-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_28/scaffold_28_1232772-1391838

-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_28-snap.311-T1
Valid prediction for snap_scaffold_28-snap.298-T1
Valid prediction for GeneMark_model.103932_t
Valid prediction for snap_scaffold_28-snap.275-T1
Valid prediction for Augustus_model.g39605.t1
Valid prediction for Augustus_model.g39606.t1
Valid prediction for snap_scaffold_28-snap.285-T1
Valid prediction for GlimmerHMM_glimmerT_59511-T1
Valid prediction for snap_scaffold_28-snap.282-T1
Valid prediction for GeneMark_model.103940_t
Valid prediction for snap_scaffold_28-snap.300-T1
Valid prediction for snap_scaffold_28-snap.301-T1
Valid prediction for GeneMark_model.103890_t
Valid prediction for GlimmerHMM_glimmerT_59519-T1
Valid prediction for GeneMark_model.103928_t
Valid prediction for snap_scaffold_28-snap.314-T1
Valid prediction for GeneMark_model.103907_t
Valid prediction for GeneMark_model.103912_t
Valid prediction for GlimmerHMM_glimmerT_59510-T1
Valid prediction for GeneMark_model.103930_t
Valid prediction for snap_scaffold_28-snap.315-T1
Valid prediction for GeneMark_model.103931_t
Couldn't classify 112324, 112476
Couldn't classify 114345, 114403
Sorry, prediction pasa_asmbl_38572.p1 fails validation.
(ATT)	 TC	112324-112476	GT	GGG
(ATC)	 AG	113390-113457	GT	TGG
(GCC)	 AG	113904-114004	GT	AGG
(AGG)	 AG	114345-114403	CA	CTC
-recovered pasa_asmbl_38572.p1, internal, 113390, 113457
-recovered pasa_asmbl_38572.p1, internal, 113904, 114004
Valid prediction for GeneMark_model.103937_t
Valid prediction for GlimmerHMM_glimmerT_59523-T1
Valid prediction for Augustus_model.g39601.t1
Valid prediction for GeneMark_model.103895_t
Valid prediction for snap_scaffold_28-snap.277-T1
Valid prediction for snap_scaffold_28-snap.290-T1
Valid prediction for GeneMark_model.103888_t
Valid prediction for GeneMark_model.103902_t
Valid prediction for GeneMark_model.103926_t
Valid prediction for GeneMark_model.103944_t
Valid prediction for GlimmerHMM_glimmerT_59526-T1
Valid prediction for Augustus_model.g39615.t1
Valid prediction for snap_scaffold_28-snap.309-T1
Valid prediction for GeneMark_model.103916_t
Valid prediction for GeneMark_model.103924_t
Valid prediction for GeneMark_model.103910_t
Valid prediction for GlimmerHMM_glimmerT_59529-T1
Valid prediction for GeneMark_model.103923_t
Valid prediction for GeneMark_model.103909_t
Valid prediction for Augustus_model.g39609.t1
Valid prediction for GeneMark_model.103942_t
Valid prediction for GlimmerHMM_glimmerT_59518-T1
Valid prediction for GlimmerHMM_glimmerT_59506-T1
Valid prediction for GeneMark_model.103892_t
Valid prediction for GeneMark_model.103905_t
Valid prediction for snap_scaffold_28-snap.280-T1
Valid prediction for GeneMark_model.103918_t
Valid prediction for snap_scaffold_28-snap.317-T1
Valid prediction for snap_scaffold_28-snap.289-T1
Valid prediction for GlimmerHMM_glimmerT_59516-T1
Valid prediction for snap_scaffold_28-snap.293-T1
Valid prediction for snap_scaffold_28-snap.303-T1
Valid prediction for GeneMark_model.103897_t
Valid prediction for GeneMark_model.103914_t
Valid prediction for snap_scaffold_28-snap.305-T1
Valid prediction for snap_scaffold_28-snap.292-T1
Valid prediction for GeneMark_model.103920_t
Valid prediction for GeneMark_model.103886_t
Valid prediction for GlimmerHMM_glimmerT_59513-T1
Valid prediction for GeneMark_model.103935_t
Valid prediction for GeneMark_model.103896_t
Valid prediction for snap_scaffold_28-snap.286-T1
Valid prediction for GlimmerHMM_glimmerT_59522-T1
Valid prediction for GeneMark_model.103898_t
Valid prediction for snap_scaffold_28-snap.307-T1
Valid prediction for Augustus_model.g39616.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 Augustus_model.g39612.t1
Valid prediction for snap_scaffold_28-snap.313-T1
Valid prediction for GeneMark_model.103917_t
Valid prediction for snap_scaffold_28-snap.287-T1
Valid prediction for GeneMark_model.103929_t
Valid prediction for snap_scaffold_28-snap.291-T1
Valid prediction for snap_scaffold_28-snap.304-T1
Valid prediction for GlimmerHMM_glimmerT_59524-T1
Valid prediction for snap_scaffold_28-snap.276-T1
Valid prediction for GeneMark_model.103906_t
Valid prediction for snap_scaffold_28-snap.288-T1
Valid prediction for Augustus_model.g39611.t1
Valid prediction for Augustus_model.g39604.t1
Valid prediction for GeneMark_model.103889_t
Valid prediction for GlimmerHMM_glimmerT_59508-T1
Valid prediction for GlimmerHMM_glimmerT_59521-T1
Valid prediction for GeneMark_model.103919_t
Valid prediction for Augustus_model.g39607.t1
Valid prediction for GlimmerHMM_glimmerT_59520-T1
Valid prediction for GeneMark_model.103936_t
Valid prediction for GeneMark_model.103911_t
Valid prediction for GeneMark_model.103939_t
Valid prediction for snap_scaffold_28-snap.302-T1
Valid prediction for GlimmerHMM_glimmerT_59509-T1
Valid prediction for GeneMark_model.103891_t
Valid prediction for GeneMark_model.103927_t
Valid prediction for snap_scaffold_28-snap.274-T1
Valid prediction for snap_scaffold_28-snap.299-T1
Valid prediction for Augustus_model.g39602.t1
Valid prediction for GeneMark_model.103922_t
Valid prediction for snap_scaffold_28-snap.319-T1
Valid prediction for snap_scaffold_28-snap.279-T1
Valid prediction for GeneMark_model.103933_t
Valid prediction for snap_scaffold_28-snap.296-T1
Valid prediction for GlimmerHMM_glimmerT_59514-T1
Valid prediction for GlimmerHMM_glimmerT_59517-T1
Valid prediction for GeneMark_model.103901_t
Valid prediction for GeneMark_model.103945_t
Valid prediction for GlimmerHMM_glimmerT_59504-T1
Valid prediction for Augustus_model.g39617.t1
Valid prediction for snap_scaffold_28-snap.308-T1
Valid prediction for Augustus_model.g39613.t1
Valid prediction for snap_scaffold_28-snap.281-T1
Valid prediction for snap_scaffold_28-snap.284-T1
Valid prediction for GlimmerHMM_glimmerT_59525-T1
Valid prediction for Augustus_model.g39608.t1
Valid prediction for snap_scaffold_28-snap.310-T1
Valid prediction for GlimmerHMM_glimmerT_59512-T1
Valid prediction for GeneMark_model.103899_t
Valid prediction for snap_scaffold_28-snap.294-T1
Valid prediction for snap_scaffold_28-snap.316-T1
Valid prediction for Augustus_model.g39610.t1
Valid prediction for Augustus_model.g39614.t1
Valid prediction for snap_scaffold_28-snap.295-T1
Valid prediction for GlimmerHMM_glimmerT_59528-T1
Valid prediction for GeneMark_model.103904_t
Valid prediction for GlimmerHMM_glimmerT_59503-T1
Valid prediction for GlimmerHMM_glimmerT_59515-T1
Valid prediction for GlimmerHMM_glimmerT_59507-T1
Valid prediction for snap_scaffold_28-snap.297-T1
Valid prediction for GeneMark_model.103941_t
Valid prediction for Augustus_model.g39603.t1
Valid prediction for snap_scaffold_28-snap.306-T1
Valid prediction for snap_scaffold_28-snap.283-T1
Valid prediction for GeneMark_model.103934_t
Valid prediction for snap_scaffold_28-snap.278-T1
Valid prediction for GeneMark_model.103925_t
Valid prediction for GlimmerHMM_glimmerT_59530-T1
Valid prediction for GeneMark_model.103908_t
Valid prediction for Augustus_model.g39618.t1
Valid prediction for snap_scaffold_28-snap.312-T1
Valid prediction for snap_scaffold_28-snap.318-T1
Valid prediction for GeneMark_model.103887_t
Valid prediction for GeneMark_model.103913_t
Valid prediction for GlimmerHMM_glimmerT_59527-T1
Valid prediction for GeneMark_model.103915_t
Valid prediction for GeneMark_model.103900_t
Valid prediction for GeneMark_model.103921_t
Valid prediction for GlimmerHMM_glimmerT_59505-T1
Valid prediction for GeneMark_model.103903_t
Valid prediction for GeneMark_model.103943_t
Valid prediction for GeneMark_model.103893_t
Valid prediction for GlimmerHMM_glimmerT_59532-T1
Valid prediction for GlimmerHMM_glimmerT_59531-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10893, rend_intergenic: 7819  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17374, rend_intergenic: 15529  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23494, rend_intergenic: 19388  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29368, rend_intergenic: 25148  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33561, rend_intergenic: 30085  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38657, rend_intergenic: 33929  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43521, rend_intergenic: 42282  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49708, rend_intergenic: 49599  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56857, rend_intergenic: 55377  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62690, rend_intergenic: 57897  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66349, rend_intergenic: 62972  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80595, rend_intergenic: 78726  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88651, rend_intergenic: 83932  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91662, rend_intergenic: 89630  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95192, rend_intergenic: 92884  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126300, rend_intergenic: 124669  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132843, rend_intergenic: 129682  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139455, rend_intergenic: 137228  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143874, rend_intergenic: 141384  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151175, rend_intergenic: 145189  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 159067
-exon list size: 706


building trellis

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96.3    
96.5    
96.6    
96.8    
96.9    
97.0    
97.2    
97.3    
97.5    
97.6    
97.7    
97.9    
98.0    
98.2    
98.3    
98.4    
98.6    
98.7    
98.9    
99.0    
99.2    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 46 predictions from path traversal
Error with prediction: snap lend_intergenic: 10893, rend_intergenic: 7819  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17374, rend_intergenic: 15529  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23494, rend_intergenic: 19388  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29368, rend_intergenic: 25148  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33561, rend_intergenic: 30085  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38657, rend_intergenic: 33929  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43521, rend_intergenic: 42282  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49708, rend_intergenic: 49599  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56857, rend_intergenic: 55377  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62690, rend_intergenic: 57897  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66349, rend_intergenic: 62972  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80595, rend_intergenic: 78726  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88651, rend_intergenic: 83932  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91662, rend_intergenic: 89630  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95192, rend_intergenic: 92884  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126300, rend_intergenic: 124669  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132843, rend_intergenic: 129682  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139455, rend_intergenic: 137228  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143874, rend_intergenic: 141384  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151175, rend_intergenic: 145189  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 10771
-exon list size: 40


building trellis

2.4    
4.8    
7.1    
9.5    
11.9    
14.3    
16.7    
19.0    
21.4    
23.8    
26.2    
28.6    
31.0    
33.3    
35.7    
38.1    
40.5    
42.9    
45.2    
47.6    
50.0    
52.4    
54.8    
57.1    
59.5    
61.9    
64.3    
66.7    
69.0    
71.4    
73.8    
76.2    
78.6    
81.0    
83.3    
85.7    
88.1    
90.5    
92.9    
95.2    
97.6    
-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