-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_8/scaffold_8_18095160-18325616

-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 11180, 11216
Sorry, prediction pasa_asmbl_52525.p1 fails validation.
(TGC)	 GT	11180-11216	GC	GGG
(GTC)	 AG	12450-12583	GT	AGG
(GCA)	 AG	12989-13067	GT	AGG
(GGA)	 AG	13271-13410	GG	GAG
-recovered pasa_asmbl_52525.p1, terminal, 13271, 13410
-recovered pasa_asmbl_52525.p1, internal, 12450, 12583
-recovered pasa_asmbl_52525.p1, internal, 12989, 13067
Valid prediction for snap_scaffold_8-snap.3372-T1
Valid prediction for GeneMark_model.37140_t
Valid prediction for Augustus_model.g14643.t1
Valid prediction for snap_scaffold_8-snap.3368-T1
Valid prediction for Augustus_model.g14624.t1
Valid prediction for GeneMark_model.37145_t
Valid prediction for GeneMark_model.37165_t
Valid prediction for GeneMark_model.37152_t
Valid prediction for GeneMark_model.37151_t
Valid prediction for HiQ_model.g14634.t1
Valid prediction for snap_scaffold_8-snap.3350-T1
Valid prediction for GeneMark_model.37136_t
Couldn't classify 122409, 122807
Sorry, prediction pasa_asmbl_52644.p1 fails validation.
(GAT)	 AG	122409-122807	GC	ACG
-recovered pasa_asmbl_52644.p1, internal, 122409, 122807
Valid prediction for Augustus_model.g14635.t1
Valid prediction for snap_scaffold_8-snap.3347-T1
Valid prediction for snap_scaffold_8-snap.3356-T1
Valid prediction for GlimmerHMM_glimmerT_21817-T1
Valid prediction for GeneMark_model.37149_t
Valid prediction for GlimmerHMM_glimmerT_21820-T1
Valid prediction for snap_scaffold_8-snap.3342-T1
Valid prediction for snap_scaffold_8-snap.3373-T1
Valid prediction for Augustus_model.g14621.t1
Valid prediction for Augustus_model.g14638.t1
Couldn't classify 53342, 53393
Couldn't classify 60608, 60784
Sorry, prediction pasa_asmbl_52529.p1 fails validation.
(TGG)	 AG	53342-53393	GT	AGG
(CGG)	 AG	54788-54944	GT	AGG
(GTG)	 AG	55069-55312	GT	CTG
(ATT)	 AG	55423-55519	GT	TCG
(CTA)	 AG	55653-55818	GT	CGG
(GGG)	 AG	55909-55998	GT	TCG
(AAT)	 AG	56169-56320	GT	AGG
(TGT)	 AG	56426-56526	GT	AGG
(CTG)	 AG	56621-56747	GT	AGG
(GTG)	 AG	56890-56967	GT	CGG
(GCA)	 AG	57156-57328	GT	AGG
(TGT)	 AG	57430-57545	GT	TGG
(TGG)	 AG	58342-58509	GT	AGG
(GGC)	 AG	58706-58964	GT	AGG
(GTG)	 AG	59206-59394	GT	AGG
(CGC)	 AG	59513-59825	GT	AGG
(ATT)	 AG	59917-60028	GT	GGG
(AGC)	 AG	60149-60296	GT	GGG
(AAA)	 AG	60608-60784	CT	ACC
-recovered pasa_asmbl_52529.p1, terminal, 53342, 53393
add_exon() Sorry, pasa_asmbl_52529.p1 56621-56747-terminal-3 is invalid.
-recovered pasa_asmbl_52529.p1, terminal, 56621, 56747
-recovered pasa_asmbl_52529.p1, internal, 53342, 53393
-recovered pasa_asmbl_52529.p1, internal, 54788, 54944
-recovered pasa_asmbl_52529.p1, internal, 55069, 55312
-recovered pasa_asmbl_52529.p1, internal, 55423, 55519
-recovered pasa_asmbl_52529.p1, internal, 55653, 55818
-recovered pasa_asmbl_52529.p1, internal, 55909, 55998
-recovered pasa_asmbl_52529.p1, internal, 56169, 56320
-recovered pasa_asmbl_52529.p1, internal, 56426, 56526
-recovered pasa_asmbl_52529.p1, internal, 56621, 56747
-recovered pasa_asmbl_52529.p1, internal, 56890, 56967
-recovered pasa_asmbl_52529.p1, internal, 57156, 57328
-recovered pasa_asmbl_52529.p1, internal, 57430, 57545
-recovered pasa_asmbl_52529.p1, internal, 58342, 58509
-recovered pasa_asmbl_52529.p1, internal, 58706, 58964
-recovered pasa_asmbl_52529.p1, internal, 59206, 59394
-recovered pasa_asmbl_52529.p1, internal, 59513, 59825
-recovered pasa_asmbl_52529.p1, internal, 59917, 60028
-recovered pasa_asmbl_52529.p1, internal, 60149, 60296
Valid prediction for GeneMark_model.37164_t
Valid prediction for snap_scaffold_8-snap.3340-T1
Valid prediction for Augustus_model.g14622.t1
Valid prediction for Augustus_model.g14615.t1
Valid prediction for GeneMark_model.37141_t
Valid prediction for GlimmerHMM_glimmerT_21812-T1
Valid prediction for snap_scaffold_8-snap.3363-T1
Valid prediction for snap_scaffold_8-snap.3341-T1
Valid prediction for snap_scaffold_8-snap.3336-T1
Valid prediction for GlimmerHMM_glimmerT_21823-T1
Valid prediction for GeneMark_model.37129_t
Valid prediction for GeneMark_model.37155_t
Valid prediction for Augustus_model.g14619.t1
Valid prediction for Augustus_model.g14629.t1
Valid prediction for GlimmerHMM_glimmerT_21828-T1
Valid prediction for snap_scaffold_8-snap.3358-T1
Valid prediction for GlimmerHMM_glimmerT_21806-T1
Valid prediction for Augustus_model.g14614.t1
Valid prediction for Augustus_model.g14644.t1
Valid prediction for pasa_asmbl_52531.p1
Valid prediction for pasa_asmbl_52537.p1
Valid prediction for snap_scaffold_8-snap.3345-T1
Valid prediction for GeneMark_model.37130_t
Valid prediction for GlimmerHMM_glimmerT_21811-T1
Valid prediction for GlimmerHMM_glimmerT_21838-T1
Valid prediction for GlimmerHMM_glimmerT_21815-T1
Valid prediction for snap_scaffold_8-snap.3357-T1
Valid prediction for GlimmerHMM_glimmerT_21824-T1
Couldn't classify 50894, 51045
Couldn't classify 51356, 51408
Sorry, prediction pasa_asmbl_52573.p1 fails validation.
(GAC)	 CT	50894-51045	GC	AGG
(AAA)	 AG	51146-51237	GT	AGG
(ACA)	 AG	51356-51408	AG	CCA
-recovered pasa_asmbl_52573.p1, internal, 51146, 51237
Valid prediction for GeneMark_model.37159_t
Valid prediction for snap_scaffold_8-snap.3346-T1
Valid prediction for Augustus_model.g14627.t1
Valid prediction for CodingQuarry_transcript_59809-T1
Couldn't classify 116747, 117436
Sorry, prediction pasa_asmbl_53580.p1 fails validation.
(TCT)	 GG	116747-117436	GA	CGG
Valid prediction for snap_scaffold_8-snap.3361-T1
Valid prediction for Augustus_model.g14630.t1
Valid prediction for CodingQuarry_transcript_59813-T1
Valid prediction for GlimmerHMM_glimmerT_21827-T1
Valid prediction for HiQ_model.g14632.t1
Valid prediction for pasa_asmbl_52523.p1
Valid prediction for GeneMark_model.37163_t
Valid prediction for GeneMark_model.37138_t
Valid prediction for GlimmerHMM_glimmerT_21831-T1
Valid prediction for GeneMark_model.37139_t
Valid prediction for snap_scaffold_8-snap.3353-T1
Valid prediction for GeneMark_model.37142_t
Couldn't classify 2661, 2780
Sorry, prediction pasa_asmbl_52521.p1 fails validation.
(ATG)	 AT	235-464	GT	AGG
(GCC)	 AG	632-734	GT	AAG
(GGG)	 AG	2661-2780	AG	TAA
-recovered pasa_asmbl_52521.p1, initial, 235, 464
-recovered pasa_asmbl_52521.p1, internal, 632, 734
Valid prediction for GlimmerHMM_glimmerT_21822-T1
Valid prediction for GlimmerHMM_glimmerT_21839-T1
Valid prediction for GlimmerHMM_glimmerT_21837-T1
Valid prediction for GeneMark_model.37162_t
Valid prediction for snap_scaffold_8-snap.3343-T1
Valid prediction for GlimmerHMM_glimmerT_21809-T1
Valid prediction for Augustus_model.g14642.t1
Valid prediction for snap_scaffold_8-snap.3359-T1
Valid prediction for GlimmerHMM_glimmerT_21840-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 Augustus_model.g14628.t1
Valid prediction for GeneMark_model.37147_t
Valid prediction for GlimmerHMM_glimmerT_21836-T1
Valid prediction for CodingQuarry_transcript_59806-T1
Valid prediction for Augustus_model.g14637.t1
Valid prediction for GeneMark_model.37148_t
Valid prediction for GeneMark_model.37134_t
Valid prediction for GlimmerHMM_glimmerT_21813-T1
Valid prediction for snap_scaffold_8-snap.3348-T1
Valid prediction for Augustus_model.g14626.t1
Valid prediction for snap_scaffold_8-snap.3374-T1
Valid prediction for GlimmerHMM_glimmerT_21835-T1
Valid prediction for Augustus_model.g14618.t1
Valid prediction for GeneMark_model.37154_t
Valid prediction for HiQ_model.g14623.t1
Valid prediction for GlimmerHMM_glimmerT_21829-T1
Valid prediction for snap_scaffold_8-snap.3365-T1
Valid prediction for Augustus_model.g14616.t1
Valid prediction for GlimmerHMM_glimmerT_21808-T1
Valid prediction for GeneMark_model.37137_t
Valid prediction for CodingQuarry_transcript_59811-T1
Valid prediction for Augustus_model.g14625.t1
Valid prediction for GeneMark_model.37132_t
Couldn't classify 123736, 123775
Couldn't classify 124683, 124758
Sorry, prediction CodingQuarry_transcript_59807-T1 fails validation.
(ATG)	 TG	122343-122437	GT	TGG
(GTT)	 AG	122556-122767	GT	AGG
(CAA)	 AG	122956-123057	GT	TGG
(GTA)	 AG	123191-123329	GT	AGG
(ACA)	 AG	123486-123573	GT	CTG
(GAC)	 AG	123736-123775	TC	CTT
(CCA)	 GT	124683-124758	GT	CGG
(GTT)	 AG	125686-125710	CA	AGC
-recovered CodingQuarry_transcript_59807-T1, initial, 122343, 122437
add_exon() Sorry, CodingQuarry_transcript_59807-T1 122556-122767-terminal-2 is invalid.
-recovered CodingQuarry_transcript_59807-T1, terminal, 122556, 122767
-recovered CodingQuarry_transcript_59807-T1, terminal, 125686, 125710
-recovered CodingQuarry_transcript_59807-T1, internal, 122556, 122767
-recovered CodingQuarry_transcript_59807-T1, internal, 122956, 123057
-recovered CodingQuarry_transcript_59807-T1, internal, 123191, 123329
-recovered CodingQuarry_transcript_59807-T1, internal, 123486, 123573
Valid prediction for snap_scaffold_8-snap.3375-T1
Couldn't classify 134384, 134692
Sorry, prediction pasa_asmbl_53528.p1 fails validation.
(CAG)	 TC	134384-134692	TC	GAT
Valid prediction for GeneMark_model.37166_t
Valid prediction for GeneMark_model.37131_t
Valid prediction for Augustus_model.g14633.t1
Valid prediction for GeneMark_model.37168_t
Valid prediction for Augustus_model.g14620.t1
Valid prediction for GlimmerHMM_glimmerT_21814-T1
Couldn't classify 163229, 163314
Sorry, prediction pasa_asmbl_53525.p1 fails validation.
(GAC)	 CA	163229-163314	GT	CGG
(GAC)	 AG	163414-163514	GT	GGG
(AAG)	 AG	163656-163845	GT	AGG
(GTT)	 AG	163923-163986	GT	TGG
(TTT)	 AG	164069-164083	AT	AGA
-recovered pasa_asmbl_53525.p1, terminal, 164069, 164083
-recovered pasa_asmbl_53525.p1, internal, 163414, 163514
-recovered pasa_asmbl_53525.p1, internal, 163656, 163845
-recovered pasa_asmbl_53525.p1, internal, 163923, 163986
Valid prediction for snap_scaffold_8-snap.3370-T1
Valid prediction for GeneMark_model.37161_t
Valid prediction for GeneMark_model.37144_t
Valid prediction for GlimmerHMM_glimmerT_21842-T1
Valid prediction for GeneMark_model.37146_t
Valid prediction for Augustus_model.g14639.t1
Valid prediction for Augustus_model.g14636.t1
Valid prediction for GlimmerHMM_glimmerT_21819-T1
Valid prediction for pasa_asmbl_53533.p1
Couldn't classify 124019, 124039
Couldn't classify 126722, 126763
Sorry, prediction pasa_asmbl_53532.p1 fails validation.
(TAC)	 GA	124019-124039	GT	CGG
(ACT)	 AG	124143-124267	GT	CCG
(ATG)	 AG	124608-124758	GT	CGG
(GTT)	 AG	125686-125769	GT	AGG
(GAT)	 AG	126252-126329	GT	AGG
(GGG)	 AG	126722-126763	CA	AAC
-recovered pasa_asmbl_53532.p1, initial, 124608, 124758
-recovered pasa_asmbl_53532.p1, internal, 124143, 124267
-recovered pasa_asmbl_53532.p1, internal, 124608, 124758
-recovered pasa_asmbl_53532.p1, internal, 125686, 125769
-recovered pasa_asmbl_53532.p1, internal, 126252, 126329
Valid prediction for GeneMark_model.37153_t
Valid prediction for snap_scaffold_8-snap.3364-T1
Valid prediction for GeneMark_model.37150_t
Valid prediction for CodingQuarry_transcript_59812-T1
Valid prediction for Augustus_model.g14631.t1
Valid prediction for snap_scaffold_8-snap.3366-T1
Valid prediction for snap_scaffold_8-snap.3362-T1
Valid prediction for GlimmerHMM_glimmerT_21830-T1
Valid prediction for snap_scaffold_8-snap.3344-T1
Valid prediction for GeneMark_model.37160_t
Valid prediction for Augustus_model.g14640.t1
Valid prediction for snap_scaffold_8-snap.3367-T1
Valid prediction for Augustus_model.g14645.t1
Couldn't classify 215181, 215258
Sorry, prediction pasa_asmbl_53517.p1 fails validation.
(CCA)	 TG	215181-215258	GT	AGG
(ATG)	 AG	215339-215509	GT	GGG
(ATA)	 AG	215629-215830	GT	AGG
(GGG)	 AG	215935-216098	AA	GAA
-recovered pasa_asmbl_53517.p1, initial, 215339, 215509
-recovered pasa_asmbl_53517.p1, terminal, 215935, 216098
-recovered pasa_asmbl_53517.p1, internal, 215339, 215509
-recovered pasa_asmbl_53517.p1, internal, 215629, 215830
Valid prediction for snap_scaffold_8-snap.3371-T1
Valid prediction for GeneMark_model.37167_t
Valid prediction for GlimmerHMM_glimmerT_21810-T1
Valid prediction for GlimmerHMM_glimmerT_21821-T1
Valid prediction for snap_scaffold_8-snap.3355-T1
Valid prediction for GeneMark_model.37156_t
Valid prediction for snap_scaffold_8-snap.3337-T1
Valid prediction for GlimmerHMM_glimmerT_21818-T1
Valid prediction for CodingQuarry_transcript_59810-T1
Valid prediction for snap_scaffold_8-snap.3369-T1
Couldn't classify 133901, 134278
Sorry, prediction pasa_asmbl_53529.p1 fails validation.
(GGC)	 AT	133901-134278	CC	CCC
Valid prediction for GlimmerHMM_glimmerT_21841-T1
Valid prediction for GlimmerHMM_glimmerT_21825-T1
Valid prediction for Augustus_model.g14641.t1
Valid prediction for snap_scaffold_8-snap.3339-T1
Valid prediction for GlimmerHMM_glimmerT_21826-T1
Valid prediction for snap_scaffold_8-snap.3338-T1
Valid prediction for snap_scaffold_8-snap.3352-T1
Valid prediction for snap_scaffold_8-snap.3354-T1
Valid prediction for GlimmerHMM_glimmerT_21816-T1
Couldn't classify 128162, 128232
Couldn't classify 129013, 129130
Sorry, prediction pasa_asmbl_53531.p1 fails validation.
(AGT)	 TT	128162-128232	GT	AGG
(GAT)	 AG	128480-128552	GT	AGG
(TGG)	 AG	128667-128872	GT	TGG
(CTG)	 AG	129013-129130	CT	GAC
-recovered pasa_asmbl_53531.p1, internal, 128480, 128552
-recovered pasa_asmbl_53531.p1, internal, 128667, 128872
Valid prediction for snap_scaffold_8-snap.3351-T1
Valid prediction for GeneMark_model.37143_t
Valid prediction for GlimmerHMM_glimmerT_21832-T1
Valid prediction for GlimmerHMM_glimmerT_21833-T1
Valid prediction for snap_scaffold_8-snap.3360-T1
Valid prediction for GeneMark_model.37133_t
Valid prediction for GlimmerHMM_glimmerT_21807-T1
Valid prediction for Augustus_model.g14617.t1
Valid prediction for GlimmerHMM_glimmerT_21834-T1
Valid prediction for snap_scaffold_8-snap.3349-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 55822, rend_intergenic: 45896  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 230457
-exon list size: 540


building trellis

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68.1    
68.3    
68.5    
68.6    
68.8    
69.0    
69.2    
69.4    
69.6    
69.7    
69.9    
70.1    
70.3    
70.5    
70.7    
70.8    
71.0    
71.2    
71.4    
71.6    
71.8    
72.0    
72.1    
72.3    
72.5    
72.7    
72.9    
73.1    
73.2    
73.4    
73.6    
73.8    
74.0    
74.2    
74.4    
74.5    
74.7    
74.9    
75.1    
75.3    
75.5    
75.6    
75.8    
76.0    
76.2    
76.4    
76.6    
76.8    
76.9    
77.1    
77.3    
77.5    
77.7    
77.9    
78.0    
78.2    
78.4    
78.6    
78.8    
79.0    
79.2    
79.3    
79.5    
79.7    
79.9    
80.1    
80.3    
80.4    
80.6    
80.8    
81.0    
81.2    
81.4    
81.5    
81.7    
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    
85.1    
85.2    
85.4    
85.6    
85.8    
86.0    
86.2    
86.3    
86.5    
86.7    
86.9    
87.1    
87.3    
87.5    
87.6    
87.8    
88.0    
88.2    
88.4    
88.6    
88.7    
88.9    
89.1    
89.3    
89.5    
89.7    
89.9    
90.0    
90.2    
90.4    
90.6    
90.8    
91.0    
91.1    
91.3    
91.5    
91.7    
91.9    
92.1    
92.3    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.5    
93.7    
93.9    
94.1    
94.3    
94.5    
94.6    
94.8    
95.0    
95.2    
95.4    
95.6    
95.8    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.0    
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 42 predictions from path traversal
Error with prediction: snap lend_intergenic: 55822, rend_intergenic: 45896  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 42 predictions persist after filtering for low support