-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_9690493-9920776

-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 snap_scaffold_20-snap.2133-T1
Valid prediction for Augustus_model.g30998.t1
Valid prediction for snap_scaffold_20-snap.2118-T1
Valid prediction for snap_scaffold_20-snap.2117-T1
Valid prediction for GlimmerHMM_glimmerT_46649-T1
Valid prediction for snap_scaffold_20-snap.2149-T1
Valid prediction for GlimmerHMM_glimmerT_46661-T1
Valid prediction for GlimmerHMM_glimmerT_46640-T1
Valid prediction for pasa_asmbl_26887.p1
Couldn't classify 36839, 36981
Sorry, prediction pasa_asmbl_26890.p1 fails validation.
(GCG)	 AG	36839-36981	GT	AGG
(TGA)	 AG	37226-37628	AG	AAA
-recovered pasa_asmbl_26890.p1, terminal, 37226, 37628
-recovered pasa_asmbl_26890.p1, internal, 36839, 36981
Valid prediction for Augustus_model.g30987.t1
Valid prediction for GlimmerHMM_glimmerT_46641-T1
Valid prediction for GlimmerHMM_glimmerT_46644-T1
Valid prediction for snap_scaffold_20-snap.2115-T1
Valid prediction for Augustus_model.g30996.t1
Valid prediction for GlimmerHMM_glimmerT_46660-T1
Valid prediction for CodingQuarry_transcript_30617-T1
Valid prediction for CodingQuarry_transcript_30613-T1
Couldn't classify 64467, 64744
Couldn't classify 65200, 65287
Sorry, prediction pasa_asmbl_26895.p2 fails validation.
(GTG)	 TG	64467-64744	GT	GGG
(ACA)	 AG	65200-65287	TT	ACT
Valid prediction for GlimmerHMM_glimmerT_46657-T1
Valid prediction for GlimmerHMM_glimmerT_46648-T1
Valid prediction for GlimmerHMM_glimmerT_46646-T1
Valid prediction for snap_scaffold_20-snap.2138-T1
Valid prediction for HiQ_model.g31000.t1
Valid prediction for Augustus_model.g30993.t1
Valid prediction for snap_scaffold_20-snap.2132-T1
Valid prediction for HiQ_model.g30992.t1
Valid prediction for GlimmerHMM_glimmerT_46645-T1
Valid prediction for HiQ_model.g30986.t1
Valid prediction for snap_scaffold_20-snap.2146-T1
Valid prediction for Augustus_model.g31002.t1
Valid prediction for snap_scaffold_20-snap.2142-T1
Valid prediction for snap_scaffold_20-snap.2124-T1
Valid prediction for GlimmerHMM_glimmerT_46654-T1
Valid prediction for CodingQuarry_transcript_30612-T1
Couldn't classify 83708, 83725
Sorry, prediction pasa_asmbl_26896.p1 fails validation.
(ATG)	 TG	81382-81481	GT	GGG
(GTT)	 AG	81600-81750	GT	TGG
(GTA)	 AG	82107-82185	GT	CAG
(ACC)	 AG	82305-82358	GT	AGG
(ACC)	 AG	82609-82704	GT	AGG
(TGG)	 AG	82803-82867	GT	GGG
(CTT)	 AG	83213-83288	GT	AGG
(CTG)	 AG	83460-83507	GT	AGG
(CCC)	 AG	83708-83725	AT	GGA
-recovered pasa_asmbl_26896.p1, initial, 81382, 81481
-recovered pasa_asmbl_26896.p1, internal, 81600, 81750
-recovered pasa_asmbl_26896.p1, internal, 82107, 82185
-recovered pasa_asmbl_26896.p1, internal, 82305, 82358
-recovered pasa_asmbl_26896.p1, internal, 82609, 82704
-recovered pasa_asmbl_26896.p1, internal, 82803, 82867
-recovered pasa_asmbl_26896.p1, internal, 83213, 83288
-recovered pasa_asmbl_26896.p1, internal, 83460, 83507
Couldn't classify 45040, 45131
Sorry, prediction pasa_asmbl_26893.p1 fails validation.
(ATG)	 GA	39976-40071	GT	AAG
(TAC)	 AG	40312-40384	GT	TGG
(GAA)	 AG	40535-40596	GT	AGG
(AAA)	 AG	40701-40745	GT	AGG
(ATC)	 AG	41092-41273	GT	AGG
(CAT)	 AG	41504-41552	GT	TGG
(GAA)	 AG	41703-41822	GT	AGG
(TTC)	 AG	42244-42372	GT	AGG
(ATG)	 AG	42518-42676	GT	AGG
(GCC)	 AG	42924-43121	GT	AGG
(GTG)	 AG	43319-43457	GT	GGG
(TGT)	 AG	43731-43912	GT	AGG
(GAC)	 AG	44435-44591	GT	CGG
(AGA)	 AG	45040-45131	GA	GCG
-recovered pasa_asmbl_26893.p1, initial, 39976, 40071
-recovered pasa_asmbl_26893.p1, initial, 42518, 42676
add_exon() Sorry, pasa_asmbl_26893.p1 41092-41273-terminal-2 is invalid.
-recovered pasa_asmbl_26893.p1, terminal, 41092, 41273
-recovered pasa_asmbl_26893.p1, internal, 40312, 40384
-recovered pasa_asmbl_26893.p1, internal, 40535, 40596
-recovered pasa_asmbl_26893.p1, internal, 40701, 40745
-recovered pasa_asmbl_26893.p1, internal, 41092, 41273
-recovered pasa_asmbl_26893.p1, internal, 41504, 41552
-recovered pasa_asmbl_26893.p1, internal, 41703, 41822
-recovered pasa_asmbl_26893.p1, internal, 42244, 42372
-recovered pasa_asmbl_26893.p1, internal, 42518, 42676
-recovered pasa_asmbl_26893.p1, internal, 42924, 43121
-recovered pasa_asmbl_26893.p1, internal, 43319, 43457
-recovered pasa_asmbl_26893.p1, internal, 43731, 43912
-recovered pasa_asmbl_26893.p1, internal, 44435, 44591
Valid prediction for GlimmerHMM_glimmerT_46659-T1
Valid prediction for snap_scaffold_20-snap.2141-T1
Valid prediction for snap_scaffold_20-snap.2116-T1
Valid prediction for Augustus_model.g30989.t1
Valid prediction for HiQ_model.g30984.t1
Valid prediction for Augustus_model.g31001.t1
Couldn't classify 115547, 115729
Couldn't classify 116226, 116507
Sorry, prediction pasa_asmbl_26901.p1 fails validation.
(AGC)	 AA	115547-115729	GT	AGG
(TCT)	 AG	116226-116507	GT	AGG
-recovered pasa_asmbl_26901.p1, internal, 116226, 116507
Couldn't classify 88570, 88680
Couldn't classify 90726, 90829
Sorry, prediction pasa_asmbl_26897.p1 fails validation.
(CTG)	 TC	88570-88680	GT	GGG
(GCG)	 AG	88863-89029	GT	AGG
(TGC)	 AG	89262-89340	GT	AGG
(TCC)	 AG	89672-89798	GT	AGG
(ATG)	 AG	90205-90312	GT	GGG
(ATG)	 AG	90726-90829	AG	CCA
add_exon() Sorry, pasa_asmbl_26897.p1 90205-90312-initial-1 is invalid.
-recovered pasa_asmbl_26897.p1, initial, 90205, 90312
-recovered pasa_asmbl_26897.p1, internal, 88863, 89029
-recovered pasa_asmbl_26897.p1, internal, 89262, 89340
-recovered pasa_asmbl_26897.p1, internal, 89672, 89798
-recovered pasa_asmbl_26897.p1, internal, 90205, 90312
Valid prediction for snap_scaffold_20-snap.2126-T1
Valid prediction for snap_scaffold_20-snap.2145-T1
Valid prediction for snap_scaffold_20-snap.2140-T1
Valid prediction for HiQ_model.g30988.t1
Valid prediction for snap_scaffold_20-snap.2136-T1
Valid prediction for snap_scaffold_20-snap.2147-T1
Valid prediction for pasa_asmbl_26888.p1
Valid prediction for snap_scaffold_20-snap.2112-T1
Valid prediction for snap_scaffold_20-snap.2123-T1
Valid prediction for GlimmerHMM_glimmerT_46647-T1
Valid prediction for snap_scaffold_20-snap.2108-T1
Valid prediction for pasa_asmbl_26908.p1
Valid prediction for GlimmerHMM_glimmerT_46656-T1
Valid prediction for GlimmerHMM_glimmerT_46652-T1
Couldn't classify 46971, 47154
Sorry, prediction pasa_asmbl_26894.p1 fails validation.
(AAC)	 AG	46971-47154	GT	CGG
(GAG)	 AG	47267-47373	GT	TGG
(GTG)	 AG	47496-47690	GT	AGG
(GAC)	 AG	48255-48423	GT	AGG
(GTC)	 AG	48698-48832	GT	AGG
(GCC)	 AG	49102-49261	GT	GAG
(TGC)	 AG	49527-49623	GT	AGG
(GAG)	 AG	49830-49976	GC	GAG
-recovered pasa_asmbl_26894.p1, terminal, 49830, 49976
-recovered pasa_asmbl_26894.p1, internal, 46971, 47154
-recovered pasa_asmbl_26894.p1, internal, 47267, 47373
-recovered pasa_asmbl_26894.p1, internal, 47496, 47690
-recovered pasa_asmbl_26894.p1, internal, 48255, 48423
-recovered pasa_asmbl_26894.p1, internal, 48698, 48832
-recovered pasa_asmbl_26894.p1, internal, 49102, 49261
-recovered pasa_asmbl_26894.p1, internal, 49527, 49623
-recovered pasa_asmbl_26894.p1, internal, 49830, 49976
Valid prediction for snap_scaffold_20-snap.2144-T1
Valid prediction for snap_scaffold_20-snap.2109-T1
Valid prediction for snap_scaffold_20-snap.2114-T1
Valid prediction for snap_scaffold_20-snap.2131-T1
Couldn't classify 213817, 214002
Sorry, prediction pasa_asmbl_26911.p1 fails validation.
(ATC)	 AG	213817-214002	GT	AGG
(CAC)	 AG	214210-214343	GT	AGG
(GTA)	 AG	214550-214847	GT	AGG
(GGC)	 AG	215127-215324	GT	AGG
(ACA)	 AG	215553-215795	GT	AGG
(GTC)	 AG	215886-215990	GT	AGG
(GGA)	 AG	216086-216193	GG	GAG
-recovered pasa_asmbl_26911.p1, terminal, 216086, 216193
-recovered pasa_asmbl_26911.p1, internal, 213817, 214002
-recovered pasa_asmbl_26911.p1, internal, 214210, 214343
-recovered pasa_asmbl_26911.p1, internal, 214550, 214847
-recovered pasa_asmbl_26911.p1, internal, 215127, 215324
-recovered pasa_asmbl_26911.p1, internal, 215553, 215795
-recovered pasa_asmbl_26911.p1, internal, 215886, 215990
Valid prediction for snap_scaffold_20-snap.2122-T1
Valid prediction for GlimmerHMM_glimmerT_46653-T1
Couldn't classify 92302, 92445
Sorry, prediction pasa_asmbl_26898.p1 fails validation.
(CAG)	 GG	92302-92445	GT	AGG
(GTG)	 AG	93578-93724	GT	CCG
(GAC)	 AG	93972-94128	GT	AGG
(CGG)	 AG	94439-95223	CA	GAC
-recovered pasa_asmbl_26898.p1, terminal, 94439, 95223
-recovered pasa_asmbl_26898.p1, internal, 93578, 93724
-recovered pasa_asmbl_26898.p1, internal, 93972, 94128
Valid prediction for snap_scaffold_20-snap.2113-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: -)Couldn't classify 114815, 115810
Sorry, prediction pasa_asmbl_26054.p1 fails validation.
(ATC)	 AC	114815-115810	CT	AAC
Couldn't classify 8745, 8892
Sorry, prediction pasa_asmbl_26060.p1 fails validation.
(GTG)	 GT	8745-8892	GT	AGG
(CCT)	 AG	9007-9070	GT	GGG
(AAC)	 AG	9190-9295	GT	AGG
(CAC)	 AG	9437-9524	GT	GGG
(CGC)	 AG	9883-10004	GT	AGG
(GAT)	 AG	10112-10192	GT	GGG
(TAT)	 AG	10833-10940	GT	AGG
(ATG)	 AG	11031-11125	GT	GGG
(GCT)	 AG	11312-11417	TG	GAT
-recovered pasa_asmbl_26060.p1, initial, 11031, 11125
-recovered pasa_asmbl_26060.p1, terminal, 11312, 11417
-recovered pasa_asmbl_26060.p1, internal, 9007, 9070
-recovered pasa_asmbl_26060.p1, internal, 9190, 9295
-recovered pasa_asmbl_26060.p1, internal, 9437, 9524
-recovered pasa_asmbl_26060.p1, internal, 9883, 10004
-recovered pasa_asmbl_26060.p1, internal, 10112, 10192
-recovered pasa_asmbl_26060.p1, internal, 10833, 10940
-recovered pasa_asmbl_26060.p1, internal, 11031, 11125
Valid prediction for pasa_asmbl_26053.p1
Valid prediction for CodingQuarry_transcript_30618-T1
Couldn't classify 91202, 91218
Sorry, prediction pasa_asmbl_26059.p1 fails validation.
(GAT)	 TC	91202-91218	GT	AGG
(GTC)	 AG	91303-91469	GT	TGG
(GGT)	 AG	91631-91693	GT	GGG
(CAT)	 AG	91870-91982	TT	AGT
-recovered pasa_asmbl_26059.p1, terminal, 91870, 91982
-recovered pasa_asmbl_26059.p1, internal, 91303, 91469
-recovered pasa_asmbl_26059.p1, internal, 91631, 91693
Valid prediction for snap_scaffold_20-snap.2130-T1
Valid prediction for Augustus_model.g30990.t1
Valid prediction for snap_scaffold_20-snap.2143-T1
Valid prediction for snap_scaffold_20-snap.2135-T1
Valid prediction for snap_scaffold_20-snap.2111-T1
Valid prediction for GlimmerHMM_glimmerT_46663-T1
Valid prediction for GlimmerHMM_glimmerT_46651-T1
Valid prediction for Augustus_model.g30991.t1
Valid prediction for snap_scaffold_20-snap.2137-T1
Valid prediction for CodingQuarry_transcript_30615-T1
Valid prediction for snap_scaffold_20-snap.2139-T1
Valid prediction for snap_scaffold_20-snap.2119-T1
Valid prediction for HiQ_model.g30994.t1
Valid prediction for HiQ_model.g30985.t1
Valid prediction for snap_scaffold_20-snap.2110-T1
Valid prediction for CodingQuarry_transcript_30616-T1
Valid prediction for snap_scaffold_20-snap.2127-T1
Valid prediction for GlimmerHMM_glimmerT_46642-T1
Valid prediction for GlimmerHMM_glimmerT_46639-T1
Valid prediction for Augustus_model.g30982.t1
Couldn't classify 3199, 3401
Sorry, prediction pasa_asmbl_26061.p1 fails validation.
(ATG)	 AC	2776-2920	GT	AGG
(GTG)	 AG	3199-3401	AA	CCA
-recovered pasa_asmbl_26061.p1, initial, 2776, 2920
Valid prediction for snap_scaffold_20-snap.2128-T1
Valid prediction for snap_scaffold_20-snap.2129-T1
Valid prediction for pasa_asmbl_26055.p1
Valid prediction for snap_scaffold_20-snap.2121-T1
Valid prediction for GlimmerHMM_glimmerT_46658-T1
Valid prediction for snap_scaffold_20-snap.2106-T1
Valid prediction for snap_scaffold_20-snap.2107-T1
Valid prediction for GlimmerHMM_glimmerT_46664-T1
Valid prediction for CodingQuarry_transcript_30611-T1
Valid prediction for snap_scaffold_20-snap.2120-T1
Valid prediction for snap_scaffold_20-snap.2125-T1
Valid prediction for snap_scaffold_20-snap.2148-T1
Valid prediction for Augustus_model.g31003.t1
Valid prediction for GlimmerHMM_glimmerT_46638-T1
Valid prediction for GlimmerHMM_glimmerT_46650-T1
Valid prediction for GlimmerHMM_glimmerT_46643-T1
Couldn't classify 6662, 6696
Couldn't classify 7289, 7477
Sorry, prediction pasa_asmbl_26331.p2 fails validation.
(CAT)	 CT	6662-6696	GT	AAG
(GCT)	 AG	7006-7102	GT	AGG
(GCA)	 AG	7289-7477	TC	AGT
-recovered pasa_asmbl_26331.p2, internal, 7006, 7102
Valid prediction for HiQ_model.g30995.t1
Valid prediction for Augustus_model.g30983.t1
Valid prediction for Augustus_model.g30997.t1
Valid prediction for GlimmerHMM_glimmerT_46662-T1
Valid prediction for snap_scaffold_20-snap.2134-T1
Valid prediction for Augustus_model.g30999.t1
Valid prediction for GlimmerHMM_glimmerT_46655-T1
Valid prediction for snap_scaffold_20-snap.2105-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 76499, rend_intergenic: 60573  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78320, rend_intergenic: 76728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92558, rend_intergenic: 88168  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157085, rend_intergenic: 155441  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 227509, rend_intergenic: 221434  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 230284
-exon list size: 552


building trellis

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65.2    
65.3    
65.5    
65.7    
65.9    
66.1    
66.2    
66.4    
66.6    
66.8    
67.0    
67.1    
67.3    
67.5    
67.7    
67.9    
68.1    
68.2    
68.4    
68.6    
68.8    
69.0    
69.1    
69.3    
69.5    
69.7    
69.9    
70.0    
70.2    
70.4    
70.6    
70.8    
70.9    
71.1    
71.3    
71.5    
71.7    
71.8    
72.0    
72.2    
72.4    
72.6    
72.7    
72.9    
73.1    
73.3    
73.5    
73.6    
73.8    
74.0    
74.2    
74.4    
74.5    
74.7    
74.9    
75.1    
75.3    
75.5    
75.6    
75.8    
76.0    
76.2    
76.4    
76.5    
76.7    
76.9    
77.1    
77.3    
77.4    
77.6    
77.8    
78.0    
78.2    
78.3    
78.5    
78.7    
78.9    
79.1    
79.2    
79.4    
79.6    
79.8    
80.0    
80.1    
80.3    
80.5    
80.7    
80.9    
81.0    
81.2    
81.4    
81.6    
81.8    
81.9    
82.1    
82.3    
82.5    
82.7    
82.9    
83.0    
83.2    
83.4    
83.6    
83.8    
83.9    
84.1    
84.3    
84.5    
84.7    
84.8    
85.0    
85.2    
85.4    
85.6    
85.7    
85.9    
86.1    
86.3    
86.5    
86.6    
86.8    
87.0    
87.2    
87.4    
87.5    
87.7    
87.9    
88.1    
88.3    
88.4    
88.6    
88.8    
89.0    
89.2    
89.4    
89.5    
89.7    
89.9    
90.1    
90.3    
90.4    
90.6    
90.8    
91.0    
91.2    
91.3    
91.5    
91.7    
91.9    
92.1    
92.2    
92.4    
92.6    
92.8    
93.0    
93.1    
93.3    
93.5    
93.7    
93.9    
94.0    
94.2    
94.4    
94.6    
94.8    
94.9    
95.1    
95.3    
95.5    
95.7    
95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
96.9    
97.1    
97.3    
97.5    
97.7    
97.8    
98.0    
98.2    
98.4    
98.6    
98.7    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 76499, rend_intergenic: 60573  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78320, rend_intergenic: 76728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92558, rend_intergenic: 88168  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157085, rend_intergenic: 155441  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 227509, rend_intergenic: 221434  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