-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_24/scaffold_24_8903312-9133193

-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 pasa_asmbl_32483.p1
Valid prediction for snap_scaffold_24-snap.1876-T1
Valid prediction for CodingQuarry_transcript_37400-T1
Valid prediction for GlimmerHMM_glimmerT_53099-T1
Couldn't classify 153720, 153805
Sorry, prediction pasa_asmbl_32484.p1 fails validation.
(CTC)	 TT	153720-153805	GT	AGG
(GCT)	 AG	153914-154172	GG	GAG
-recovered pasa_asmbl_32484.p1, terminal, 153914, 154172
Valid prediction for Augustus_model.g35354.t1
Valid prediction for HiQ_model.g35366.t1
Valid prediction for Augustus_model.g35345.t1
Valid prediction for pasa_asmbl_32503.p1
Valid prediction for GlimmerHMM_glimmerT_53084-T1
Couldn't classify 59774, 59911
Sorry, prediction pasa_asmbl_32468.p1 fails validation.
(GTG)	 AG	59774-59911	GT	AGG
(GTG)	 AG	60235-60360	GT	TGG
(ATG)	 AG	60621-60866	GT	AGG
(GCA)	 AG	61089-61325	GT	AGG
-recovered pasa_asmbl_32468.p1, initial, 60621, 60866
-recovered pasa_asmbl_32468.p1, terminal, 61089, 61325
-recovered pasa_asmbl_32468.p1, internal, 59774, 59911
-recovered pasa_asmbl_32468.p1, internal, 60235, 60360
-recovered pasa_asmbl_32468.p1, internal, 60621, 60866
-recovered pasa_asmbl_32468.p1, internal, 61089, 61325
Valid prediction for snap_scaffold_24-snap.1856-T1
Valid prediction for GlimmerHMM_glimmerT_53093-T1
Valid prediction for HiQ_model.g35369.t1
Valid prediction for snap_scaffold_24-snap.1887-T1
Valid prediction for snap_scaffold_24-snap.1857-T1
Valid prediction for GlimmerHMM_glimmerT_53067-T1
Valid prediction for Augustus_model.g35353.t1
Valid prediction for GlimmerHMM_glimmerT_53065-T1
Valid prediction for snap_scaffold_24-snap.1890-T1
Couldn't classify 84149, 84553
Couldn't classify 84989, 85044
Sorry, prediction pasa_asmbl_32474.p1 fails validation.
(CTG)	 CG	84149-84553	GT	AGG
(AGG)	 AG	84693-84723	GT	TGG
(TGC)	 AG	84989-85044	TA	ACT
-recovered pasa_asmbl_32474.p1, internal, 84693, 84723
Valid prediction for snap_scaffold_24-snap.1871-T1
Valid prediction for GlimmerHMM_glimmerT_53080-T1
Valid prediction for GlimmerHMM_glimmerT_53074-T1
Valid prediction for GlimmerHMM_glimmerT_53075-T1
Valid prediction for snap_scaffold_24-snap.1886-T1
Valid prediction for snap_scaffold_24-snap.1874-T1
Valid prediction for snap_scaffold_24-snap.1888-T1
Valid prediction for GlimmerHMM_glimmerT_53089-T1
Couldn't classify 159062, 159089
Sorry, prediction pasa_asmbl_32485.p1 fails validation.
(AGA)	 GT	159062-159089	GT	TGG
(CTC)	 AG	159659-159695	GT	AGG
(ACC)	 AG	159891-159959	GT	AGG
(TCT)	 AG	160070-160190	GT	GGG
(AGC)	 AG	160291-160470	GT	AGG
(GTG)	 AG	160713-160759	GT	AGG
(CTG)	 AG	161071-161159	GT	AGG
(GTT)	 AG	161266-161363	AA	GAA
-recovered pasa_asmbl_32485.p1, terminal, 161266, 161363
-recovered pasa_asmbl_32485.p1, internal, 159659, 159695
-recovered pasa_asmbl_32485.p1, internal, 159891, 159959
-recovered pasa_asmbl_32485.p1, internal, 160070, 160190
-recovered pasa_asmbl_32485.p1, internal, 160291, 160470
-recovered pasa_asmbl_32485.p1, internal, 160713, 160759
-recovered pasa_asmbl_32485.p1, internal, 161071, 161159
Valid prediction for GlimmerHMM_glimmerT_53072-T1
Valid prediction for Augustus_model.g35352.t1
Valid prediction for snap_scaffold_24-snap.1851-T1
Couldn't classify 219798, 219879
Sorry, prediction pasa_asmbl_32521.p1 fails validation.
(TCT)	 CC	219798-219879	GT	GGG
(ACA)	 AG	220186-220317	GT	CAG
(GTG)	 AG	221245-221619	GT	TGG
(ATC)	 AG	222150-222269	GT	GGG
(AAA)	 AG	222368-222493	GT	AGG
(GAG)	 AG	223075-223246	GT	AGG
(GAT)	 AG	223400-223615	GT	GGG
(TCT)	 AG	223811-223929	GT	AGG
(ATG)	 AG	224172-224311	GT	AGG
(GGA)	 AG	224443-224584	GT	AGG
(AAT)	 AG	224844-224918	GT	CGG
(TGT)	 AG	225064-225222	GT	AGG
(GAC)	 AG	225496-225548	CA	AGC
add_exon() Sorry, pasa_asmbl_32521.p1 224172-224311-initial-1 is invalid.
-recovered pasa_asmbl_32521.p1, initial, 224172, 224311
add_exon() Sorry, pasa_asmbl_32521.p1 223811-223929-terminal-2 is invalid.
-recovered pasa_asmbl_32521.p1, terminal, 223811, 223929
-recovered pasa_asmbl_32521.p1, terminal, 225496, 225548
-recovered pasa_asmbl_32521.p1, internal, 220186, 220317
-recovered pasa_asmbl_32521.p1, internal, 221245, 221619
-recovered pasa_asmbl_32521.p1, internal, 222150, 222269
-recovered pasa_asmbl_32521.p1, internal, 222368, 222493
-recovered pasa_asmbl_32521.p1, internal, 223075, 223246
-recovered pasa_asmbl_32521.p1, internal, 223400, 223615
-recovered pasa_asmbl_32521.p1, internal, 223811, 223929
-recovered pasa_asmbl_32521.p1, internal, 224172, 224311
-recovered pasa_asmbl_32521.p1, internal, 224443, 224584
-recovered pasa_asmbl_32521.p1, internal, 224844, 224918
-recovered pasa_asmbl_32521.p1, internal, 225064, 225222
Valid prediction for pasa_asmbl_32464.p1
Valid prediction for CodingQuarry_transcript_37398-T1
Valid prediction for CodingQuarry_transcript_37402-T1
Valid prediction for snap_scaffold_24-snap.1883-T1
Valid prediction for GlimmerHMM_glimmerT_53090-T1
Valid prediction for GlimmerHMM_glimmerT_53098-T1
Valid prediction for GlimmerHMM_glimmerT_53086-T1
Valid prediction for snap_scaffold_24-snap.1861-T1
Valid prediction for snap_scaffold_24-snap.1860-T1
Valid prediction for CodingQuarry_transcript_37401-T1
Valid prediction for snap_scaffold_24-snap.1882-T1
Valid prediction for GlimmerHMM_glimmerT_53083-T1
Valid prediction for snap_scaffold_24-snap.1870-T1
Couldn't classify 117123, 117206
Sorry, prediction pasa_asmbl_32477.p1 fails validation.
(ATG)	 AA	114714-114754	GT	ATG
(CCT)	 AG	115473-115630	GT	CAG
(CTC)	 AG	115791-115915	GT	AGG
(CCC)	 AG	116560-116674	GT	GGG
(TAA)	 AG	116947-117032	GT	TTG
(GGG)	 AG	117123-117206	AG	GCA
-recovered pasa_asmbl_32477.p1, initial, 114714, 114754
-recovered pasa_asmbl_32477.p1, internal, 115473, 115630
-recovered pasa_asmbl_32477.p1, internal, 115791, 115915
-recovered pasa_asmbl_32477.p1, internal, 116560, 116674
-recovered pasa_asmbl_32477.p1, internal, 116947, 117032
Valid prediction for GlimmerHMM_glimmerT_53076-T1
Valid prediction for Augustus_model.g35358.t1
Valid prediction for Augustus_model.g35370.t1
Valid prediction for pasa_asmbl_32500.p1
Valid prediction for Augustus_model.g35351.t1
Valid prediction for Augustus_model.g35355.t1
Valid prediction for snap_scaffold_24-snap.1879-T1
Valid prediction for HiQ_model.g35350.t1
Valid prediction for snap_scaffold_24-snap.1866-T1
Valid prediction for CodingQuarry_transcript_37393-T1
Valid prediction for CodingQuarry_transcript_37394-T1
Valid prediction for snap_scaffold_24-snap.1881-T1
Valid prediction for snap_scaffold_24-snap.1852-T1
Valid prediction for snap_scaffold_24-snap.1868-T1
Valid prediction for GlimmerHMM_glimmerT_53091-T1
Valid prediction for HiQ_model.g35367.t1
Valid prediction for snap_scaffold_24-snap.1867-T1
Valid prediction for snap_scaffold_24-snap.1863-T1
Valid prediction for GlimmerHMM_glimmerT_53082-T1
Valid prediction for snap_scaffold_24-snap.1884-T1
Valid prediction for pasa_asmbl_32490.p1
Valid prediction for Augustus_model.g35359.t1
Valid prediction for GlimmerHMM_glimmerT_53096-T1
Valid prediction for Augustus_model.g35362.t1
Valid prediction for snap_scaffold_24-snap.1858-T1
Valid prediction for CodingQuarry_transcript_37399-T1
Valid prediction for snap_scaffold_24-snap.1862-T1
Valid prediction for pasa_asmbl_32509.p1
Valid prediction for GlimmerHMM_glimmerT_53071-T1
Valid prediction for pasa_asmbl_32480.p1
Valid prediction for snap_scaffold_24-snap.1872-T1
Valid prediction for snap_scaffold_24-snap.1875-T1
Couldn't classify 87228, 87404
Sorry, prediction pasa_asmbl_32475.p1 fails validation.
(CAG)	 CC	87228-87404	GT	AGG
(GTA)	 AG	87526-87738	GT	GAG
(GAC)	 AG	88167-88286	GT	TTG
(ATA)	 AG	88500-88640	GT	AGG
(ATC)	 AG	88732-88803	GG	GAG
-recovered pasa_asmbl_32475.p1, terminal, 88732, 88803
-recovered pasa_asmbl_32475.p1, internal, 87526, 87738
-recovered pasa_asmbl_32475.p1, internal, 88167, 88286
-recovered pasa_asmbl_32475.p1, internal, 88500, 88640
Valid prediction for CodingQuarry_transcript_37405-T1
Valid prediction for snap_scaffold_24-snap.1864-T1
Valid prediction for Augustus_model.g35360.t1
Valid prediction for snap_scaffold_24-snap.1877-T1
Valid prediction for HiQ_model.g35364.t1
Valid prediction for GlimmerHMM_glimmerT_53095-T1
Couldn't classify 127848, 128068
Couldn't classify 128269, 128551
Sorry, prediction pasa_asmbl_32479.p1 fails validation.
(GGA)	 TG	127848-128068	GT	ATG
(CAA)	 AG	128269-128551	GT	AGG
-recovered pasa_asmbl_32479.p1, internal, 128269, 128551
Valid prediction for pasa_asmbl_32473.p2
Valid prediction for Augustus_model.g35356.t1
Valid prediction for HiQ_model.g35349.t1
Valid prediction for CodingQuarry_transcript_37404-T1
Valid prediction for HiQ_model.g35361.t1
Valid prediction for snap_scaffold_24-snap.1891-T1
Valid prediction for GlimmerHMM_glimmerT_53064-T1
Valid prediction for GlimmerHMM_glimmerT_53066-T1
Valid prediction for GlimmerHMM_glimmerT_53097-T1
Valid prediction for GlimmerHMM_glimmerT_53077-T1
Couldn't classify 81070, 81117
Sorry, prediction pasa_asmbl_32471.p2 fails validation.
(ATG)	 AC	80451-80513	GT	TGG
(ATA)	 AG	80700-80888	GT	AGG
(GAA)	 AG	81070-81117	GA	CTG
-recovered pasa_asmbl_32471.p2, initial, 80451, 80513
-recovered pasa_asmbl_32471.p2, internal, 80700, 80888
Valid prediction for GlimmerHMM_glimmerT_53073-T1
Couldn't classify 218906, 218993
Sorry, prediction pasa_asmbl_32516.p1 fails validation.
(ATG)	 CT	217857-217907	GT	GGG
(CAC)	 AG	218186-218235	GT	AGG
(GAC)	 AG	218543-218680	GT	GGG
(CCA)	 AG	218906-218993	CT	CAC
-recovered pasa_asmbl_32516.p1, initial, 217857, 217907
-recovered pasa_asmbl_32516.p1, internal, 218186, 218235
-recovered pasa_asmbl_32516.p1, internal, 218543, 218680
Valid prediction for Augustus_model.g35346.t1
Valid prediction for CodingQuarry_transcript_37392-T1
Valid prediction for snap_scaffold_24-snap.1853-T1
Valid prediction for GlimmerHMM_glimmerT_53100-T1
Valid prediction for GlimmerHMM_glimmerT_53088-T1
Valid prediction for GlimmerHMM_glimmerT_53094-T1
Valid prediction for snap_scaffold_24-snap.1889-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 GlimmerHMM_glimmerT_53063-T1
Valid prediction for GlimmerHMM_glimmerT_53087-T1
Couldn't classify 67247, 67354
Couldn't classify 67520, 67636
Sorry, prediction CodingQuarry_transcript_37396-T1 fails validation.
(ATG)	 TT	65448-65505	GT	AGG
(GTG)	 AG	66449-66594	GT	AAG
(ATT)	 AG	66762-66825	GT	TGG
(GTA)	 AG	66946-67013	GT	AGG
(GGT)	 AG	67247-67354	CA	TCC
(AGG)	 TC	67520-67636	TC	GAT
-recovered CodingQuarry_transcript_37396-T1, initial, 65448, 65505
-recovered CodingQuarry_transcript_37396-T1, internal, 66449, 66594
-recovered CodingQuarry_transcript_37396-T1, internal, 66762, 66825
-recovered CodingQuarry_transcript_37396-T1, internal, 66946, 67013
Valid prediction for snap_scaffold_24-snap.1859-T1
Valid prediction for snap_scaffold_24-snap.1878-T1
Valid prediction for GlimmerHMM_glimmerT_53092-T1
Valid prediction for snap_scaffold_24-snap.1880-T1
Valid prediction for pasa_asmbl_33131.p1
Valid prediction for snap_scaffold_24-snap.1885-T1
Valid prediction for GlimmerHMM_glimmerT_53085-T1
Valid prediction for GlimmerHMM_glimmerT_53079-T1
Valid prediction for Augustus_model.g35363.t1
Valid prediction for CodingQuarry_transcript_37397-T1
Valid prediction for CodingQuarry_transcript_37390-T1
Valid prediction for snap_scaffold_24-snap.1850-T1
Valid prediction for CodingQuarry_transcript_37391-T1
Valid prediction for Augustus_model.g35344.t1
Valid prediction for Augustus_model.g35357.t1
Valid prediction for HiQ_model.g35368.t1
Valid prediction for GlimmerHMM_glimmerT_53078-T1
Valid prediction for GlimmerHMM_glimmerT_53069-T1
Valid prediction for CodingQuarry_transcript_37403-T1
Valid prediction for GlimmerHMM_glimmerT_53068-T1
Valid prediction for GlimmerHMM_glimmerT_53070-T1
Valid prediction for GlimmerHMM_glimmerT_53081-T1
Valid prediction for snap_scaffold_24-snap.1855-T1
Valid prediction for snap_scaffold_24-snap.1869-T1
Valid prediction for HiQ_model.g35365.t1
Valid prediction for snap_scaffold_24-snap.1873-T1
Couldn't classify 190098, 190173
Sorry, prediction pasa_asmbl_33124.p1 fails validation.
(TTT)	 CA	190098-190173	GT	CGG
(GTT)	 AG	190283-190479	GT	AGG
(GCT)	 AG	190825-190997	GT	AGG
(AGT)	 AG	191159-191298	GT	CGG
(ACA)	 AG	191536-191594	AG	AAA
add_exon() Sorry, pasa_asmbl_33124.p1 190825-190997-terminal-2 is invalid.
-recovered pasa_asmbl_33124.p1, terminal, 190825, 190997
-recovered pasa_asmbl_33124.p1, terminal, 191536, 191594
-recovered pasa_asmbl_33124.p1, internal, 190283, 190479
-recovered pasa_asmbl_33124.p1, internal, 190825, 190997
-recovered pasa_asmbl_33124.p1, internal, 191159, 191298
Valid prediction for snap_scaffold_24-snap.1865-T1
Valid prediction for HiQ_model.g35347.t1
Valid prediction for pasa_asmbl_33127.p1
Valid prediction for snap_scaffold_24-snap.1854-T1
Valid prediction for pasa_asmbl_33130.p1
Valid prediction for HiQ_model.g35348.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 96996, rend_intergenic: 94168  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 229882
-exon list size: 473


building trellis

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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 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 96996, rend_intergenic: 94168  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 31 predictions persist after filtering for low support