-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_28/scaffold_28_5799678-6041950

-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_28-snap.1348-T1
Couldn't classify 22802, 22897
Sorry, prediction pasa_asmbl_37605.p1 fails validation.
(TCC)	 CT	22802-22897	GT	AGG
(GCT)	 AG	23115-23218	GT	GAG
(TAT)	 AG	23430-23527	GT	ATG
(TCG)	 AG	23724-23862	GT	AGG
(CCT)	 AG	23955-24247	GT	AGG
(AGA)	 AG	24334-24399	GT	GGG
(CTG)	 AG	24627-24700	AT	AAA
-recovered pasa_asmbl_37605.p1, terminal, 24627, 24700
-recovered pasa_asmbl_37605.p1, internal, 23115, 23218
-recovered pasa_asmbl_37605.p1, internal, 23430, 23527
-recovered pasa_asmbl_37605.p1, internal, 23724, 23862
-recovered pasa_asmbl_37605.p1, internal, 23955, 24247
-recovered pasa_asmbl_37605.p1, internal, 24334, 24399
Valid prediction for GlimmerHMM_glimmerT_58875-T1
Couldn't classify 16120, 16332
Couldn't classify 16779, 16976
Sorry, prediction pasa_asmbl_37853.p1 fails validation.
(TTG)	 AG	16120-16332	GT	TGG
(ATG)	 AG	16454-16606	GT	ACG
(ATC)	 AG	16779-16976	GA	GAG
-recovered pasa_asmbl_37853.p1, initial, 16454, 16606
-recovered pasa_asmbl_37853.p1, internal, 16120, 16332
-recovered pasa_asmbl_37853.p1, internal, 16454, 16606
Valid prediction for GlimmerHMM_glimmerT_58876-T1
Valid prediction for GlimmerHMM_glimmerT_58884-T1
Valid prediction for GlimmerHMM_glimmerT_58861-T1
Valid prediction for HiQ_model.g39021.t1
Valid prediction for GlimmerHMM_glimmerT_58887-T1
Valid prediction for snap_scaffold_28-snap.1324-T1
Valid prediction for snap_scaffold_28-snap.1334-T1
Valid prediction for snap_scaffold_28-snap.1341-T1
Valid prediction for GlimmerHMM_glimmerT_58895-T1
Valid prediction for snap_scaffold_28-snap.1332-T1
Valid prediction for GlimmerHMM_glimmerT_58877-T1
Valid prediction for GlimmerHMM_glimmerT_58892-T1
Couldn't classify 49357, 49498
Sorry, prediction pasa_asmbl_37607.p1 fails validation.
(AAC)	 AG	49357-49498	GT	ACG
(ACA)	 AG	49791-49872	GT	AAG
(CTA)	 AG	49963-50047	GT	CTG
(ACT)	 AG	50161-50247	GT	TGG
(GAC)	 AG	50334-50510	GT	AGG
(GCA)	 AG	50700-50783	GT	AGG
(ATC)	 AG	50918-51055	GT	TGG
(CCC)	 AG	51321-51472	GT	GAG
(CAG)	 AG	52285-52432	GT	AGG
(CTC)	 AG	52568-52718	GT	CAG
(GTT)	 AG	53094-53212	GT	AGG
(TTC)	 AG	53363-53446	AA	AGA
-recovered pasa_asmbl_37607.p1, terminal, 53363, 53446
-recovered pasa_asmbl_37607.p1, internal, 49357, 49498
-recovered pasa_asmbl_37607.p1, internal, 49791, 49872
-recovered pasa_asmbl_37607.p1, internal, 49963, 50047
-recovered pasa_asmbl_37607.p1, internal, 50161, 50247
-recovered pasa_asmbl_37607.p1, internal, 50334, 50510
-recovered pasa_asmbl_37607.p1, internal, 50700, 50783
-recovered pasa_asmbl_37607.p1, internal, 50918, 51055
-recovered pasa_asmbl_37607.p1, internal, 51321, 51472
-recovered pasa_asmbl_37607.p1, internal, 52285, 52432
-recovered pasa_asmbl_37607.p1, internal, 52568, 52718
-recovered pasa_asmbl_37607.p1, internal, 53094, 53212
Valid prediction for Augustus_model.g39042.t1
Valid prediction for GlimmerHMM_glimmerT_58874-T1
Valid prediction for snap_scaffold_28-snap.1314-T1
Valid prediction for Augustus_model.g39020.t1
Valid prediction for Augustus_model.g39034.t1
Valid prediction for HiQ_model.g39029.t1
Valid prediction for CodingQuarry_transcript_43687-T1
Valid prediction for Augustus_model.g39017.t1
Valid prediction for snap_scaffold_28-snap.1320-T1
Valid prediction for Augustus_model.g39030.t1
Valid prediction for HiQ_model.g39033.t1
Couldn't classify 118993, 119082
Sorry, prediction pasa_asmbl_37611.p1 fails validation.
(ATG)	 CC	114659-114665	GT	AGG
(GCG)	 AG	115287-115355	GT	AGG
(CTG)	 AG	115740-115837	GT	AGG
(AGC)	 AG	115934-116099	GT	TGG
(ATA)	 AG	116194-116306	GT	GGG
(GTA)	 AG	116464-116641	GT	TAG
(ACA)	 AG	116740-116904	GT	ATG
(TGT)	 AG	117261-117430	GT	AGG
(GTC)	 AG	118993-119082	AG	ACA
-recovered pasa_asmbl_37611.p1, initial, 114659, 114665
-recovered pasa_asmbl_37611.p1, internal, 115287, 115355
-recovered pasa_asmbl_37611.p1, internal, 115740, 115837
-recovered pasa_asmbl_37611.p1, internal, 115934, 116099
-recovered pasa_asmbl_37611.p1, internal, 116194, 116306
-recovered pasa_asmbl_37611.p1, internal, 116464, 116641
-recovered pasa_asmbl_37611.p1, internal, 116740, 116904
-recovered pasa_asmbl_37611.p1, internal, 117261, 117430
Valid prediction for Augustus_model.g39025.t1
Valid prediction for snap_scaffold_28-snap.1316-T1
Valid prediction for GlimmerHMM_glimmerT_58868-T1
Valid prediction for snap_scaffold_28-snap.1353-T1
Valid prediction for snap_scaffold_28-snap.1333-T1
Valid prediction for GlimmerHMM_glimmerT_58893-T1
Valid prediction for snap_scaffold_28-snap.1327-T1
Valid prediction for Augustus_model.g39035.t1
Valid prediction for snap_scaffold_28-snap.1343-T1
Valid prediction for snap_scaffold_28-snap.1317-T1
Valid prediction for GlimmerHMM_glimmerT_58859-T1
Valid prediction for pasa_asmbl_37614.p1
Valid prediction for snap_scaffold_28-snap.1335-T1
Valid prediction for GlimmerHMM_glimmerT_58865-T1
Valid prediction for GlimmerHMM_glimmerT_58894-T1
Valid prediction for snap_scaffold_28-snap.1326-T1
Valid prediction for GlimmerHMM_glimmerT_58872-T1
Valid prediction for snap_scaffold_28-snap.1319-T1
Valid prediction for HiQ_model.g39038.t1
Valid prediction for GlimmerHMM_glimmerT_58866-T1
Valid prediction for GlimmerHMM_glimmerT_58881-T1
Valid prediction for Augustus_model.g39026.t1
Valid prediction for snap_scaffold_28-snap.1318-T1
Valid prediction for snap_scaffold_28-snap.1352-T1
Valid prediction for snap_scaffold_28-snap.1331-T1
Valid prediction for GlimmerHMM_glimmerT_58883-T1
Valid prediction for snap_scaffold_28-snap.1344-T1
Valid prediction for Augustus_model.g39028.t1
Valid prediction for GlimmerHMM_glimmerT_58870-T1
Valid prediction for GlimmerHMM_glimmerT_58862-T1
Valid prediction for pasa_asmbl_37616.p1
Couldn't classify 45647, 45689
Couldn't classify 47938, 48027
Sorry, prediction pasa_asmbl_37606.p1 fails validation.
(AAG)	 GG	45647-45689	GT	TGG
(GGC)	 AG	45953-46107	GT	AAG
(TTT)	 AG	46278-46363	GT	ACG
(GCT)	 AG	46657-46813	GT	TTG
(AAC)	 AG	47008-47048	GT	CGG
(ATA)	 AG	47166-47256	GT	AGG
(TGG)	 AG	47427-47546	GT	AAG
(ATG)	 AG	47938-48027	GT	TGG
-recovered pasa_asmbl_37606.p1, initial, 47938, 48027
-recovered pasa_asmbl_37606.p1, internal, 45953, 46107
-recovered pasa_asmbl_37606.p1, internal, 46278, 46363
-recovered pasa_asmbl_37606.p1, internal, 46657, 46813
-recovered pasa_asmbl_37606.p1, internal, 47008, 47048
-recovered pasa_asmbl_37606.p1, internal, 47166, 47256
-recovered pasa_asmbl_37606.p1, internal, 47427, 47546
-recovered pasa_asmbl_37606.p1, internal, 47938, 48027
Valid prediction for GlimmerHMM_glimmerT_58860-T1
Valid prediction for Augustus_model.g39019.t1
Valid prediction for GlimmerHMM_glimmerT_58878-T1
Valid prediction for Augustus_model.g39018.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_28-snap.1339-T1
Valid prediction for GlimmerHMM_glimmerT_58889-T1
Valid prediction for snap_scaffold_28-snap.1354-T1
Valid prediction for Augustus_model.g39022.t1
Valid prediction for Augustus_model.g39027.t1
Valid prediction for GlimmerHMM_glimmerT_58880-T1
Valid prediction for snap_scaffold_28-snap.1350-T1
Valid prediction for Augustus_model.g39032.t1
Valid prediction for GlimmerHMM_glimmerT_58879-T1
Valid prediction for snap_scaffold_28-snap.1340-T1
Valid prediction for snap_scaffold_28-snap.1351-T1
Couldn't classify 41389, 41463
Couldn't classify 42063, 42134
Sorry, prediction pasa_asmbl_38331.p1 fails validation.
(CCG)	 AG	41389-41463	GT	AGG
(GAG)	 AG	41592-41672	GT	AGG
(ATT)	 AG	41885-41968	GT	AGG
(AGC)	 AG	42063-42134	AC	AGA
-recovered pasa_asmbl_38331.p1, internal, 41389, 41463
-recovered pasa_asmbl_38331.p1, internal, 41592, 41672
-recovered pasa_asmbl_38331.p1, internal, 41885, 41968
Valid prediction for pasa_asmbl_38327.p1
Valid prediction for snap_scaffold_28-snap.1325-T1
Valid prediction for Augustus_model.g39023.t1
Valid prediction for snap_scaffold_28-snap.1329-T1
Valid prediction for snap_scaffold_28-snap.1321-T1
Valid prediction for snap_scaffold_28-snap.1313-T1
Valid prediction for HiQ_model.g39037.t1
Valid prediction for snap_scaffold_28-snap.1347-T1
Valid prediction for Augustus_model.g39031.t1
Valid prediction for Augustus_model.g39039.t1
Valid prediction for snap_scaffold_28-snap.1315-T1
Valid prediction for snap_scaffold_28-snap.1330-T1
Valid prediction for GlimmerHMM_glimmerT_58867-T1
Valid prediction for Augustus_model.g39036.t1
Valid prediction for GlimmerHMM_glimmerT_58873-T1
Valid prediction for pasa_asmbl_38329.p1
Valid prediction for snap_scaffold_28-snap.1338-T1
Valid prediction for GlimmerHMM_glimmerT_58871-T1
Valid prediction for CodingQuarry_transcript_43685-T1
Valid prediction for GlimmerHMM_glimmerT_58890-T1
Valid prediction for GlimmerHMM_glimmerT_58857-T1
Valid prediction for GlimmerHMM_glimmerT_58886-T1
Valid prediction for snap_scaffold_28-snap.1337-T1
Valid prediction for GlimmerHMM_glimmerT_58896-T1
Valid prediction for GlimmerHMM_glimmerT_58888-T1
Valid prediction for GlimmerHMM_glimmerT_58882-T1
Valid prediction for snap_scaffold_28-snap.1328-T1
Valid prediction for snap_scaffold_28-snap.1349-T1
Valid prediction for snap_scaffold_28-snap.1346-T1
Couldn't classify 38062, 38202
Sorry, prediction pasa_asmbl_38332.p1 fails validation.
(ATG)	 CC	35395-35439	GT	CGG
(AAC)	 AG	35750-35913	GT	AAG
(GCG)	 AG	36015-36186	GT	AGG
(CCT)	 AG	36326-36518	GT	GGG
(ATG)	 AG	36770-36825	GT	AGG
(GAG)	 AG	36907-37005	GT	ACG
(CTG)	 AG	37155-37307	GT	AGG
(ACG)	 AG	37440-37539	GT	GAG
(TCC)	 AG	37658-37794	GT	GGG
(GAG)	 AG	37895-37975	GT	AGG
(TCC)	 AG	38062-38202	GC	CCG
-recovered pasa_asmbl_38332.p1, initial, 35395, 35439
add_exon() Sorry, pasa_asmbl_38332.p1 36770-36825-initial-1 is invalid.
-recovered pasa_asmbl_38332.p1, initial, 36770, 36825
-recovered pasa_asmbl_38332.p1, terminal, 37440, 37539
-recovered pasa_asmbl_38332.p1, internal, 35750, 35913
-recovered pasa_asmbl_38332.p1, internal, 36015, 36186
-recovered pasa_asmbl_38332.p1, internal, 36326, 36518
-recovered pasa_asmbl_38332.p1, internal, 36770, 36825
-recovered pasa_asmbl_38332.p1, internal, 36907, 37005
-recovered pasa_asmbl_38332.p1, internal, 37155, 37307
-recovered pasa_asmbl_38332.p1, internal, 37440, 37539
-recovered pasa_asmbl_38332.p1, internal, 37658, 37794
-recovered pasa_asmbl_38332.p1, internal, 37895, 37975
-recovered pasa_asmbl_38332.p1, internal, 38062, 38202
Valid prediction for snap_scaffold_28-snap.1322-T1
Valid prediction for CodingQuarry_transcript_43686-T1
Valid prediction for Augustus_model.g39043.t1
Valid prediction for GlimmerHMM_glimmerT_58891-T1
Valid prediction for Augustus_model.g39024.t1
Valid prediction for GlimmerHMM_glimmerT_58858-T1
Valid prediction for GlimmerHMM_glimmerT_58863-T1
Valid prediction for snap_scaffold_28-snap.1323-T1
Valid prediction for snap_scaffold_28-snap.1345-T1
Couldn't classify 42063, 42169
Sorry, prediction pasa_asmbl_38330.p1 fails validation.
(AGC)	 AG	42063-42169	GT	ATG
(GTG)	 AG	42278-42396	GT	TGG
(GTG)	 AG	42553-42707	GT	AGG
(GTG)	 AG	42820-43009	GT	GTG
(CCT)	 AG	43183-43356	GT	GGG
(TGT)	 AG	43560-43720	GT	AGG
(GTG)	 AG	43928-44155	GT	GGG
(CCG)	 AG	44267-44458	GT	AGG
(GGC)	 AG	44619-44797	GT	AGG
(GTT)	 AG	44901-45052	GT	TGG
(GTG)	 AG	45165-45273	GT	GCG
(GTA)	 AG	45403-45511	GT	AGG
(GAT)	 AG	45703-45892	GT	GGG
(GCA)	 AG	46120-46284	GT	CGG
(AGT)	 AG	46420-46541	GT	AGG
(CTG)	 AG	46635-46778	GT	AGG
(GCG)	 AG	46884-47060	GT	AGG
(GGT)	 AG	47192-47352	GT	AGG
(TGG)	 AG	47476-47557	GT	AGG
(AAA)	 AG	47694-47786	GT	AGG
(GTG)	 AG	47899-48048	GG	GAG
-recovered pasa_asmbl_38330.p1, terminal, 47899, 48048
-recovered pasa_asmbl_38330.p1, internal, 42063, 42169
-recovered pasa_asmbl_38330.p1, internal, 42278, 42396
-recovered pasa_asmbl_38330.p1, internal, 42553, 42707
-recovered pasa_asmbl_38330.p1, internal, 42820, 43009
-recovered pasa_asmbl_38330.p1, internal, 43183, 43356
-recovered pasa_asmbl_38330.p1, internal, 43560, 43720
-recovered pasa_asmbl_38330.p1, internal, 43928, 44155
-recovered pasa_asmbl_38330.p1, internal, 44267, 44458
-recovered pasa_asmbl_38330.p1, internal, 44619, 44797
-recovered pasa_asmbl_38330.p1, internal, 44901, 45052
-recovered pasa_asmbl_38330.p1, internal, 45165, 45273
-recovered pasa_asmbl_38330.p1, internal, 45403, 45511
-recovered pasa_asmbl_38330.p1, internal, 45703, 45892
-recovered pasa_asmbl_38330.p1, internal, 46120, 46284
-recovered pasa_asmbl_38330.p1, internal, 46420, 46541
-recovered pasa_asmbl_38330.p1, internal, 46635, 46778
-recovered pasa_asmbl_38330.p1, internal, 46884, 47060
-recovered pasa_asmbl_38330.p1, internal, 47192, 47352
-recovered pasa_asmbl_38330.p1, internal, 47476, 47557
-recovered pasa_asmbl_38330.p1, internal, 47694, 47786
Valid prediction for GlimmerHMM_glimmerT_58885-T1
Valid prediction for snap_scaffold_28-snap.1336-T1
Valid prediction for Augustus_model.g39041.t1
Valid prediction for Augustus_model.g39040.t1
Valid prediction for snap_scaffold_28-snap.1342-T1
Valid prediction for Augustus_model.g39016.t1
Valid prediction for GlimmerHMM_glimmerT_58869-T1
Valid prediction for GlimmerHMM_glimmerT_58864-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 18306, rend_intergenic: 15254  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22084, rend_intergenic: 18343  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163182, rend_intergenic: 161442  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166560, rend_intergenic: 163882  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176198, rend_intergenic: 166720  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 242273
-exon list size: 623


building trellis

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51.7    
51.8    
52.0    
52.2    
52.3    
52.5    
52.6    
52.8    
53.0    
53.1    
53.3    
53.4    
53.6    
53.8    
53.9    
54.1    
54.2    
54.4    
54.6    
54.7    
54.9    
55.0    
55.2    
55.4    
55.5    
55.7    
55.8    
56.0    
56.2    
56.3    
56.5    
56.6    
56.8    
57.0    
57.1    
57.3    
57.4    
57.6    
57.8    
57.9    
58.1    
58.2    
58.4    
58.6    
58.7    
58.9    
59.0    
59.2    
59.4    
59.5    
59.7    
59.8    
60.0    
60.2    
60.3    
60.5    
60.6    
60.8    
61.0    
61.1    
61.3    
61.4    
61.6    
61.8    
61.9    
62.1    
62.2    
62.4    
62.6    
62.7    
62.9    
63.0    
63.2    
63.4    
63.5    
63.7    
63.8    
64.0    
64.2    
64.3    
64.5    
64.6    
64.8    
65.0    
65.1    
65.3    
65.4    
65.6    
65.8    
65.9    
66.1    
66.2    
66.4    
66.6    
66.7    
66.9    
67.0    
67.2    
67.4    
67.5    
67.7    
67.8    
68.0    
68.2    
68.3    
68.5    
68.6    
68.8    
69.0    
69.1    
69.3    
69.4    
69.6    
69.8    
69.9    
70.1    
70.2    
70.4    
70.6    
70.7    
70.9    
71.0    
71.2    
71.4    
71.5    
71.7    
71.8    
72.0    
72.2    
72.3    
72.5    
72.6    
72.8    
73.0    
73.1    
73.3    
73.4    
73.6    
73.8    
73.9    
74.1    
74.2    
74.4    
74.6    
74.7    
74.9    
75.0    
75.2    
75.4    
75.5    
75.7    
75.8    
76.0    
76.2    
76.3    
76.5    
76.6    
76.8    
77.0    
77.1    
77.3    
77.4    
77.6    
77.8    
77.9    
78.1    
78.2    
78.4    
78.6    
78.7    
78.9    
79.0    
79.2    
79.4    
79.5    
79.7    
79.8    
80.0    
80.2    
80.3    
80.5    
80.6    
80.8    
81.0    
81.1    
81.3    
81.4    
81.6    
81.8    
81.9    
82.1    
82.2    
82.4    
82.6    
82.7    
82.9    
83.0    
83.2    
83.4    
83.5    
83.7    
83.8    
84.0    
84.2    
84.3    
84.5    
84.6    
84.8    
85.0    
85.1    
85.3    
85.4    
85.6    
85.8    
85.9    
86.1    
86.2    
86.4    
86.6    
86.7    
86.9    
87.0    
87.2    
87.4    
87.5    
87.7    
87.8    
88.0    
88.2    
88.3    
88.5    
88.6    
88.8    
89.0    
89.1    
89.3    
89.4    
89.6    
89.8    
89.9    
90.1    
90.2    
90.4    
90.6    
90.7    
90.9    
91.0    
91.2    
91.4    
91.5    
91.7    
91.8    
92.0    
92.2    
92.3    
92.5    
92.6    
92.8    
93.0    
93.1    
93.3    
93.4    
93.6    
93.8    
93.9    
94.1    
94.2    
94.4    
94.6    
94.7    
94.9    
95.0    
95.2    
95.4    
95.5    
95.7    
95.8    
96.0    
96.2    
96.3    
96.5    
96.6    
96.8    
97.0    
97.1    
97.3    
97.4    
97.6    
97.8    
97.9    
98.1    
98.2    
98.4    
98.6    
98.7    
98.9    
99.0    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 38 predictions from path traversal
Error with prediction: snap lend_intergenic: 18306, rend_intergenic: 15254  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22084, rend_intergenic: 18343  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163182, rend_intergenic: 161442  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166560, rend_intergenic: 163882  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176198, rend_intergenic: 166720  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 36 predictions persist after filtering for low support