-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_19/scaffold_19_1489043-1650481

-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 GlimmerHMM_glimmerT_44652-T1
Valid prediction for GeneMark_model.77778_t
Valid prediction for GeneMark_model.77780_t
Valid prediction for GlimmerHMM_glimmerT_44646-T1
Valid prediction for GeneMark_model.77763_t
Valid prediction for GeneMark_model.77768_t
Valid prediction for GeneMark_model.77753_t
Valid prediction for CodingQuarry_transcript_25541-T1
Valid prediction for snap_scaffold_19-snap.335-T1
Valid prediction for GeneMark_model.77784_t
Valid prediction for GeneMark_model.77767_t
Valid prediction for snap_scaffold_19-snap.353-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g29809.t1
Valid prediction for GeneMark_model.77754_t
Valid prediction for snap_scaffold_19-snap.346-T1
Couldn't classify 159061, 159195
Sorry, prediction pasa_asmbl_22052.p1 fails validation.
(GGG)	 GT	159061-159195	GT	GGG
(AGA)	 AG	159593-159703	GT	AGG
(GCT)	 AG	159791-159941	GT	GGG
(GTA)	 AG	160311-160399	TC	AAT
-recovered pasa_asmbl_22052.p1, terminal, 160311, 160399
-recovered pasa_asmbl_22052.p1, internal, 159593, 159703
-recovered pasa_asmbl_22052.p1, internal, 159791, 159941
Valid prediction for snap_scaffold_19-snap.350-T1
Valid prediction for GeneMark_model.77775_t
Valid prediction for CodingQuarry_transcript_25539-T1
Valid prediction for snap_scaffold_19-snap.341-T1
Valid prediction for GeneMark_model.77752_t
Valid prediction for snap_scaffold_19-snap.351-T1
Valid prediction for HiQ_model.g29816.t1
Valid prediction for GlimmerHMM_glimmerT_44647-T1
Valid prediction for GeneMark_model.77760_t
Valid prediction for snap_scaffold_19-snap.358-T1
Valid prediction for GlimmerHMM_glimmerT_44659-T1
Valid prediction for snap_scaffold_19-snap.331-T1
Valid prediction for snap_scaffold_19-snap.355-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_19-snap.333-T1
Sorry, intron length (4) is less than minimum required (10)
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for snap_scaffold_19-snap.330-T1
Valid prediction for GlimmerHMM_glimmerT_44651-T1
Valid prediction for snap_scaffold_19-snap.361-T1
Valid prediction for pasa_asmbl_22046.p2
Valid prediction for snap_scaffold_19-snap.345-T1
Valid prediction for snap_scaffold_19-snap.337-T1
Valid prediction for snap_scaffold_19-snap.349-T1
Valid prediction for snap_scaffold_19-snap.328-T1
Valid prediction for GlimmerHMM_glimmerT_44660-T1
Valid prediction for pasa_asmbl_22049.p1
Valid prediction for GeneMark_model.77773_t
Valid prediction for Augustus_model.g29812.t1
Valid prediction for GeneMark_model.77777_t
Valid prediction for snap_scaffold_19-snap.329-T1
Valid prediction for Augustus_model.g29808.t1
Valid prediction for GeneMark_model.77787_t
Valid prediction for Augustus_model.g29806.t1
Valid prediction for snap_scaffold_19-snap.348-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_44653-T1
Valid prediction for snap_scaffold_19-snap.356-T1
Valid prediction for pasa_asmbl_22047.p1
Valid prediction for GeneMark_model.77765_t
Valid prediction for GlimmerHMM_glimmerT_44636-T1
Valid prediction for GlimmerHMM_glimmerT_44643-T1
Valid prediction for GeneMark_model.77758_t
Valid prediction for GlimmerHMM_glimmerT_44635-T1
Valid prediction for GlimmerHMM_glimmerT_44640-T1
Couldn't classify 9990, 15542
Couldn't classify 15564, 16202
Sorry, prediction CodingQuarry_transcript_25540-T1 fails validation.
(ATG)	 GA	7467-7577	GT	AGG
(ATG)	 AG	8344-8413	GT	AGG
(TCA)	 AG	9450-9553	GT	AGG
(ATT)	 AG	9990-15542	AT	ACA
(ATT)	 AC	15564-16202	TG	GAT
-recovered CodingQuarry_transcript_25540-T1, initial, 7467, 7577
-recovered CodingQuarry_transcript_25540-T1, initial, 8344, 8413
-recovered CodingQuarry_transcript_25540-T1, internal, 8344, 8413
-recovered CodingQuarry_transcript_25540-T1, internal, 9450, 9553
Valid prediction for GlimmerHMM_glimmerT_44642-T1
Valid prediction for HiQ_model.g29811.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 GlimmerHMM_glimmerT_44650-T1
Valid prediction for GlimmerHMM_glimmerT_44649-T1
Valid prediction for snap_scaffold_19-snap.352-T1
Valid prediction for Augustus_model.g29813.t1
Valid prediction for GeneMark_model.77783_t
Valid prediction for GlimmerHMM_glimmerT_44638-T1
Valid prediction for GlimmerHMM_glimmerT_44645-T1
Valid prediction for GeneMark_model.77766_t
Valid prediction for GlimmerHMM_glimmerT_44641-T1
Valid prediction for snap_scaffold_19-snap.339-T1
Valid prediction for GeneMark_model.77764_t
Valid prediction for GeneMark_model.77774_t
Valid prediction for GlimmerHMM_glimmerT_44637-T1
Valid prediction for GeneMark_model.77776_t
Valid prediction for Augustus_model.g29807.t1
Valid prediction for snap_scaffold_19-snap.360-T1
Valid prediction for GeneMark_model.77782_t
Valid prediction for snap_scaffold_19-snap.357-T1
Valid prediction for GeneMark_model.77786_t
Valid prediction for Augustus_model.g29810.t1
Valid prediction for GlimmerHMM_glimmerT_44639-T1
Valid prediction for GlimmerHMM_glimmerT_44658-T1
Valid prediction for GlimmerHMM_glimmerT_44657-T1
Valid prediction for snap_scaffold_19-snap.336-T1
Valid prediction for Augustus_model.g29815.t1
Valid prediction for GlimmerHMM_glimmerT_44644-T1
Valid prediction for GlimmerHMM_glimmerT_44655-T1
Valid prediction for GeneMark_model.77779_t
Valid prediction for snap_scaffold_19-snap.334-T1
Valid prediction for snap_scaffold_19-snap.342-T1
Valid prediction for GeneMark_model.77762_t
Valid prediction for GeneMark_model.77759_t
Valid prediction for snap_scaffold_19-snap.359-T1
Valid prediction for GeneMark_model.77769_t
Valid prediction for GeneMark_model.77761_t
Valid prediction for GlimmerHMM_glimmerT_44656-T1
Valid prediction for snap_scaffold_19-snap.327-T1
Valid prediction for snap_scaffold_19-snap.347-T1
Valid prediction for snap_scaffold_19-snap.340-T1
Valid prediction for snap_scaffold_19-snap.332-T1
Valid prediction for Augustus_model.g29814.t1
Valid prediction for snap_scaffold_19-snap.338-T1
Valid prediction for GeneMark_model.77771_t
Valid prediction for snap_scaffold_19-snap.343-T1
Valid prediction for GlimmerHMM_glimmerT_44654-T1
Valid prediction for GeneMark_model.77757_t
Valid prediction for GeneMark_model.77785_t
Valid prediction for GeneMark_model.77756_t
Valid prediction for snap_scaffold_19-snap.344-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_44648-T1
Valid prediction for GeneMark_model.77772_t
Valid prediction for snap_scaffold_19-snap.354-T1
Valid prediction for GeneMark_model.77770_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6636, rend_intergenic: 4439  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38975, rend_intergenic: 37345  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43170, rend_intergenic: 40697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43841, rend_intergenic: 43170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53806, rend_intergenic: 49167  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85060, rend_intergenic: 76334  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89773, rend_intergenic: 88153  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120463, rend_intergenic: 100533  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135689, rend_intergenic: 133858  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147832, rend_intergenic: 138309  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151039, rend_intergenic: 148746  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153072, rend_intergenic: 151998  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159882, rend_intergenic: 158258  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 161439
-exon list size: 540


building trellis

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31.9    
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32.8    
33.0    
33.2    
33.4    
33.6    
33.8    
33.9    
34.1    
34.3    
34.5    
34.7    
34.9    
35.1    
35.2    
35.4    
35.6    
35.8    
36.0    
36.2    
36.3    
36.5    
36.7    
36.9    
37.1    
37.3    
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38.2    
38.4    
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38.7    
38.9    
39.1    
39.3    
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39.7    
39.9    
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40.2    
40.4    
40.6    
40.8    
41.0    
41.1    
41.3    
41.5    
41.7    
41.9    
42.1    
42.3    
42.4    
42.6    
42.8    
43.0    
43.2    
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44.1    
44.3    
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44.6    
44.8    
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45.2    
45.4    
45.6    
45.8    
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46.9    
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52.8    
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55.2    
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56.1    
56.3    
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56.8    
57.0    
57.2    
57.4    
57.6    
57.7    
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58.1    
58.3    
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59.6    
59.8    
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60.1    
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61.3    
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66.6    
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67.2    
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68.1    
68.3    
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68.6    
68.8    
69.0    
69.2    
69.4    
69.6    
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70.8    
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71.2    
71.4    
71.6    
71.8    
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72.3    
72.5    
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72.9    
73.1    
73.2    
73.4    
73.6    
73.8    
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74.2    
74.4    
74.5    
74.7    
74.9    
75.1    
75.3    
75.5    
75.6    
75.8    
76.0    
76.2    
76.4    
76.6    
76.8    
76.9    
77.1    
77.3    
77.5    
77.7    
77.9    
78.0    
78.2    
78.4    
78.6    
78.8    
79.0    
79.2    
79.3    
79.5    
79.7    
79.9    
80.1    
80.3    
80.4    
80.6    
80.8    
81.0    
81.2    
81.4    
81.5    
81.7    
81.9    
82.1    
82.3    
82.5    
82.7    
82.8    
83.0    
83.2    
83.4    
83.6    
83.8    
83.9    
84.1    
84.3    
84.5    
84.7    
84.9    
85.1    
85.2    
85.4    
85.6    
85.8    
86.0    
86.2    
86.3    
86.5    
86.7    
86.9    
87.1    
87.3    
87.5    
87.6    
87.8    
88.0    
88.2    
88.4    
88.6    
88.7    
88.9    
89.1    
89.3    
89.5    
89.7    
89.9    
90.0    
90.2    
90.4    
90.6    
90.8    
91.0    
91.1    
91.3    
91.5    
91.7    
91.9    
92.1    
92.3    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.5    
93.7    
93.9    
94.1    
94.3    
94.5    
94.6    
94.8    
95.0    
95.2    
95.4    
95.6    
95.8    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.0    
97.2    
97.4    
97.6    
97.8    
98.0    
98.2    
98.3    
98.5    
98.7    
98.9    
99.1    
99.3    
99.4    
99.6    
99.8    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 6636, rend_intergenic: 4439  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38975, rend_intergenic: 37345  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43170, rend_intergenic: 40697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43841, rend_intergenic: 43170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53806, rend_intergenic: 49167  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85060, rend_intergenic: 76334  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89773, rend_intergenic: 88153  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120463, rend_intergenic: 100533  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135689, rend_intergenic: 133858  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147832, rend_intergenic: 138309  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151039, rend_intergenic: 148746  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153072, rend_intergenic: 151998  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159882, rend_intergenic: 158258  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support