-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_18/scaffold_18_7059401-7259178

-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.75331_t
Valid prediction for GlimmerHMM_glimmerT_43628-T1
Valid prediction for GlimmerHMM_glimmerT_43608-T1
Valid prediction for Augustus_model.g29212.t1
Valid prediction for snap_scaffold_18-snap.1492-T1
Valid prediction for CodingQuarry_transcript_23755-T1
Valid prediction for GeneMark_model.75319_t
Valid prediction for Augustus_model.g29188.t1
Valid prediction for CodingQuarry_transcript_23759-T1
Valid prediction for snap_scaffold_18-snap.1488-T1
Valid prediction for HiQ_model.g29203.t1
Valid prediction for pasa_asmbl_20755.p1
Valid prediction for snap_scaffold_18-snap.1513-T1
Valid prediction for CodingQuarry_transcript_23751-T1
Valid prediction for GeneMark_model.75326_t
Valid prediction for pasa_asmbl_20739.p1
Valid prediction for GeneMark_model.75316_t
Valid prediction for pasa_asmbl_20748.p1
Valid prediction for GeneMark_model.75296_t
Valid prediction for Augustus_model.g29201.t1
Valid prediction for CodingQuarry_transcript_23752-T1
Couldn't classify 182178, 182481
Sorry, prediction pasa_asmbl_20759.p1 fails validation.
(ACA)	 AC	182178-182481	GT	AGG
(ATT)	 AG	182573-182619	GT	CGG
(TTG)	 AG	182763-182911	GT	ATG
(AGC)	 AG	183117-183248	GT	AGG
(TGG)	 AG	183395-183517	GT	AGG
(AAT)	 AG	183786-183935	GT	AGG
(GAC)	 AG	184198-184321	GT	ATG
(TAT)	 AG	184594-184681	GT	AGG
(CCG)	 AG	184821-184945	GT	AGG
(GAC)	 AG	185138-185155	AT	AAA
-recovered pasa_asmbl_20759.p1, terminal, 185138, 185155
-recovered pasa_asmbl_20759.p1, internal, 182573, 182619
-recovered pasa_asmbl_20759.p1, internal, 182763, 182911
-recovered pasa_asmbl_20759.p1, internal, 183117, 183248
-recovered pasa_asmbl_20759.p1, internal, 183395, 183517
-recovered pasa_asmbl_20759.p1, internal, 183786, 183935
-recovered pasa_asmbl_20759.p1, internal, 184198, 184321
-recovered pasa_asmbl_20759.p1, internal, 184594, 184681
-recovered pasa_asmbl_20759.p1, internal, 184821, 184945
Valid prediction for snap_scaffold_18-snap.1504-T1
Valid prediction for GeneMark_model.75314_t
Valid prediction for GlimmerHMM_glimmerT_43614-T1
Valid prediction for HiQ_model.g29196.t1
Valid prediction for snap_scaffold_18-snap.1482-T1
Valid prediction for GeneMark_model.75317_t
Valid prediction for CodingQuarry_transcript_23753-T1
Valid prediction for snap_scaffold_18-snap.1499-T1
Valid prediction for GeneMark_model.75332_t
Valid prediction for GlimmerHMM_glimmerT_43607-T1
Couldn't classify 120061, 120106
Sorry, prediction pasa_asmbl_20743.p1 fails validation.
(CCT)	 GG	120061-120106	GT	AGG
(ATG)	 AG	120346-121160	CC	GAC
-recovered pasa_asmbl_20743.p1, terminal, 120346, 121160
Valid prediction for GeneMark_model.75322_t
Valid prediction for snap_scaffold_18-snap.1516-T1
Valid prediction for pasa_asmbl_20744.p1
Valid prediction for GeneMark_model.75312_t
Valid prediction for snap_scaffold_18-snap.1502-T1
Couldn't classify 188971, 189064
Sorry, prediction pasa_asmbl_20762.p2 fails validation.
(ATG)	 AA	188676-188884	GT	TGG
(GGT)	 AG	188971-189064	GA	AGG
-recovered pasa_asmbl_20762.p2, initial, 188676, 188884
Valid prediction for snap_scaffold_18-snap.1514-T1
Valid prediction for GeneMark_model.75328_t
Valid prediction for GlimmerHMM_glimmerT_43605-T1
Couldn't classify 149704, 149724
Couldn't classify 152355, 152480
Sorry, prediction pasa_asmbl_21097.p1 fails validation.
(GTG)	 AC	149704-149724	GT	GGG
(GAT)	 AG	150199-150342	GT	CTG
(CCG)	 AG	150742-150828	GT	AGG
(GTA)	 AG	152355-152480	AG	GCA
-recovered pasa_asmbl_21097.p1, internal, 150199, 150342
-recovered pasa_asmbl_21097.p1, internal, 150742, 150828
Valid prediction for HiQ_model.g29211.t1
Valid prediction for pasa_asmbl_20740.p1
Valid prediction for snap_scaffold_18-snap.1520-T1
Valid prediction for Augustus_model.g29193.t1
Valid prediction for GlimmerHMM_glimmerT_43624-T1
Valid prediction for GeneMark_model.75300_t
Valid prediction for snap_scaffold_18-snap.1493-T1
Valid prediction for GeneMark_model.75308_t
Valid prediction for CodingQuarry_transcript_23745-T1
Valid prediction for snap_scaffold_18-snap.1518-T1
Valid prediction for CodingQuarry_transcript_23757-T1
Valid prediction for snap_scaffold_18-snap.1503-T1
Valid prediction for snap_scaffold_18-snap.1506-T1
Valid prediction for CodingQuarry_transcript_23760-T1
Valid prediction for GeneMark_model.75330_t
Valid prediction for GeneMark_model.75310_t
Valid prediction for snap_scaffold_18-snap.1519-T1
Valid prediction for HiQ_model.g29198.t1
Valid prediction for CodingQuarry_transcript_23758-T1
Valid prediction for GlimmerHMM_glimmerT_43629-T1
Valid prediction for GeneMark_model.75288_t
Valid prediction for GlimmerHMM_glimmerT_43609-T1
Valid prediction for snap_scaffold_18-snap.1485-T1
Valid prediction for snap_scaffold_18-snap.1509-T1
Valid prediction for GlimmerHMM_glimmerT_43618-T1
Valid prediction for snap_scaffold_18-snap.1486-T1
Valid prediction for snap_scaffold_18-snap.1511-T1
Valid prediction for snap_scaffold_18-snap.1497-T1
Valid prediction for snap_scaffold_18-snap.1489-T1
Valid prediction for snap_scaffold_18-snap.1480-T1
Valid prediction for Augustus_model.g29194.t1
Valid prediction for GeneMark_model.75324_t
Valid prediction for snap_scaffold_18-snap.1491-T1
Valid prediction for HiQ_model.g29205.t1
Valid prediction for GeneMark_model.75304_t
Valid prediction for GlimmerHMM_glimmerT_43616-T1
Valid prediction for GeneMark_model.75291_t
Valid prediction for HiQ_model.g29210.t1
Valid prediction for GeneMark_model.75306_t
Valid prediction for Augustus_model.g29207.t1
Valid prediction for GeneMark_model.75290_t
Valid prediction for CodingQuarry_transcript_23754-T1
Valid prediction for GlimmerHMM_glimmerT_43622-T1
Valid prediction for Augustus_model.g29189.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_19959.p1
Valid prediction for GeneMark_model.75289_t
Valid prediction for snap_scaffold_18-snap.1483-T1
Valid prediction for snap_scaffold_18-snap.1521-T1
Valid prediction for GlimmerHMM_glimmerT_43611-T1
Valid prediction for snap_scaffold_18-snap.1494-T1
Valid prediction for GeneMark_model.75309_t
Valid prediction for GeneMark_model.75321_t
Valid prediction for GeneMark_model.75318_t
Valid prediction for snap_scaffold_18-snap.1510-T1
Valid prediction for GlimmerHMM_glimmerT_43627-T1
Valid prediction for Augustus_model.g29195.t1
Valid prediction for snap_scaffold_18-snap.1501-T1
Valid prediction for GlimmerHMM_glimmerT_43623-T1
Valid prediction for GlimmerHMM_glimmerT_43610-T1
Valid prediction for pasa_asmbl_19969.p1
Valid prediction for GlimmerHMM_glimmerT_43621-T1
Couldn't classify 95191, 95220
Couldn't classify 95344, 95446
Sorry, prediction CodingQuarry_transcript_23747-T1 fails validation.
(ATG)	 GA	95191-95220	AG	AAA
(GCA)	 CA	95344-95446	GT	GGG
(GGC)	 AG	95557-95771	GT	CTG
(GAG)	 AG	96095-96210	GT	AGG
(AAA)	 AG	96308-96392	GT	AGG
(TAC)	 AG	96526-96672	GT	AGG
(GAG)	 AG	96789-97008	GT	CCG
(CCC)	 AG	97299-97378	GT	ATG
(TGT)	 AG	98561-98770	GT	AGG
(GTT)	 AG	99024-99143	GT	AGG
(ATC)	 AG	99242-99339	GT	CGG
(GGA)	 AG	99476-99620	GG	GAG
add_exon() Sorry, CodingQuarry_transcript_23747-T1 96095-96210-terminal-2 is invalid.
-recovered CodingQuarry_transcript_23747-T1, terminal, 96095, 96210
-recovered CodingQuarry_transcript_23747-T1, terminal, 99476, 99620
-recovered CodingQuarry_transcript_23747-T1, internal, 95557, 95771
-recovered CodingQuarry_transcript_23747-T1, internal, 96095, 96210
-recovered CodingQuarry_transcript_23747-T1, internal, 96308, 96392
-recovered CodingQuarry_transcript_23747-T1, internal, 96526, 96672
-recovered CodingQuarry_transcript_23747-T1, internal, 96789, 97008
-recovered CodingQuarry_transcript_23747-T1, internal, 97299, 97378
-recovered CodingQuarry_transcript_23747-T1, internal, 98561, 98770
-recovered CodingQuarry_transcript_23747-T1, internal, 99024, 99143
-recovered CodingQuarry_transcript_23747-T1, internal, 99242, 99339
Valid prediction for snap_scaffold_18-snap.1490-T1
Valid prediction for GeneMark_model.75327_t
Valid prediction for snap_scaffold_18-snap.1500-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.75315_t
Valid prediction for GeneMark_model.75302_t
Valid prediction for Augustus_model.g29190.t1
Valid prediction for GeneMark_model.75329_t
Valid prediction for Augustus_model.g29191.t1
Valid prediction for GeneMark_model.75292_t
Valid prediction for GlimmerHMM_glimmerT_43619-T1
Valid prediction for snap_scaffold_18-snap.1498-T1
Valid prediction for GlimmerHMM_glimmerT_43615-T1
Valid prediction for GlimmerHMM_glimmerT_43630-T1
Valid prediction for GeneMark_model.75325_t
Valid prediction for snap_scaffold_18-snap.1495-T1
Valid prediction for HiQ_model.g29202.t1
Valid prediction for Augustus_model.g29204.t1
Valid prediction for pasa_asmbl_19961.p2
Valid prediction for HiQ_model.g29213.t1
Valid prediction for GlimmerHMM_glimmerT_43613-T1
Valid prediction for snap_scaffold_18-snap.1487-T1
Valid prediction for HiQ_model.g29200.t1
Valid prediction for Augustus_model.g29208.t1
Valid prediction for GeneMark_model.75311_t
Valid prediction for GeneMark_model.75323_t
Valid prediction for snap_scaffold_18-snap.1484-T1
Valid prediction for snap_scaffold_18-snap.1481-T1
Valid prediction for GeneMark_model.75294_t
Valid prediction for GeneMark_model.75313_t
Valid prediction for CodingQuarry_transcript_23749-T1
Valid prediction for snap_scaffold_18-snap.1515-T1
Valid prediction for Augustus_model.g29209.t1
Valid prediction for GeneMark_model.75307_t
Valid prediction for GeneMark_model.75301_t
Valid prediction for GeneMark_model.75297_t
Valid prediction for CodingQuarry_transcript_23748-T1
Valid prediction for GeneMark_model.75299_t
Valid prediction for GeneMark_model.75305_t
Valid prediction for GlimmerHMM_glimmerT_43625-T1
Valid prediction for GlimmerHMM_glimmerT_43617-T1
Valid prediction for snap_scaffold_18-snap.1496-T1
Valid prediction for snap_scaffold_18-snap.1517-T1
Valid prediction for snap_scaffold_18-snap.1507-T1
Valid prediction for pasa_asmbl_19966.p1
Valid prediction for GlimmerHMM_glimmerT_43606-T1
Valid prediction for GlimmerHMM_glimmerT_43612-T1
Valid prediction for snap_scaffold_18-snap.1505-T1
Valid prediction for GeneMark_model.75320_t
Valid prediction for Augustus_model.g29192.t1
Valid prediction for GeneMark_model.75295_t
Valid prediction for GeneMark_model.75303_t
Valid prediction for CodingQuarry_transcript_23746-T1
Valid prediction for HiQ_model.g29197.t1
Valid prediction for snap_scaffold_18-snap.1508-T1
Valid prediction for GlimmerHMM_glimmerT_43620-T1
Valid prediction for GeneMark_model.75293_t
Valid prediction for Augustus_model.g29206.t1
Valid prediction for HiQ_model.g29199.t1
Valid prediction for snap_scaffold_18-snap.1512-T1
Valid prediction for GlimmerHMM_glimmerT_43626-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11175, rend_intergenic: 9606  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15703, rend_intergenic: 12609  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36485, rend_intergenic: 28294  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76881, rend_intergenic: 57834  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77665, rend_intergenic: 77005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110670, rend_intergenic: 106200  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162214, rend_intergenic: 161113  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163579, rend_intergenic: 162285  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172442, rend_intergenic: 163990  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 199778
-exon list size: 628


building trellis

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85.2    
85.4    
85.6    
85.7    
85.9    
86.0    
86.2    
86.3    
86.5    
86.7    
86.8    
87.0    
87.1    
87.3    
87.5    
87.6    
87.8    
87.9    
88.1    
88.3    
88.4    
88.6    
88.7    
88.9    
89.0    
89.2    
89.4    
89.5    
89.7    
89.8    
90.0    
90.2    
90.3    
90.5    
90.6    
90.8    
91.0    
91.1    
91.3    
91.4    
91.6    
91.7    
91.9    
92.1    
92.2    
92.4    
92.5    
92.7    
92.9    
93.0    
93.2    
93.3    
93.5    
93.7    
93.8    
94.0    
94.1    
94.3    
94.4    
94.6    
94.8    
94.9    
95.1    
95.2    
95.4    
95.6    
95.7    
95.9    
96.0    
96.2    
96.3    
96.5    
96.7    
96.8    
97.0    
97.1    
97.3    
97.5    
97.6    
97.8    
97.9    
98.1    
98.3    
98.4    
98.6    
98.7    
98.9    
99.0    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 11175, rend_intergenic: 9606  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15703, rend_intergenic: 12609  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36485, rend_intergenic: 28294  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76881, rend_intergenic: 57834  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77665, rend_intergenic: 77005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110670, rend_intergenic: 106200  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162214, rend_intergenic: 161113  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163579, rend_intergenic: 162285  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172442, rend_intergenic: 163990  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 26 predictions persist after filtering for low support