-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_14/scaffold_14_10272577-10463288

-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 GeneMark_model.60602_t
Valid prediction for GeneMark_model.60597_t
Valid prediction for snap_scaffold_14-snap.2154-T1
Valid prediction for GeneMark_model.60569_t
Valid prediction for CodingQuarry_transcript_15759-T1
Valid prediction for CodingQuarry_transcript_15761-T1
Valid prediction for snap_scaffold_14-snap.2161-T1
Valid prediction for GlimmerHMM_glimmerT_35300-T1
Valid prediction for snap_scaffold_14-snap.2134-T1
Valid prediction for GeneMark_model.60608_t
Valid prediction for snap_scaffold_14-snap.2158-T1
Valid prediction for snap_scaffold_14-snap.2132-T1
Couldn't classify 102386, 102418
Couldn't classify 103065, 103165
Sorry, prediction pasa_asmbl_12722.p1 fails validation.
(GGA)	 AT	102386-102418	GT	AGG
(CAC)	 AG	102661-102847	GT	TTG
(ATG)	 AG	103065-103165	CT	CCC
-recovered pasa_asmbl_12722.p1, internal, 102661, 102847
Valid prediction for GeneMark_model.60578_t
Valid prediction for GeneMark_model.60604_t
Valid prediction for snap_scaffold_14-snap.2143-T1
Valid prediction for GlimmerHMM_glimmerT_35291-T1
Valid prediction for GeneMark_model.60576_t
Valid prediction for snap_scaffold_14-snap.2135-T1
Couldn't classify 125118, 125221
Couldn't classify 126861, 126940
Sorry, prediction pasa_asmbl_12296.p1 fails validation.
(GGC)	 TG	125118-125221	GT	GCG
(GAA)	 AG	125788-125870	GT	AGG
(AGC)	 AG	125977-126094	GT	ATG
(GAA)	 AG	126321-126427	GT	AGG
(AGC)	 AG	126861-126940	GG	ACG
-recovered pasa_asmbl_12296.p1, internal, 125788, 125870
-recovered pasa_asmbl_12296.p1, internal, 125977, 126094
-recovered pasa_asmbl_12296.p1, internal, 126321, 126427
Valid prediction for snap_scaffold_14-snap.2167-T1
Valid prediction for Augustus_model.g23738.t1
Valid prediction for pasa_asmbl_12744.p1
Valid prediction for GlimmerHMM_glimmerT_35290-T1
Valid prediction for GeneMark_model.60592_t
Valid prediction for GeneMark_model.60598_t
Valid prediction for GeneMark_model.60575_t
Valid prediction for GeneMark_model.60588_t
Valid prediction for GeneMark_model.60570_t
Valid prediction for HiQ_model.g23741.t1
Valid prediction for Augustus_model.g23740.t1
Valid prediction for GlimmerHMM_glimmerT_35304-T1
Valid prediction for HiQ_model.g23736.t1
Valid prediction for snap_scaffold_14-snap.2138-T1
Valid prediction for GeneMark_model.60606_t
Valid prediction for GeneMark_model.60572_t
Valid prediction for snap_scaffold_14-snap.2142-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_14-snap.2149-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_35303-T1
Valid prediction for GeneMark_model.60580_t
Valid prediction for GlimmerHMM_glimmerT_35296-T1
Valid prediction for GeneMark_model.60593_t
Valid prediction for GeneMark_model.60595_t
Valid prediction for GeneMark_model.60568_t
Valid prediction for snap_scaffold_14-snap.2159-T1
Valid prediction for snap_scaffold_14-snap.2137-T1
Valid prediction for snap_scaffold_14-snap.2163-T1
Valid prediction for snap_scaffold_14-snap.2152-T1
Valid prediction for GeneMark_model.60600_t
Couldn't classify 109445, 109459
Sorry, prediction pasa_asmbl_12293.p1 fails validation.
(TAC)	 GA	109445-109459	GT	AGG
(ATC)	 AG	109750-109855	GT	CGG
(GTT)	 AG	109951-110137	GT	AGG
(GCA)	 AG	110266-110422	GT	AGG
(GCT)	 AG	110560-110622	GG	GAG
-recovered pasa_asmbl_12293.p1, terminal, 110560, 110622
-recovered pasa_asmbl_12293.p1, internal, 109750, 109855
-recovered pasa_asmbl_12293.p1, internal, 109951, 110137
-recovered pasa_asmbl_12293.p1, internal, 110266, 110422
Valid prediction for Augustus_model.g23729.t1
Couldn't classify 127952, 128041
Sorry, prediction pasa_asmbl_12297.p1 fails validation.
(GGG)	 AC	127952-128041	GT	AGG
(GGT)	 AG	128167-128238	GT	ATG
(GTC)	 AG	128327-128455	GT	TGG
(ATG)	 AG	128781-128890	GT	TGG
(GAT)	 AG	129014-129272	GT	AGG
(GTT)	 AG	129988-130035	TA	GAT
-recovered pasa_asmbl_12297.p1, initial, 128781, 128890
-recovered pasa_asmbl_12297.p1, terminal, 129988, 130035
-recovered pasa_asmbl_12297.p1, internal, 128167, 128238
-recovered pasa_asmbl_12297.p1, internal, 128327, 128455
-recovered pasa_asmbl_12297.p1, internal, 128781, 128890
-recovered pasa_asmbl_12297.p1, internal, 129014, 129272
Valid prediction for GeneMark_model.60590_t
Valid prediction for GeneMark_model.60582_t
Valid prediction for snap_scaffold_14-snap.2147-T1
Valid prediction for snap_scaffold_14-snap.2144-T1
Couldn't classify 120919, 121323
Sorry, prediction pasa_asmbl_12295.p1 fails validation.
(ATA)	 AG	120919-121323	AG	CCA
Valid prediction for snap_scaffold_14-snap.2141-T1
Valid prediction for GlimmerHMM_glimmerT_35293-T1
Valid prediction for snap_scaffold_14-snap.2160-T1
Valid prediction for GlimmerHMM_glimmerT_35307-T1
Valid prediction for snap_scaffold_14-snap.2164-T1
Valid prediction for snap_scaffold_14-snap.2155-T1
Valid prediction for pasa_asmbl_12298.p1
Valid prediction for GlimmerHMM_glimmerT_35298-T1
Valid prediction for GeneMark_model.60579_t
Valid prediction for GeneMark_model.60585_t
Valid prediction for GeneMark_model.60567_t
Valid prediction for GeneMark_model.60605_t
Valid prediction for snap_scaffold_14-snap.2140-T1
Valid prediction for GeneMark_model.60583_t
Valid prediction for GlimmerHMM_glimmerT_35289-T1
Valid prediction for GlimmerHMM_glimmerT_35301-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 GeneMark_model.60573_t
Valid prediction for snap_scaffold_14-snap.2153-T1
Valid prediction for CodingQuarry_transcript_15760-T1
Valid prediction for snap_scaffold_14-snap.2165-T1
Valid prediction for snap_scaffold_14-snap.2139-T1
Valid prediction for GeneMark_model.60577_t
Valid prediction for GeneMark_model.60589_t
Valid prediction for GlimmerHMM_glimmerT_35306-T1
Valid prediction for HiQ_model.g23737.t1
Valid prediction for Augustus_model.g23742.t1
Valid prediction for snap_scaffold_14-snap.2150-T1
Valid prediction for snap_scaffold_14-snap.2148-T1
Valid prediction for GeneMark_model.60584_t
Valid prediction for GlimmerHMM_glimmerT_35294-T1
Valid prediction for Augustus_model.g23746.t1
Valid prediction for GlimmerHMM_glimmerT_35297-T1
Couldn't classify 97967, 97981
Sorry, prediction pasa_asmbl_13399.p1 fails validation.
(ATG)	 AG	97195-97233	GT	TGG
(ACG)	 AG	97518-97695	GT	GGG
(CAG)	 AG	97808-97866	GT	AAG
(CCC)	 AG	97967-97981	GA	AGG
-recovered pasa_asmbl_13399.p1, initial, 97195, 97233
-recovered pasa_asmbl_13399.p1, internal, 97195, 97233
-recovered pasa_asmbl_13399.p1, internal, 97518, 97695
-recovered pasa_asmbl_13399.p1, internal, 97808, 97866
Valid prediction for GeneMark_model.60571_t
Valid prediction for Augustus_model.g23733.t1
Valid prediction for Augustus_model.g23735.t1
Valid prediction for GlimmerHMM_glimmerT_35302-T1
Valid prediction for GlimmerHMM_glimmerT_35292-T1
Valid prediction for Augustus_model.g23730.t1
Valid prediction for GeneMark_model.60603_t
Couldn't classify 136386, 136730
Sorry, prediction pasa_asmbl_13392.p1 fails validation.
(CAG)	 TC	136386-136730	TC	CCT
Valid prediction for pasa_asmbl_13400.p1
Valid prediction for Augustus_model.g23745.t1
Valid prediction for GeneMark_model.60601_t
Valid prediction for pasa_asmbl_13398.p1
Valid prediction for Augustus_model.g23732.t1
Couldn't classify 113928, 114690
Couldn't classify 114841, 115025
Sorry, prediction pasa_asmbl_13396.p1 fails validation.
(CGC)	 CC	113928-114690	GT	TGG
(GCT)	 AG	114841-115025	CT	GCC
Couldn't classify 118651, 118695
Couldn't classify 127580, 127735
Sorry, prediction pasa_asmbl_13395.p1 fails validation.
(CTC)	 TA	118651-118695	GC	AGG
(GAT)	 AG	119672-119771	GT	TGG
(GTG)	 AG	121233-121317	GT	AGG
(CAG)	 AG	121574-121700	GT	AGG
(CTG)	 AG	123211-123288	GT	AGG
(TTG)	 AG	124938-125024	GT	TGG
(GCG)	 AG	127580-127735	AG	GGA
-recovered pasa_asmbl_13395.p1, internal, 119672, 119771
-recovered pasa_asmbl_13395.p1, internal, 121233, 121317
-recovered pasa_asmbl_13395.p1, internal, 121574, 121700
-recovered pasa_asmbl_13395.p1, internal, 123211, 123288
-recovered pasa_asmbl_13395.p1, internal, 124938, 125024
Valid prediction for Augustus_model.g23731.t1
Valid prediction for snap_scaffold_14-snap.2162-T1
Valid prediction for GeneMark_model.60607_t
Valid prediction for GeneMark_model.60587_t
Valid prediction for snap_scaffold_14-snap.2151-T1
Valid prediction for snap_scaffold_14-snap.2157-T1
Valid prediction for Augustus_model.g23739.t1
Valid prediction for GlimmerHMM_glimmerT_35305-T1
Valid prediction for Augustus_model.g23743.t1
Valid prediction for GeneMark_model.60581_t
Valid prediction for GlimmerHMM_glimmerT_35299-T1
Couldn't classify 46469, 46761
Sorry, prediction pasa_asmbl_13802.p1 fails validation.
(ATG)	 CC	40702-40742	GT	AGG
(CAT)	 AG	41000-41130	GT	GGG
(ACC)	 AG	41316-41554	GT	AGG
(AAA)	 AG	41664-41725	GT	AGG
(GTT)	 AG	41881-42046	GT	AGG
(GTG)	 AG	42141-42248	GT	AAG
(GAT)	 AG	42576-42692	GT	AGG
(GCG)	 AG	42950-43108	GT	AGG
(GCT)	 AG	43202-43337	GT	TGG
(CCG)	 AG	43658-43705	GT	AGG
(ACA)	 AG	45133-45251	GT	AGG
(GTG)	 AG	45434-45551	GT	AGG
(GGC)	 AG	45891-46025	GT	GGG
(GTG)	 AG	46469-46761	GG	ACG
-recovered pasa_asmbl_13802.p1, initial, 40702, 40742
-recovered pasa_asmbl_13802.p1, internal, 41000, 41130
-recovered pasa_asmbl_13802.p1, internal, 41316, 41554
-recovered pasa_asmbl_13802.p1, internal, 41664, 41725
-recovered pasa_asmbl_13802.p1, internal, 41881, 42046
-recovered pasa_asmbl_13802.p1, internal, 42141, 42248
-recovered pasa_asmbl_13802.p1, internal, 42576, 42692
-recovered pasa_asmbl_13802.p1, internal, 42950, 43108
-recovered pasa_asmbl_13802.p1, internal, 43202, 43337
-recovered pasa_asmbl_13802.p1, internal, 43658, 43705
-recovered pasa_asmbl_13802.p1, internal, 45133, 45251
-recovered pasa_asmbl_13802.p1, internal, 45434, 45551
-recovered pasa_asmbl_13802.p1, internal, 45891, 46025
Valid prediction for snap_scaffold_14-snap.2166-T1
Couldn't classify 36790, 36992
Couldn't classify 40184, 40257
Sorry, prediction pasa_asmbl_13405.p1 fails validation.
(GAC)	 CG	36790-36992	GT	CAG
(CTC)	 AG	38203-38244	GT	TTG
(ATT)	 AG	38665-39034	GT	AGG
(GCG)	 AG	39148-39417	GT	AGG
(GAG)	 AG	39530-39694	GT	GGG
(GCA)	 AG	39834-39951	GT	AGG
(CAG)	 AG	40184-40257	TC	CGT
-recovered pasa_asmbl_13405.p1, internal, 38203, 38244
-recovered pasa_asmbl_13405.p1, internal, 38665, 39034
-recovered pasa_asmbl_13405.p1, internal, 39148, 39417
-recovered pasa_asmbl_13405.p1, internal, 39530, 39694
-recovered pasa_asmbl_13405.p1, internal, 39834, 39951
Valid prediction for GeneMark_model.60596_t
Valid prediction for GeneMark_model.60594_t
Valid prediction for Augustus_model.g23744.t1
Valid prediction for snap_scaffold_14-snap.2146-T1
Valid prediction for snap_scaffold_14-snap.2133-T1
Valid prediction for snap_scaffold_14-snap.2145-T1
Valid prediction for GeneMark_model.60599_t
Valid prediction for snap_scaffold_14-snap.2156-T1
Couldn't classify 47692, 47853
Sorry, prediction pasa_asmbl_13404.p1 fails validation.
(CAG)	 AC	47692-47853	GT	CGG
(ATC)	 AG	48373-48634	GT	AGG
(GCT)	 AG	48887-49005	GT	TGG
(CTG)	 AG	49112-49240	GT	CGG
(ATA)	 AG	49358-49540	GT	AGG
(AAG)	 AG	49711-49881	GT	AGG
(ACC)	 AG	50148-50360	GT	AGG
(ATG)	 AG	50462-50600	GT	CAG
(GGT)	 AG	51255-51379	AT	GAA
-recovered pasa_asmbl_13404.p1, initial, 50462, 50600
-recovered pasa_asmbl_13404.p1, terminal, 51255, 51379
-recovered pasa_asmbl_13404.p1, internal, 48373, 48634
-recovered pasa_asmbl_13404.p1, internal, 48887, 49005
-recovered pasa_asmbl_13404.p1, internal, 49112, 49240
-recovered pasa_asmbl_13404.p1, internal, 49358, 49540
-recovered pasa_asmbl_13404.p1, internal, 49711, 49881
-recovered pasa_asmbl_13404.p1, internal, 50148, 50360
-recovered pasa_asmbl_13404.p1, internal, 50462, 50600
Valid prediction for GlimmerHMM_glimmerT_35295-T1
Valid prediction for GeneMark_model.60591_t
Valid prediction for GeneMark_model.60566_t
Valid prediction for snap_scaffold_14-snap.2136-T1
Valid prediction for GeneMark_model.60574_t
Valid prediction for GeneMark_model.60586_t
Valid prediction for Augustus_model.g23734.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 37917, rend_intergenic: 37685  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59072, rend_intergenic: 50383  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61064, rend_intergenic: 59291  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71667, rend_intergenic: 61068  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80800, rend_intergenic: 74977  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110622, rend_intergenic: 100858  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129320, rend_intergenic: 121452  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136855, rend_intergenic: 132012  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161602, rend_intergenic: 140784  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171419, rend_intergenic: 168569  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181573, rend_intergenic: 175406  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 190712
-exon list size: 642


building trellis

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60.2    
60.4    
60.6    
60.7    
60.9    
61.0    
61.2    
61.3    
61.5    
61.6    
61.8    
62.0    
62.1    
62.3    
62.4    
62.6    
62.7    
62.9    
63.0    
63.2    
63.4    
63.5    
63.7    
63.8    
64.0    
64.1    
64.3    
64.4    
64.6    
64.8    
64.9    
65.1    
65.2    
65.4    
65.5    
65.7    
65.8    
66.0    
66.1    
66.3    
66.5    
66.6    
66.8    
66.9    
67.1    
67.2    
67.4    
67.5    
67.7    
67.9    
68.0    
68.2    
68.3    
68.5    
68.6    
68.8    
68.9    
69.1    
69.3    
69.4    
69.6    
69.7    
69.9    
70.0    
70.2    
70.3    
70.5    
70.7    
70.8    
71.0    
71.1    
71.3    
71.4    
71.6    
71.7    
71.9    
72.0    
72.2    
72.4    
72.5    
72.7    
72.8    
73.0    
73.1    
73.3    
73.4    
73.6    
73.8    
73.9    
74.1    
74.2    
74.4    
74.5    
74.7    
74.8    
75.0    
75.2    
75.3    
75.5    
75.6    
75.8    
75.9    
76.1    
76.2    
76.4    
76.6    
76.7    
76.9    
77.0    
77.2    
77.3    
77.5    
77.6    
77.8    
78.0    
78.1    
78.3    
78.4    
78.6    
78.7    
78.9    
79.0    
79.2    
79.3    
79.5    
79.7    
79.8    
80.0    
80.1    
80.3    
80.4    
80.6    
80.7    
80.9    
81.1    
81.2    
81.4    
81.5    
81.7    
81.8    
82.0    
82.1    
82.3    
82.5    
82.6    
82.8    
82.9    
83.1    
83.2    
83.4    
83.5    
83.7    
83.9    
84.0    
84.2    
84.3    
84.5    
84.6    
84.8    
84.9    
85.1    
85.2    
85.4    
85.6    
85.7    
85.9    
86.0    
86.2    
86.3    
86.5    
86.6    
86.8    
87.0    
87.1    
87.3    
87.4    
87.6    
87.7    
87.9    
88.0    
88.2    
88.4    
88.5    
88.7    
88.8    
89.0    
89.1    
89.3    
89.4    
89.6    
89.8    
89.9    
90.1    
90.2    
90.4    
90.5    
90.7    
90.8    
91.0    
91.1    
91.3    
91.5    
91.6    
91.8    
91.9    
92.1    
92.2    
92.4    
92.5    
92.7    
92.9    
93.0    
93.2    
93.3    
93.5    
93.6    
93.8    
93.9    
94.1    
94.3    
94.4    
94.6    
94.7    
94.9    
95.0    
95.2    
95.3    
95.5    
95.7    
95.8    
96.0    
96.1    
96.3    
96.4    
96.6    
96.7    
96.9    
97.0    
97.2    
97.4    
97.5    
97.7    
97.8    
98.0    
98.1    
98.3    
98.4    
98.6    
98.8    
98.9    
99.1    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 37917, rend_intergenic: 37685  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59072, rend_intergenic: 50383  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61064, rend_intergenic: 59291  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71667, rend_intergenic: 61068  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80800, rend_intergenic: 74977  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110622, rend_intergenic: 100858  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129320, rend_intergenic: 121452  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136855, rend_intergenic: 132012  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161602, rend_intergenic: 140784  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171419, rend_intergenic: 168569  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181573, rend_intergenic: 175406  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 15407
-exon list size: 14


building trellis

6.2    
12.5    
18.8    
25.0    
31.2    
37.5    
43.8    
50.0    
56.2    
62.5    
68.8    
75.0    
81.2    
87.5    
93.8    
-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