-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_20/scaffold_20_10584454-10954032

-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 CodingQuarry_transcript_30654-T1
Valid prediction for snap_scaffold_20-snap.2253-T1
Valid prediction for snap_scaffold_20-snap.2267-T1
Valid prediction for pasa_asmbl_26995.p1
Valid prediction for GlimmerHMM_glimmerT_46768-T1
Valid prediction for snap_scaffold_20-snap.2259-T1
Valid prediction for GlimmerHMM_glimmerT_46763-T1
Valid prediction for snap_scaffold_20-snap.2265-T1
Valid prediction for GlimmerHMM_glimmerT_46751-T1
Valid prediction for GlimmerHMM_glimmerT_46767-T1
Valid prediction for Augustus_model.g31080.t1
Valid prediction for HiQ_model.g31100.t1
Valid prediction for GlimmerHMM_glimmerT_46765-T1
Valid prediction for snap_scaffold_20-snap.2270-T1
Valid prediction for Augustus_model.g31098.t1
Valid prediction for GlimmerHMM_glimmerT_46743-T1
Valid prediction for Augustus_model.g31101.t1
Valid prediction for snap_scaffold_20-snap.2274-T1
Valid prediction for snap_scaffold_20-snap.2292-T1
Valid prediction for GlimmerHMM_glimmerT_46750-T1
Couldn't classify 289199, 289288
Couldn't classify 290164, 290279
Sorry, prediction pasa_asmbl_27001.p1 fails validation.
(GAA)	 AT	289199-289288	GT	GGG
(ATG)	 AG	289428-289507	GT	AGG
(GCG)	 AG	289597-289639	GT	AGG
(ACC)	 AG	289761-289840	GT	AGG
(ACT)	 AG	289976-290046	GT	AGG
(AGC)	 AG	290164-290279	GG	GGG
-recovered pasa_asmbl_27001.p1, initial, 289428, 289507
-recovered pasa_asmbl_27001.p1, internal, 289428, 289507
-recovered pasa_asmbl_27001.p1, internal, 289597, 289639
-recovered pasa_asmbl_27001.p1, internal, 289761, 289840
-recovered pasa_asmbl_27001.p1, internal, 289976, 290046
Valid prediction for snap_scaffold_20-snap.2275-T1
Valid prediction for Augustus_model.g31090.t1
Valid prediction for GlimmerHMM_glimmerT_46760-T1
Valid prediction for HiQ_model.g31084.t1
Valid prediction for pasa_asmbl_26980.p1
Valid prediction for snap_scaffold_20-snap.2256-T1
Valid prediction for CodingQuarry_transcript_30655-T1
Valid prediction for snap_scaffold_20-snap.2279-T1
Couldn't classify 72576, 72680
Sorry, prediction pasa_asmbl_26974.p1 fails validation.
(ATG)	 TC	65729-65784	GT	AGG
(GAG)	 AG	66433-66497	GT	CGG
(TGA)	 AG	68100-68155	GT	AGG
(GGG)	 AG	68499-68546	GT	AGG
(GGA)	 AG	69369-69411	GT	AGG
(CTG)	 AG	70157-70229	GT	TGG
(GAT)	 AG	70667-70798	GT	AGG
(GGC)	 AG	71224-71286	GT	TGG
(GAC)	 AG	71928-72009	GT	AGG
(CAT)	 AG	72576-72680	GA	AGG
-recovered pasa_asmbl_26974.p1, initial, 65729, 65784
add_exon() Sorry, pasa_asmbl_26974.p1 69369-69411-terminal-3 is invalid.
-recovered pasa_asmbl_26974.p1, terminal, 69369, 69411
-recovered pasa_asmbl_26974.p1, internal, 66433, 66497
-recovered pasa_asmbl_26974.p1, internal, 68100, 68155
-recovered pasa_asmbl_26974.p1, internal, 68499, 68546
-recovered pasa_asmbl_26974.p1, internal, 69369, 69411
-recovered pasa_asmbl_26974.p1, internal, 70157, 70229
-recovered pasa_asmbl_26974.p1, internal, 70667, 70798
-recovered pasa_asmbl_26974.p1, internal, 71224, 71286
-recovered pasa_asmbl_26974.p1, internal, 71928, 72009
Valid prediction for GlimmerHMM_glimmerT_46744-T1
Valid prediction for Augustus_model.g31099.t1
Valid prediction for pasa_asmbl_26996.p1
Valid prediction for CodingQuarry_transcript_30658-T1
Valid prediction for CodingQuarry_transcript_30659-T1
Couldn't classify 123593, 123853
Sorry, prediction pasa_asmbl_26987.p1 fails validation.
(ATG)	 TC	113778-114306	GT	AGG
(ATC)	 AG	117187-117268	GT	AGG
(GTT)	 AG	117443-117565	GT	CGG
(AGT)	 AG	117742-117845	GT	AGG
(GCA)	 AG	118314-118536	GT	AGG
(GGC)	 AG	121170-121289	GT	AAG
(GTG)	 AG	121604-121766	GT	AGG
(CAA)	 AG	122114-122231	GT	TGG
(GGA)	 AG	122816-122988	GT	GAG
(AAG)	 AG	123177-123293	GT	TTG
(GCC)	 AG	123593-123853	CC	GCC
-recovered pasa_asmbl_26987.p1, initial, 113778, 114306
-recovered pasa_asmbl_26987.p1, internal, 117187, 117268
-recovered pasa_asmbl_26987.p1, internal, 117443, 117565
-recovered pasa_asmbl_26987.p1, internal, 117742, 117845
-recovered pasa_asmbl_26987.p1, internal, 118314, 118536
-recovered pasa_asmbl_26987.p1, internal, 121170, 121289
-recovered pasa_asmbl_26987.p1, internal, 121604, 121766
-recovered pasa_asmbl_26987.p1, internal, 122114, 122231
-recovered pasa_asmbl_26987.p1, internal, 122816, 122988
-recovered pasa_asmbl_26987.p1, internal, 123177, 123293
Valid prediction for snap_scaffold_20-snap.2290-T1
Valid prediction for GlimmerHMM_glimmerT_46753-T1
Valid prediction for snap_scaffold_20-snap.2251-T1
Valid prediction for Augustus_model.g31095.t1
Valid prediction for snap_scaffold_20-snap.2291-T1
Valid prediction for CodingQuarry_transcript_30653-T1
Valid prediction for snap_scaffold_20-snap.2271-T1
Valid prediction for Augustus_model.g31082.t1
Valid prediction for Augustus_model.g31073.t1
Valid prediction for snap_scaffold_20-snap.2263-T1
Valid prediction for snap_scaffold_20-snap.2264-T1
Valid prediction for Augustus_model.g31076.t1
Valid prediction for snap_scaffold_20-snap.2305-T1
Valid prediction for GlimmerHMM_glimmerT_46771-T1
Valid prediction for GlimmerHMM_glimmerT_46772-T1
Valid prediction for Augustus_model.g31072.t1
Valid prediction for snap_scaffold_20-snap.2262-T1
Valid prediction for snap_scaffold_20-snap.2258-T1
Valid prediction for GlimmerHMM_glimmerT_46762-T1
Valid prediction for GlimmerHMM_glimmerT_46776-T1
Valid prediction for snap_scaffold_20-snap.2266-T1
Valid prediction for HiQ_model.g31077.t1
Valid prediction for snap_scaffold_20-snap.2252-T1
Valid prediction for snap_scaffold_20-snap.2293-T1
Valid prediction for snap_scaffold_20-snap.2272-T1
Couldn't classify 125514, 125549
Sorry, prediction pasa_asmbl_26988.p1 fails validation.
(CCT)	 GG	125514-125549	GT	AGG
(ATG)	 AG	125799-126368	GA	AAG
-recovered pasa_asmbl_26988.p1, terminal, 125799, 126368
Valid prediction for snap_scaffold_20-snap.2278-T1
Valid prediction for GlimmerHMM_glimmerT_46766-T1
Valid prediction for CodingQuarry_transcript_30663-T1
Valid prediction for Augustus_model.g31093.t1
Valid prediction for GlimmerHMM_glimmerT_46746-T1
Valid prediction for snap_scaffold_20-snap.2285-T1
Couldn't classify 194658, 194954
Sorry, prediction pasa_asmbl_26990.p1 fails validation.
(GGT)	 TA	194658-194954	GT	AGG
(TCG)	 AG	196511-196645	GT	AGG
(GTG)	 AG	196818-196922	GT	AGG
(GTT)	 AG	197015-197065	GT	AGG
(CTC)	 AG	198479-198535	GT	AGG
(ACT)	 AG	198672-198764	GT	AAG
(GTC)	 AG	198953-199091	GT	GGG
(ATA)	 AG	199191-199318	GT	AGG
(GCG)	 AG	199498-199554	GT	AGG
(GCA)	 AG	199746-199817	GT	AGG
(AAC)	 AG	200019-200024	CA	GAC
-recovered pasa_asmbl_26990.p1, terminal, 200019, 200024
-recovered pasa_asmbl_26990.p1, internal, 196511, 196645
-recovered pasa_asmbl_26990.p1, internal, 196818, 196922
-recovered pasa_asmbl_26990.p1, internal, 197015, 197065
-recovered pasa_asmbl_26990.p1, internal, 198479, 198535
-recovered pasa_asmbl_26990.p1, internal, 198672, 198764
-recovered pasa_asmbl_26990.p1, internal, 198953, 199091
-recovered pasa_asmbl_26990.p1, internal, 199191, 199318
-recovered pasa_asmbl_26990.p1, internal, 199498, 199554
-recovered pasa_asmbl_26990.p1, internal, 199746, 199817
Valid prediction for GlimmerHMM_glimmerT_46747-T1
Valid prediction for GlimmerHMM_glimmerT_46758-T1
Valid prediction for snap_scaffold_20-snap.2269-T1
Valid prediction for HiQ_model.g31091.t1
Valid prediction for snap_scaffold_20-snap.2286-T1
Valid prediction for Augustus_model.g31094.t1
Valid prediction for snap_scaffold_20-snap.2294-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for snap_scaffold_20-snap.2277-T1
Valid prediction for HiQ_model.g31083.t1
Valid prediction for CodingQuarry_transcript_30660-T1
Valid prediction for snap_scaffold_20-snap.2260-T1
Valid prediction for snap_scaffold_20-snap.2295-T1
Valid prediction for Augustus_model.g31078.t1
Valid prediction for snap_scaffold_20-snap.2257-T1
Valid prediction for GlimmerHMM_glimmerT_46749-T1
Valid prediction for GlimmerHMM_glimmerT_46775-T1
Valid prediction for snap_scaffold_20-snap.2261-T1
Valid prediction for GlimmerHMM_glimmerT_46754-T1
Valid prediction for snap_scaffold_20-snap.2276-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 snap_scaffold_20-snap.2268-T1
Valid prediction for snap_scaffold_20-snap.2281-T1
Valid prediction for HiQ_model.g31086.t1
Valid prediction for GlimmerHMM_glimmerT_46770-T1
Valid prediction for snap_scaffold_20-snap.2296-T1
Valid prediction for snap_scaffold_20-snap.2280-T1
Valid prediction for GlimmerHMM_glimmerT_46773-T1
Valid prediction for snap_scaffold_20-snap.2287-T1
Valid prediction for snap_scaffold_20-snap.2303-T1
Valid prediction for CodingQuarry_transcript_30662-T1
Valid prediction for CodingQuarry_transcript_30661-T1
Valid prediction for HiQ_model.g31092.t1
Valid prediction for snap_scaffold_20-snap.2297-T1
Couldn't classify 88437, 88458
Sorry, prediction pasa_asmbl_26122.p1 fails validation.
(CTA)	 TA	88437-88458	GT	TGG
(ATC)	 AG	89140-89180	GT	CTG
(GTT)	 AG	90914-90961	GT	AGG
(AGA)	 AG	91145-91287	GT	AGG
(ACC)	 AG	91437-91509	TC	AAT
-recovered pasa_asmbl_26122.p1, terminal, 91437, 91509
-recovered pasa_asmbl_26122.p1, internal, 89140, 89180
-recovered pasa_asmbl_26122.p1, internal, 90914, 90961
-recovered pasa_asmbl_26122.p1, internal, 91145, 91287
Valid prediction for snap_scaffold_20-snap.2254-T1
Valid prediction for snap_scaffold_20-snap.2306-T1
Valid prediction for pasa_asmbl_26116.p1
Valid prediction for GlimmerHMM_glimmerT_46748-T1
Valid prediction for snap_scaffold_20-snap.2273-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g31074.t1
Valid prediction for snap_scaffold_20-snap.2302-T1
Valid prediction for GlimmerHMM_glimmerT_46745-T1
Valid prediction for Augustus_model.g31088.t1
Valid prediction for Augustus_model.g31075.t1
Valid prediction for Augustus_model.g31087.t1
Couldn't classify 148206, 148460
Sorry, prediction pasa_asmbl_26120.p1 fails validation.
(ATG)	 GA	145736-146176	GT	AGG
(GCG)	 AG	148206-148460	AC	GCA
-recovered pasa_asmbl_26120.p1, initial, 145736, 146176
Valid prediction for snap_scaffold_20-snap.2298-T1
Valid prediction for GlimmerHMM_glimmerT_46764-T1
Valid prediction for snap_scaffold_20-snap.2289-T1
Valid prediction for Augustus_model.g31096.t1
Valid prediction for GlimmerHMM_glimmerT_46757-T1
Couldn't classify 38166, 38241
Couldn't classify 45239, 45258
Sorry, prediction pasa_asmbl_26125.p1 fails validation.
(AGG)	 TC	38166-38241	GT	TGG
(ATG)	 AG	38650-38734	GT	CAG
(GTA)	 AG	41456-41626	GT	AGG
(TAA)	 AG	41853-41988	GT	CAG
(ATA)	 AG	42532-42694	GT	GGG
(CTG)	 AG	45239-45258	CC	CCC
add_exon() Sorry, pasa_asmbl_26125.p1 38650-38734-initial-1 is invalid.
-recovered pasa_asmbl_26125.p1, initial, 38650, 38734
-recovered pasa_asmbl_26125.p1, internal, 38650, 38734
-recovered pasa_asmbl_26125.p1, internal, 41456, 41626
-recovered pasa_asmbl_26125.p1, internal, 41853, 41988
-recovered pasa_asmbl_26125.p1, internal, 42532, 42694
Valid prediction for pasa_asmbl_26115.p1
Valid prediction for HiQ_model.g31079.t1
Valid prediction for snap_scaffold_20-snap.2283-T1
Couldn't classify 47212, 47235
Sorry, prediction pasa_asmbl_26124.p1 fails validation.
(GAG)	 AC	47212-47235	GT	ATG
(CTT)	 AG	49900-50075	GT	AAG
(GTG)	 AG	50648-50695	GT	CGG
(AGG)	 AG	50831-50952	GT	TGG
(AGC)	 AG	51162-51329	GT	AGG
(AGC)	 AG	51916-52056	GT	AGG
(GAC)	 AG	52309-52410	GT	AGG
(GGA)	 AG	52611-52697	GT	CAG
(GTC)	 AG	53000-53169	TT	GAT
-recovered pasa_asmbl_26124.p1, terminal, 53000, 53169
-recovered pasa_asmbl_26124.p1, internal, 49900, 50075
-recovered pasa_asmbl_26124.p1, internal, 50648, 50695
-recovered pasa_asmbl_26124.p1, internal, 50831, 50952
-recovered pasa_asmbl_26124.p1, internal, 51162, 51329
-recovered pasa_asmbl_26124.p1, internal, 51916, 52056
-recovered pasa_asmbl_26124.p1, internal, 52309, 52410
-recovered pasa_asmbl_26124.p1, internal, 52611, 52697
Valid prediction for GlimmerHMM_glimmerT_46774-T1
Valid prediction for snap_scaffold_20-snap.2284-T1
Valid prediction for GlimmerHMM_glimmerT_46761-T1
Valid prediction for GlimmerHMM_glimmerT_46755-T1
Valid prediction for GlimmerHMM_glimmerT_46752-T1
Valid prediction for snap_scaffold_20-snap.2304-T1
Valid prediction for GlimmerHMM_glimmerT_46756-T1
Valid prediction for GlimmerHMM_glimmerT_46769-T1
Valid prediction for Augustus_model.g31097.t1
Valid prediction for snap_scaffold_20-snap.2288-T1
Couldn't classify 152575, 152833
Sorry, prediction pasa_asmbl_26118.p1 fails validation.
(GAC)	 AG	152575-152833	GT	CGG
(GTG)	 AG	153777-153935	GT	AGG
(GAG)	 AG	155160-155270	GT	AGG
(TGA)	 AG	155923-156099	GT	CGG
(GTG)	 AG	156480-156535	GT	CGG
(ATG)	 AG	156838-156927	CC	GAC
-recovered pasa_asmbl_26118.p1, terminal, 156838, 156927
-recovered pasa_asmbl_26118.p1, internal, 152575, 152833
-recovered pasa_asmbl_26118.p1, internal, 153777, 153935
-recovered pasa_asmbl_26118.p1, internal, 155160, 155270
-recovered pasa_asmbl_26118.p1, internal, 155923, 156099
-recovered pasa_asmbl_26118.p1, internal, 156480, 156535
Valid prediction for pasa_asmbl_26121.p1
Valid prediction for HiQ_model.g31085.t1
Valid prediction for GlimmerHMM_glimmerT_46759-T1
Valid prediction for snap_scaffold_20-snap.2282-T1
Valid prediction for Augustus_model.g31089.t1
Valid prediction for snap_scaffold_20-snap.2299-T1
Valid prediction for snap_scaffold_20-snap.2301-T1
Valid prediction for snap_scaffold_20-snap.2255-T1
Valid prediction for Augustus_model.g31081.t1
Valid prediction for snap_scaffold_20-snap.2300-T1
Sorry, intron length (7) is less than minimum required (10)

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 165476, rend_intergenic: 163857  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 363315, rend_intergenic: 362507  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 126368, rend_intergenic: 126365  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 369579
-exon list size: 473


building trellis

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68.8    
69.1    
69.3    
69.5    
69.7    
69.9    
70.1    
70.3    
70.5    
70.7    
70.9    
71.2    
71.4    
71.6    
71.8    
72.0    
72.2    
72.4    
72.6    
72.8    
73.1    
73.3    
73.5    
73.7    
73.9    
74.1    
74.3    
74.5    
74.7    
74.9    
75.2    
75.4    
75.6    
75.8    
76.0    
76.2    
76.4    
76.6    
76.8    
77.1    
77.3    
77.5    
77.7    
77.9    
78.1    
78.3    
78.5    
78.7    
78.9    
79.2    
79.4    
79.6    
79.8    
80.0    
80.2    
80.4    
80.6    
80.8    
81.1    
81.3    
81.5    
81.7    
81.9    
82.1    
82.3    
82.5    
82.7    
82.9    
83.2    
83.4    
83.6    
83.8    
84.0    
84.2    
84.4    
84.6    
84.8    
85.1    
85.3    
85.5    
85.7    
85.9    
86.1    
86.3    
86.5    
86.7    
86.9    
87.2    
87.4    
87.6    
87.8    
88.0    
88.2    
88.4    
88.6    
88.8    
89.1    
89.3    
89.5    
89.7    
89.9    
90.1    
90.3    
90.5    
90.7    
90.9    
91.2    
91.4    
91.6    
91.8    
92.0    
92.2    
92.4    
92.6    
92.8    
93.1    
93.3    
93.5    
93.7    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.2    
95.4    
95.6    
95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
97.1    
97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.2    
99.4    
99.6    
99.8    
-found 38 predictions from path traversal
Error with prediction: snap lend_intergenic: 165476, rend_intergenic: 163857  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 363315, rend_intergenic: 362507  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 126368, rend_intergenic: 126365  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 37 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 11837
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-found 1 predictions from path traversal

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