-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_13/scaffold_13_11869856-12010065

-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 GeneMark_model.56663_t
Valid prediction for GlimmerHMM_glimmerT_33194-T1
Valid prediction for GeneMark_model.56643_t
Valid prediction for GeneMark_model.56642_t
Valid prediction for Augustus_model.g22309.t1
Valid prediction for GeneMark_model.56655_t
Valid prediction for snap_scaffold_13-snap.2230-T1
Valid prediction for GlimmerHMM_glimmerT_33205-T1
Valid prediction for GlimmerHMM_glimmerT_33188-T1
Valid prediction for snap_scaffold_13-snap.2232-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_33198-T1
Valid prediction for GeneMark_model.56620_t
Valid prediction for GeneMark_model.56623_t
Valid prediction for snap_scaffold_13-snap.2217-T1
Valid prediction for GlimmerHMM_glimmerT_33192-T1
Valid prediction for snap_scaffold_13-snap.2224-T1
Valid prediction for Augustus_model.g22314.t1
Valid prediction for snap_scaffold_13-snap.2241-T1
Valid prediction for CodingQuarry_transcript_13230-T1
Valid prediction for GlimmerHMM_glimmerT_33199-T1
Valid prediction for GlimmerHMM_glimmerT_33187-T1
Valid prediction for GeneMark_model.56621_t
Valid prediction for GeneMark_model.56638_t
Valid prediction for GeneMark_model.56634_t
Valid prediction for GlimmerHMM_glimmerT_33201-T1
Valid prediction for snap_scaffold_13-snap.2212-T1
Valid prediction for snap_scaffold_13-snap.2225-T1
Valid prediction for Augustus_model.g22317.t1
Valid prediction for snap_scaffold_13-snap.2221-T1
Valid prediction for Augustus_model.g22308.t1
Valid prediction for snap_scaffold_13-snap.2220-T1
Valid prediction for GeneMark_model.56630_t
Valid prediction for snap_scaffold_13-snap.2208-T1
Valid prediction for snap_scaffold_13-snap.2239-T1
Valid prediction for snap_scaffold_13-snap.2227-T1
Valid prediction for GeneMark_model.56632_t
Valid prediction for GeneMark_model.56636_t
Couldn't classify 61888, 61941
Couldn't classify 65242, 65424
Sorry, prediction pasa_asmbl_11298.p2 fails validation.
(AGA)	 GA	61888-61941	GT	AGG
(GAG)	 AG	63700-63808	GT	CGG
(CTT)	 AG	64527-64632	GT	AGG
(ACT)	 AG	64848-65055	GT	GTG
(GAT)	 AG	65242-65424	GC	AGG
-recovered pasa_asmbl_11298.p2, internal, 63700, 63808
-recovered pasa_asmbl_11298.p2, internal, 64527, 64632
-recovered pasa_asmbl_11298.p2, internal, 64848, 65055
-recovered pasa_asmbl_11298.p2, internal, 65242, 65424
Valid prediction for snap_scaffold_13-snap.2218-T1
Valid prediction for GeneMark_model.56650_t
Valid prediction for GlimmerHMM_glimmerT_33185-T1
Valid prediction for snap_scaffold_13-snap.2234-T1
Valid prediction for GeneMark_model.56652_t
Valid prediction for Augustus_model.g22312.t1
Valid prediction for GeneMark_model.56645_t
Valid prediction for GeneMark_model.56647_t
Valid prediction for GlimmerHMM_glimmerT_33183-T1
Valid prediction for GeneMark_model.56661_t
Couldn't classify 83581, 84030
Sorry, prediction pasa_asmbl_10079.p1 fails validation.
(GGG)	 GA	83581-84030	TT	AAT
Valid prediction for GeneMark_model.56640_t
Valid prediction for HiQ_model.g22310.t1
Valid prediction for GlimmerHMM_glimmerT_33193-T1
Couldn't classify 131490, 132095
Sorry, prediction pasa_asmbl_11303.p1 fails validation.
(AGA)	 TT	131490-132095	GT	AGG
(GAG)	 AG	132209-132271	GT	AGG
(GAG)	 AG	132438-132559	GT	GGG
(AAT)	 AG	132792-132858	GT	TGG
(GTG)	 AG	133652-133791	GT	AGG
(ATC)	 AG	134466-134676	CA	GAC
-recovered pasa_asmbl_11303.p1, terminal, 134466, 134676
-recovered pasa_asmbl_11303.p1, internal, 132209, 132271
-recovered pasa_asmbl_11303.p1, internal, 132438, 132559
-recovered pasa_asmbl_11303.p1, internal, 132792, 132858
-recovered pasa_asmbl_11303.p1, internal, 133652, 133791
Valid prediction for GlimmerHMM_glimmerT_33191-T1
Valid prediction for GeneMark_model.56657_t
Valid prediction for snap_scaffold_13-snap.2210-T1
Valid prediction for GeneMark_model.56624_t
Valid prediction for GlimmerHMM_glimmerT_33204-T1
Valid prediction for snap_scaffold_13-snap.2238-T1
Valid prediction for snap_scaffold_13-snap.2229-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.56625_t
Valid prediction for GlimmerHMM_glimmerT_33206-T1
Valid prediction for GeneMark_model.56641_t
Valid prediction for GlimmerHMM_glimmerT_33202-T1
Valid prediction for pasa_asmbl_10074.p1
Valid prediction for CodingQuarry_transcript_13233-T1
Valid prediction for GeneMark_model.56646_t
Valid prediction for snap_scaffold_13-snap.2226-T1
Valid prediction for pasa_asmbl_10077.p1
Valid prediction for Augustus_model.g22313.t1
Valid prediction for CodingQuarry_transcript_13231-T1
Valid prediction for GeneMark_model.56622_t
Valid prediction for snap_scaffold_13-snap.2211-T1
Valid prediction for CodingQuarry_transcript_13232-T1
Valid prediction for GlimmerHMM_glimmerT_33196-T1
Valid prediction for Augustus_model.g22318.t1
Valid prediction for Augustus_model.g22305.t1
Valid prediction for GlimmerHMM_glimmerT_33203-T1
Valid prediction for GeneMark_model.56658_t
Valid prediction for GeneMark_model.56644_t
Valid prediction for Augustus_model.g22315.t1
Valid prediction for GlimmerHMM_glimmerT_33189-T1
Valid prediction for Augustus_model.g22304.t1
Valid prediction for GeneMark_model.56629_t
Valid prediction for snap_scaffold_13-snap.2228-T1
Valid prediction for Augustus_model.g22307.t1
Valid prediction for snap_scaffold_13-snap.2222-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for snap_scaffold_13-snap.2213-T1
Valid prediction for GeneMark_model.56635_t
Valid prediction for GeneMark_model.56631_t
Valid prediction for GeneMark_model.56656_t
Valid prediction for snap_scaffold_13-snap.2216-T1
Valid prediction for snap_scaffold_13-snap.2240-T1
Valid prediction for GlimmerHMM_glimmerT_33190-T1
Valid prediction for CodingQuarry_transcript_13234-T1
Valid prediction for GeneMark_model.56654_t
Valid prediction for snap_scaffold_13-snap.2242-T1
Valid prediction for GeneMark_model.56651_t
Valid prediction for GeneMark_model.56664_t
Valid prediction for snap_scaffold_13-snap.2231-T1
Valid prediction for snap_scaffold_13-snap.2215-T1
Valid prediction for Augustus_model.g22306.t1
Valid prediction for GlimmerHMM_glimmerT_33195-T1
Valid prediction for GeneMark_model.56628_t
Valid prediction for GlimmerHMM_glimmerT_33184-T1
Valid prediction for snap_scaffold_13-snap.2223-T1
Valid prediction for snap_scaffold_13-snap.2214-T1
Valid prediction for snap_scaffold_13-snap.2236-T1
Valid prediction for GeneMark_model.56653_t
Valid prediction for GeneMark_model.56626_t
Valid prediction for GlimmerHMM_glimmerT_33200-T1
Valid prediction for GeneMark_model.56649_t
Valid prediction for GeneMark_model.56627_t
Valid prediction for GeneMark_model.56619_t
Valid prediction for snap_scaffold_13-snap.2237-T1
Valid prediction for snap_scaffold_13-snap.2235-T1
Sorry, intron length (7) is less than minimum required (10)
Couldn't classify 21201, 21298
Sorry, prediction pasa_asmbl_10084.p1 fails validation.
(ATG)	 CC	15626-15647	GT	AGG
(GTG)	 AG	16238-16327	GT	CGG
(TCT)	 AG	17137-17187	GT	CAG
(AGT)	 AG	17328-17413	GT	GGG
(CGT)	 AG	17681-17809	GT	CGG
(GAG)	 AG	18012-18072	GT	AGG
(GCC)	 AG	18399-18454	GT	AGG
(GCG)	 AG	19147-19323	GT	AGG
(GAC)	 AG	20187-20284	GT	AGG
(GCT)	 AG	20441-20527	GT	AGG
(GTT)	 AG	20617-20752	GT	AGG
(GAG)	 AG	20962-21049	GT	TGG
(GCT)	 AG	21201-21298	CA	ACC
-recovered pasa_asmbl_10084.p1, initial, 15626, 15647
add_exon() Sorry, pasa_asmbl_10084.p1 20441-20527-terminal-1 is invalid.
-recovered pasa_asmbl_10084.p1, terminal, 20441, 20527
-recovered pasa_asmbl_10084.p1, internal, 16238, 16327
-recovered pasa_asmbl_10084.p1, internal, 17137, 17187
-recovered pasa_asmbl_10084.p1, internal, 17328, 17413
-recovered pasa_asmbl_10084.p1, internal, 17681, 17809
-recovered pasa_asmbl_10084.p1, internal, 18012, 18072
-recovered pasa_asmbl_10084.p1, internal, 18399, 18454
-recovered pasa_asmbl_10084.p1, internal, 19147, 19323
-recovered pasa_asmbl_10084.p1, internal, 20187, 20284
-recovered pasa_asmbl_10084.p1, internal, 20441, 20527
-recovered pasa_asmbl_10084.p1, internal, 20617, 20752
-recovered pasa_asmbl_10084.p1, internal, 20962, 21049
Valid prediction for GlimmerHMM_glimmerT_33197-T1
Valid prediction for GlimmerHMM_glimmerT_33186-T1
Valid prediction for snap_scaffold_13-snap.2219-T1
Valid prediction for HiQ_model.g22311.t1
Valid prediction for Augustus_model.g22316.t1
Valid prediction for snap_scaffold_13-snap.2209-T1
Valid prediction for GeneMark_model.56660_t
Valid prediction for GeneMark_model.56662_t
Valid prediction for snap_scaffold_13-snap.2233-T1
Valid prediction for GeneMark_model.56637_t
Valid prediction for GeneMark_model.56648_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 18151, rend_intergenic: 16274  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51462, rend_intergenic: 47496  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61311, rend_intergenic: 59586  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66594, rend_intergenic: 63880  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77097, rend_intergenic: 72246  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87671, rend_intergenic: 85825  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98640, rend_intergenic: 87749  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99838, rend_intergenic: 98698  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102390, rend_intergenic: 99857  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104887, rend_intergenic: 103015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109267, rend_intergenic: 105413  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124214, rend_intergenic: 120820  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127513, rend_intergenic: 126040  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 140210
-exon list size: 488


building trellis

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17.3    
17.6    
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18.6    
18.8    
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20.6    
20.8    
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21.2    
21.4    
21.6    
21.8    
22.0    
22.2    
22.4    
22.7    
22.9    
23.1    
23.3    
23.5    
23.7    
23.9    
24.1    
24.3    
24.5    
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24.9    
25.1    
25.3    
25.5    
25.7    
25.9    
26.1    
26.3    
26.5    
26.7    
26.9    
27.1    
27.3    
27.6    
27.8    
28.0    
28.2    
28.4    
28.6    
28.8    
29.0    
29.2    
29.4    
29.6    
29.8    
30.0    
30.2    
30.4    
30.6    
30.8    
31.0    
31.2    
31.4    
31.6    
31.8    
32.0    
32.2    
32.4    
32.7    
32.9    
33.1    
33.3    
33.5    
33.7    
33.9    
34.1    
34.3    
34.5    
34.7    
34.9    
35.1    
35.3    
35.5    
35.7    
35.9    
36.1    
36.3    
36.5    
36.7    
36.9    
37.1    
37.3    
37.6    
37.8    
38.0    
38.2    
38.4    
38.6    
38.8    
39.0    
39.2    
39.4    
39.6    
39.8    
40.0    
40.2    
40.4    
40.6    
40.8    
41.0    
41.2    
41.4    
41.6    
41.8    
42.0    
42.2    
42.4    
42.7    
42.9    
43.1    
43.3    
43.5    
43.7    
43.9    
44.1    
44.3    
44.5    
44.7    
44.9    
45.1    
45.3    
45.5    
45.7    
45.9    
46.1    
46.3    
46.5    
46.7    
46.9    
47.1    
47.3    
47.6    
47.8    
48.0    
48.2    
48.4    
48.6    
48.8    
49.0    
49.2    
49.4    
49.6    
49.8    
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50.2    
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50.8    
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51.6    
51.8    
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57.8    
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61.2    
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61.6    
61.8    
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62.4    
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62.9    
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63.3    
63.5    
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64.1    
64.3    
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65.3    
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65.9    
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66.3    
66.5    
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67.6    
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78.2    
78.4    
78.6    
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79.0    
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80.0    
80.2    
80.4    
80.6    
80.8    
81.0    
81.2    
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82.0    
82.2    
82.4    
82.7    
82.9    
83.1    
83.3    
83.5    
83.7    
83.9    
84.1    
84.3    
84.5    
84.7    
84.9    
85.1    
85.3    
85.5    
85.7    
85.9    
86.1    
86.3    
86.5    
86.7    
86.9    
87.1    
87.3    
87.6    
87.8    
88.0    
88.2    
88.4    
88.6    
88.8    
89.0    
89.2    
89.4    
89.6    
89.8    
90.0    
90.2    
90.4    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.8    
92.0    
92.2    
92.4    
92.7    
92.9    
93.1    
93.3    
93.5    
93.7    
93.9    
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94.3    
94.5    
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94.9    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.3    
97.6    
97.8    
98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 18151, rend_intergenic: 16274  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51462, rend_intergenic: 47496  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61311, rend_intergenic: 59586  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66594, rend_intergenic: 63880  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77097, rend_intergenic: 72246  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87671, rend_intergenic: 85825  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98640, rend_intergenic: 87749  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99838, rend_intergenic: 98698  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102390, rend_intergenic: 99857  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104887, rend_intergenic: 103015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109267, rend_intergenic: 105413  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124214, rend_intergenic: 120820  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127513, rend_intergenic: 126040  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 29 predictions persist after filtering for low support