-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_23/scaffold_23_3384074-3642730

-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: +)Couldn't classify 206905, 207062
Sorry, prediction pasa_asmbl_31451.p1 fails validation.
(GAG)	 AG	206905-207062	GT	AGG
(GGA)	 AG	207815-207962	GT	TTG
(GCG)	 AG	208055-208246	GT	AGG
(AAA)	 AG	208641-208732	GT	AGG
(CAA)	 AG	209126-209245	GT	AGG
(GTC)	 AG	211201-211379	GT	AGG
(GTG)	 AG	212996-213114	GT	CGG
(ACC)	 AG	213378-213451	GT	CCG
(GCA)	 AG	213570-213621	GT	AGG
(ACG)	 AG	213745-213897	GT	AGG
(ACC)	 AG	214891-215010	AG	GAA
-recovered pasa_asmbl_31451.p1, terminal, 214891, 215010
-recovered pasa_asmbl_31451.p1, internal, 206905, 207062
-recovered pasa_asmbl_31451.p1, internal, 207815, 207962
-recovered pasa_asmbl_31451.p1, internal, 208055, 208246
-recovered pasa_asmbl_31451.p1, internal, 208641, 208732
-recovered pasa_asmbl_31451.p1, internal, 209126, 209245
-recovered pasa_asmbl_31451.p1, internal, 211201, 211379
-recovered pasa_asmbl_31451.p1, internal, 212996, 213114
-recovered pasa_asmbl_31451.p1, internal, 213378, 213451
-recovered pasa_asmbl_31451.p1, internal, 213570, 213621
-recovered pasa_asmbl_31451.p1, internal, 213745, 213897
Valid prediction for snap_scaffold_23-snap.721-T1
Valid prediction for GlimmerHMM_glimmerT_50811-T1
Valid prediction for snap_scaffold_23-snap.688-T1
Valid prediction for snap_scaffold_23-snap.693-T1
Valid prediction for GlimmerHMM_glimmerT_50843-T1
Valid prediction for CodingQuarry_transcript_35611-T1
Valid prediction for GlimmerHMM_glimmerT_50810-T1
Valid prediction for snap_scaffold_23-snap.684-T1
Valid prediction for Augustus_model.g33976.t1
Valid prediction for Augustus_model.g33974.t1
Valid prediction for snap_scaffold_23-snap.680-T1
Valid prediction for GlimmerHMM_glimmerT_50833-T1
Valid prediction for snap_scaffold_23-snap.718-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for pasa_asmbl_31442.p1
Valid prediction for GlimmerHMM_glimmerT_50823-T1
Couldn't classify 123640, 123772
Sorry, prediction pasa_asmbl_31440.p1 fails validation.
(CGT)	 GT	123640-123772	GT	TGG
(GCG)	 AG	123865-125126	GT	GAG
-recovered pasa_asmbl_31440.p1, terminal, 123865, 125126
-recovered pasa_asmbl_31440.p1, internal, 123865, 125126
Valid prediction for Augustus_model.g33972.t1
Valid prediction for GlimmerHMM_glimmerT_50825-T1
Valid prediction for CodingQuarry_transcript_35608-T1
Valid prediction for snap_scaffold_23-snap.711-T1
Valid prediction for HiQ_model.g33971.t1
Valid prediction for snap_scaffold_23-snap.716-T1
Valid prediction for snap_scaffold_23-snap.702-T1
Valid prediction for snap_scaffold_23-snap.726-T1
Valid prediction for snap_scaffold_23-snap.725-T1
Valid prediction for snap_scaffold_23-snap.717-T1
Valid prediction for GlimmerHMM_glimmerT_50814-T1
Valid prediction for GlimmerHMM_glimmerT_50841-T1
Valid prediction for snap_scaffold_23-snap.728-T1
Valid prediction for snap_scaffold_23-snap.727-T1
Valid prediction for GlimmerHMM_glimmerT_50845-T1
Valid prediction for CodingQuarry_transcript_35615-T1
Valid prediction for HiQ_model.g33977.t1
Valid prediction for snap_scaffold_23-snap.719-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_23-snap.687-T1
Valid prediction for snap_scaffold_23-snap.703-T1
Valid prediction for GlimmerHMM_glimmerT_50821-T1
Valid prediction for Augustus_model.g33950.t1
Valid prediction for GlimmerHMM_glimmerT_50819-T1
Valid prediction for Augustus_model.g33964.t1
Valid prediction for snap_scaffold_23-snap.706-T1
Valid prediction for HiQ_model.g33978.t1
Valid prediction for snap_scaffold_23-snap.677-T1
Valid prediction for snap_scaffold_23-snap.695-T1
Valid prediction for Augustus_model.g33958.t1
Valid prediction for Augustus_model.g33970.t1
Couldn't classify 45672, 45758
Sorry, prediction pasa_asmbl_31435.p1 fails validation.
(GGT)	 GG	45672-45758	GT	TTG
(GGG)	 AG	46018-46106	GT	TGG
(GCC)	 AG	46236-46299	GT	ATG
(TGC)	 AG	47833-47924	GT	AGG
(AAT)	 AG	49524-49601	GT	AGG
(TGG)	 AG	50248-50363	GT	AGG
(GTT)	 AG	51034-51124	GT	AGG
(TTC)	 AG	51223-51306	GT	AGG
(CGG)	 AG	52350-52463	GT	AGG
(GAA)	 AG	52881-52928	GT	CGG
(GTC)	 AG	53307-53384	GT	CGG
(GTC)	 AG	53735-53854	GT	TCG
(GCG)	 AG	54056-54103	GT	CAG
(GAA)	 AG	54207-54275	GT	GAG
(AAC)	 AG	54436-54546	GT	AAG
(CTC)	 AG	54701-54779	GT	AGG
(AAG)	 AG	54963-55073	CC	GAC
-recovered pasa_asmbl_31435.p1, terminal, 54963, 55073
-recovered pasa_asmbl_31435.p1, internal, 46018, 46106
-recovered pasa_asmbl_31435.p1, internal, 46236, 46299
-recovered pasa_asmbl_31435.p1, internal, 47833, 47924
-recovered pasa_asmbl_31435.p1, internal, 49524, 49601
-recovered pasa_asmbl_31435.p1, internal, 50248, 50363
-recovered pasa_asmbl_31435.p1, internal, 51034, 51124
-recovered pasa_asmbl_31435.p1, internal, 51223, 51306
-recovered pasa_asmbl_31435.p1, internal, 52350, 52463
-recovered pasa_asmbl_31435.p1, internal, 52881, 52928
-recovered pasa_asmbl_31435.p1, internal, 53307, 53384
-recovered pasa_asmbl_31435.p1, internal, 53735, 53854
-recovered pasa_asmbl_31435.p1, internal, 54056, 54103
-recovered pasa_asmbl_31435.p1, internal, 54207, 54275
-recovered pasa_asmbl_31435.p1, internal, 54436, 54546
-recovered pasa_asmbl_31435.p1, internal, 54701, 54779
Valid prediction for GlimmerHMM_glimmerT_50816-T1
Valid prediction for snap_scaffold_23-snap.705-T1
Valid prediction for HiQ_model.g33975.t1
Valid prediction for snap_scaffold_23-snap.720-T1
Valid prediction for snap_scaffold_23-snap.723-T1
Valid prediction for snap_scaffold_23-snap.676-T1
Valid prediction for GlimmerHMM_glimmerT_50829-T1
Valid prediction for GlimmerHMM_glimmerT_50840-T1
Valid prediction for Augustus_model.g33955.t1
Valid prediction for snap_scaffold_23-snap.682-T1
Valid prediction for HiQ_model.g33954.t1
Valid prediction for GlimmerHMM_glimmerT_50844-T1
Valid prediction for pasa_asmbl_31441.p1
Valid prediction for snap_scaffold_23-snap.729-T1
Valid prediction for HiQ_model.g33969.t1
Valid prediction for GlimmerHMM_glimmerT_50812-T1
Valid prediction for pasa_asmbl_31455.p1
Valid prediction for snap_scaffold_23-snap.730-T1
Valid prediction for snap_scaffold_23-snap.673-T1
Valid prediction for snap_scaffold_23-snap.692-T1
Valid prediction for Augustus_model.g33959.t1
Valid prediction for pasa_asmbl_31457.p1
Valid prediction for CodingQuarry_transcript_35614-T1
Valid prediction for GlimmerHMM_glimmerT_50839-T1
Valid prediction for snap_scaffold_23-snap.722-T1
Valid prediction for snap_scaffold_23-snap.675-T1
Valid prediction for snap_scaffold_23-snap.689-T1
Valid prediction for GlimmerHMM_glimmerT_50831-T1
Valid prediction for GlimmerHMM_glimmerT_50837-T1
Valid prediction for GlimmerHMM_glimmerT_50817-T1
Couldn't classify 121104, 121231
Couldn't classify 123228, 123458
Sorry, prediction pasa_asmbl_31439.p1 fails validation.
(GTT)	 TT	121104-121231	GT	AGG
(TCC)	 AG	121452-121523	GT	GGG
(CCG)	 AG	121901-122036	GT	GAG
(ACC)	 AG	122160-122288	GT	AGG
(TTC)	 AG	123228-123458	TG	CGT
-recovered pasa_asmbl_31439.p1, internal, 121452, 121523
-recovered pasa_asmbl_31439.p1, internal, 121901, 122036
-recovered pasa_asmbl_31439.p1, internal, 122160, 122288
Valid prediction for Augustus_model.g33962.t1
Couldn't classify 120314, 120527
Couldn't classify 120689, 120771
Sorry, prediction pasa_asmbl_31930.p1 fails validation.
(GCC)	 AG	120314-120527	GT	CAG
(ATT)	 AG	120689-120771	AA	TCA
-recovered pasa_asmbl_31930.p1, internal, 120314, 120527
Valid prediction for snap_scaffold_23-snap.714-T1
Valid prediction for snap_scaffold_23-snap.696-T1
Valid prediction for snap_scaffold_23-snap.686-T1
Couldn't classify 222562, 222687
Sorry, prediction pasa_asmbl_31454.p1 fails validation.
(GGG)	 TG	222562-222687	GT	ACG
(ATC)	 AG	222958-223065	GT	AGG
(GTG)	 AG	223212-223331	GT	AGG
(GGG)	 AG	223460-223570	GT	AGG
(CAT)	 AG	223666-223794	CA	GAC
-recovered pasa_asmbl_31454.p1, terminal, 223666, 223794
-recovered pasa_asmbl_31454.p1, internal, 222958, 223065
-recovered pasa_asmbl_31454.p1, internal, 223212, 223331
-recovered pasa_asmbl_31454.p1, internal, 223460, 223570

-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_50836-T1
Valid prediction for Augustus_model.g33967.t1
Valid prediction for snap_scaffold_23-snap.712-T1
Valid prediction for snap_scaffold_23-snap.713-T1
Valid prediction for HiQ_model.g33963.t1
Valid prediction for GlimmerHMM_glimmerT_50827-T1
Valid prediction for snap_scaffold_23-snap.671-T1
Valid prediction for snap_scaffold_23-snap.690-T1
Valid prediction for HiQ_model.g33968.t1
Valid prediction for snap_scaffold_23-snap.700-T1
Valid prediction for Augustus_model.g33966.t1
Valid prediction for snap_scaffold_23-snap.698-T1
Valid prediction for GlimmerHMM_glimmerT_50820-T1
Valid prediction for pasa_asmbl_30808.p1
Valid prediction for snap_scaffold_23-snap.694-T1
Valid prediction for Augustus_model.g33951.t1
Valid prediction for CodingQuarry_transcript_35607-T1
Valid prediction for snap_scaffold_23-snap.707-T1
Valid prediction for GlimmerHMM_glimmerT_50830-T1
Valid prediction for snap_scaffold_23-snap.674-T1
Valid prediction for GlimmerHMM_glimmerT_50813-T1
Valid prediction for Augustus_model.g33960.t1
Valid prediction for GlimmerHMM_glimmerT_50834-T1
Couldn't classify 187184, 187327
Sorry, prediction pasa_asmbl_30795.p1 fails validation.
(ACC)	 AG	187184-187327	GT	GTG
(GCC)	 AG	187417-187615	GT	AGG
(GTT)	 AG	187704-187748	GT	TGG
(GTA)	 AG	187870-188039	GT	TCG
(AAT)	 AG	188609-188738	GT	AGG
(AGT)	 AG	188844-188976	GT	GGG
(GAA)	 AG	189310-189652	TT	GAT
-recovered pasa_asmbl_30795.p1, terminal, 189310, 189652
-recovered pasa_asmbl_30795.p1, internal, 187184, 187327
-recovered pasa_asmbl_30795.p1, internal, 187417, 187615
-recovered pasa_asmbl_30795.p1, internal, 187704, 187748
-recovered pasa_asmbl_30795.p1, internal, 187870, 188039
-recovered pasa_asmbl_30795.p1, internal, 188609, 188738
-recovered pasa_asmbl_30795.p1, internal, 188844, 188976
Valid prediction for snap_scaffold_23-snap.708-T1
Valid prediction for snap_scaffold_23-snap.681-T1
Valid prediction for snap_scaffold_23-snap.710-T1
Valid prediction for GlimmerHMM_glimmerT_50822-T1
Valid prediction for GlimmerHMM_glimmerT_50828-T1
Valid prediction for Augustus_model.g33952.t1
Valid prediction for snap_scaffold_23-snap.672-T1
Valid prediction for GlimmerHMM_glimmerT_50832-T1
Valid prediction for GlimmerHMM_glimmerT_50824-T1
Valid prediction for GlimmerHMM_glimmerT_50838-T1
Valid prediction for snap_scaffold_23-snap.709-T1
Valid prediction for GlimmerHMM_glimmerT_50818-T1
Valid prediction for snap_scaffold_23-snap.704-T1
Valid prediction for Augustus_model.g33973.t1
Valid prediction for GlimmerHMM_glimmerT_50826-T1
Valid prediction for Augustus_model.g33957.t1
Valid prediction for Augustus_model.g33961.t1
Valid prediction for pasa_asmbl_30802.p1
Valid prediction for snap_scaffold_23-snap.724-T1
Couldn't classify 30112, 30399
Sorry, prediction pasa_asmbl_30811.p1 fails validation.
(TTG)	 GC	30112-30399	GT	AGG
(ATC)	 AG	30530-30715	GT	AGG
(GTT)	 AG	30914-31056	GT	AGG
(TGT)	 AG	31405-31511	GT	AGG
(GGC)	 AG	32705-32868	GT	AGG
(GTC)	 AG	33103-33190	GT	AGG
(GTC)	 AG	33558-33751	TC	GAT
-recovered pasa_asmbl_30811.p1, terminal, 33558, 33751
-recovered pasa_asmbl_30811.p1, internal, 30530, 30715
-recovered pasa_asmbl_30811.p1, internal, 30914, 31056
-recovered pasa_asmbl_30811.p1, internal, 31405, 31511
-recovered pasa_asmbl_30811.p1, internal, 32705, 32868
-recovered pasa_asmbl_30811.p1, internal, 33103, 33190
Valid prediction for snap_scaffold_23-snap.691-T1
Valid prediction for snap_scaffold_23-snap.715-T1
Valid prediction for snap_scaffold_23-snap.701-T1
Valid prediction for Augustus_model.g33965.t1
Valid prediction for CodingQuarry_transcript_35610-T1
Valid prediction for snap_scaffold_23-snap.685-T1
Valid prediction for snap_scaffold_23-snap.697-T1
Valid prediction for Augustus_model.g33953.t1
Valid prediction for snap_scaffold_23-snap.678-T1
Valid prediction for CodingQuarry_transcript_35612-T1
Valid prediction for GlimmerHMM_glimmerT_50835-T1
Valid prediction for Augustus_model.g33956.t1
Valid prediction for snap_scaffold_23-snap.679-T1
Valid prediction for snap_scaffold_23-snap.699-T1
Couldn't classify 77038, 77223
Sorry, prediction CodingQuarry_transcript_35613-T1 fails validation.
(ATG)	 CA	75049-75088	GT	AGG
(AGC)	 AG	75492-76750	GC	ATG
(CAA)	 AT	77038-77223	TT	AGT
-recovered CodingQuarry_transcript_35613-T1, initial, 75049, 75088
-recovered CodingQuarry_transcript_35613-T1, internal, 75492, 76750
Valid prediction for snap_scaffold_23-snap.683-T1
Valid prediction for GlimmerHMM_glimmerT_50815-T1
Valid prediction for GlimmerHMM_glimmerT_50842-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12543, rend_intergenic: 9191  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22738, rend_intergenic: 13895  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25028, rend_intergenic: 22954  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28624, rend_intergenic: 25369  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35905, rend_intergenic: 31488  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36949, rend_intergenic: 35929  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42540, rend_intergenic: 38558  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44828, rend_intergenic: 42975  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75722, rend_intergenic: 70977  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80384, rend_intergenic: 77509  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93822, rend_intergenic: 81993  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172910, rend_intergenic: 171055  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 96827, rend_intergenic: 96824  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 258657
-exon list size: 546


building trellis

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58.8    
58.9    
59.1    
59.3    
59.5    
59.7    
59.9    
60.0    
60.2    
60.4    
60.6    
60.8    
60.9    
61.1    
61.3    
61.5    
61.7    
61.9    
62.0    
62.2    
62.4    
62.6    
62.8    
63.0    
63.1    
63.3    
63.5    
63.7    
63.9    
64.1    
64.2    
64.4    
64.6    
64.8    
65.0    
65.1    
65.3    
65.5    
65.7    
65.9    
66.1    
66.2    
66.4    
66.6    
66.8    
67.0    
67.2    
67.3    
67.5    
67.7    
67.9    
68.1    
68.2    
68.4    
68.6    
68.8    
69.0    
69.2    
69.3    
69.5    
69.7    
69.9    
70.1    
70.3    
70.4    
70.6    
70.8    
71.0    
71.2    
71.4    
71.5    
71.7    
71.9    
72.1    
72.3    
72.4    
72.6    
72.8    
73.0    
73.2    
73.4    
73.5    
73.7    
73.9    
74.1    
74.3    
74.5    
74.6    
74.8    
75.0    
75.2    
75.4    
75.5    
75.7    
75.9    
76.1    
76.3    
76.5    
76.6    
76.8    
77.0    
77.2    
77.4    
77.6    
77.7    
77.9    
78.1    
78.3    
78.5    
78.6    
78.8    
79.0    
79.2    
79.4    
79.6    
79.7    
79.9    
80.1    
80.3    
80.5    
80.7    
80.8    
81.0    
81.2    
81.4    
81.6    
81.8    
81.9    
82.1    
82.3    
82.5    
82.7    
82.8    
83.0    
83.2    
83.4    
83.6    
83.8    
83.9    
84.1    
84.3    
84.5    
84.7    
84.9    
85.0    
85.2    
85.4    
85.6    
85.8    
85.9    
86.1    
86.3    
86.5    
86.7    
86.9    
87.0    
87.2    
87.4    
87.6    
87.8    
88.0    
88.1    
88.3    
88.5    
88.7    
88.9    
89.1    
89.2    
89.4    
89.6    
89.8    
90.0    
90.1    
90.3    
90.5    
90.7    
90.9    
91.1    
91.2    
91.4    
91.6    
91.8    
92.0    
92.2    
92.3    
92.5    
92.7    
92.9    
93.1    
93.2    
93.4    
93.6    
93.8    
94.0    
94.2    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.4    
95.6    
95.8    
96.0    
96.2    
96.4    
96.5    
96.7    
96.9    
97.1    
97.3    
97.4    
97.6    
97.8    
98.0    
98.2    
98.4    
98.5    
98.7    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 44 predictions from path traversal
Error with prediction: snap lend_intergenic: 12543, rend_intergenic: 9191  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22738, rend_intergenic: 13895  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25028, rend_intergenic: 22954  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28624, rend_intergenic: 25369  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35905, rend_intergenic: 31488  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36949, rend_intergenic: 35929  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42540, rend_intergenic: 38558  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44828, rend_intergenic: 42975  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75722, rend_intergenic: 70977  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80384, rend_intergenic: 77509  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93822, rend_intergenic: 81993  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172910, rend_intergenic: 171055  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 96827, rend_intergenic: 96824  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 33 predictions persist after filtering for low support