-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_17/scaffold_17_6294644-6639150

-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_17-snap.1286-T1
Valid prediction for Augustus_model.g26942.t1
Valid prediction for snap_scaffold_17-snap.1294-T1
Valid prediction for snap_scaffold_17-snap.1308-T1
Valid prediction for GlimmerHMM_glimmerT_40426-T1
Valid prediction for snap_scaffold_17-snap.1280-T1
Valid prediction for Augustus_model.g26934.t1
Valid prediction for snap_scaffold_17-snap.1281-T1
Valid prediction for CodingQuarry_transcript_22000-T1
Valid prediction for GlimmerHMM_glimmerT_40420-T1
Couldn't classify 316749, 316891
Couldn't classify 319957, 320122
Sorry, prediction pasa_asmbl_18861.p1 fails validation.
(GGC)	 CA	316749-316891	GT	CGG
(GAG)	 AG	317060-317293	GT	AGG
(GGG)	 AG	319957-320122	GG	TGG
-recovered pasa_asmbl_18861.p1, internal, 317060, 317293
Valid prediction for Augustus_model.g26947.t1
Valid prediction for snap_scaffold_17-snap.1301-T1
Valid prediction for Augustus_model.g26950.t1
Valid prediction for snap_scaffold_17-snap.1287-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_40419-T1
Valid prediction for snap_scaffold_17-snap.1295-T1
Valid prediction for GlimmerHMM_glimmerT_40418-T1
Valid prediction for snap_scaffold_17-snap.1306-T1
Valid prediction for GlimmerHMM_glimmerT_40438-T1
Valid prediction for HiQ_model.g26937.t1
Valid prediction for GlimmerHMM_glimmerT_40421-T1
Valid prediction for GlimmerHMM_glimmerT_40444-T1
Valid prediction for CodingQuarry_transcript_22001-T1
Valid prediction for GlimmerHMM_glimmerT_40446-T1
Valid prediction for snap_scaffold_17-snap.1316-T1
Couldn't classify 293724, 293813
Couldn't classify 295065, 295200
Sorry, prediction pasa_asmbl_18856.p1 fails validation.
(AGC)	 GG	293724-293813	GT	AGG
(CCA)	 AG	293929-294096	GT	TGG
(ATC)	 AG	294206-294347	GT	AGG
(TGA)	 AG	294440-294618	GT	CGG
(CAA)	 AG	294805-294950	GT	GGG
(GAA)	 AG	295065-295200	CC	AGC
-recovered pasa_asmbl_18856.p1, internal, 293929, 294096
-recovered pasa_asmbl_18856.p1, internal, 294206, 294347
-recovered pasa_asmbl_18856.p1, internal, 294440, 294618
-recovered pasa_asmbl_18856.p1, internal, 294805, 294950
Valid prediction for snap_scaffold_17-snap.1307-T1
Valid prediction for GlimmerHMM_glimmerT_40440-T1
Valid prediction for GlimmerHMM_glimmerT_40413-T1
Valid prediction for snap_scaffold_17-snap.1305-T1
Valid prediction for snap_scaffold_17-snap.1278-T1
Valid prediction for GlimmerHMM_glimmerT_40428-T1
Valid prediction for snap_scaffold_17-snap.1312-T1
Valid prediction for snap_scaffold_17-snap.1311-T1
Valid prediction for Augustus_model.g26933.t1
Valid prediction for snap_scaffold_17-snap.1315-T1
Valid prediction for snap_scaffold_17-snap.1302-T1
Valid prediction for HiQ_model.g26938.t1
Valid prediction for Augustus_model.g26935.t1
Valid prediction for snap_scaffold_17-snap.1292-T1
Valid prediction for snap_scaffold_17-snap.1298-T1
Valid prediction for snap_scaffold_17-snap.1285-T1
Valid prediction for Augustus_model.g26945.t1
Valid prediction for GlimmerHMM_glimmerT_40427-T1
Valid prediction for pasa_asmbl_18855.p1
Valid prediction for GlimmerHMM_glimmerT_40449-T1
Valid prediction for snap_scaffold_17-snap.1275-T1
Valid prediction for snap_scaffold_17-snap.1284-T1
Valid prediction for Augustus_model.g26930.t1
Valid prediction for GlimmerHMM_glimmerT_40441-T1
Valid prediction for Augustus_model.g26932.t1
Valid prediction for snap_scaffold_17-snap.1288-T1
Valid prediction for GlimmerHMM_glimmerT_40433-T1
Valid prediction for Augustus_model.g26936.t1
Valid prediction for GlimmerHMM_glimmerT_40415-T1
Valid prediction for Augustus_model.g26949.t1
Valid prediction for Augustus_model.g26941.t1
Valid prediction for GlimmerHMM_glimmerT_40417-T1
Couldn't classify 308709, 308792
Couldn't classify 312116, 313173
Sorry, prediction pasa_asmbl_18860.p1 fails validation.
(AAC)	 GG	308709-308792	GT	AGG
(GGG)	 AG	309001-309151	GT	AGG
(GTT)	 AG	310218-310308	GT	AGG
(GAA)	 AG	311110-311276	GT	AGG
(GTG)	 AG	312116-313173	GG	CTG
add_exon() Sorry, pasa_asmbl_18860.p1 310218-310308-terminal-3 is invalid.
-recovered pasa_asmbl_18860.p1, terminal, 310218, 310308
-recovered pasa_asmbl_18860.p1, internal, 309001, 309151
-recovered pasa_asmbl_18860.p1, internal, 310218, 310308
-recovered pasa_asmbl_18860.p1, internal, 311110, 311276
Valid prediction for Augustus_model.g26943.t1
Couldn't classify 74975, 75087
Sorry, prediction pasa_asmbl_18848.p1 fails validation.
(GGA)	 TA	74975-75087	GT	GAG
(AGA)	 AG	75256-75379	GT	AGG
(GTG)	 AG	75522-75797	GT	ACG
(TTT)	 AG	75936-76016	GT	CTG
(GGT)	 AG	78741-78794	GT	AGG
(GGA)	 AG	78879-78932	GT	AAG
(GGT)	 AG	79027-79080	GT	AGG
(GGA)	 AG	79941-79994	GT	CTG
(GGG)	 AG	80094-80138	GT	GGG
(GGA)	 AG	81220-81273	GT	ATG
(GGT)	 AG	81374-81427	GT	AGG
(GGA)	 AG	81799-81834	GT	TGG
(GTT)	 AG	81939-81968	GT	CTG
(GGG)	 AG	82184-82237	GT	CAG
(GGT)	 AG	82374-82427	GT	GGG
(GGA)	 AG	83614-83667	GT	CTG
(GGT)	 AG	84206-84259	GT	CTG
(GGT)	 AG	84352-84405	GT	CCG
(GGT)	 AG	84515-84568	GT	AGG
(GGC)	 AG	84788-84841	GT	AGG
(GGT)	 AG	84963-85007	GT	GGG
(GGA)	 AG	85117-85179	GT	AGG
(GGT)	 AG	85329-85382	GT	AGG
(GGT)	 AG	85538-85579	GT	ACG
(GTT)	 AG	85733-85765	GT	CAG
(GGT)	 AG	85967-86020	GT	TGG
(GGT)	 AG	86356-86409	GT	AGG
(GGT)	 AG	86553-86606	GT	CGG
(GGT)	 AG	86690-86743	GT	TGG
(GGA)	 AG	86862-86915	GT	GGG
(GGG)	 AG	87300-87404	GT	ATG
(GGG)	 AG	88048-88092	GT	AGG
(GGT)	 AG	88775-88852	GT	AGG
(GGA)	 AG	89006-89041	GT	AGG
(GGC)	 AG	89130-89183	GT	ATG
(GGT)	 AG	89412-89456	GT	CAG
(GGG)	 AG	89610-89645	GT	AGG
(GAT)	 AG	89748-89861	GT	AAG
(GGC)	 AG	90153-90206	GT	AGG
(GGT)	 AG	90363-90416	GT	AGG
(GGA)	 AG	90538-90591	GT	CTG
(GGT)	 AG	90684-90737	GT	AGG
(GGC)	 AG	90919-90972	GT	TGG
(GGA)	 AG	91071-91124	GT	ATG
(GGC)	 AG	91237-91290	GT	CCG
(GGC)	 AG	91377-91421	GT	AGG
(GGT)	 AG	91935-91988	GT	ACG
(GGT)	 AG	92080-92133	GT	CGG
(GGT)	 AG	92322-92375	GT	CGG
(GGT)	 AG	92753-92824	GT	CGG
(GGT)	 AG	93010-93045	GT	AGG
(GGG)	 AG	93131-93175	GT	GAG
(GGT)	 AG	93429-93608	GT	GAG
(GGA)	 AG	93895-93961	GT	TGG
(CCA)	 AG	94060-94242	GT	AGG
(GTG)	 AG	94378-94455	GT	AGG
(GCC)	 AG	94577-94770	AA	AAA
-recovered pasa_asmbl_18848.p1, terminal, 94378, 94455
-recovered pasa_asmbl_18848.p1, terminal, 94577, 94770
-recovered pasa_asmbl_18848.p1, internal, 75256, 75379
-recovered pasa_asmbl_18848.p1, internal, 75522, 75797
-recovered pasa_asmbl_18848.p1, internal, 75936, 76016
-recovered pasa_asmbl_18848.p1, internal, 78741, 78794
-recovered pasa_asmbl_18848.p1, internal, 78879, 78932
-recovered pasa_asmbl_18848.p1, internal, 79027, 79080
-recovered pasa_asmbl_18848.p1, internal, 79941, 79994
-recovered pasa_asmbl_18848.p1, internal, 80094, 80138
-recovered pasa_asmbl_18848.p1, internal, 81220, 81273
-recovered pasa_asmbl_18848.p1, internal, 81374, 81427
-recovered pasa_asmbl_18848.p1, internal, 81799, 81834
-recovered pasa_asmbl_18848.p1, internal, 81939, 81968
-recovered pasa_asmbl_18848.p1, internal, 82184, 82237
-recovered pasa_asmbl_18848.p1, internal, 82374, 82427
-recovered pasa_asmbl_18848.p1, internal, 83614, 83667
-recovered pasa_asmbl_18848.p1, internal, 84206, 84259
-recovered pasa_asmbl_18848.p1, internal, 84352, 84405
-recovered pasa_asmbl_18848.p1, internal, 84515, 84568
-recovered pasa_asmbl_18848.p1, internal, 84788, 84841
-recovered pasa_asmbl_18848.p1, internal, 84963, 85007
-recovered pasa_asmbl_18848.p1, internal, 85117, 85179
-recovered pasa_asmbl_18848.p1, internal, 85329, 85382
-recovered pasa_asmbl_18848.p1, internal, 85538, 85579
-recovered pasa_asmbl_18848.p1, internal, 85733, 85765
-recovered pasa_asmbl_18848.p1, internal, 85967, 86020
-recovered pasa_asmbl_18848.p1, internal, 86356, 86409
-recovered pasa_asmbl_18848.p1, internal, 86553, 86606
-recovered pasa_asmbl_18848.p1, internal, 86690, 86743
-recovered pasa_asmbl_18848.p1, internal, 86862, 86915
-recovered pasa_asmbl_18848.p1, internal, 87300, 87404
-recovered pasa_asmbl_18848.p1, internal, 88048, 88092
-recovered pasa_asmbl_18848.p1, internal, 88775, 88852
-recovered pasa_asmbl_18848.p1, internal, 89006, 89041
-recovered pasa_asmbl_18848.p1, internal, 89130, 89183
-recovered pasa_asmbl_18848.p1, internal, 89412, 89456
-recovered pasa_asmbl_18848.p1, internal, 89610, 89645
-recovered pasa_asmbl_18848.p1, internal, 89748, 89861
-recovered pasa_asmbl_18848.p1, internal, 90153, 90206
-recovered pasa_asmbl_18848.p1, internal, 90363, 90416
-recovered pasa_asmbl_18848.p1, internal, 90538, 90591
-recovered pasa_asmbl_18848.p1, internal, 90684, 90737
-recovered pasa_asmbl_18848.p1, internal, 90919, 90972
-recovered pasa_asmbl_18848.p1, internal, 91071, 91124
-recovered pasa_asmbl_18848.p1, internal, 91237, 91290
-recovered pasa_asmbl_18848.p1, internal, 91377, 91421
-recovered pasa_asmbl_18848.p1, internal, 91935, 91988
-recovered pasa_asmbl_18848.p1, internal, 92080, 92133
-recovered pasa_asmbl_18848.p1, internal, 92322, 92375
-recovered pasa_asmbl_18848.p1, internal, 92753, 92824
-recovered pasa_asmbl_18848.p1, internal, 93010, 93045
-recovered pasa_asmbl_18848.p1, internal, 93131, 93175
-recovered pasa_asmbl_18848.p1, internal, 93429, 93608
-recovered pasa_asmbl_18848.p1, internal, 93895, 93961
-recovered pasa_asmbl_18848.p1, internal, 94060, 94242
-recovered pasa_asmbl_18848.p1, internal, 94378, 94455
Valid prediction for GlimmerHMM_glimmerT_40439-T1
Valid prediction for GlimmerHMM_glimmerT_40448-T1
Valid prediction for snap_scaffold_17-snap.1313-T1
Couldn't classify 67579, 68060
Sorry, prediction pasa_asmbl_18847.p1 fails validation.
(ATG)	 AG	67382-67472	GT	AGG
(GGT)	 AG	67579-68060	CC	AGC
-recovered pasa_asmbl_18847.p1, initial, 67382, 67472
-recovered pasa_asmbl_18847.p1, internal, 67382, 67472
Valid prediction for GlimmerHMM_glimmerT_40422-T1
Valid prediction for GlimmerHMM_glimmerT_40430-T1
Valid prediction for snap_scaffold_17-snap.1293-T1
Couldn't classify 296350, 296460
Sorry, prediction pasa_asmbl_18857.p1 fails validation.
(CTG)	 AG	296350-296460	GT	AGG
(GTC)	 AG	296766-296856	GT	AGG
(ATG)	 AG	297070-297154	GT	CGG
(GAT)	 AG	297478-297619	GT	GAG
(ATC)	 AG	297712-297864	GT	AGG
(ATC)	 AG	298009-298185	GT	GGG
(GAT)	 AG	298381-298447	GT	GGG
(TGT)	 AG	298562-298609	GT	AGG
(CCA)	 AG	298719-298874	GT	TGG
(CTA)	 AG	299021-299150	GT	AGG
(GAT)	 AG	299322-299460	GT	TAG
(ATC)	 AG	299563-299610	GA	GAG
-recovered pasa_asmbl_18857.p1, initial, 297070, 297154
-recovered pasa_asmbl_18857.p1, terminal, 299563, 299610
-recovered pasa_asmbl_18857.p1, internal, 296350, 296460
-recovered pasa_asmbl_18857.p1, internal, 296766, 296856
-recovered pasa_asmbl_18857.p1, internal, 297070, 297154
-recovered pasa_asmbl_18857.p1, internal, 297478, 297619
-recovered pasa_asmbl_18857.p1, internal, 297712, 297864
-recovered pasa_asmbl_18857.p1, internal, 298009, 298185
-recovered pasa_asmbl_18857.p1, internal, 298381, 298447
-recovered pasa_asmbl_18857.p1, internal, 298562, 298609
-recovered pasa_asmbl_18857.p1, internal, 298719, 298874
-recovered pasa_asmbl_18857.p1, internal, 299021, 299150
-recovered pasa_asmbl_18857.p1, internal, 299322, 299460
Valid prediction for snap_scaffold_17-snap.1282-T1
Couldn't classify 35855, 36103
Sorry, prediction pasa_asmbl_18846.p1 fails validation.
(TGC)	 CC	35855-36103	GT	CGG
(GTG)	 AG	37170-37349	TG	AGT
-recovered pasa_asmbl_18846.p1, terminal, 37170, 37349
Valid prediction for snap_scaffold_17-snap.1314-T1
Valid prediction for snap_scaffold_17-snap.1283-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_40423-T1
Valid prediction for snap_scaffold_17-snap.1289-T1
Valid prediction for GlimmerHMM_glimmerT_40437-T1
Valid prediction for snap_scaffold_17-snap.1279-T1
Valid prediction for GlimmerHMM_glimmerT_40429-T1
Valid prediction for snap_scaffold_17-snap.1296-T1
Valid prediction for Augustus_model.g26948.t1
Valid prediction for snap_scaffold_17-snap.1304-T1
Valid prediction for Augustus_model.g26946.t1
Valid prediction for GlimmerHMM_glimmerT_40414-T1
Valid prediction for snap_scaffold_17-snap.1299-T1
Valid prediction for snap_scaffold_17-snap.1300-T1
Valid prediction for GlimmerHMM_glimmerT_40443-T1
Valid prediction for Augustus_model.g26940.t1
Valid prediction for snap_scaffold_17-snap.1274-T1
Valid prediction for snap_scaffold_17-snap.1303-T1
Valid prediction for snap_scaffold_17-snap.1297-T1
Valid prediction for GlimmerHMM_glimmerT_40425-T1
Valid prediction for GlimmerHMM_glimmerT_40416-T1
Valid prediction for GlimmerHMM_glimmerT_40431-T1
Valid prediction for GlimmerHMM_glimmerT_40434-T1
Valid prediction for snap_scaffold_17-snap.1310-T1
Valid prediction for Augustus_model.g26939.t1
Valid prediction for GlimmerHMM_glimmerT_40442-T1
Valid prediction for snap_scaffold_17-snap.1309-T1
Valid prediction for GlimmerHMM_glimmerT_40412-T1
Valid prediction for GlimmerHMM_glimmerT_40436-T1
Valid prediction for snap_scaffold_17-snap.1276-T1
Valid prediction for GlimmerHMM_glimmerT_40435-T1
Valid prediction for GlimmerHMM_glimmerT_40424-T1
Valid prediction for snap_scaffold_17-snap.1290-T1
Valid prediction for Augustus_model.g26944.t1
Valid prediction for snap_scaffold_17-snap.1277-T1
Valid prediction for snap_scaffold_17-snap.1291-T1
Valid prediction for GlimmerHMM_glimmerT_40445-T1
Valid prediction for pasa_asmbl_17977.p1
Valid prediction for Augustus_model.g26931.t1
Valid prediction for GlimmerHMM_glimmerT_40432-T1
Valid prediction for GlimmerHMM_glimmerT_40447-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 19260, rend_intergenic: 12932  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30688, rend_intergenic: 27639  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37720, rend_intergenic: 31115  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 299610, rend_intergenic: 293712  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 344507
-exon list size: 564


building trellis

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48.1    
48.2    
48.4    
48.6    
48.8    
48.9    
49.1    
49.3    
49.5    
49.6    
49.8    
50.0    
50.2    
50.4    
50.5    
50.7    
50.9    
51.1    
51.2    
51.4    
51.6    
51.8    
51.9    
52.1    
52.3    
52.5    
52.7    
52.8    
53.0    
53.2    
53.4    
53.5    
53.7    
53.9    
54.1    
54.2    
54.4    
54.6    
54.8    
54.9    
55.1    
55.3    
55.5    
55.7    
55.8    
56.0    
56.2    
56.4    
56.5    
56.7    
56.9    
57.1    
57.2    
57.4    
57.6    
57.8    
58.0    
58.1    
58.3    
58.5    
58.7    
58.8    
59.0    
59.2    
59.4    
59.5    
59.7    
59.9    
60.1    
60.2    
60.4    
60.6    
60.8    
61.0    
61.1    
61.3    
61.5    
61.7    
61.8    
62.0    
62.2    
62.4    
62.5    
62.7    
62.9    
63.1    
63.3    
63.4    
63.6    
63.8    
64.0    
64.1    
64.3    
64.5    
64.7    
64.8    
65.0    
65.2    
65.4    
65.5    
65.7    
65.9    
66.1    
66.3    
66.4    
66.6    
66.8    
67.0    
67.1    
67.3    
67.5    
67.7    
67.8    
68.0    
68.2    
68.4    
68.6    
68.7    
68.9    
69.1    
69.3    
69.4    
69.6    
69.8    
70.0    
70.1    
70.3    
70.5    
70.7    
70.8    
71.0    
71.2    
71.4    
71.6    
71.7    
71.9    
72.1    
72.3    
72.4    
72.6    
72.8    
73.0    
73.1    
73.3    
73.5    
73.7    
73.9    
74.0    
74.2    
74.4    
74.6    
74.7    
74.9    
75.1    
75.3    
75.4    
75.6    
75.8    
76.0    
76.1    
76.3    
76.5    
76.7    
76.9    
77.0    
77.2    
77.4    
77.6    
77.7    
77.9    
78.1    
78.3    
78.4    
78.6    
78.8    
79.0    
79.2    
79.3    
79.5    
79.7    
79.9    
80.0    
80.2    
80.4    
80.6    
80.7    
80.9    
81.1    
81.3    
81.4    
81.6    
81.8    
82.0    
82.2    
82.3    
82.5    
82.7    
82.9    
83.0    
83.2    
83.4    
83.6    
83.7    
83.9    
84.1    
84.3    
84.5    
84.6    
84.8    
85.0    
85.2    
85.3    
85.5    
85.7    
85.9    
86.0    
86.2    
86.4    
86.6    
86.7    
86.9    
87.1    
87.3    
87.5    
87.6    
87.8    
88.0    
88.2    
88.3    
88.5    
88.7    
88.9    
89.0    
89.2    
89.4    
89.6    
89.8    
89.9    
90.1    
90.3    
90.5    
90.6    
90.8    
91.0    
91.2    
91.3    
91.5    
91.7    
91.9    
92.0    
92.2    
92.4    
92.6    
92.8    
92.9    
93.1    
93.3    
93.5    
93.6    
93.8    
94.0    
94.2    
94.3    
94.5    
94.7    
94.9    
95.1    
95.2    
95.4    
95.6    
95.8    
95.9    
96.1    
96.3    
96.5    
96.6    
96.8    
97.0    
97.2    
97.3    
97.5    
97.7    
97.9    
98.1    
98.2    
98.4    
98.6    
98.8    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 19260, rend_intergenic: 12932  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30688, rend_intergenic: 27639  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37720, rend_intergenic: 31115  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 299610, rend_intergenic: 293712  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 27 predictions persist after filtering for low support