-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_19/scaffold_19_7977618-8170898

-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_19-snap.1591-T1
Valid prediction for snap_scaffold_19-snap.1567-T1
Valid prediction for GeneMark_model.79421_t
Valid prediction for GeneMark_model.79403_t
Valid prediction for snap_scaffold_19-snap.1570-T1
Valid prediction for snap_scaffold_19-snap.1576-T1
Valid prediction for GlimmerHMM_glimmerT_45475-T1
Valid prediction for snap_scaffold_19-snap.1585-T1
Valid prediction for GeneMark_model.79382_t
Valid prediction for GeneMark_model.79415_t
Valid prediction for GlimmerHMM_glimmerT_45469-T1
Valid prediction for GeneMark_model.79418_t
Valid prediction for Augustus_model.g30315.t1
Valid prediction for Augustus_model.g30309.t1
Valid prediction for Augustus_model.g30324.t1
Valid prediction for Augustus_model.g30322.t1
Valid prediction for GlimmerHMM_glimmerT_45478-T1
Valid prediction for snap_scaffold_19-snap.1559-T1
Valid prediction for snap_scaffold_19-snap.1587-T1
Valid prediction for snap_scaffold_19-snap.1573-T1
Valid prediction for snap_scaffold_19-snap.1582-T1
Valid prediction for GeneMark_model.79405_t
Valid prediction for GeneMark_model.79383_t
Valid prediction for Augustus_model.g30310.t1
Valid prediction for Augustus_model.g30313.t1
Valid prediction for pasa_asmbl_22300.p1
Valid prediction for GeneMark_model.79390_t
Valid prediction for snap_scaffold_19-snap.1555-T1
Valid prediction for Augustus_model.g30318.t1
Valid prediction for snap_scaffold_19-snap.1569-T1
Valid prediction for GeneMark_model.79381_t
Valid prediction for GlimmerHMM_glimmerT_45482-T1
Valid prediction for snap_scaffold_19-snap.1554-T1
Valid prediction for Augustus_model.g30308.t1
Valid prediction for GlimmerHMM_glimmerT_45457-T1
Valid prediction for GlimmerHMM_glimmerT_45480-T1
Valid prediction for snap_scaffold_19-snap.1589-T1
Valid prediction for snap_scaffold_19-snap.1572-T1
Valid prediction for GeneMark_model.79396_t
Valid prediction for GeneMark_model.79412_t
Valid prediction for snap_scaffold_19-snap.1568-T1
Valid prediction for GeneMark_model.79410_t
Valid prediction for HiQ_model.g30329.t1
Valid prediction for Augustus_model.g30326.t1
Valid prediction for GlimmerHMM_glimmerT_45473-T1
Valid prediction for GlimmerHMM_glimmerT_45471-T1
Valid prediction for CodingQuarry_transcript_25665-T1
Valid prediction for snap_scaffold_19-snap.1578-T1
Valid prediction for snap_scaffold_19-snap.1583-T1
Valid prediction for GeneMark_model.79419_t
Valid prediction for GeneMark_model.79387_t
Valid prediction for Augustus_model.g30316.t1
Valid prediction for snap_scaffold_19-snap.1575-T1
Valid prediction for GeneMark_model.79417_t
Valid prediction for GlimmerHMM_glimmerT_45461-T1
Valid prediction for GlimmerHMM_glimmerT_45459-T1
Valid prediction for GeneMark_model.79392_t
Valid prediction for GlimmerHMM_glimmerT_45474-T1
Valid prediction for GeneMark_model.79389_t
Valid prediction for Augustus_model.g30328.t1
Valid prediction for GeneMark_model.79407_t
Valid prediction for Augustus_model.g30317.t1
Valid prediction for snap_scaffold_19-snap.1558-T1
Valid prediction for GeneMark_model.79400_t
Valid prediction for GlimmerHMM_glimmerT_45463-T1
Valid prediction for snap_scaffold_19-snap.1579-T1
Valid prediction for Augustus_model.g30307.t1
Valid prediction for GeneMark_model.79384_t
Valid prediction for GeneMark_model.79408_t
Valid prediction for snap_scaffold_19-snap.1577-T1
Valid prediction for Augustus_model.g30319.t1
Valid prediction for snap_scaffold_19-snap.1588-T1
Valid prediction for snap_scaffold_19-snap.1590-T1
Valid prediction for GlimmerHMM_glimmerT_45468-T1
Valid prediction for GeneMark_model.79397_t
Valid prediction for GlimmerHMM_glimmerT_45460-T1
Valid prediction for GlimmerHMM_glimmerT_45458-T1
Valid prediction for Augustus_model.g30312.t1
Valid prediction for Augustus_model.g30327.t1
Valid prediction for GeneMark_model.79413_t
Valid prediction for GeneMark_model.79394_t
Valid prediction for GlimmerHMM_glimmerT_45481-T1
Valid prediction for snap_scaffold_19-snap.1560-T1
Valid prediction for GlimmerHMM_glimmerT_45467-T1
Valid prediction for snap_scaffold_19-snap.1553-T1
Valid prediction for GeneMark_model.79416_t

-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 HiQ_model.g30323.t1
Valid prediction for Augustus_model.g30320.t1
Valid prediction for snap_scaffold_19-snap.1565-T1
Valid prediction for GeneMark_model.79404_t
Valid prediction for HiQ_model.g30325.t1
Valid prediction for GlimmerHMM_glimmerT_45477-T1
Valid prediction for GlimmerHMM_glimmerT_45472-T1
Couldn't classify 89668, 89793
Sorry, prediction pasa_asmbl_21478.p1 fails validation.
(AAC)	 AC	89668-89793	GT	AGG
(GTG)	 AG	89943-90149	GT	AGG
(GGC)	 AG	90370-90486	GT	AGG
(ATG)	 AG	90708-90794	CC	AGC
-recovered pasa_asmbl_21478.p1, terminal, 90708, 90794
-recovered pasa_asmbl_21478.p1, internal, 89943, 90149
-recovered pasa_asmbl_21478.p1, internal, 90370, 90486
Valid prediction for CodingQuarry_transcript_25664-T1
Valid prediction for GeneMark_model.79406_t
Couldn't classify 57509, 57559
Sorry, prediction pasa_asmbl_21483.p1 fails validation.
(ATG)	 CC	55687-55699	GT	CGG
(GGG)	 AG	56184-56338	GT	AGG
(ATA)	 AG	56445-56544	GT	AGG
(GTA)	 AG	56641-56828	GT	AGG
(GGT)	 AG	56938-57060	GT	AGG
(ATC)	 AG	57162-57368	GT	AGG
(GTG)	 AG	57509-57559	AT	CGA
-recovered pasa_asmbl_21483.p1, initial, 55687, 55699
-recovered pasa_asmbl_21483.p1, internal, 56184, 56338
-recovered pasa_asmbl_21483.p1, internal, 56445, 56544
-recovered pasa_asmbl_21483.p1, internal, 56641, 56828
-recovered pasa_asmbl_21483.p1, internal, 56938, 57060
-recovered pasa_asmbl_21483.p1, internal, 57162, 57368
Valid prediction for Augustus_model.g30314.t1
Valid prediction for GeneMark_model.79401_t
Valid prediction for GeneMark_model.79422_t
Valid prediction for snap_scaffold_19-snap.1566-T1
Valid prediction for GeneMark_model.79386_t
Valid prediction for pasa_asmbl_21484.p1
Valid prediction for snap_scaffold_19-snap.1592-T1
Valid prediction for GeneMark_model.79398_t
Valid prediction for snap_scaffold_19-snap.1563-T1
Couldn't classify 87155, 87231
Couldn't classify 89259, 89347
Sorry, prediction pasa_asmbl_21479.p1 fails validation.
(CCT)	 CC	87155-87231	GT	AGG
(CAT)	 AG	88367-88514	GT	GGG
(ATG)	 AG	88655-88892	GT	CGG
(GGC)	 AG	89029-89085	GT	TGG
(CAG)	 AG	89259-89347	GC	GGG
-recovered pasa_asmbl_21479.p1, initial, 88655, 88892
-recovered pasa_asmbl_21479.p1, internal, 88367, 88514
-recovered pasa_asmbl_21479.p1, internal, 88655, 88892
-recovered pasa_asmbl_21479.p1, internal, 89029, 89085
-recovered pasa_asmbl_21479.p1, internal, 89259, 89347
Valid prediction for snap_scaffold_19-snap.1581-T1
Valid prediction for GlimmerHMM_glimmerT_45466-T1
Valid prediction for GeneMark_model.79399_t
Valid prediction for GlimmerHMM_glimmerT_45476-T1
Valid prediction for snap_scaffold_19-snap.1557-T1
Valid prediction for snap_scaffold_19-snap.1562-T1
Valid prediction for GlimmerHMM_glimmerT_45479-T1
Valid prediction for GlimmerHMM_glimmerT_45483-T1
Valid prediction for GeneMark_model.79411_t
Valid prediction for Augustus_model.g30321.t1
Valid prediction for GlimmerHMM_glimmerT_45462-T1
Valid prediction for GeneMark_model.79409_t
Valid prediction for Augustus_model.g30330.t1
Valid prediction for snap_scaffold_19-snap.1580-T1
Valid prediction for GlimmerHMM_glimmerT_45465-T1
Valid prediction for GeneMark_model.79414_t
Valid prediction for snap_scaffold_19-snap.1556-T1
Valid prediction for snap_scaffold_19-snap.1571-T1
Valid prediction for snap_scaffold_19-snap.1561-T1
Valid prediction for snap_scaffold_19-snap.1584-T1
Valid prediction for pasa_asmbl_21480.p1
Valid prediction for snap_scaffold_19-snap.1593-T1
Valid prediction for GeneMark_model.79393_t
Valid prediction for Augustus_model.g30311.t1
Valid prediction for GeneMark_model.79402_t
Valid prediction for GlimmerHMM_glimmerT_45470-T1
Valid prediction for GeneMark_model.79388_t
Valid prediction for GlimmerHMM_glimmerT_45464-T1
Valid prediction for snap_scaffold_19-snap.1586-T1
Valid prediction for GeneMark_model.79385_t
Valid prediction for snap_scaffold_19-snap.1574-T1
Valid prediction for GeneMark_model.79391_t
Valid prediction for GeneMark_model.79420_t
Valid prediction for snap_scaffold_19-snap.1564-T1
Valid prediction for GeneMark_model.79395_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 34285, rend_intergenic: 32248  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94819, rend_intergenic: 91660  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119777, rend_intergenic: 105966  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123036, rend_intergenic: 121858  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 99050, rend_intergenic: 99047  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 193281
-exon list size: 596


building trellis

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86.3    
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87.1    
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88.0    
88.1    
88.3    
88.5    
88.6    
88.8    
89.0    
89.1    
89.3    
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90.0    
90.1    
90.3    
90.5    
90.6    
90.8    
91.0    
91.1    
91.3    
91.5    
91.6    
91.8    
92.0    
92.1    
92.3    
92.5    
92.6    
92.8    
93.0    
93.1    
93.3    
93.5    
93.6    
93.8    
94.0    
94.1    
94.3    
94.5    
94.6    
94.8    
95.0    
95.2    
95.3    
95.5    
95.7    
95.8    
96.0    
96.2    
96.3    
96.5    
96.7    
96.8    
97.0    
97.2    
97.3    
97.5    
97.7    
97.8    
98.0    
98.2    
98.3    
98.5    
98.7    
98.8    
99.0    
99.2    
99.3    
99.5    
99.7    
99.8    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 34285, rend_intergenic: 32248  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94819, rend_intergenic: 91660  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119777, rend_intergenic: 105966  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123036, rend_intergenic: 121858  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 99050, rend_intergenic: 99047  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 28 predictions persist after filtering for low support