-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_17299449-17441748

-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_1-snap.3151-T1
Valid prediction for snap_scaffold_1-snap.3164-T1
Valid prediction for snap_scaffold_1-snap.3163-T1
Valid prediction for GlimmerHMM_glimmerT_2370-T1
Valid prediction for snap_scaffold_1-snap.3152-T1
Valid prediction for GeneMark_model.3454_t
Valid prediction for GlimmerHMM_glimmerT_2365-T1
Valid prediction for GeneMark_model.3425_t
Valid prediction for snap_scaffold_1-snap.3141-T1
Valid prediction for GeneMark_model.3448_t
Valid prediction for GlimmerHMM_glimmerT_2363-T1
Valid prediction for GeneMark_model.3428_t
Valid prediction for snap_scaffold_1-snap.3161-T1
Valid prediction for GlimmerHMM_glimmerT_2378-T1
Valid prediction for GlimmerHMM_glimmerT_2376-T1
Valid prediction for Augustus_model.g1730.t1
Valid prediction for snap_scaffold_1-snap.3142-T1
Valid prediction for GeneMark_model.3439_t
Valid prediction for GlimmerHMM_glimmerT_2375-T1
Valid prediction for snap_scaffold_1-snap.3162-T1
Valid prediction for GeneMark_model.3450_t
Valid prediction for GeneMark_model.3457_t
Valid prediction for snap_scaffold_1-snap.3154-T1
Valid prediction for GeneMark_model.3444_t
Valid prediction for GeneMark_model.3433_t
Valid prediction for GlimmerHMM_glimmerT_2372-T1
Valid prediction for Augustus_model.g1724.t1
Valid prediction for snap_scaffold_1-snap.3157-T1
Valid prediction for GeneMark_model.3441_t
Valid prediction for GeneMark_model.3446_t
Valid prediction for GlimmerHMM_glimmerT_2366-T1
Valid prediction for snap_scaffold_1-snap.3136-T1
Valid prediction for snap_scaffold_1-snap.3135-T1
Valid prediction for Augustus_model.g1728.t1
Valid prediction for GeneMark_model.3431_t
Valid prediction for snap_scaffold_1-snap.3148-T1
Valid prediction for GeneMark_model.3437_t
Valid prediction for snap_scaffold_1-snap.3140-T1
Valid prediction for GeneMark_model.3442_t
Valid prediction for snap_scaffold_1-snap.3159-T1
Valid prediction for Augustus_model.g1722.t1
Valid prediction for Augustus_model.g1715.t1
Valid prediction for GeneMark_model.3452_t
Valid prediction for snap_scaffold_1-snap.3155-T1
Valid prediction for GeneMark_model.3458_t
Valid prediction for Augustus_model.g1726.t1
Valid prediction for snap_scaffold_1-snap.3150-T1
Valid prediction for GeneMark_model.3459_t
Valid prediction for GeneMark_model.3435_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 snap_scaffold_1-snap.3143-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.3436_t
Valid prediction for GeneMark_model.3449_t
Valid prediction for Augustus_model.g1727.t1
Valid prediction for snap_scaffold_1-snap.3134-T1
Valid prediction for Augustus_model.g1720.t1
Valid prediction for snap_scaffold_1-snap.3166-T1
Valid prediction for GeneMark_model.3440_t
Valid prediction for snap_scaffold_1-snap.3147-T1
Valid prediction for GeneMark_model.3424_t
Valid prediction for GeneMark_model.3455_t
Valid prediction for GeneMark_model.3451_t
Valid prediction for GlimmerHMM_glimmerT_2364-T1
Valid prediction for Augustus_model.g1718.t1
Valid prediction for snap_scaffold_1-snap.3146-T1
Valid prediction for snap_scaffold_1-snap.3139-T1
Valid prediction for GlimmerHMM_glimmerT_2361-T1
Valid prediction for Augustus_model.g1723.t1
Valid prediction for snap_scaffold_1-snap.3137-T1
Valid prediction for snap_scaffold_1-snap.3156-T1
Valid prediction for GeneMark_model.3429_t
Valid prediction for Augustus_model.g1729.t1
Couldn't classify 101382, 101438
Sorry, prediction GlimmerHMM_glimmerT_2367-T1 fails validation.
(ATG)	 TG	100625-100738	GT	ACG
(NNN)	 AN	101382-101438	GT	TGG
(GTG)	 AG	102132-103067	GT	AGG
(GGG)	 AG	107817-107891	AG	AGA
-recovered GlimmerHMM_glimmerT_2367-T1, initial, 100625, 100738
-recovered GlimmerHMM_glimmerT_2367-T1, terminal, 107817, 107891
-recovered GlimmerHMM_glimmerT_2367-T1, internal, 102132, 103067
Valid prediction for GeneMark_model.3432_t
Valid prediction for snap_scaffold_1-snap.3133-T1
Valid prediction for snap_scaffold_1-snap.3144-T1
Valid prediction for Augustus_model.g1719.t1
Valid prediction for Augustus_model.g1717.t1
Valid prediction for GeneMark_model.3427_t
Valid prediction for snap_scaffold_1-snap.3145-T1
Valid prediction for GeneMark_model.3445_t
Valid prediction for Augustus_model.g1732.t1
Valid prediction for GeneMark_model.3426_t
Valid prediction for snap_scaffold_1-snap.3160-T1
Valid prediction for snap_scaffold_1-snap.3167-T1
Valid prediction for GeneMark_model.3443_t
Valid prediction for GlimmerHMM_glimmerT_2369-T1
Valid prediction for Augustus_model.g1716.t1
Valid prediction for GlimmerHMM_glimmerT_2368-T1
Valid prediction for GlimmerHMM_glimmerT_2377-T1
Valid prediction for snap_scaffold_1-snap.3138-T1
Valid prediction for snap_scaffold_1-snap.3149-T1
Valid prediction for GeneMark_model.3430_t
Valid prediction for snap_scaffold_1-snap.3153-T1
Valid prediction for Augustus_model.g1721.t1
Valid prediction for Augustus_model.g1725.t1
Valid prediction for snap_scaffold_1-snap.3158-T1
Valid prediction for GeneMark_model.3438_t
Valid prediction for GlimmerHMM_glimmerT_2371-T1
Valid prediction for GeneMark_model.3447_t
Valid prediction for GlimmerHMM_glimmerT_2362-T1
Valid prediction for GeneMark_model.3456_t
Valid prediction for Augustus_model.g1731.t1
Valid prediction for GlimmerHMM_glimmerT_2373-T1
Valid prediction for GeneMark_model.3434_t
Valid prediction for GlimmerHMM_glimmerT_2374-T1
Valid prediction for snap_scaffold_1-snap.3165-T1
Valid prediction for GeneMark_model.3453_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 41676, rend_intergenic: 30681  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41793, rend_intergenic: 41737  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71957, rend_intergenic: 63384  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82212, rend_intergenic: 76369  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87403, rend_intergenic: 86092  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96893, rend_intergenic: 94500  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101066, rend_intergenic: 99506  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 142300
-exon list size: 458


building trellis

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-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 41676, rend_intergenic: 30681  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41793, rend_intergenic: 41737  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71957, rend_intergenic: 63384  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82212, rend_intergenic: 76369  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87403, rend_intergenic: 86092  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96893, rend_intergenic: 94500  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101066, rend_intergenic: 99506  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 129596 - 142300
-exon list size: 15


building trellis

5.9    
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41.2    
47.1    
52.9    
58.8    
64.7    
70.6    
76.5    
82.4    
88.2    
94.1    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support