-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_21/scaffold_21_3550108-3742336

-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_21-snap.705-T1
Valid prediction for snap_scaffold_21-snap.691-T1
Valid prediction for GeneMark_model.84367_t
Valid prediction for snap_scaffold_21-snap.702-T1
Valid prediction for GeneMark_model.84366_t
Valid prediction for snap_scaffold_21-snap.703-T1
Valid prediction for snap_scaffold_21-snap.694-T1
Valid prediction for snap_scaffold_21-snap.707-T1
Valid prediction for GeneMark_model.84358_t
Valid prediction for GlimmerHMM_glimmerT_48600-T1
Valid prediction for Augustus_model.g32513.t1
Valid prediction for GeneMark_model.84381_t
Valid prediction for snap_scaffold_21-snap.701-T1
Valid prediction for GlimmerHMM_glimmerT_48587-T1
Couldn't classify 168981, 169121
Sorry, prediction pasa_asmbl_28510.p1 fails validation.
(GTG)	 AG	168981-169121	GT	TCG
(TTC)	 AG	170810-171064	GT	AGG
(ATC)	 AG	171376-171714	CT	AGC
-recovered pasa_asmbl_28510.p1, terminal, 171376, 171714
-recovered pasa_asmbl_28510.p1, internal, 168981, 169121
-recovered pasa_asmbl_28510.p1, internal, 170810, 171064
Valid prediction for Augustus_model.g32518.t1
Valid prediction for GlimmerHMM_glimmerT_48594-T1
Valid prediction for GeneMark_model.84380_t
Valid prediction for snap_scaffold_21-snap.695-T1
Valid prediction for GeneMark_model.84355_t
Valid prediction for GeneMark_model.84359_t
Valid prediction for snap_scaffold_21-snap.680-T1
Valid prediction for snap_scaffold_21-snap.677-T1
Valid prediction for snap_scaffold_21-snap.676-T1
Valid prediction for snap_scaffold_21-snap.698-T1
Valid prediction for snap_scaffold_21-snap.675-T1
Valid prediction for GeneMark_model.84362_t
Valid prediction for GlimmerHMM_glimmerT_48591-T1
Valid prediction for GlimmerHMM_glimmerT_48590-T1
Valid prediction for GlimmerHMM_glimmerT_48598-T1
Valid prediction for snap_scaffold_21-snap.678-T1
Valid prediction for Augustus_model.g32511.t1
Valid prediction for snap_scaffold_21-snap.704-T1
Valid prediction for Augustus_model.g32510.t1
Valid prediction for GlimmerHMM_glimmerT_48606-T1
Valid prediction for Augustus_model.g32516.t1
Valid prediction for GeneMark_model.84370_t
Valid prediction for GlimmerHMM_glimmerT_48589-T1
Valid prediction for Augustus_model.g32512.t1
Valid prediction for GeneMark_model.84364_t
Valid prediction for GeneMark_model.84374_t
Valid prediction for GeneMark_model.84378_t
Valid prediction for GeneMark_model.84371_t
Valid prediction for GlimmerHMM_glimmerT_48592-T1
Valid prediction for snap_scaffold_21-snap.686-T1
Valid prediction for snap_scaffold_21-snap.681-T1
Valid prediction for Augustus_model.g32515.t1
Valid prediction for GeneMark_model.84372_t
Valid prediction for GeneMark_model.84357_t
Valid prediction for snap_scaffold_21-snap.690-T1
Valid prediction for snap_scaffold_21-snap.672-T1
Couldn't classify 168727, 168774
Sorry, prediction pasa_asmbl_28509.p1 fails validation.
(ATG)	 CA	168245-168358	GT	AGG
(GGT)	 AG	168480-168614	GT	AGG
(GCT)	 AG	168727-168774	GC	TGG
-recovered pasa_asmbl_28509.p1, initial, 168245, 168358
-recovered pasa_asmbl_28509.p1, internal, 168480, 168614
-recovered pasa_asmbl_28509.p1, internal, 168727, 168774
Valid prediction for GlimmerHMM_glimmerT_48608-T1
Valid prediction for snap_scaffold_21-snap.685-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 GeneMark_model.84361_t
Valid prediction for GeneMark_model.84376_t
Valid prediction for snap_scaffold_21-snap.673-T1
Valid prediction for snap_scaffold_21-snap.699-T1
Valid prediction for GeneMark_model.84379_t
Valid prediction for Augustus_model.g32514.t1
Couldn't classify 8934, 8943
Sorry, prediction pasa_asmbl_27554.p1 fails validation.
(CTC)	 TC	8934-8943	GT	AGG
(GGG)	 AG	9220-9415	GT	AGG
(TTA)	 AG	10275-10461	GT	AGG
(GTA)	 AG	12211-12372	GT	ACG
(GCT)	 AG	13299-13395	GT	AGG
(TGG)	 AG	15203-15371	GT	AGG
(TCT)	 AG	15461-15593	GT	AGG
(CTG)	 AG	15811-15980	GT	AAG
(TTA)	 AG	16921-16924	TT	AAT
-recovered pasa_asmbl_27554.p1, terminal, 16921, 16924
-recovered pasa_asmbl_27554.p1, internal, 9220, 9415
-recovered pasa_asmbl_27554.p1, internal, 10275, 10461
-recovered pasa_asmbl_27554.p1, internal, 12211, 12372
-recovered pasa_asmbl_27554.p1, internal, 13299, 13395
-recovered pasa_asmbl_27554.p1, internal, 15203, 15371
-recovered pasa_asmbl_27554.p1, internal, 15461, 15593
-recovered pasa_asmbl_27554.p1, internal, 15811, 15980
Valid prediction for snap_scaffold_21-snap.684-T1
Valid prediction for GlimmerHMM_glimmerT_48601-T1
Valid prediction for GeneMark_model.84365_t
Valid prediction for GeneMark_model.84373_t
Valid prediction for snap_scaffold_21-snap.700-T1
Valid prediction for snap_scaffold_21-snap.682-T1
Valid prediction for GlimmerHMM_glimmerT_48607-T1
Valid prediction for GlimmerHMM_glimmerT_48605-T1
Valid prediction for snap_scaffold_21-snap.679-T1
Valid prediction for GeneMark_model.84363_t
Valid prediction for GeneMark_model.84369_t
Valid prediction for snap_scaffold_21-snap.687-T1
Valid prediction for snap_scaffold_21-snap.696-T1
Valid prediction for GlimmerHMM_glimmerT_48593-T1
Valid prediction for GeneMark_model.84377_t
Valid prediction for snap_scaffold_21-snap.683-T1
Valid prediction for GeneMark_model.84356_t
Valid prediction for Augustus_model.g32517.t1
Valid prediction for GeneMark_model.84353_t
Valid prediction for GeneMark_model.84360_t
Valid prediction for GlimmerHMM_glimmerT_48597-T1
Valid prediction for GlimmerHMM_glimmerT_48595-T1
Valid prediction for GlimmerHMM_glimmerT_48602-T1
Valid prediction for snap_scaffold_21-snap.688-T1
Valid prediction for snap_scaffold_21-snap.692-T1
Valid prediction for GlimmerHMM_glimmerT_48588-T1
Valid prediction for GlimmerHMM_glimmerT_48596-T1
Valid prediction for GlimmerHMM_glimmerT_48603-T1
Valid prediction for snap_scaffold_21-snap.706-T1
Valid prediction for GeneMark_model.84354_t
Valid prediction for GeneMark_model.84368_t
Valid prediction for GlimmerHMM_glimmerT_48599-T1
Valid prediction for GlimmerHMM_glimmerT_48604-T1
Valid prediction for snap_scaffold_21-snap.693-T1
Valid prediction for GeneMark_model.84375_t
Valid prediction for snap_scaffold_21-snap.697-T1
Valid prediction for snap_scaffold_21-snap.674-T1
Valid prediction for snap_scaffold_21-snap.689-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 100601, rend_intergenic: 98341  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152629, rend_intergenic: 147958  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156079, rend_intergenic: 152726  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179183, rend_intergenic: 175831  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 192229
-exon list size: 334


building trellis

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3.6    
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10.7    
11.0    
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11.6    
11.9    
12.2    
12.5    
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13.4    
13.7    
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14.3    
14.6    
14.9    
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17.6    
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18.8    
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19.6    
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21.4    
21.7    
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24.7    
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25.6    
25.9    
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26.5    
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27.1    
27.4    
27.7    
28.0    
28.3    
28.6    
28.9    
29.2    
29.5    
29.8    
30.1    
30.4    
30.7    
31.0    
31.2    
31.5    
31.8    
32.1    
32.4    
32.7    
33.0    
33.3    
33.6    
33.9    
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34.8    
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35.4    
35.7    
36.0    
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38.1    
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38.7    
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39.6    
39.9    
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40.5    
40.8    
41.1    
41.4    
41.7    
42.0    
42.3    
42.6    
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44.0    
44.3    
44.6    
44.9    
45.2    
45.5    
45.8    
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46.4    
46.7    
47.0    
47.3    
47.6    
47.9    
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49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.2    
51.5    
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52.1    
52.4    
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53.0    
53.3    
53.6    
53.9    
54.2    
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55.4    
55.7    
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56.2    
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58.0    
58.3    
58.6    
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59.2    
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60.4    
60.7    
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61.6    
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63.4    
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64.3    
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65.2    
65.5    
65.8    
66.1    
66.4    
66.7    
67.0    
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67.6    
67.9    
68.2    
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69.3    
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72.0    
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78.0    
78.3    
78.6    
78.9    
79.2    
79.5    
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80.1    
80.4    
80.7    
81.0    
81.2    
81.5    
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82.4    
82.7    
83.0    
83.3    
83.6    
83.9    
84.2    
84.5    
84.8    
85.1    
85.4    
85.7    
86.0    
86.3    
86.6    
86.9    
87.2    
87.5    
87.8    
88.1    
88.4    
88.7    
89.0    
89.3    
89.6    
89.9    
90.2    
90.5    
90.8    
91.1    
91.4    
91.7    
92.0    
92.3    
92.6    
92.9    
93.2    
93.5    
93.8    
94.0    
94.3    
94.6    
94.9    
95.2    
95.5    
95.8    
96.1    
96.4    
96.7    
97.0    
97.3    
97.6    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 20 predictions from path traversal
Error with prediction: snap lend_intergenic: 100601, rend_intergenic: 98341  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152629, rend_intergenic: 147958  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156079, rend_intergenic: 152726  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179183, rend_intergenic: 175831  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 10 predictions persist after filtering for low support