-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_4/scaffold_4_17538657-17712559

-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 pasa_asmbl_43406.p1
Valid prediction for GlimmerHMM_glimmerT_11280-T1
Valid prediction for snap_scaffold_4-snap.3623-T1
Valid prediction for GlimmerHMM_glimmerT_11274-T1
Valid prediction for snap_scaffold_4-snap.3608-T1
Valid prediction for snap_scaffold_4-snap.3607-T1
Valid prediction for GeneMark_model.18491_t
Valid prediction for GeneMark_model.18521_t
Valid prediction for snap_scaffold_4-snap.3622-T1
Valid prediction for GeneMark_model.18484_t
Valid prediction for snap_scaffold_4-snap.3617-T1
Valid prediction for GeneMark_model.18487_t
Valid prediction for pasa_asmbl_43407.p1
Valid prediction for HiQ_model.g7448.t1
Valid prediction for GlimmerHMM_glimmerT_11275-T1
Valid prediction for GeneMark_model.18496_t
Valid prediction for GlimmerHMM_glimmerT_11278-T1
Valid prediction for CodingQuarry_transcript_49231-T1
Valid prediction for snap_scaffold_4-snap.3612-T1
Valid prediction for snap_scaffold_4-snap.3616-T1
Valid prediction for GlimmerHMM_glimmerT_11276-T1
Valid prediction for CodingQuarry_transcript_49239-T1
Valid prediction for snap_scaffold_4-snap.3602-T1
Valid prediction for CodingQuarry_transcript_49243-T1
Valid prediction for CodingQuarry_transcript_49241-T1
Valid prediction for GeneMark_model.18497_t
Valid prediction for GeneMark_model.18507_t
Valid prediction for GlimmerHMM_glimmerT_11271-T1
Valid prediction for pasa_asmbl_43588.p1
Valid prediction for GlimmerHMM_glimmerT_11267-T1
Valid prediction for CodingQuarry_transcript_49237-T1
Valid prediction for HiQ_model.g7452.t1
Valid prediction for GeneMark_model.18509_t
Valid prediction for GlimmerHMM_glimmerT_11273-T1
Valid prediction for snap_scaffold_4-snap.3605-T1
Valid prediction for GeneMark_model.18515_t
Valid prediction for GeneMark_model.18511_t
Valid prediction for Augustus_model.g7459.t1
Valid prediction for snap_scaffold_4-snap.3614-T1
Valid prediction for CodingQuarry_transcript_49233-T1
Valid prediction for GeneMark_model.18494_t
Valid prediction for GeneMark_model.18499_t
Valid prediction for CodingQuarry_transcript_49242-T1
Valid prediction for pasa_asmbl_43402.p1
Valid prediction for HiQ_model.g7446.t1
Valid prediction for GlimmerHMM_glimmerT_11277-T1
Valid prediction for snap_scaffold_4-snap.3600-T1
Valid prediction for GeneMark_model.18517_t
Valid prediction for GlimmerHMM_glimmerT_11269-T1
Couldn't classify 16279, 16341
Sorry, prediction pasa_asmbl_43524.p1 fails validation.
(ATG)	 AA	14718-14764	GT	TGG
(GTC)	 AG	15212-15344	GT	AGG
(GCT)	 AG	15600-15743	GT	CTG
(TAT)	 AG	16014-16091	GT	AGG
(CCT)	 AG	16279-16341	CC	CCC
-recovered pasa_asmbl_43524.p1, initial, 14718, 14764
-recovered pasa_asmbl_43524.p1, internal, 15212, 15344
-recovered pasa_asmbl_43524.p1, internal, 15600, 15743
-recovered pasa_asmbl_43524.p1, internal, 16014, 16091
Valid prediction for CodingQuarry_transcript_49240-T1
Valid prediction for HiQ_model.g7442.t1
Valid prediction for GeneMark_model.18508_t
Valid prediction for GeneMark_model.18481_t
Valid prediction for GeneMark_model.18485_t
Valid prediction for GeneMark_model.18513_t
Valid prediction for snap_scaffold_4-snap.3610-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.18478_t
Valid prediction for snap_scaffold_4-snap.3632-T1
Valid prediction for GeneMark_model.18479_t
Valid prediction for pasa_asmbl_43410.p1
Valid prediction for pasa_asmbl_43397.p1
Valid prediction for GlimmerHMM_glimmerT_11266-T1
Valid prediction for Augustus_model.g7445.t1
Valid prediction for Augustus_model.g7449.t1
Valid prediction for snap_scaffold_4-snap.3603-T1
Valid prediction for CodingQuarry_transcript_49247-T1
Valid prediction for HiQ_model.g7439.t1
Valid prediction for GeneMark_model.18488_t
Valid prediction for CodingQuarry_transcript_49238-T1
Valid prediction for snap_scaffold_4-snap.3599-T1
Valid prediction for GeneMark_model.18489_t
Valid prediction for Augustus_model.g7454.t1
Valid prediction for CodingQuarry_transcript_49244-T1
Valid prediction for snap_scaffold_4-snap.3611-T1
Valid prediction for GlimmerHMM_glimmerT_11281-T1
Valid prediction for GlimmerHMM_glimmerT_11287-T1
Valid prediction for snap_scaffold_4-snap.3630-T1
Valid prediction for snap_scaffold_4-snap.3609-T1
Valid prediction for Augustus_model.g7447.t1
Valid prediction for snap_scaffold_4-snap.3625-T1
Valid prediction for HiQ_model.g7440.t1
Valid prediction for snap_scaffold_4-snap.3635-T1
Valid prediction for GeneMark_model.18503_t
Valid prediction for snap_scaffold_4-snap.3628-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 pasa_asmbl_42386.p1
Valid prediction for GlimmerHMM_glimmerT_11279-T1
Couldn't classify 23076, 23672
Sorry, prediction pasa_asmbl_42054.p1 fails validation.
(CGA)	 AT	23076-23672	GT	TGG
Valid prediction for snap_scaffold_4-snap.3629-T1
Valid prediction for GlimmerHMM_glimmerT_11282-T1
Valid prediction for snap_scaffold_4-snap.3618-T1
Valid prediction for GlimmerHMM_glimmerT_11286-T1
Couldn't classify 68901, 68971
Sorry, prediction pasa_asmbl_42047.p1 fails validation.
(GAT)	 GC	68901-68971	GT	CGG
(AAA)	 AG	69337-69402	GT	AGG
(CTC)	 AG	70191-70437	GT	AGG
(CTC)	 AG	70527-70567	GT	AGG
(GAC)	 AG	71093-71165	GA	AGG
-recovered pasa_asmbl_42047.p1, terminal, 71093, 71165
-recovered pasa_asmbl_42047.p1, internal, 69337, 69402
-recovered pasa_asmbl_42047.p1, internal, 70191, 70437
-recovered pasa_asmbl_42047.p1, internal, 70527, 70567
Valid prediction for GeneMark_model.18490_t
Valid prediction for GeneMark_model.18512_t
Couldn't classify 82737, 82878
Sorry, prediction pasa_asmbl_42042.p1 fails validation.
(ATG)	 CC	79474-79498	GT	AGG
(GTG)	 AG	79711-79778	GT	AGG
(CTT)	 AG	79859-79933	GT	AAG
(CGA)	 AG	80023-80112	GT	CGG
(CAA)	 AG	80270-80398	GT	CGG
(AAC)	 AG	80489-80584	GT	AGG
(GAT)	 AG	80747-80960	GT	ACG
(CTC)	 AG	81089-81216	GT	CAG
(GAG)	 AG	81314-81370	GT	AGG
(TCA)	 AG	81499-82420	GT	GAG
(GTT)	 AG	82511-82616	GT	CCG
(GAT)	 AG	82737-82878	GT	AGG
-recovered pasa_asmbl_42042.p1, initial, 79474, 79498
-recovered pasa_asmbl_42042.p1, internal, 79711, 79778
-recovered pasa_asmbl_42042.p1, internal, 79859, 79933
-recovered pasa_asmbl_42042.p1, internal, 80023, 80112
-recovered pasa_asmbl_42042.p1, internal, 80270, 80398
-recovered pasa_asmbl_42042.p1, internal, 80489, 80584
-recovered pasa_asmbl_42042.p1, internal, 80747, 80960
-recovered pasa_asmbl_42042.p1, internal, 81089, 81216
-recovered pasa_asmbl_42042.p1, internal, 81314, 81370
-recovered pasa_asmbl_42042.p1, internal, 81499, 82420
-recovered pasa_asmbl_42042.p1, internal, 82511, 82616
-recovered pasa_asmbl_42042.p1, internal, 82737, 82878
Valid prediction for GeneMark_model.18492_t
Valid prediction for Augustus_model.g7453.t1
Valid prediction for snap_scaffold_4-snap.3626-T1
Valid prediction for CodingQuarry_transcript_49245-T1
Valid prediction for snap_scaffold_4-snap.3606-T1
Valid prediction for Augustus_model.g7450.t1
Valid prediction for Augustus_model.g7443.t1
Valid prediction for snap_scaffold_4-snap.3624-T1
Valid prediction for GeneMark_model.18486_t
Valid prediction for snap_scaffold_4-snap.3634-T1
Valid prediction for GlimmerHMM_glimmerT_11283-T1
Valid prediction for GeneMark_model.18502_t
Valid prediction for GeneMark_model.18483_t
Valid prediction for GlimmerHMM_glimmerT_11268-T1
Valid prediction for snap_scaffold_4-snap.3631-T1
Valid prediction for GlimmerHMM_glimmerT_11284-T1
Valid prediction for Augustus_model.g7441.t1
Valid prediction for GlimmerHMM_glimmerT_11285-T1
Couldn't classify 84564, 84626
Sorry, prediction pasa_asmbl_42328.p1 fails validation.
(GGG)	 CA	84564-84626	GT	AGG
(GCT)	 AG	85946-86057	GT	AGG
(ACA)	 AG	86210-86408	GT	AGG
(ACA)	 AG	86534-86666	GT	AGG
(GGC)	 AG	86930-87055	GT	AGG
(GGC)	 AG	87398-87496	AG	GAA
-recovered pasa_asmbl_42328.p1, terminal, 87398, 87496
-recovered pasa_asmbl_42328.p1, internal, 85946, 86057
-recovered pasa_asmbl_42328.p1, internal, 86210, 86408
-recovered pasa_asmbl_42328.p1, internal, 86534, 86666
-recovered pasa_asmbl_42328.p1, internal, 86930, 87055
Valid prediction for pasa_asmbl_42038.p1
Valid prediction for CodingQuarry_transcript_49236-T1
Valid prediction for snap_scaffold_4-snap.3633-T1
Valid prediction for GeneMark_model.18495_t
Couldn't classify 31861, 31962
Sorry, prediction pasa_asmbl_42050.p1 fails validation.
(ATG)	 GA	28468-28534	GT	CAG
(TCC)	 AG	30998-31148	GT	AGG
(TAA)	 AG	31618-31684	GT	AGG
(GGC)	 AG	31861-31962	GA	GAG
-recovered pasa_asmbl_42050.p1, initial, 28468, 28534
-recovered pasa_asmbl_42050.p1, internal, 30998, 31148
-recovered pasa_asmbl_42050.p1, internal, 31618, 31684
Valid prediction for GeneMark_model.18493_t
Valid prediction for snap_scaffold_4-snap.3619-T1
Valid prediction for CodingQuarry_transcript_49248-T1
Valid prediction for Augustus_model.g7444.t1
Couldn't classify 161044, 161188
Sorry, prediction pasa_asmbl_42032.p1 fails validation.
(GAA)	 AA	161044-161188	GT	AAG
(ACG)	 AG	162446-163401	GG	AGG
-recovered pasa_asmbl_42032.p1, terminal, 162446, 163401
Valid prediction for pasa_asmbl_42057.p1
Valid prediction for HiQ_model.g7455.t1
Valid prediction for CodingQuarry_transcript_49234-T1
Valid prediction for Augustus_model.g7456.t1
Valid prediction for Augustus_model.g7458.t1
Valid prediction for CodingQuarry_transcript_49235-T1
Valid prediction for snap_scaffold_4-snap.3620-T1
Valid prediction for CodingQuarry_transcript_49246-T1
Valid prediction for snap_scaffold_4-snap.3621-T1
Valid prediction for GeneMark_model.18482_t
Valid prediction for GeneMark_model.18505_t
Valid prediction for snap_scaffold_4-snap.3627-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for HiQ_model.g7457.t1
Valid prediction for snap_scaffold_4-snap.3601-T1
Valid prediction for snap_scaffold_4-snap.3613-T1
Valid prediction for GeneMark_model.18500_t
Couldn't classify 24312, 24677
Sorry, prediction pasa_asmbl_42052.p1 fails validation.
(CCC)	 AC	24312-24677	GT	AGG
(GTC)	 AG	25221-25283	GC	GAG
-recovered pasa_asmbl_42052.p1, terminal, 25221, 25283
-recovered pasa_asmbl_42052.p1, internal, 25221, 25283
Valid prediction for HiQ_model.g7451.t1
Valid prediction for GeneMark_model.18520_t
Valid prediction for GeneMark_model.18498_t
Valid prediction for GeneMark_model.18504_t
Valid prediction for GeneMark_model.18522_t
Valid prediction for CodingQuarry_transcript_49249-T1
Valid prediction for snap_scaffold_4-snap.3615-T1
Valid prediction for GeneMark_model.18510_t
Valid prediction for GeneMark_model.18519_t
Valid prediction for GeneMark_model.18514_t
Valid prediction for GlimmerHMM_glimmerT_11272-T1
Valid prediction for snap_scaffold_4-snap.3604-T1
Valid prediction for GlimmerHMM_glimmerT_11270-T1
Couldn't classify 23670, 24140
Sorry, prediction pasa_asmbl_42053.p1 fails validation.
(GTG)	 GG	23670-24140	CC	CCC
Valid prediction for GeneMark_model.18516_t
Valid prediction for GeneMark_model.18506_t
Valid prediction for GeneMark_model.18501_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 36557, rend_intergenic: 32646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65018, rend_intergenic: 64569  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69106, rend_intergenic: 66230  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77436, rend_intergenic: 72410  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89669, rend_intergenic: 86408  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113840, rend_intergenic: 105077  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127891, rend_intergenic: 120160  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138110, rend_intergenic: 136630  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143685, rend_intergenic: 138898  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155892, rend_intergenic: 151199  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 173903
-exon list size: 647


building trellis

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77.2    
77.3    
77.5    
77.7    
77.8    
78.0    
78.1    
78.3    
78.4    
78.6    
78.7    
78.9    
79.0    
79.2    
79.4    
79.5    
79.7    
79.8    
80.0    
80.1    
80.3    
80.4    
80.6    
80.7    
80.9    
81.0    
81.2    
81.4    
81.5    
81.7    
81.8    
82.0    
82.1    
82.3    
82.4    
82.6    
82.7    
82.9    
83.1    
83.2    
83.4    
83.5    
83.7    
83.8    
84.0    
84.1    
84.3    
84.4    
84.6    
84.7    
84.9    
85.1    
85.2    
85.4    
85.5    
85.7    
85.8    
86.0    
86.1    
86.3    
86.4    
86.6    
86.7    
86.9    
87.1    
87.2    
87.4    
87.5    
87.7    
87.8    
88.0    
88.1    
88.3    
88.4    
88.6    
88.8    
88.9    
89.1    
89.2    
89.4    
89.5    
89.7    
89.8    
90.0    
90.1    
90.3    
90.4    
90.6    
90.8    
90.9    
91.1    
91.2    
91.4    
91.5    
91.7    
91.8    
92.0    
92.1    
92.3    
92.4    
92.6    
92.8    
92.9    
93.1    
93.2    
93.4    
93.5    
93.7    
93.8    
94.0    
94.1    
94.3    
94.5    
94.6    
94.8    
94.9    
95.1    
95.2    
95.4    
95.5    
95.7    
95.8    
96.0    
96.1    
96.3    
96.5    
96.6    
96.8    
96.9    
97.1    
97.2    
97.4    
97.5    
97.7    
97.8    
98.0    
98.2    
98.3    
98.5    
98.6    
98.8    
98.9    
99.1    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 36557, rend_intergenic: 32646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65018, rend_intergenic: 64569  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69106, rend_intergenic: 66230  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77436, rend_intergenic: 72410  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89669, rend_intergenic: 86408  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113840, rend_intergenic: 105077  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127891, rend_intergenic: 120160  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138110, rend_intergenic: 136630  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143685, rend_intergenic: 138898  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155892, rend_intergenic: 151199  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support