-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_18/scaffold_18_10856163-11118717

-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.2349-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_18-snap.2335-T1
Valid prediction for snap_scaffold_18-snap.2305-T1
Valid prediction for Augustus_model.g28720.t1
Valid prediction for snap_scaffold_18-snap.2299-T1
Valid prediction for Augustus_model.g28718.t1
Valid prediction for GlimmerHMM_glimmerT_43095-T1
Valid prediction for snap_scaffold_18-snap.2348-T1
Valid prediction for snap_scaffold_18-snap.2317-T1
Valid prediction for Augustus_model.g28722.t1
Valid prediction for snap_scaffold_18-snap.2312-T1
Valid prediction for Augustus_model.g28719.t1
Valid prediction for Augustus_model.g28723.t1
Valid prediction for snap_scaffold_18-snap.2345-T1
Valid prediction for snap_scaffold_18-snap.2309-T1
Valid prediction for Augustus_model.g28713.t1
Valid prediction for snap_scaffold_18-snap.2302-T1
Valid prediction for GlimmerHMM_glimmerT_43082-T1
Valid prediction for snap_scaffold_18-snap.2339-T1
Valid prediction for Augustus_model.g28714.t1
Valid prediction for snap_scaffold_18-snap.2341-T1
Valid prediction for snap_scaffold_18-snap.2352-T1
Couldn't classify 82883, 83070
Couldn't classify 84961, 85078
Sorry, prediction pasa_asmbl_20928.p2 fails validation.
(TCG)	 TG	82883-83070	GT	AGG
(TTC)	 AG	84961-85078	CG	CCC
Valid prediction for GlimmerHMM_glimmerT_43088-T1
Valid prediction for snap_scaffold_18-snap.2332-T1
Valid prediction for HiQ_model.g28721.t1
Valid prediction for snap_scaffold_18-snap.2315-T1
Valid prediction for snap_scaffold_18-snap.2331-T1
Couldn't classify 76910, 76986
Couldn't classify 79325, 79516
Sorry, prediction pasa_asmbl_20927.p1 fails validation.
(GCG)	 TG	76910-76986	GT	AGG
(GAC)	 AG	78716-78905	GT	AGG
(GTG)	 AG	79325-79516	CT	TGC
-recovered pasa_asmbl_20927.p1, internal, 78716, 78905
Valid prediction for GlimmerHMM_glimmerT_43085-T1
Valid prediction for GlimmerHMM_glimmerT_43096-T1
Valid prediction for snap_scaffold_18-snap.2308-T1
Valid prediction for Augustus_model.g28724.t1
Valid prediction for GlimmerHMM_glimmerT_43099-T1
Valid prediction for GlimmerHMM_glimmerT_43097-T1
Valid prediction for snap_scaffold_18-snap.2304-T1
Valid prediction for snap_scaffold_18-snap.2297-T1
Valid prediction for Augustus_model.g28716.t1
Valid prediction for snap_scaffold_18-snap.2321-T1
Valid prediction for snap_scaffold_18-snap.2301-T1
Valid prediction for GlimmerHMM_glimmerT_43087-T1
Valid prediction for snap_scaffold_18-snap.2326-T1
Valid prediction for snap_scaffold_18-snap.2318-T1
Valid prediction for GlimmerHMM_glimmerT_43101-T1
Valid prediction for snap_scaffold_18-snap.2323-T1
Valid prediction for snap_scaffold_18-snap.2336-T1
Valid prediction for snap_scaffold_18-snap.2307-T1
Valid prediction for GlimmerHMM_glimmerT_43084-T1
Valid prediction for GlimmerHMM_glimmerT_43098-T1
Valid prediction for GlimmerHMM_glimmerT_43086-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.2313-T1
Valid prediction for snap_scaffold_18-snap.2329-T1
Valid prediction for Augustus_model.g28711.t1
Valid prediction for snap_scaffold_18-snap.2319-T1
Valid prediction for GlimmerHMM_glimmerT_43093-T1
Valid prediction for GlimmerHMM_glimmerT_43083-T1
Valid prediction for snap_scaffold_18-snap.2298-T1
Valid prediction for snap_scaffold_18-snap.2330-T1
Valid prediction for snap_scaffold_18-snap.2350-T1
Valid prediction for GlimmerHMM_glimmerT_43089-T1
Valid prediction for GlimmerHMM_glimmerT_43092-T1
Valid prediction for GlimmerHMM_glimmerT_43094-T1
Valid prediction for snap_scaffold_18-snap.2344-T1
Valid prediction for snap_scaffold_18-snap.2322-T1
Valid prediction for GlimmerHMM_glimmerT_43100-T1
Valid prediction for GlimmerHMM_glimmerT_43091-T1
Valid prediction for snap_scaffold_18-snap.2343-T1
Valid prediction for snap_scaffold_18-snap.2351-T1
Valid prediction for Augustus_model.g28710.t1
Valid prediction for snap_scaffold_18-snap.2334-T1
Valid prediction for snap_scaffold_18-snap.2314-T1
Valid prediction for snap_scaffold_18-snap.2340-T1
Valid prediction for snap_scaffold_18-snap.2324-T1
Valid prediction for snap_scaffold_18-snap.2346-T1
Valid prediction for snap_scaffold_18-snap.2342-T1
Valid prediction for snap_scaffold_18-snap.2325-T1
Valid prediction for snap_scaffold_18-snap.2310-T1
Valid prediction for snap_scaffold_18-snap.2338-T1
Valid prediction for snap_scaffold_18-snap.2300-T1
Valid prediction for snap_scaffold_18-snap.2316-T1
Valid prediction for snap_scaffold_18-snap.2337-T1
Valid prediction for Augustus_model.g28717.t1
Valid prediction for Augustus_model.g28712.t1
Valid prediction for Augustus_model.g28715.t1
Valid prediction for snap_scaffold_18-snap.2311-T1
Valid prediction for snap_scaffold_18-snap.2320-T1
Valid prediction for snap_scaffold_18-snap.2303-T1
Valid prediction for snap_scaffold_18-snap.2347-T1
Valid prediction for snap_scaffold_18-snap.2328-T1
Valid prediction for snap_scaffold_18-snap.2333-T1
Valid prediction for GlimmerHMM_glimmerT_43081-T1
Valid prediction for snap_scaffold_18-snap.2306-T1
Valid prediction for GlimmerHMM_glimmerT_43090-T1
Valid prediction for snap_scaffold_18-snap.2327-T1
Couldn't classify 189762, 189989
Sorry, prediction pasa_asmbl_20119.p2 fails validation.
(ATG)	 AC	186931-187011	GT	GGG
(CTC)	 AG	187797-188066	GT	AGG
(CCC)	 AG	189762-189989	GA	GTG
-recovered pasa_asmbl_20119.p2, initial, 186931, 187011
-recovered pasa_asmbl_20119.p2, internal, 187797, 188066
Valid prediction for snap_scaffold_18-snap.2353-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7296, rend_intergenic: 4619  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14769, rend_intergenic: 7479  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20144, rend_intergenic: 14777  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31804, rend_intergenic: 21138  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34583, rend_intergenic: 34510  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42145, rend_intergenic: 34630  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44297, rend_intergenic: 42198  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50939, rend_intergenic: 45615  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57047, rend_intergenic: 52539  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70765, rend_intergenic: 58474  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80003, rend_intergenic: 77926  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88120, rend_intergenic: 80469  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93395, rend_intergenic: 88517  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96640, rend_intergenic: 93443  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105368, rend_intergenic: 98643  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105872, rend_intergenic: 105531  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118603, rend_intergenic: 108353  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128715, rend_intergenic: 119617  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131840, rend_intergenic: 128776  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155383, rend_intergenic: 132061  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162391, rend_intergenic: 158228  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168208, rend_intergenic: 162478  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176009, rend_intergenic: 169237  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186684, rend_intergenic: 179474  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192314, rend_intergenic: 190868  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211684, rend_intergenic: 193671  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 222206, rend_intergenic: 212823  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 232111, rend_intergenic: 222505  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 233207, rend_intergenic: 232407  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 245002, rend_intergenic: 237391  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 255877, rend_intergenic: 250102  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 262555
-exon list size: 458


building trellis

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-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 7296, rend_intergenic: 4619  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14769, rend_intergenic: 7479  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20144, rend_intergenic: 14777  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31804, rend_intergenic: 21138  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34583, rend_intergenic: 34510  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42145, rend_intergenic: 34630  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44297, rend_intergenic: 42198  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50939, rend_intergenic: 45615  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57047, rend_intergenic: 52539  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70765, rend_intergenic: 58474  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80003, rend_intergenic: 77926  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88120, rend_intergenic: 80469  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93395, rend_intergenic: 88517  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96640, rend_intergenic: 93443  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105368, rend_intergenic: 98643  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105872, rend_intergenic: 105531  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118603, rend_intergenic: 108353  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128715, rend_intergenic: 119617  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131840, rend_intergenic: 128776  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155383, rend_intergenic: 132061  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162391, rend_intergenic: 158228  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168208, rend_intergenic: 162478  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176009, rend_intergenic: 169237  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186684, rend_intergenic: 179474  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192314, rend_intergenic: 190868  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211684, rend_intergenic: 193671  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 222206, rend_intergenic: 212823  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 232111, rend_intergenic: 222505  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 233207, rend_intergenic: 232407  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 245002, rend_intergenic: 237391  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 255877, rend_intergenic: 250102  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 13 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 33743
-exon list size: 23


building trellis

4.0    
8.0    
12.0    
16.0    
20.0    
24.0    
28.0    
32.0    
36.0    
40.0    
44.0    
48.0    
52.0    
56.0    
60.0    
64.0    
68.0    
72.0    
76.0    
80.0    
84.0    
88.0    
92.0    
96.0    
-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

-building DP trellis

-building trellis in range 1 - 24404
-exon list size: 11


building trellis

7.7    
15.4    
23.1    
30.8    
38.5    
46.2    
53.8    
61.5    
69.2    
76.9    
84.6    
92.3    
-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

-building DP trellis

-building trellis in range 4632 - 24404
-exon list size: 9


building trellis

9.1    
18.2    
27.3    
36.4    
45.5    
54.5    
63.6    
72.7    
81.8    
90.9    
-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

-building DP trellis

-building trellis in range 4632 - 20106
-exon list size: 7


building trellis

11.1    
22.2    
33.3    
44.4    
55.6    
66.7    
77.8    
88.9    
-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

-building DP trellis

-building trellis in range 250954 - 262555
-exon list size: 10


building trellis

8.3    
16.7    
25.0    
33.3    
41.7    
50.0    
58.3    
66.7    
75.0    
83.3    
91.7    
-found 1 predictions from path traversal

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