-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_10/scaffold_10_5997918-6280500

-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 GlimmerHMM_glimmerT_24850-T1
Valid prediction for HiQ_model.g16524.t1
Valid prediction for pasa_asmbl_3214.p1
Valid prediction for Augustus_model.g16529.t1
Valid prediction for snap_scaffold_10-snap.1295-T1
Valid prediction for snap_scaffold_10-snap.1290-T1
Valid prediction for snap_scaffold_10-snap.1264-T1
Valid prediction for GlimmerHMM_glimmerT_24830-T1
Valid prediction for snap_scaffold_10-snap.1300-T1
Valid prediction for Augustus_model.g16548.t1
Valid prediction for Augustus_model.g16546.t1
Valid prediction for snap_scaffold_10-snap.1257-T1
Valid prediction for HiQ_model.g16550.t1
Valid prediction for GlimmerHMM_glimmerT_24835-T1
Valid prediction for snap_scaffold_10-snap.1285-T1
Valid prediction for snap_scaffold_10-snap.1286-T1
Valid prediction for pasa_asmbl_3232.p1
Valid prediction for HiQ_model.g16526.t1
Valid prediction for Augustus_model.g16542.t1
Valid prediction for GlimmerHMM_glimmerT_24834-T1
Valid prediction for GlimmerHMM_glimmerT_24852-T1
Valid prediction for GlimmerHMM_glimmerT_24828-T1
Valid prediction for CodingQuarry_transcript_5431-T1
Valid prediction for GlimmerHMM_glimmerT_24836-T1
Valid prediction for pasa_asmbl_3215.p1
Valid prediction for HiQ_model.g16525.t1
Valid prediction for snap_scaffold_10-snap.1288-T1
Valid prediction for CodingQuarry_transcript_5430-T1
Valid prediction for Augustus_model.g16536.t1
Valid prediction for GlimmerHMM_glimmerT_24844-T1
Couldn't classify 279087, 279184
Sorry, prediction CodingQuarry_transcript_5440-T1 fails validation.
(ATG)	 CA	277745-278054	GT	AGG
(ACT)	 AG	278611-278757	GT	AAG
(CAG)	 GG	279087-279184	CA	GAC
-recovered CodingQuarry_transcript_5440-T1, initial, 277745, 278054
-recovered CodingQuarry_transcript_5440-T1, internal, 278611, 278757
Valid prediction for Augustus_model.g16530.t1
Valid prediction for CodingQuarry_transcript_5439-T1
Valid prediction for GlimmerHMM_glimmerT_24851-T1
Valid prediction for GlimmerHMM_glimmerT_24857-T1
Valid prediction for snap_scaffold_10-snap.1258-T1
Valid prediction for snap_scaffold_10-snap.1262-T1
Valid prediction for GlimmerHMM_glimmerT_24849-T1
Valid prediction for snap_scaffold_10-snap.1256-T1
Valid prediction for Augustus_model.g16543.t1
Valid prediction for Augustus_model.g16544.t1
Valid prediction for Augustus_model.g16545.t1
Valid prediction for snap_scaffold_10-snap.1296-T1
Valid prediction for GlimmerHMM_glimmerT_24856-T1
Valid prediction for snap_scaffold_10-snap.1301-T1
Valid prediction for GlimmerHMM_glimmerT_24838-T1
Valid prediction for GlimmerHMM_glimmerT_24831-T1
Valid prediction for snap_scaffold_10-snap.1259-T1
Valid prediction for snap_scaffold_10-snap.1289-T1
Valid prediction for GlimmerHMM_glimmerT_24861-T1
Valid prediction for snap_scaffold_10-snap.1284-T1
Valid prediction for GlimmerHMM_glimmerT_24854-T1
Valid prediction for pasa_asmbl_3216.p1
Valid prediction for snap_scaffold_10-snap.1267-T1
Valid prediction for HiQ_model.g16531.t1
Valid prediction for GlimmerHMM_glimmerT_24847-T1
Valid prediction for snap_scaffold_10-snap.1287-T1
Valid prediction for GlimmerHMM_glimmerT_24829-T1
Valid prediction for snap_scaffold_10-snap.1273-T1
Valid prediction for snap_scaffold_10-snap.1282-T1
Valid prediction for snap_scaffold_10-snap.1283-T1
Valid prediction for pasa_asmbl_3225.p1

-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_24832-T1
Valid prediction for HiQ_model.g16527.t1
Valid prediction for GlimmerHMM_glimmerT_24853-T1
Valid prediction for CodingQuarry_transcript_5438-T1
Valid prediction for Augustus_model.g16538.t1
Couldn't classify 21120, 21152
Couldn't classify 22145, 22222
Sorry, prediction pasa_asmbl_4445.p1 fails validation.
(AAT)	 GG	21120-21152	GT	AGG
(GAG)	 AG	21240-21407	GT	AGG
(TTC)	 AG	21783-22022	GT	AGG
(GAA)	 AG	22145-22222	GA	GAG
-recovered pasa_asmbl_4445.p1, internal, 21240, 21407
-recovered pasa_asmbl_4445.p1, internal, 21783, 22022
Valid prediction for snap_scaffold_10-snap.1292-T1
Couldn't classify 29595, 29681
Couldn't classify 30143, 30231
Sorry, prediction pasa_asmbl_4442.p1 fails validation.
(TTC)	 CT	29595-29681	GT	AGG
(GAC)	 AG	29839-30064	GT	AGG
(ACG)	 AG	30143-30231	AA	CCA
-recovered pasa_asmbl_4442.p1, internal, 29839, 30064
Valid prediction for snap_scaffold_10-snap.1271-T1
Valid prediction for GlimmerHMM_glimmerT_24841-T1
Valid prediction for snap_scaffold_10-snap.1277-T1
Valid prediction for Augustus_model.g16540.t1
Valid prediction for GlimmerHMM_glimmerT_24845-T1
Valid prediction for snap_scaffold_10-snap.1275-T1
Valid prediction for snap_scaffold_10-snap.1276-T1
Valid prediction for snap_scaffold_10-snap.1278-T1
Valid prediction for snap_scaffold_10-snap.1272-T1
Valid prediction for Augustus_model.g16547.t1
Valid prediction for snap_scaffold_10-snap.1293-T1
Valid prediction for CodingQuarry_transcript_5433-T1
Valid prediction for snap_scaffold_10-snap.1281-T1
Valid prediction for GlimmerHMM_glimmerT_24846-T1
Valid prediction for GlimmerHMM_glimmerT_24858-T1
Valid prediction for CodingQuarry_transcript_5434-T1
Valid prediction for GlimmerHMM_glimmerT_24848-T1
Valid prediction for snap_scaffold_10-snap.1297-T1
Valid prediction for snap_scaffold_10-snap.1265-T1
Couldn't classify 12280, 12333
Couldn't classify 12671, 12843
Sorry, prediction pasa_asmbl_5215.p1 fails validation.
(AGA)	 TT	12280-12333	GT	AGG
(GTG)	 AG	12435-12579	GT	CGG
(AGA)	 AG	12671-12843	TA	GGT
-recovered pasa_asmbl_5215.p1, internal, 12435, 12579
Valid prediction for GlimmerHMM_glimmerT_24833-T1
Valid prediction for Augustus_model.g16549.t1
Valid prediction for snap_scaffold_10-snap.1268-T1
Couldn't classify 22342, 22549
Couldn't classify 23222, 23255
Sorry, prediction pasa_asmbl_4444.p2 fails validation.
(CAG)	 TG	22342-22549	GT	AGG
(GCG)	 AG	22643-22922	GT	AGG
(CTT)	 AG	23222-23255	CT	CCC
-recovered pasa_asmbl_4444.p2, internal, 22643, 22922
Valid prediction for snap_scaffold_10-snap.1291-T1
Couldn't classify 145724, 145751
Couldn't classify 149523, 149609
Sorry, prediction pasa_asmbl_4437.p1 fails validation.
(GGG)	 CA	145724-145751	GT	AGG
(GTC)	 AG	146243-146373	GT	TGG
(GGT)	 AG	147778-147813	GT	AGG
(GGA)	 AG	148699-148734	GT	CAG
(GGC)	 AG	149523-149609	AG	GCA
-recovered pasa_asmbl_4437.p1, internal, 146243, 146373
-recovered pasa_asmbl_4437.p1, internal, 147778, 147813
-recovered pasa_asmbl_4437.p1, internal, 148699, 148734
Valid prediction for snap_scaffold_10-snap.1269-T1
Valid prediction for pasa_asmbl_4436.p1
Couldn't classify 141699, 141753
Couldn't classify 142702, 142838
Sorry, prediction pasa_asmbl_5086.p1 fails validation.
(AGG)	 GC	141699-141753	GT	AGG
(ACT)	 AG	142201-142335	GT	GGG
(ACA)	 AG	142702-142838	GG	GAG
-recovered pasa_asmbl_5086.p1, internal, 142201, 142335
Couldn't classify 18203, 18390
Couldn't classify 19078, 19298
Sorry, prediction pasa_asmbl_4446.p1 fails validation.
(GGG)	 CC	18203-18390	GT	AGG
(GGA)	 AG	18530-18608	GT	AGG
(TCA)	 AG	18702-18750	GT	GGG
(GTC)	 AG	19078-19298	GC	GGG
-recovered pasa_asmbl_4446.p1, internal, 18530, 18608
-recovered pasa_asmbl_4446.p1, internal, 18702, 18750
-recovered pasa_asmbl_4446.p1, internal, 19078, 19298
Valid prediction for snap_scaffold_10-snap.1260-T1
Couldn't classify 35455, 35596
Sorry, prediction pasa_asmbl_4439.p1 fails validation.
(CAG)	 GG	35455-35596	GT	AGG
(GCT)	 AG	35697-35878	GT	AGG
(CTG)	 AG	36040-36195	GT	AGG
(GTG)	 AG	36595-36717	GT	AGG
(AAA)	 AG	36804-36906	GT	AGG
(AGC)	 AG	37074-37243	GT	AGG
(TTG)	 AG	37354-37486	GT	AGG
(GTG)	 AG	37596-37759	GT	AGG
(GTG)	 AG	37873-38042	GT	AGG
(GGG)	 AG	38203-38368	GT	AGG
(GAG)	 AG	38500-38576	GT	AGG
(GTT)	 AG	38670-38922	GT	TGG
(ATG)	 AG	39114-39266	GT	AGG
(GTA)	 AG	39410-39715	GT	GGG
(CCC)	 AG	39870-40055	CC	AAC
-recovered pasa_asmbl_4439.p1, initial, 39114, 39266
-recovered pasa_asmbl_4439.p1, terminal, 39870, 40055
-recovered pasa_asmbl_4439.p1, internal, 35697, 35878
-recovered pasa_asmbl_4439.p1, internal, 36040, 36195
-recovered pasa_asmbl_4439.p1, internal, 36595, 36717
-recovered pasa_asmbl_4439.p1, internal, 36804, 36906
-recovered pasa_asmbl_4439.p1, internal, 37074, 37243
-recovered pasa_asmbl_4439.p1, internal, 37354, 37486
-recovered pasa_asmbl_4439.p1, internal, 37596, 37759
-recovered pasa_asmbl_4439.p1, internal, 37873, 38042
-recovered pasa_asmbl_4439.p1, internal, 38203, 38368
-recovered pasa_asmbl_4439.p1, internal, 38500, 38576
-recovered pasa_asmbl_4439.p1, internal, 38670, 38922
-recovered pasa_asmbl_4439.p1, internal, 39114, 39266
-recovered pasa_asmbl_4439.p1, internal, 39410, 39715
Couldn't classify 187845, 188273
Sorry, prediction pasa_asmbl_4433.p1 fails validation.
(ATT)	 AG	187845-188273	AT	ACA
Couldn't classify 30301, 30420
Couldn't classify 30830, 30941
Sorry, prediction pasa_asmbl_4441.p2 fails validation.
(CTG)	 AG	30301-30420	GT	GGG
(GTC)	 AG	30561-30688	GT	AGG
(CGA)	 AG	30830-30941	TG	TCT
-recovered pasa_asmbl_4441.p2, internal, 30301, 30420
-recovered pasa_asmbl_4441.p2, internal, 30561, 30688
Valid prediction for Augustus_model.g16528.t1
Valid prediction for CodingQuarry_transcript_5437-T1
Valid prediction for snap_scaffold_10-snap.1279-T1
Valid prediction for pasa_asmbl_4431.p1
Valid prediction for snap_scaffold_10-snap.1299-T1
Valid prediction for snap_scaffold_10-snap.1274-T1
Valid prediction for pasa_asmbl_4430.p1
Valid prediction for snap_scaffold_10-snap.1298-T1
Valid prediction for snap_scaffold_10-snap.1280-T1
Valid prediction for Augustus_model.g16537.t1
Valid prediction for GlimmerHMM_glimmerT_24837-T1
Couldn't classify 23727, 24009
Couldn't classify 29123, 29190
Sorry, prediction pasa_asmbl_5119.p1 fails validation.
(TCC)	 AG	23727-24009	GT	AGG
(AAT)	 AG	24163-24376	GT	CAG
(ATC)	 AG	24543-24595	GT	GGG
(AGC)	 AG	26021-26104	GT	AGG
(GGG)	 AG	26572-26758	GT	AGG
(TCT)	 AG	27281-27417	GT	AGG
(ACT)	 AG	27642-27850	GT	AGG
(GGT)	 AG	27990-28258	GT	AGG
(GAT)	 AG	28601-28653	GT	CGG
(ACG)	 AG	28748-28945	GT	AGG
(GGA)	 AG	29123-29190	CA	CTC
-recovered pasa_asmbl_5119.p1, internal, 23727, 24009
-recovered pasa_asmbl_5119.p1, internal, 24163, 24376
-recovered pasa_asmbl_5119.p1, internal, 24543, 24595
-recovered pasa_asmbl_5119.p1, internal, 26021, 26104
-recovered pasa_asmbl_5119.p1, internal, 26572, 26758
-recovered pasa_asmbl_5119.p1, internal, 27281, 27417
-recovered pasa_asmbl_5119.p1, internal, 27642, 27850
-recovered pasa_asmbl_5119.p1, internal, 27990, 28258
-recovered pasa_asmbl_5119.p1, internal, 28601, 28653
-recovered pasa_asmbl_5119.p1, internal, 28748, 28945
Valid prediction for GlimmerHMM_glimmerT_24859-T1
Valid prediction for snap_scaffold_10-snap.1270-T1
Valid prediction for Augustus_model.g16535.t1
Valid prediction for GlimmerHMM_glimmerT_24860-T1
Valid prediction for snap_scaffold_10-snap.1261-T1
Couldn't classify 31115, 31316
Couldn't classify 34892, 34987
Sorry, prediction pasa_asmbl_4440.p1 fails validation.
(GAG)	 TG	31115-31316	GT	AGG
(CCC)	 AG	31477-31604	GT	CTG
(GAG)	 AG	31998-32197	GT	GCG
(GGG)	 AG	32308-32422	GT	AGG
(CGT)	 AG	32584-32715	GT	AGG
(GAT)	 AG	32885-32986	GT	AGG
(GAT)	 AG	33123-33296	GT	GGG
(AGC)	 AG	33993-34277	GT	TGG
(GAC)	 AG	34454-34519	GT	AGG
(GAC)	 AG	34892-34987	CT	CTC
-recovered pasa_asmbl_4440.p1, internal, 31477, 31604
-recovered pasa_asmbl_4440.p1, internal, 31998, 32197
-recovered pasa_asmbl_4440.p1, internal, 32308, 32422
-recovered pasa_asmbl_4440.p1, internal, 32584, 32715
-recovered pasa_asmbl_4440.p1, internal, 32885, 32986
-recovered pasa_asmbl_4440.p1, internal, 33123, 33296
-recovered pasa_asmbl_4440.p1, internal, 33993, 34277
-recovered pasa_asmbl_4440.p1, internal, 34454, 34519
Valid prediction for GlimmerHMM_glimmerT_24842-T1
Couldn't classify 190849, 190968
Sorry, prediction pasa_asmbl_5102.p1 fails validation.
(AGT)	 TA	190849-190968	GT	AGG
(GAC)	 AG	191078-191578	GA	AGG
-recovered pasa_asmbl_5102.p1, terminal, 191078, 191578
Valid prediction for GlimmerHMM_glimmerT_24843-T1
Valid prediction for Augustus_model.g16541.t1
Couldn't classify 23289, 23600
Sorry, prediction pasa_asmbl_4443.p1 fails validation.
(TGT)	 AG	23289-23600	GG	CAG
Valid prediction for CodingQuarry_transcript_5435-T1
Valid prediction for GlimmerHMM_glimmerT_24855-T1
Valid prediction for snap_scaffold_10-snap.1266-T1
Valid prediction for GlimmerHMM_glimmerT_24839-T1
Couldn't classify 257284, 257634
Sorry, prediction pasa_asmbl_5131.p1 fails validation.
(CAC)	 CC	257284-257634	AC	CGA
Valid prediction for HiQ_model.g16532.t1
Valid prediction for HiQ_model.g16539.t1
Valid prediction for CodingQuarry_transcript_5436-T1
Valid prediction for Augustus_model.g16533.t1
Valid prediction for snap_scaffold_10-snap.1294-T1
Valid prediction for GlimmerHMM_glimmerT_24840-T1
Valid prediction for Augustus_model.g16534.t1
Valid prediction for pasa_asmbl_4416.p1
Couldn't classify 186705, 187514
Sorry, prediction pasa_asmbl_4435.p1 fails validation.
(ATG)	 AG	186705-187514	CC	TAC
Valid prediction for snap_scaffold_10-snap.1263-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 66824, rend_intergenic: 58271  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82840, rend_intergenic: 81791  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 256525, rend_intergenic: 245828  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 261225, rend_intergenic: 257268  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 273803, rend_intergenic: 267388  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 282583
-exon list size: 543


building trellis

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63.7    
63.9    
64.0    
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    
68.3    
68.4    
68.6    
68.8    
69.0    
69.2    
69.4    
69.5    
69.7    
69.9    
70.1    
70.3    
70.5    
70.6    
70.8    
71.0    
71.2    
71.4    
71.6    
71.7    
71.9    
72.1    
72.3    
72.5    
72.7    
72.8    
73.0    
73.2    
73.4    
73.6    
73.8    
73.9    
74.1    
74.3    
74.5    
74.7    
74.9    
75.0    
75.2    
75.4    
75.6    
75.8    
76.0    
76.1    
76.3    
76.5    
76.7    
76.9    
77.1    
77.2    
77.4    
77.6    
77.8    
78.0    
78.2    
78.3    
78.5    
78.7    
78.9    
79.1    
79.3    
79.4    
79.6    
79.8    
80.0    
80.2    
80.4    
80.6    
80.7    
80.9    
81.1    
81.3    
81.5    
81.7    
81.8    
82.0    
82.2    
82.4    
82.6    
82.8    
82.9    
83.1    
83.3    
83.5    
83.7    
83.9    
84.0    
84.2    
84.4    
84.6    
84.8    
85.0    
85.1    
85.3    
85.5    
85.7    
85.9    
86.1    
86.2    
86.4    
86.6    
86.8    
87.0    
87.2    
87.3    
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    
90.5    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.7    
91.9    
92.1    
92.3    
92.5    
92.7    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.0    
95.2    
95.4    
95.6    
95.8    
96.0    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.2    
97.4    
97.6    
97.8    
98.0    
98.2    
98.3    
98.5    
98.7    
98.9    
99.1    
99.3    
99.4    
99.6    
99.8    
-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 66824, rend_intergenic: 58271  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82840, rend_intergenic: 81791  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 256525, rend_intergenic: 245828  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 261225, rend_intergenic: 257268  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 273803, rend_intergenic: 267388  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