-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_24/scaffold_24_1330034-1424735

-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 Augustus_model.g35688.t1
Valid prediction for GeneMark_model.92691_t
Valid prediction for snap_scaffold_24-snap.318-T1
Valid prediction for snap_scaffold_24-snap.321-T1
Valid prediction for GeneMark_model.92690_t
Couldn't classify 9572, 9623
Sorry, prediction pasa_asmbl_32082.p1 fails validation.
(ATG)	 CC	8302-8335	GT	GGG
(ATT)	 AG	8501-8564	GT	GGG
(CGG)	 AG	8809-8916	GT	CGG
(CAC)	 AG	9076-9183	GT	AAG
(GCT)	 AG	9572-9623	GA	ATG
-recovered pasa_asmbl_32082.p1, initial, 8302, 8335
-recovered pasa_asmbl_32082.p1, internal, 8501, 8564
-recovered pasa_asmbl_32082.p1, internal, 8809, 8916
-recovered pasa_asmbl_32082.p1, internal, 9076, 9183
Valid prediction for snap_scaffold_24-snap.333-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.92687_t
Valid prediction for GlimmerHMM_glimmerT_53279-T1
Valid prediction for HiQ_model.g35695.t1
Couldn't classify 60503, 60715
Sorry, prediction pasa_asmbl_32083.p1 fails validation.
(CCA)	 AC	60503-60715	GT	TGG
(CAA)	 AG	61979-62098	GT	AGG
(GGT)	 AG	62692-62769	GT	AGG
(GTG)	 AG	63369-63503	AC	AAA
-recovered pasa_asmbl_32083.p1, terminal, 63369, 63503
-recovered pasa_asmbl_32083.p1, internal, 61979, 62098
-recovered pasa_asmbl_32083.p1, internal, 62692, 62769
Valid prediction for GlimmerHMM_glimmerT_53270-T1
Valid prediction for snap_scaffold_24-snap.340-T1
Valid prediction for GeneMark_model.92673_t
Valid prediction for snap_scaffold_24-snap.332-T1
Valid prediction for snap_scaffold_24-snap.322-T1
Valid prediction for snap_scaffold_24-snap.323-T1
Valid prediction for Augustus_model.g35694.t1
Valid prediction for snap_scaffold_24-snap.343-T1
Valid prediction for snap_scaffold_24-snap.345-T1
Valid prediction for snap_scaffold_24-snap.338-T1
Valid prediction for snap_scaffold_24-snap.328-T1
Valid prediction for snap_scaffold_24-snap.319-T1
Valid prediction for GeneMark_model.92682_t
Valid prediction for GeneMark_model.92684_t
Valid prediction for GlimmerHMM_glimmerT_53277-T1
Valid prediction for GeneMark_model.92693_t
Valid prediction for GlimmerHMM_glimmerT_53278-T1
Valid prediction for GeneMark_model.92678_t
Valid prediction for HiQ_model.g35689.t1
Valid prediction for snap_scaffold_24-snap.315-T1
Valid prediction for GlimmerHMM_glimmerT_53276-T1
Valid prediction for GeneMark_model.92675_t
Valid prediction for GeneMark_model.92685_t
Couldn't classify 59482, 59898
Sorry, prediction pasa_asmbl_32646.p1 fails validation.
(CCA)	 TA	59482-59898	CC	GAC
Valid prediction for snap_scaffold_24-snap.346-T1
Valid prediction for Augustus_model.g35696.t1
Valid prediction for snap_scaffold_24-snap.326-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_24-snap.317-T1
Valid prediction for snap_scaffold_24-snap.327-T1
Valid prediction for GeneMark_model.92692_t
Couldn't classify 6863, 6974
Sorry, prediction pasa_asmbl_32718.p1 fails validation.
(CTG)	 TA	6863-6974	GT	AGG
(GTA)	 AG	8424-8553	GC	ATG
(TTT)	 AG	9581-9728	GT	AGG
(GAT)	 AG	10503-10541	GC	GAG
-recovered pasa_asmbl_32718.p1, terminal, 10503, 10541
-recovered pasa_asmbl_32718.p1, internal, 8424, 8553
-recovered pasa_asmbl_32718.p1, internal, 9581, 9728
-recovered pasa_asmbl_32718.p1, internal, 10503, 10541
Valid prediction for snap_scaffold_24-snap.329-T1
Valid prediction for GlimmerHMM_glimmerT_53275-T1
Valid prediction for GeneMark_model.92674_t
Valid prediction for snap_scaffold_24-snap.325-T1
Valid prediction for GlimmerHMM_glimmerT_53272-T1
Valid prediction for GeneMark_model.92680_t
Valid prediction for snap_scaffold_24-snap.344-T1
Valid prediction for GeneMark_model.92689_t
Valid prediction for Augustus_model.g35691.t1
Valid prediction for GlimmerHMM_glimmerT_53274-T1
Valid prediction for GeneMark_model.92677_t
Valid prediction for snap_scaffold_24-snap.324-T1
Valid prediction for snap_scaffold_24-snap.337-T1
Valid prediction for snap_scaffold_24-snap.330-T1
Valid prediction for CodingQuarry_transcript_37166-T1
Valid prediction for GeneMark_model.92686_t
Valid prediction for snap_scaffold_24-snap.341-T1
Valid prediction for CodingQuarry_transcript_37167-T1
Valid prediction for pasa_asmbl_32719.p1
Valid prediction for snap_scaffold_24-snap.339-T1
Valid prediction for GlimmerHMM_glimmerT_53273-T1
Valid prediction for HiQ_model.g35697.t1
Valid prediction for GeneMark_model.92679_t
Valid prediction for snap_scaffold_24-snap.347-T1
Valid prediction for GeneMark_model.92683_t
Valid prediction for snap_scaffold_24-snap.335-T1
Valid prediction for snap_scaffold_24-snap.334-T1
Valid prediction for snap_scaffold_24-snap.331-T1
Valid prediction for GeneMark_model.92676_t
Valid prediction for HiQ_model.g35698.t1
Valid prediction for CodingQuarry_transcript_37168-T1
Valid prediction for snap_scaffold_24-snap.336-T1
Valid prediction for GlimmerHMM_glimmerT_53280-T1
Valid prediction for Augustus_model.g35692.t1
Valid prediction for GeneMark_model.92681_t
Valid prediction for GlimmerHMM_glimmerT_53271-T1
Valid prediction for snap_scaffold_24-snap.342-T1
Valid prediction for Augustus_model.g35693.t1
Valid prediction for snap_scaffold_24-snap.320-T1
Valid prediction for GeneMark_model.92688_t
Valid prediction for Augustus_model.g35690.t1
Valid prediction for snap_scaffold_24-snap.316-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6985, rend_intergenic: 4343  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11263, rend_intergenic: 8302  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14655, rend_intergenic: 13676  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27108, rend_intergenic: 15039  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28651, rend_intergenic: 27172  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30677, rend_intergenic: 29170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38577, rend_intergenic: 31151  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43598, rend_intergenic: 40965  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48043, rend_intergenic: 44608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59898, rend_intergenic: 49027  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63496, rend_intergenic: 61680  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70425, rend_intergenic: 68592  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79561, rend_intergenic: 71199  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91327, rend_intergenic: 84694  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 94702
-exon list size: 502


building trellis

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13.1    
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13.7    
13.9    
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16.1    
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16.9    
17.1    
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18.3    
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25.4    
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25.8    
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27.6    
27.8    
28.0    
28.2    
28.4    
28.6    
28.8    
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29.2    
29.4    
29.6    
29.8    
30.0    
30.2    
30.4    
30.6    
30.8    
31.0    
31.2    
31.3    
31.5    
31.7    
31.9    
32.1    
32.3    
32.5    
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    
37.5    
37.7    
37.9    
38.1    
38.3    
38.5    
38.7    
38.9    
39.1    
39.3    
39.5    
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40.1    
40.3    
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41.3    
41.5    
41.7    
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42.1    
42.3    
42.5    
42.7    
42.9    
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43.3    
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44.4    
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48.8    
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49.4    
49.6    
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53.6    
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54.6    
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55.2    
55.4    
55.6    
55.8    
56.0    
56.2    
56.3    
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56.9    
57.1    
57.3    
57.5    
57.7    
57.9    
58.1    
58.3    
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58.7    
58.9    
59.1    
59.3    
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59.7    
59.9    
60.1    
60.3    
60.5    
60.7    
60.9    
61.1    
61.3    
61.5    
61.7    
61.9    
62.1    
62.3    
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63.3    
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63.7    
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64.1    
64.3    
64.5    
64.7    
64.9    
65.1    
65.3    
65.5    
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65.9    
66.1    
66.3    
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67.3    
67.5    
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68.1    
68.3    
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76.4    
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76.8    
77.0    
77.2    
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78.2    
78.4    
78.6    
78.8    
79.0    
79.2    
79.4    
79.6    
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80.0    
80.2    
80.4    
80.6    
80.8    
81.0    
81.2    
81.3    
81.5    
81.7    
81.9    
82.1    
82.3    
82.5    
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    
87.5    
87.7    
87.9    
88.1    
88.3    
88.5    
88.7    
88.9    
89.1    
89.3    
89.5    
89.7    
89.9    
90.1    
90.3    
90.5    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
91.9    
92.1    
92.3    
92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.7    
93.8    
94.0    
94.2    
94.4    
94.6    
94.8    
95.0    
95.2    
95.4    
95.6    
95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
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 16 predictions from path traversal
Error with prediction: snap lend_intergenic: 6985, rend_intergenic: 4343  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11263, rend_intergenic: 8302  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14655, rend_intergenic: 13676  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27108, rend_intergenic: 15039  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28651, rend_intergenic: 27172  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30677, rend_intergenic: 29170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38577, rend_intergenic: 31151  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43598, rend_intergenic: 40965  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48043, rend_intergenic: 44608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59898, rend_intergenic: 49027  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63496, rend_intergenic: 61680  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70425, rend_intergenic: 68592  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79561, rend_intergenic: 71199  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91327, rend_intergenic: 84694  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