-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_4/scaffold_4_14056321-14440770

-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 29464, 30079
Sorry, prediction pasa_asmbl_41838.p1 fails validation.
(AGT)	 TT	29464-30079	GT	AGG
(GTA)	 AG	30434-30684	GT	GGG
(GAG)	 AG	30800-30916	AC	GAA
-recovered pasa_asmbl_41838.p1, terminal, 30800, 30916
-recovered pasa_asmbl_41838.p1, internal, 30434, 30684
Couldn't classify 238841, 239578
Sorry, prediction pasa_asmbl_41859.p1 fails validation.
(TCA)	 CC	238841-239578	GT	AGG
(GGA)	 AG	239772-239956	GT	CTG
(GGG)	 AG	240080-240184	GT	AGG
(CTC)	 AG	240497-240635	GT	AGG
(CTG)	 AG	240791-240904	GT	AGG
(CCT)	 AG	241241-241861	GA	GAG
-recovered pasa_asmbl_41859.p1, terminal, 241241, 241861
-recovered pasa_asmbl_41859.p1, internal, 239772, 239956
-recovered pasa_asmbl_41859.p1, internal, 240080, 240184
-recovered pasa_asmbl_41859.p1, internal, 240497, 240635
-recovered pasa_asmbl_41859.p1, internal, 240791, 240904
Valid prediction for snap_scaffold_4-snap.2894-T1
Valid prediction for GlimmerHMM_glimmerT_10564-T1
Valid prediction for GlimmerHMM_glimmerT_10549-T1
Couldn't classify 199928, 200085
Sorry, prediction pasa_asmbl_41853.p1 fails validation.
(ATG)	 CC	189600-189699	GT	AGG
(AGC)	 AG	189894-189982	GT	AGG
(GTT)	 AG	190130-190347	GT	AGG
(TAT)	 AG	190453-190584	GT	AGG
(ACC)	 AG	190818-190973	GT	AGG
(GTT)	 AG	191730-191903	GT	AAG
(GTG)	 AG	192055-192192	GT	ACG
(GAG)	 AG	194228-194308	GT	AAG
(GGC)	 AG	197293-197351	GT	TGG
(ACG)	 AG	197578-197628	GT	TGG
(GAA)	 AG	199928-200085	AA	GTA
-recovered pasa_asmbl_41853.p1, initial, 189600, 189699
-recovered pasa_asmbl_41853.p1, internal, 189894, 189982
-recovered pasa_asmbl_41853.p1, internal, 190130, 190347
-recovered pasa_asmbl_41853.p1, internal, 190453, 190584
-recovered pasa_asmbl_41853.p1, internal, 190818, 190973
-recovered pasa_asmbl_41853.p1, internal, 191730, 191903
-recovered pasa_asmbl_41853.p1, internal, 192055, 192192
-recovered pasa_asmbl_41853.p1, internal, 194228, 194308
-recovered pasa_asmbl_41853.p1, internal, 197293, 197351
-recovered pasa_asmbl_41853.p1, internal, 197578, 197628
Valid prediction for snap_scaffold_4-snap.2874-T1
Valid prediction for Augustus_model.g6915.t1
Valid prediction for snap_scaffold_4-snap.2898-T1
Valid prediction for snap_scaffold_4-snap.2888-T1
Valid prediction for snap_scaffold_4-snap.2885-T1
Valid prediction for pasa_asmbl_41865.p1
Valid prediction for GlimmerHMM_glimmerT_10575-T1
Valid prediction for CodingQuarry_transcript_49223-T1
Valid prediction for GlimmerHMM_glimmerT_10570-T1
Valid prediction for Augustus_model.g6916.t1
Valid prediction for GlimmerHMM_glimmerT_10571-T1
Valid prediction for CodingQuarry_transcript_49225-T1
Valid prediction for snap_scaffold_4-snap.2889-T1
Valid prediction for CodingQuarry_transcript_49217-T1
Valid prediction for snap_scaffold_4-snap.2879-T1
Valid prediction for Augustus_model.g6928.t1
Valid prediction for HiQ_model.g6933.t1
Valid prediction for GlimmerHMM_glimmerT_10573-T1
Valid prediction for pasa_asmbl_41844.p1
Valid prediction for snap_scaffold_4-snap.2890-T1
Valid prediction for snap_scaffold_4-snap.2914-T1
Valid prediction for pasa_asmbl_41836.p1
Valid prediction for HiQ_model.g6909.t1
Valid prediction for snap_scaffold_4-snap.2912-T1
Valid prediction for GlimmerHMM_glimmerT_10558-T1
Valid prediction for GlimmerHMM_glimmerT_10572-T1
Valid prediction for GlimmerHMM_glimmerT_10556-T1
Valid prediction for Augustus_model.g6929.t1
Valid prediction for CodingQuarry_transcript_49215-T1
Valid prediction for snap_scaffold_4-snap.2883-T1
Valid prediction for HiQ_model.g6911.t1
Couldn't classify 233056, 233131
Couldn't classify 235881, 235909
Sorry, prediction pasa_asmbl_41856.p1 fails validation.
(ACA)	 GG	233056-233131	GT	TGG
(GTG)	 AG	233402-233451	GT	AGG
(GGT)	 AG	233600-233731	GT	TGG
(GGT)	 AG	233820-233900	GT	AGG
(GTG)	 AG	234080-234211	GT	ATG
(CTA)	 AG	234315-234362	GT	GGG
(TTG)	 AG	234454-234510	GT	AGG
(GGT)	 AG	234666-234724	GT	AAG
(GTT)	 AG	234816-234895	GT	AGG
(GTG)	 AG	235055-235169	GT	AGG
(TGA)	 AG	235254-235319	GT	GAG
(GCA)	 AG	235504-235649	GT	GGG
(TCC)	 AG	235881-235909	GC	AGG
-recovered pasa_asmbl_41856.p1, internal, 233402, 233451
-recovered pasa_asmbl_41856.p1, internal, 233600, 233731
-recovered pasa_asmbl_41856.p1, internal, 233820, 233900
-recovered pasa_asmbl_41856.p1, internal, 234080, 234211
-recovered pasa_asmbl_41856.p1, internal, 234315, 234362
-recovered pasa_asmbl_41856.p1, internal, 234454, 234510
-recovered pasa_asmbl_41856.p1, internal, 234666, 234724
-recovered pasa_asmbl_41856.p1, internal, 234816, 234895
-recovered pasa_asmbl_41856.p1, internal, 235055, 235169
-recovered pasa_asmbl_41856.p1, internal, 235254, 235319
-recovered pasa_asmbl_41856.p1, internal, 235504, 235649
-recovered pasa_asmbl_41856.p1, internal, 235881, 235909
Valid prediction for HiQ_model.g6908.t1
Valid prediction for CodingQuarry_transcript_49224-T1
Couldn't classify 60795, 60851
Sorry, prediction pasa_asmbl_41852.p1 fails validation.
(CAT)	 AA	60795-60851	GT	CTG
(ATG)	 AG	60987-61294	GT	AGG
(AAT)	 AG	61491-61671	TG	GAT
-recovered pasa_asmbl_41852.p1, initial, 60987, 61294
-recovered pasa_asmbl_41852.p1, terminal, 61491, 61671
-recovered pasa_asmbl_41852.p1, internal, 60987, 61294
Couldn't classify 236093, 236195
Couldn't classify 237121, 238783
Sorry, prediction pasa_asmbl_41858.p1 fails validation.
(GAG)	 CA	236093-236195	GT	AGG
(AGG)	 AG	236308-236462	GC	AGG
(AGG)	 AG	236626-236957	GT	AGG
(GGA)	 AG	237121-238783	TC	CGT
-recovered pasa_asmbl_41858.p1, internal, 236308, 236462
-recovered pasa_asmbl_41858.p1, internal, 236626, 236957
Valid prediction for snap_scaffold_4-snap.2887-T1
Valid prediction for snap_scaffold_4-snap.2873-T1
Valid prediction for snap_scaffold_4-snap.2903-T1
Valid prediction for Augustus_model.g6932.t1
Valid prediction for Augustus_model.g6914.t1
Valid prediction for snap_scaffold_4-snap.2886-T1
Valid prediction for GlimmerHMM_glimmerT_10568-T1
Valid prediction for HiQ_model.g6907.t1
Valid prediction for GlimmerHMM_glimmerT_10574-T1
Valid prediction for GlimmerHMM_glimmerT_10548-T1
Valid prediction for snap_scaffold_4-snap.2915-T1
Valid prediction for HiQ_model.g6918.t1
Valid prediction for CodingQuarry_transcript_49216-T1
Valid prediction for snap_scaffold_4-snap.2911-T1
Valid prediction for Augustus_model.g6924.t1
Valid prediction for CodingQuarry_transcript_49222-T1
Valid prediction for snap_scaffold_4-snap.2891-T1
Valid prediction for GlimmerHMM_glimmerT_10553-T1
Valid prediction for Augustus_model.g6930.t1
Valid prediction for HiQ_model.g6934.t1
Valid prediction for GlimmerHMM_glimmerT_10550-T1
Couldn't classify 207804, 209114
Sorry, prediction pasa_asmbl_41854.p1 fails validation.
(GGT)	 AA	207804-209114	GG	GAG
Valid prediction for snap_scaffold_4-snap.2907-T1
Valid prediction for snap_scaffold_4-snap.2892-T1
Valid prediction for GlimmerHMM_glimmerT_10561-T1
Valid prediction for GlimmerHMM_glimmerT_10566-T1
Valid prediction for pasa_asmbl_41870.p1
Valid prediction for Augustus_model.g6927.t1
Valid prediction for snap_scaffold_4-snap.2875-T1
Valid prediction for GlimmerHMM_glimmerT_10559-T1
Valid prediction for Augustus_model.g6931.t1
Valid prediction for GlimmerHMM_glimmerT_10576-T1
Valid prediction for snap_scaffold_4-snap.2910-T1
Valid prediction for pasa_asmbl_41872.p1
Valid prediction for snap_scaffold_4-snap.2878-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_10555-T1
Valid prediction for Augustus_model.g6913.t1
Valid prediction for snap_scaffold_4-snap.2877-T1
Valid prediction for pasa_asmbl_43043.p1
Valid prediction for HiQ_model.g6920.t1
Couldn't classify 69935, 69947
Couldn't classify 72334, 72387
Sorry, prediction pasa_asmbl_43049.p2 fails validation.
(CAA)	 CT	69935-69947	GT	CGG
(AGG)	 AG	70034-70103	GT	AGG
(CTA)	 AG	70300-70375	GT	AAG
(GTG)	 AG	70465-70590	GT	AGG
(TCT)	 AG	70974-71092	GT	GGG
(GAA)	 AG	71568-71695	GT	CGG
(TGA)	 AG	71916-71975	GT	GGG
(ATG)	 AG	72117-72154	GT	AGG
(GAC)	 AG	72334-72387	GA	AGG
add_exon() Sorry, pasa_asmbl_43049.p2 72117-72154-initial-1 is invalid.
-recovered pasa_asmbl_43049.p2, initial, 72117, 72154
-recovered pasa_asmbl_43049.p2, internal, 70034, 70103
-recovered pasa_asmbl_43049.p2, internal, 70300, 70375
-recovered pasa_asmbl_43049.p2, internal, 70465, 70590
-recovered pasa_asmbl_43049.p2, internal, 70974, 71092
-recovered pasa_asmbl_43049.p2, internal, 71568, 71695
-recovered pasa_asmbl_43049.p2, internal, 71916, 71975
-recovered pasa_asmbl_43049.p2, internal, 72117, 72154
Valid prediction for snap_scaffold_4-snap.2870-T1
Valid prediction for snap_scaffold_4-snap.2902-T1
Valid prediction for HiQ_model.g6910.t1
Valid prediction for Augustus_model.g6922.t1
Valid prediction for snap_scaffold_4-snap.2884-T1
Valid prediction for GlimmerHMM_glimmerT_10552-T1
Valid prediction for snap_scaffold_4-snap.2904-T1
Valid prediction for HiQ_model.g6926.t1
Valid prediction for GlimmerHMM_glimmerT_10563-T1
Valid prediction for Augustus_model.g6921.t1
Valid prediction for snap_scaffold_4-snap.2871-T1
Valid prediction for snap_scaffold_4-snap.2908-T1
Valid prediction for snap_scaffold_4-snap.2900-T1
Valid prediction for CodingQuarry_transcript_49219-T1
Valid prediction for snap_scaffold_4-snap.2901-T1
Valid prediction for CodingQuarry_transcript_49221-T1
Valid prediction for snap_scaffold_4-snap.2909-T1
Valid prediction for pasa_asmbl_43037.p1
Valid prediction for Augustus_model.g6925.t1
Valid prediction for snap_scaffold_4-snap.2880-T1
Valid prediction for snap_scaffold_4-snap.2893-T1
Valid prediction for GlimmerHMM_glimmerT_10546-T1
Valid prediction for GlimmerHMM_glimmerT_10554-T1
Valid prediction for GlimmerHMM_glimmerT_10565-T1
Valid prediction for GlimmerHMM_glimmerT_10551-T1
Valid prediction for snap_scaffold_4-snap.2906-T1
Valid prediction for GlimmerHMM_glimmerT_10547-T1
Valid prediction for snap_scaffold_4-snap.2913-T1
Valid prediction for GlimmerHMM_glimmerT_10567-T1
Couldn't classify 320459, 320638
Sorry, prediction pasa_asmbl_43035.p1 fails validation.
(AAA)	 CT	320459-320638	GT	AGG
(GTG)	 AG	320804-321046	GT	GAG
-recovered pasa_asmbl_43035.p1, terminal, 320804, 321046
-recovered pasa_asmbl_43035.p1, internal, 320804, 321046
Valid prediction for snap_scaffold_4-snap.2896-T1
Couldn't classify 136476, 136775
Couldn't classify 137410, 137513
Sorry, prediction pasa_asmbl_43042.p1 fails validation.
(CCC)	 AG	136476-136775	GT	AGG
(CTG)	 AG	136883-136968	GT	AGG
(GAT)	 AG	137156-137238	GT	AGG
(GGC)	 AG	137410-137513	AT	CCA
-recovered pasa_asmbl_43042.p1, internal, 136476, 136775
-recovered pasa_asmbl_43042.p1, internal, 136883, 136968
-recovered pasa_asmbl_43042.p1, internal, 137156, 137238
Valid prediction for GlimmerHMM_glimmerT_10557-T1
Couldn't classify 138125, 138277
Couldn't classify 138493, 138735
Sorry, prediction pasa_asmbl_43041.p1 fails validation.
(CTA)	 TC	138125-138277	GT	AGG
(GAG)	 AG	138493-138735	TG	ACT
Valid prediction for snap_scaffold_4-snap.2899-T1
Valid prediction for snap_scaffold_4-snap.2872-T1
Valid prediction for snap_scaffold_4-snap.2876-T1
Valid prediction for snap_scaffold_4-snap.2897-T1
Valid prediction for pasa_asmbl_43050.p1
Valid prediction for GlimmerHMM_glimmerT_10560-T1
Valid prediction for CodingQuarry_transcript_49220-T1
Valid prediction for snap_scaffold_4-snap.2881-T1
Couldn't classify 73126, 73146
Couldn't classify 78794, 78955
Sorry, prediction pasa_asmbl_43536.p1 fails validation.
(CTG)	 CG	73126-73146	GT	AGG
(ATC)	 AG	73379-73489	GT	AGG
(AGT)	 AG	73641-73700	GT	AGG
(GCT)	 AG	73846-74104	GT	GGG
(AGG)	 AG	74316-74477	GT	GGG
(AGA)	 AG	75747-75802	GT	AGG
(GCC)	 AG	76477-76624	GT	AGG
(ACA)	 AG	76833-77011	GT	AGG
(CAT)	 AG	77519-77653	GT	CAG
(CTG)	 AG	78794-78955	CC	GCC
-recovered pasa_asmbl_43536.p1, internal, 73379, 73489
-recovered pasa_asmbl_43536.p1, internal, 73641, 73700
-recovered pasa_asmbl_43536.p1, internal, 73846, 74104
-recovered pasa_asmbl_43536.p1, internal, 74316, 74477
-recovered pasa_asmbl_43536.p1, internal, 75747, 75802
-recovered pasa_asmbl_43536.p1, internal, 76477, 76624
-recovered pasa_asmbl_43536.p1, internal, 76833, 77011
-recovered pasa_asmbl_43536.p1, internal, 77519, 77653
Valid prediction for Augustus_model.g6923.t1
Couldn't classify 135409, 135486
Couldn't classify 136250, 136352
Sorry, prediction pasa_asmbl_43581.p1 fails validation.
(GAC)	 GC	135409-135486	GT	TGG
(GAT)	 AG	135721-135836	GT	GGG
(GTT)	 AG	136250-136352	TT	GCT
-recovered pasa_asmbl_43581.p1, internal, 135721, 135836
Valid prediction for HiQ_model.g6917.t1
Valid prediction for Augustus_model.g6919.t1
Valid prediction for snap_scaffold_4-snap.2895-T1
Valid prediction for HiQ_model.g6912.t1
Valid prediction for Augustus_model.g6906.t1
Valid prediction for pasa_asmbl_43031.p1
Valid prediction for snap_scaffold_4-snap.2869-T1
Valid prediction for GlimmerHMM_glimmerT_10562-T1
Valid prediction for snap_scaffold_4-snap.2905-T1
Valid prediction for GlimmerHMM_glimmerT_10569-T1
Valid prediction for snap_scaffold_4-snap.2882-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 299981, rend_intergenic: 299978  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 332515, rend_intergenic: 327207  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 367131, rend_intergenic: 363131  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 384450
-exon list size: 509


building trellis

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69.3    
69.5    
69.7    
69.9    
70.1    
70.3    
70.5    
70.6    
70.8    
71.0    
71.2    
71.4    
71.6    
71.8    
72.0    
72.2    
72.4    
72.6    
72.8    
73.0    
73.2    
73.4    
73.6    
73.8    
74.0    
74.2    
74.4    
74.6    
74.8    
75.0    
75.1    
75.3    
75.5    
75.7    
75.9    
76.1    
76.3    
76.5    
76.7    
76.9    
77.1    
77.3    
77.5    
77.7    
77.9    
78.1    
78.3    
78.5    
78.7    
78.9    
79.1    
79.3    
79.5    
79.6    
79.8    
80.0    
80.2    
80.4    
80.6    
80.8    
81.0    
81.2    
81.4    
81.6    
81.8    
82.0    
82.2    
82.4    
82.6    
82.8    
83.0    
83.2    
83.4    
83.6    
83.8    
84.0    
84.1    
84.3    
84.5    
84.7    
84.9    
85.1    
85.3    
85.5    
85.7    
85.9    
86.1    
86.3    
86.5    
86.7    
86.9    
87.1    
87.3    
87.5    
87.7    
87.9    
88.1    
88.3    
88.5    
88.6    
88.8    
89.0    
89.2    
89.4    
89.6    
89.8    
90.0    
90.2    
90.4    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.8    
92.0    
92.2    
92.4    
92.6    
92.8    
93.0    
93.2    
93.3    
93.5    
93.7    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.3    
97.5    
97.7    
97.8    
98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 40 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 299981, rend_intergenic: 299978  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 332515, rend_intergenic: 327207  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 367131, rend_intergenic: 363131  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 34 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 10101
-exon list size: 1


building trellis

33.3    
66.7    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support