-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_19/scaffold_19_8620434-8800183

-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_45541-T1
Valid prediction for CodingQuarry_transcript_25692-T1
Valid prediction for Augustus_model.g30388.t1
Valid prediction for snap_scaffold_19-snap.1688-T1
Valid prediction for GlimmerHMM_glimmerT_45552-T1
Valid prediction for snap_scaffold_19-snap.1665-T1
Valid prediction for GlimmerHMM_glimmerT_45565-T1
Valid prediction for snap_scaffold_19-snap.1671-T1
Valid prediction for GlimmerHMM_glimmerT_45558-T1
Valid prediction for HiQ_model.g30391.t1
Valid prediction for snap_scaffold_19-snap.1696-T1
Valid prediction for GeneMark_model.79526_t
Valid prediction for snap_scaffold_19-snap.1676-T1
Valid prediction for GeneMark_model.79509_t
Valid prediction for snap_scaffold_19-snap.1694-T1
Valid prediction for GeneMark_model.79507_t
Valid prediction for Augustus_model.g30376.t1
Valid prediction for GlimmerHMM_glimmerT_45544-T1
Valid prediction for snap_scaffold_19-snap.1685-T1
Valid prediction for GeneMark_model.79504_t
Couldn't classify 133868, 134679
Couldn't classify 134776, 134908
Sorry, prediction CodingQuarry_transcript_25693-T1 fails validation.
(ATG)	 AT	132518-132650	GT	AGG
(ACA)	 AG	132782-132927	GT	GGG
(GCA)	 AG	133320-133437	GT	TGG
(GTG)	 AG	133868-134679	GA	AAG
(GAG)	 AT	134776-134908	GT	TGG
(AGG)	 AG	135037-135194	GT	CTG
(GCG)	 AG	135311-135428	GT	GGG
(GTG)	 AG	135690-136075	GG	AGG
-recovered CodingQuarry_transcript_25693-T1, initial, 132518, 132650
-recovered CodingQuarry_transcript_25693-T1, terminal, 135690, 136075
-recovered CodingQuarry_transcript_25693-T1, internal, 132782, 132927
-recovered CodingQuarry_transcript_25693-T1, internal, 133320, 133437
-recovered CodingQuarry_transcript_25693-T1, internal, 135037, 135194
-recovered CodingQuarry_transcript_25693-T1, internal, 135311, 135428
Valid prediction for GeneMark_model.79506_t
Couldn't classify 6194, 6360
Sorry, prediction pasa_asmbl_22342.p1 fails validation.
(GTC)	 AT	6194-6360	GT	AGG
(GTA)	 AG	7616-7791	GT	CAG
(GTG)	 AG	8658-8875	TA	AAT
-recovered pasa_asmbl_22342.p1, terminal, 8658, 8875
-recovered pasa_asmbl_22342.p1, internal, 7616, 7791
Valid prediction for GeneMark_model.79530_t
Valid prediction for GlimmerHMM_glimmerT_45563-T1
Valid prediction for GeneMark_model.79512_t
Valid prediction for snap_scaffold_19-snap.1692-T1
Valid prediction for snap_scaffold_19-snap.1690-T1
Valid prediction for GlimmerHMM_glimmerT_45553-T1
Valid prediction for GlimmerHMM_glimmerT_45549-T1
Valid prediction for GeneMark_model.79532_t
Valid prediction for HiQ_model.g30372.t1
Valid prediction for snap_scaffold_19-snap.1674-T1
Valid prediction for GeneMark_model.79510_t
Valid prediction for GeneMark_model.79528_t
Couldn't classify 122613, 123150
Couldn't classify 125508, 125708
Couldn't classify 125945, 125964
Sorry, prediction pasa_asmbl_22348.p1 fails validation.
(TCA)	 AG	122613-123150	GT	AGG
(GCA)	 AG	123264-123559	GT	TGG
(GAA)	 AG	123899-124018	GT	AGG
(GAG)	 AG	124756-124969	GT	GGG
(GTC)	 AG	125270-125414	GT	AGG
(TGA)	 AG	125508-125708	AT	GAA
(GTT)	 AC	125945-125964	GT	TGG
(AAT)	 AG	126727-126848	AG	GAA
-recovered pasa_asmbl_22348.p1, terminal, 126727, 126848
-recovered pasa_asmbl_22348.p1, internal, 122613, 123150
-recovered pasa_asmbl_22348.p1, internal, 123264, 123559
-recovered pasa_asmbl_22348.p1, internal, 123899, 124018
-recovered pasa_asmbl_22348.p1, internal, 124756, 124969
-recovered pasa_asmbl_22348.p1, internal, 125270, 125414
Valid prediction for snap_scaffold_19-snap.1700-T1
Valid prediction for GlimmerHMM_glimmerT_45566-T1
Valid prediction for GeneMark_model.79514_t
Valid prediction for GlimmerHMM_glimmerT_45561-T1
Valid prediction for Augustus_model.g30395.t1
Valid prediction for pasa_asmbl_22352.p1
Couldn't classify 176574, 176691
Couldn't classify 177384, 177590
Sorry, prediction pasa_asmbl_22355.p1 fails validation.
(TTC)	 GA	176574-176691	GT	AGG
(GTG)	 AG	177184-177266	GT	ATG
(ATG)	 AG	177384-177590	GG	CCG
-recovered pasa_asmbl_22355.p1, internal, 177184, 177266
Valid prediction for GeneMark_model.79533_t
Valid prediction for CodingQuarry_transcript_25691-T1
Valid prediction for pasa_asmbl_22351.p1
Valid prediction for Augustus_model.g30383.t1
Couldn't classify 120931, 120995
Couldn't classify 121824, 121964
Sorry, prediction pasa_asmbl_22346.p1 fails validation.
(AAC)	 CC	120931-120995	GT	AGG
(TAC)	 AG	121152-121253	GT	AGG
(TTC)	 AG	121395-121455	GT	AGG
(GAG)	 AG	121593-121736	GT	AGG
(TGT)	 AG	121824-121964	CA	AGC
-recovered pasa_asmbl_22346.p1, internal, 121152, 121253
-recovered pasa_asmbl_22346.p1, internal, 121395, 121455
-recovered pasa_asmbl_22346.p1, internal, 121593, 121736
Valid prediction for Augustus_model.g30390.t1
Valid prediction for CodingQuarry_transcript_25686-T1
Valid prediction for snap_scaffold_19-snap.1666-T1
Valid prediction for snap_scaffold_19-snap.1679-T1
Valid prediction for GeneMark_model.79518_t
Valid prediction for snap_scaffold_19-snap.1699-T1
Couldn't classify 112078, 112443
Sorry, prediction pasa_asmbl_22344.p1 fails validation.
(CGT)	 GA	112078-112443	GA	GGG
Valid prediction for GeneMark_model.79525_t
Valid prediction for Augustus_model.g30394.t1
Valid prediction for GlimmerHMM_glimmerT_45560-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_45548-T1
Valid prediction for HiQ_model.g30392.t1
Valid prediction for GeneMark_model.79502_t
Valid prediction for GeneMark_model.79519_t
Valid prediction for snap_scaffold_19-snap.1668-T1
Valid prediction for GeneMark_model.79524_t
Valid prediction for snap_scaffold_19-snap.1697-T1
Valid prediction for snap_scaffold_19-snap.1678-T1
Valid prediction for GlimmerHMM_glimmerT_45556-T1
Valid prediction for Augustus_model.g30377.t1
Valid prediction for snap_scaffold_19-snap.1702-T1
Valid prediction for Augustus_model.g30386.t1
Valid prediction for GlimmerHMM_glimmerT_45546-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_19-snap.1669-T1
Valid prediction for GlimmerHMM_glimmerT_45555-T1
Valid prediction for GeneMark_model.79517_t
Valid prediction for Augustus_model.g30379.t1
Valid prediction for snap_scaffold_19-snap.1698-T1
Valid prediction for GeneMark_model.79531_t
Valid prediction for pasa_asmbl_21512.p1
Valid prediction for pasa_asmbl_21518.p1
Valid prediction for snap_scaffold_19-snap.1695-T1
Valid prediction for snap_scaffold_19-snap.1703-T1
Valid prediction for CodingQuarry_transcript_25689-T1
Valid prediction for snap_scaffold_19-snap.1701-T1
Valid prediction for GeneMark_model.79516_t
Valid prediction for GeneMark_model.79508_t
Valid prediction for snap_scaffold_19-snap.1693-T1
Valid prediction for GeneMark_model.79511_t
Valid prediction for Augustus_model.g30375.t1
Valid prediction for pasa_asmbl_21514.p1
Valid prediction for GlimmerHMM_glimmerT_45551-T1
Valid prediction for GlimmerHMM_glimmerT_45547-T1
Valid prediction for HiQ_model.g30393.t1
Valid prediction for CodingQuarry_transcript_25687-T1
Valid prediction for pasa_asmbl_21516.p1
Valid prediction for HiQ_model.g30389.t1
Valid prediction for snap_scaffold_19-snap.1684-T1
Valid prediction for snap_scaffold_19-snap.1667-T1
Valid prediction for GeneMark_model.79529_t
Valid prediction for Augustus_model.g30384.t1
Valid prediction for Augustus_model.g30373.t1
Valid prediction for snap_scaffold_19-snap.1682-T1
Valid prediction for Augustus_model.g30380.t1
Valid prediction for snap_scaffold_19-snap.1672-T1
Valid prediction for GlimmerHMM_glimmerT_45545-T1
Valid prediction for snap_scaffold_19-snap.1691-T1
Valid prediction for GlimmerHMM_glimmerT_45543-T1
Valid prediction for HiQ_model.g30387.t1
Valid prediction for Augustus_model.g30378.t1
Valid prediction for snap_scaffold_19-snap.1673-T1
Valid prediction for GlimmerHMM_glimmerT_45562-T1
Valid prediction for snap_scaffold_19-snap.1687-T1
Valid prediction for snap_scaffold_19-snap.1686-T1
Valid prediction for CodingQuarry_transcript_25690-T1
Valid prediction for snap_scaffold_19-snap.1675-T1
Valid prediction for GlimmerHMM_glimmerT_45554-T1
Valid prediction for snap_scaffold_19-snap.1670-T1
Valid prediction for snap_scaffold_19-snap.1680-T1
Valid prediction for GeneMark_model.79520_t
Valid prediction for GlimmerHMM_glimmerT_45550-T1
Valid prediction for GeneMark_model.79503_t
Valid prediction for GeneMark_model.79527_t
Valid prediction for GlimmerHMM_glimmerT_45559-T1
Valid prediction for GlimmerHMM_glimmerT_45557-T1
Valid prediction for Augustus_model.g30382.t1
Valid prediction for Augustus_model.g30381.t1
Couldn't classify 71348, 71385
Couldn't classify 72650, 72805
Sorry, prediction pasa_asmbl_21511.p1 fails validation.
(GAA)	 AA	71348-71385	GT	AGG
(GTT)	 AG	71658-71787	GT	AGG
(GAG)	 AG	71889-72005	GT	AGG
(GTG)	 AG	72141-72215	GT	AGG
(AAG)	 AG	72650-72805	AC	CGA
-recovered pasa_asmbl_21511.p1, internal, 71658, 71787
-recovered pasa_asmbl_21511.p1, internal, 71889, 72005
-recovered pasa_asmbl_21511.p1, internal, 72141, 72215
Valid prediction for GeneMark_model.79515_t
Valid prediction for snap_scaffold_19-snap.1681-T1
Valid prediction for snap_scaffold_19-snap.1689-T1
Valid prediction for snap_scaffold_19-snap.1683-T1
Valid prediction for snap_scaffold_19-snap.1677-T1
Valid prediction for GeneMark_model.79513_t
Valid prediction for CodingQuarry_transcript_25688-T1
Valid prediction for GlimmerHMM_glimmerT_45542-T1
Valid prediction for GeneMark_model.79523_t
Valid prediction for GlimmerHMM_glimmerT_45564-T1
Valid prediction for GeneMark_model.79505_t
Valid prediction for Augustus_model.g30374.t1
Valid prediction for HiQ_model.g30385.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 55918, rend_intergenic: 52763  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60882, rend_intergenic: 56706  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69973, rend_intergenic: 64313  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123586, rend_intergenic: 120730  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124590, rend_intergenic: 123866  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127529, rend_intergenic: 124750  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128730, rend_intergenic: 127747  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143228, rend_intergenic: 138011  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148630, rend_intergenic: 143446  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170554, rend_intergenic: 162392  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178759, rend_intergenic: 172951  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 179750
-exon list size: 481


building trellis

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98.1    
98.3    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 55918, rend_intergenic: 52763  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60882, rend_intergenic: 56706  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69973, rend_intergenic: 64313  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123586, rend_intergenic: 120730  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124590, rend_intergenic: 123866  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127529, rend_intergenic: 124750  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128730, rend_intergenic: 127747  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143228, rend_intergenic: 138011  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148630, rend_intergenic: 143446  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170554, rend_intergenic: 162392  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178759, rend_intergenic: 172951  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