-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_18/scaffold_18_1376299-1551352

-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 snap_scaffold_18-snap.308-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for snap_scaffold_18-snap.301-T1
Valid prediction for GlimmerHMM_glimmerT_42726-T1
Valid prediction for CodingQuarry_transcript_23614-T1
Valid prediction for snap_scaffold_18-snap.271-T1
Valid prediction for snap_scaffold_18-snap.270-T1
Valid prediction for GeneMark_model.73868_t
Valid prediction for snap_scaffold_18-snap.285-T1
Valid prediction for pasa_asmbl_20385.p1
Valid prediction for GlimmerHMM_glimmerT_42737-T1
Valid prediction for Augustus_model.g28579.t1
Valid prediction for snap_scaffold_18-snap.297-T1
Valid prediction for pasa_asmbl_20382.p1
Valid prediction for HiQ_model.g28589.t1
Valid prediction for snap_scaffold_18-snap.288-T1
Valid prediction for snap_scaffold_18-snap.292-T1
Valid prediction for GlimmerHMM_glimmerT_42729-T1
Couldn't classify 50269, 50463
Sorry, prediction pasa_asmbl_20374.p1 fails validation.
(ATG)	 CT	48269-48388	GT	CGG
(ATG)	 AG	50269-50463	AC	TCA
-recovered pasa_asmbl_20374.p1, initial, 48269, 48388
Valid prediction for GlimmerHMM_glimmerT_42730-T1
Valid prediction for GeneMark_model.73871_t
Couldn't classify 55874, 55888
Couldn't classify 56963, 57078
Sorry, prediction CodingQuarry_transcript_23607-T1 fails validation.
(ATG)	 TC	55874-55888	AA	GGA
(CAG)	 CA	56963-57078	GT	AGG
(TGC)	 AG	57680-57740	CC	AGC
-recovered CodingQuarry_transcript_23607-T1, terminal, 57680, 57740
Valid prediction for GeneMark_model.73862_t
Valid prediction for snap_scaffold_18-snap.279-T1
Couldn't classify 53624, 53643
Sorry, prediction pasa_asmbl_20375.p1 fails validation.
(ATG)	 GG	53015-53080	GT	AGG
(CTG)	 AG	53195-53286	GT	CCG
(GGA)	 AG	53383-53522	GT	AGG
(ATC)	 AG	53624-53643	AT	TGA
-recovered pasa_asmbl_20375.p1, initial, 53015, 53080
add_exon() Sorry, pasa_asmbl_20375.p1 53383-53522-terminal-2 is invalid.
-recovered pasa_asmbl_20375.p1, terminal, 53383, 53522
-recovered pasa_asmbl_20375.p1, internal, 53195, 53286
-recovered pasa_asmbl_20375.p1, internal, 53383, 53522
Couldn't classify 122990, 123046
Sorry, prediction pasa_asmbl_20379.p1 fails validation.
(TCG)	 TC	122990-123046	GT	TGG
(ACT)	 AG	123438-123518	GT	CGG
(TCG)	 AG	123644-123752	GT	AGG
(TCA)	 AG	123848-123945	TT	AGT
-recovered pasa_asmbl_20379.p1, terminal, 123848, 123945
-recovered pasa_asmbl_20379.p1, internal, 123438, 123518
-recovered pasa_asmbl_20379.p1, internal, 123644, 123752
Valid prediction for snap_scaffold_18-snap.304-T1
Valid prediction for Augustus_model.g28571.t1
Valid prediction for CodingQuarry_transcript_23609-T1
Valid prediction for snap_scaffold_18-snap.283-T1
Valid prediction for GlimmerHMM_glimmerT_42716-T1
Valid prediction for CodingQuarry_transcript_23612-T1
Valid prediction for GlimmerHMM_glimmerT_42724-T1
Valid prediction for snap_scaffold_18-snap.290-T1
Valid prediction for GeneMark_model.73882_t
Valid prediction for snap_scaffold_18-snap.287-T1
Couldn't classify 1731, 2145
Couldn't classify 2167, 2180
Sorry, prediction pasa_asmbl_20370.p1 fails validation.
(CTC)	 GC	1731-2145	GT	AGG
(GCA)	 AG	2167-2180	GG	AGG
Valid prediction for snap_scaffold_18-snap.299-T1
Valid prediction for GeneMark_model.73864_t
Valid prediction for Augustus_model.g28577.t1
Valid prediction for GeneMark_model.73880_t
Valid prediction for HiQ_model.g28587.t1
Valid prediction for snap_scaffold_18-snap.307-T1
Valid prediction for GlimmerHMM_glimmerT_42735-T1
Couldn't classify 53788, 53815
Couldn't classify 55240, 55336
Sorry, prediction pasa_asmbl_20376.p1 fails validation.
(ACC)	 CT	53788-53815	GT	AGG
(GTA)	 AG	53961-54052	GT	AGG
(CTT)	 AG	54172-54248	GT	CGG
(ACA)	 AG	54387-54447	GT	AGG
(ATT)	 AG	54532-54672	GT	AGG
(ATG)	 AG	54787-54903	GT	AGG
(GCT)	 AG	55022-55116	GT	AGG
(GTT)	 AG	55240-55336	GC	ACG
-recovered pasa_asmbl_20376.p1, initial, 54787, 54903
-recovered pasa_asmbl_20376.p1, internal, 53961, 54052
-recovered pasa_asmbl_20376.p1, internal, 54172, 54248
-recovered pasa_asmbl_20376.p1, internal, 54387, 54447
-recovered pasa_asmbl_20376.p1, internal, 54532, 54672
-recovered pasa_asmbl_20376.p1, internal, 54787, 54903
-recovered pasa_asmbl_20376.p1, internal, 55022, 55116
-recovered pasa_asmbl_20376.p1, internal, 55240, 55336
Valid prediction for GlimmerHMM_glimmerT_42717-T1
Valid prediction for GlimmerHMM_glimmerT_42720-T1
Valid prediction for HiQ_model.g28585.t1
Valid prediction for snap_scaffold_18-snap.295-T1
Couldn't classify 1272, 1721
Sorry, prediction pasa_asmbl_20369.p1 fails validation.
(ATC)	 AG	1272-1721	CC	CCC
Valid prediction for pasa_asmbl_20373.p1
Valid prediction for GlimmerHMM_glimmerT_42738-T1
Valid prediction for snap_scaffold_18-snap.273-T1
Valid prediction for snap_scaffold_18-snap.275-T1
Valid prediction for HiQ_model.g28573.t1
Valid prediction for CodingQuarry_transcript_23606-T1
Valid prediction for snap_scaffold_18-snap.303-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 snap_scaffold_18-snap.293-T1
Valid prediction for GlimmerHMM_glimmerT_42734-T1
Valid prediction for snap_scaffold_18-snap.294-T1
Valid prediction for GlimmerHMM_glimmerT_42727-T1
Valid prediction for GeneMark_model.73867_t
Valid prediction for GeneMark_model.73876_t
Valid prediction for GeneMark_model.73870_t
Valid prediction for Augustus_model.g28575.t1
Couldn't classify 113687, 114071
Sorry, prediction pasa_asmbl_19659.p1 fails validation.
(GAT)	 CG	113687-114071	GT	AGG
(GAC)	 AG	114289-114407	GT	AGG
(GTG)	 AG	114854-115042	GT	AAG
-recovered pasa_asmbl_19659.p1, terminal, 114854, 115042
-recovered pasa_asmbl_19659.p1, internal, 114289, 114407
-recovered pasa_asmbl_19659.p1, internal, 114854, 115042
Valid prediction for GeneMark_model.73874_t
Valid prediction for Augustus_model.g28591.t1
Valid prediction for CodingQuarry_transcript_23611-T1
Valid prediction for GlimmerHMM_glimmerT_42733-T1
Valid prediction for snap_scaffold_18-snap.269-T1
Valid prediction for GeneMark_model.73875_t
Valid prediction for GlimmerHMM_glimmerT_42743-T1
Valid prediction for GeneMark_model.73883_t
Valid prediction for snap_scaffold_18-snap.305-T1
Valid prediction for pasa_asmbl_19661.p1
Valid prediction for GlimmerHMM_glimmerT_42723-T1
Valid prediction for snap_scaffold_18-snap.291-T1
Valid prediction for snap_scaffold_18-snap.284-T1
Valid prediction for snap_scaffold_18-snap.277-T1
Valid prediction for GlimmerHMM_glimmerT_42741-T1
Valid prediction for Augustus_model.g28578.t1
Valid prediction for GeneMark_model.73861_t
Valid prediction for GlimmerHMM_glimmerT_42721-T1
Valid prediction for Augustus_model.g28576.t1
Valid prediction for Augustus_model.g28583.t1
Valid prediction for GlimmerHMM_glimmerT_42725-T1
Valid prediction for CodingQuarry_transcript_23605-T1
Valid prediction for snap_scaffold_18-snap.278-T1
Valid prediction for snap_scaffold_18-snap.268-T1
Valid prediction for Augustus_model.g28588.t1
Valid prediction for GlimmerHMM_glimmerT_42728-T1
Valid prediction for GeneMark_model.73878_t
Valid prediction for GlimmerHMM_glimmerT_42731-T1
Valid prediction for Augustus_model.g28570.t1
Valid prediction for GeneMark_model.73884_t
Valid prediction for snap_scaffold_18-snap.289-T1
Valid prediction for pasa_asmbl_19660.p1
Valid prediction for GeneMark_model.73881_t
Valid prediction for snap_scaffold_18-snap.272-T1
Valid prediction for snap_scaffold_18-snap.286-T1
Valid prediction for snap_scaffold_18-snap.296-T1
Valid prediction for Augustus_model.g28582.t1
Valid prediction for snap_scaffold_18-snap.298-T1
Valid prediction for GlimmerHMM_glimmerT_42718-T1
Valid prediction for snap_scaffold_18-snap.281-T1
Valid prediction for snap_scaffold_18-snap.280-T1
Valid prediction for snap_scaffold_18-snap.276-T1
Valid prediction for GeneMark_model.73877_t
Valid prediction for GlimmerHMM_glimmerT_42719-T1
Valid prediction for pasa_asmbl_19651.p1
Valid prediction for GeneMark_model.73863_t
Valid prediction for GlimmerHMM_glimmerT_42744-T1
Valid prediction for HiQ_model.g28572.t1
Valid prediction for GeneMark_model.73872_t
Valid prediction for pasa_asmbl_19647.p1
Couldn't classify 41052, 41120
Sorry, prediction pasa_asmbl_19662.p1 fails validation.
(TCA)	 CA	41052-41120	GT	TGG
(GAG)	 AG	41207-41260	GT	AGG
(ACA)	 AG	41356-41465	GT	AGG
(GAG)	 AG	41596-41698	GT	CTG
(GAC)	 AG	41824-41898	GT	TGG
(TTG)	 AG	42272-42394	CA	GAC
-recovered pasa_asmbl_19662.p1, terminal, 42272, 42394
-recovered pasa_asmbl_19662.p1, internal, 41207, 41260
-recovered pasa_asmbl_19662.p1, internal, 41356, 41465
-recovered pasa_asmbl_19662.p1, internal, 41596, 41698
-recovered pasa_asmbl_19662.p1, internal, 41824, 41898
Valid prediction for GlimmerHMM_glimmerT_42732-T1
Couldn't classify 49553, 49674
Sorry, prediction CodingQuarry_transcript_23610-T1 fails validation.
(ATG)	 TT	47606-47609	GT	GGG
(TTG)	 AG	48132-48212	GT	CGG
(GCT)	 AG	48906-49015	GT	AGG
(GGC)	 AG	49157-49228	GT	TGG
(CTG)	 AG	49553-49674	AA	AGA
(TGG)	 AG	49773-50070	TT	GAT
-recovered CodingQuarry_transcript_23610-T1, initial, 47606, 47609
-recovered CodingQuarry_transcript_23610-T1, terminal, 49773, 50070
-recovered CodingQuarry_transcript_23610-T1, internal, 48132, 48212
-recovered CodingQuarry_transcript_23610-T1, internal, 48906, 49015
-recovered CodingQuarry_transcript_23610-T1, internal, 49157, 49228
Valid prediction for HiQ_model.g28586.t1
Valid prediction for GlimmerHMM_glimmerT_42722-T1
Valid prediction for snap_scaffold_18-snap.282-T1
Valid prediction for HiQ_model.g28584.t1
Valid prediction for GlimmerHMM_glimmerT_42736-T1
Valid prediction for GlimmerHMM_glimmerT_42715-T1
Valid prediction for GeneMark_model.73873_t
Valid prediction for GlimmerHMM_glimmerT_42742-T1
Valid prediction for CodingQuarry_transcript_23613-T1
Valid prediction for GlimmerHMM_glimmerT_42745-T1
Valid prediction for CodingQuarry_transcript_23608-T1
Valid prediction for GeneMark_model.73866_t
Valid prediction for GlimmerHMM_glimmerT_42740-T1
Valid prediction for snap_scaffold_18-snap.302-T1
Valid prediction for Augustus_model.g28590.t1
Valid prediction for snap_scaffold_18-snap.306-T1
Valid prediction for Augustus_model.g28574.t1
Valid prediction for Augustus_model.g28581.t1
Valid prediction for GeneMark_model.73865_t
Valid prediction for snap_scaffold_18-snap.300-T1
Valid prediction for GlimmerHMM_glimmerT_42739-T1
Valid prediction for GeneMark_model.73879_t
Valid prediction for Augustus_model.g28580.t1
Valid prediction for snap_scaffold_18-snap.274-T1
Valid prediction for GeneMark_model.73869_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15362, rend_intergenic: 7961  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21544, rend_intergenic: 15979  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22951, rend_intergenic: 22648  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25696, rend_intergenic: 22961  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58040, rend_intergenic: 53294  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93281, rend_intergenic: 91141  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105491, rend_intergenic: 102464  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109679, rend_intergenic: 106542  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141157, rend_intergenic: 139073  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151970, rend_intergenic: 143158  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160935, rend_intergenic: 152584  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172083, rend_intergenic: 164813  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 175054
-exon list size: 617


building trellis

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82.4    
82.6    
82.7    
82.9    
83.0    
83.2    
83.4    
83.5    
83.7    
83.8    
84.0    
84.2    
84.3    
84.5    
84.7    
84.8    
85.0    
85.1    
85.3    
85.5    
85.6    
85.8    
85.9    
86.1    
86.3    
86.4    
86.6    
86.8    
86.9    
87.1    
87.2    
87.4    
87.6    
87.7    
87.9    
88.0    
88.2    
88.4    
88.5    
88.7    
88.9    
89.0    
89.2    
89.3    
89.5    
89.7    
89.8    
90.0    
90.1    
90.3    
90.5    
90.6    
90.8    
91.0    
91.1    
91.3    
91.4    
91.6    
91.8    
91.9    
92.1    
92.2    
92.4    
92.6    
92.7    
92.9    
93.1    
93.2    
93.4    
93.5    
93.7    
93.9    
94.0    
94.2    
94.3    
94.5    
94.7    
94.8    
95.0    
95.2    
95.3    
95.5    
95.6    
95.8    
96.0    
96.1    
96.3    
96.4    
96.6    
96.8    
96.9    
97.1    
97.3    
97.4    
97.6    
97.7    
97.9    
98.1    
98.2    
98.4    
98.5    
98.7    
98.9    
99.0    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 15362, rend_intergenic: 7961  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21544, rend_intergenic: 15979  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22951, rend_intergenic: 22648  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25696, rend_intergenic: 22961  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58040, rend_intergenic: 53294  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93281, rend_intergenic: 91141  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105491, rend_intergenic: 102464  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109679, rend_intergenic: 106542  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141157, rend_intergenic: 139073  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151970, rend_intergenic: 143158  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160935, rend_intergenic: 152584  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172083, rend_intergenic: 164813  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support