-snap.2223-T1
Valid prediction for Augustus_model.g12245.t1
Valid prediction for GlimmerHMM_glimmerT_18166-T1
Valid prediction for GlimmerHMM_glimmerT_18168-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 HiQ_model.g12244.t1
Valid prediction for Augustus_model.g12230.t1
Valid prediction for Augustus_model.g12223.t1
Valid prediction for HiQ_model.g12243.t1
Valid prediction for Augustus_model.g12237.t1
Valid prediction for GlimmerHMM_glimmerT_18192-T1
Valid prediction for Augustus_model.g12221.t1
Valid prediction for snap_scaffold_7-snap.2240-T1
Valid prediction for GlimmerHMM_glimmerT_18187-T1
Valid prediction for Augustus_model.g12227.t1
Valid prediction for Augustus_model.g12228.t1
Valid prediction for snap_scaffold_7-snap.2256-T1
Valid prediction for snap_scaffold_7-snap.2260-T1
Valid prediction for snap_scaffold_7-snap.2236-T1
Valid prediction for snap_scaffold_7-snap.2231-T1
Valid prediction for Augustus_model.g12218.t1
Valid prediction for GlimmerHMM_glimmerT_18191-T1
Valid prediction for Augustus_model.g12229.t1
Couldn't classify 8310, 8491
Couldn't classify 8702, 8715
Sorry, prediction CodingQuarry_transcript_57645-T1 fails validation.
(ATG)	 CA	7603-7759	GT	TGG
(GCC)	 AG	8098-8176	GT	AAG
(ATT)	 AG	8310-8491	AA	GGA
(TGC)	 GG	8702-8715	TA	GAT
-recovered CodingQuarry_transcript_57645-T1, initial, 7603, 7759
-recovered CodingQuarry_transcript_57645-T1, internal, 8098, 8176
Valid prediction for GlimmerHMM_glimmerT_18178-T1
Valid prediction for snap_scaffold_7-snap.2235-T1
Valid prediction for GlimmerHMM_glimmerT_18183-T1
Valid prediction for GlimmerHMM_glimmerT_18173-T1
Valid prediction for GlimmerHMM_glimmerT_18193-T1
Couldn't classify 15417, 15551
Sorry, prediction pasa_asmbl_51179.p1 fails validation.
(GGT)	 CA	15417-15551	GT	AGG
(GTC)	 AG	15693-15863	GT	AGG
(CTG)	 AG	16000-16156	GT	GGG
(GTA)	 AG	16247-16443	GT	TGG
(ATC)	 AG	16530-16780	GT	AAG
(GAG)	 AG	16888-17770	TT	GAT
-recovered pasa_asmbl_51179.p1, terminal, 16888, 17770
-recovered pasa_asmbl_51179.p1, internal, 15693, 15863
-recovered pasa_asmbl_51179.p1, internal, 16000, 16156
-recovered pasa_asmbl_51179.p1, internal, 16247, 16443
-recovered pasa_asmbl_51179.p1, internal, 16530, 16780
Valid prediction for GlimmerHMM_glimmerT_18172-T1
Valid prediction for snap_scaffold_7-snap.2230-T1
Couldn't classify 133653, 133823
Sorry, prediction pasa_asmbl_51173.p1 fails validation.
(CCC)	 CC	133653-133823	GT	TCG
(CTC)	 AG	135795-135905	GT	CTG
(TAC)	 AG	136007-136127	GT	CGG
(ATG)	 AG	137006-137097	GT	AGG
(TCT)	 AG	137720-137831	GT	TGG
(GGG)	 AG	139290-139457	GT	TGG
(GCT)	 AG	139590-139862	GT	AGG
(ACA)	 AG	140496-140557	GT	GGG
(GAC)	 AG	141289-141361	GT	CTG
(GCC)	 AG	141481-141548	GT	AGG
(CCT)	 AG	141658-141753	GA	GAG
add_exon() Sorry, pasa_asmbl_51173.p1 137006-137097-initial-1 is invalid.
-recovered pasa_asmbl_51173.p1, initial, 137006, 137097
-recovered pasa_asmbl_51173.p1, terminal, 141658, 141753
-recovered pasa_asmbl_51173.p1, internal, 135795, 135905
-recovered pasa_asmbl_51173.p1, internal, 136007, 136127
-recovered pasa_asmbl_51173.p1, internal, 137006, 137097
-recovered pasa_asmbl_51173.p1, internal, 137720, 137831
-recovered pasa_asmbl_51173.p1, internal, 139290, 139457
-recovered pasa_asmbl_51173.p1, internal, 139590, 139862
-recovered pasa_asmbl_51173.p1, internal, 140496, 140557
-recovered pasa_asmbl_51173.p1, internal, 141289, 141361
-recovered pasa_asmbl_51173.p1, internal, 141481, 141548
Valid prediction for GlimmerHMM_glimmerT_18174-T1
Valid prediction for GlimmerHMM_glimmerT_18186-T1
Valid prediction for GlimmerHMM_glimmerT_18189-T1
Valid prediction for Augustus_model.g12241.t1
Valid prediction for snap_scaffold_7-snap.2253-T1
Valid prediction for snap_scaffold_7-snap.2263-T1
Valid prediction for Augustus_model.g12235.t1
Valid prediction for snap_scaffold_7-snap.2251-T1
Valid prediction for snap_scaffold_7-snap.2237-T1
Valid prediction for GlimmerHMM_glimmerT_18182-T1
Valid prediction for snap_scaffold_7-snap.2252-T1
Valid prediction for snap_scaffold_7-snap.2232-T1
Valid prediction for GlimmerHMM_glimmerT_18164-T1
Valid prediction for Augustus_model.g12225.t1
Couldn't classify 186012, 186131
Sorry, prediction pasa_asmbl_51165.p1 fails validation.
(GGC)	 CA	186012-186131	GT	CAG
(GTC)	 AG	186316-186430	GT	AGG
(TGG)	 AG	186688-186869	GT	GGG
(GTG)	 AG	188283-188510	GG	GAG
-recovered pasa_asmbl_51165.p1, terminal, 188283, 188510
-recovered pasa_asmbl_51165.p1, internal, 186316, 186430
-recovered pasa_asmbl_51165.p1, internal, 186688, 186869
Valid prediction for GlimmerHMM_glimmerT_18167-T1
Couldn't classify 175036, 175081
Couldn't classify 179720, 179808
Sorry, prediction pasa_asmbl_51167.p1 fails validation.
(CTC)	 GC	175036-175081	GT	CAG
(CCA)	 AG	177737-177760	GT	AGG
(GCC)	 AG	178990-179157	GT	AGG
(ATG)	 AG	179720-179808	GG	AAG
-recovered pasa_asmbl_51167.p1, internal, 177737, 177760
-recovered pasa_asmbl_51167.p1, internal, 178990, 179157
Valid prediction for Augustus_model.g12236.t1
Valid prediction for snap_scaffold_7-snap.2228-T1
Valid prediction for snap_scaffold_7-snap.2261-T1
Valid prediction for snap_scaffold_7-snap.2220-T1
Valid prediction for HiQ_model.g12233.t1
Valid prediction for snap_scaffold_7-snap.2238-T1
Valid prediction for snap_scaffold_7-snap.2222-T1
Valid prediction for pasa_asmbl_51180.p1
Valid prediction for snap_scaffold_7-snap.2247-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g12217.t1
Valid prediction for snap_scaffold_7-snap.2245-T1
Valid prediction for CodingQuarry_transcript_57644-T1
Valid prediction for GlimmerHMM_glimmerT_18179-T1
Valid prediction for Augustus_model.g12219.t1
Valid prediction for snap_scaffold_7-snap.2250-T1
Valid prediction for GlimmerHMM_glimmerT_18171-T1
Valid prediction for snap_scaffold_7-snap.2258-T1
Valid prediction for GlimmerHMM_glimmerT_18180-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_18176-T1
Valid prediction for GlimmerHMM_glimmerT_18165-T1
Valid prediction for GlimmerHMM_glimmerT_18169-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13303, rend_intergenic: 13208  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18955, rend_intergenic: 17436  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34445, rend_intergenic: 29980  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87251, rend_intergenic: 79370  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114381, rend_intergenic: 108613  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146561, rend_intergenic: 141152  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149927, rend_intergenic: 149335  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 210015, rend_intergenic: 206837  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 282904
-exon list size: 496


building trellis

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79.3    
79.5    
79.7    
79.9    
80.1    
80.3    
80.5    
80.7    
80.9    
81.1    
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    
83.9    
84.1    
84.3    
84.5    
84.7    
84.9    
85.1    
85.3    
85.5    
85.7    
85.9    
86.1    
86.3    
86.5    
86.7    
86.9    
87.1    
87.3    
87.6    
87.8    
88.0    
88.2    
88.4    
88.6    
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    
91.4    
91.6    
91.8    
92.0    
92.2    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
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    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.8    
98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 38 predictions from path traversal
Error with prediction: snap lend_intergenic: 13303, rend_intergenic: 13208  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18955, rend_intergenic: 17436  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34445, rend_intergenic: 29980  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87251, rend_intergenic: 79370  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114381, rend_intergenic: 108613  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146561, rend_intergenic: 141152  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149927, rend_intergenic: 149335  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 210015, rend_intergenic: 206837  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 32 predictions persist after filtering for low support