-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_22/scaffold_22_3483578-3638145

-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.87247_t
Valid prediction for snap_scaffold_22-snap.640-T1
Valid prediction for Augustus_model.g33817.t1
Valid prediction for GlimmerHMM_glimmerT_50420-T1
Valid prediction for snap_scaffold_22-snap.645-T1
Valid prediction for GlimmerHMM_glimmerT_50415-T1
Valid prediction for GlimmerHMM_glimmerT_50431-T1
Valid prediction for Augustus_model.g33815.t1
Valid prediction for GeneMark_model.87232_t
Valid prediction for GlimmerHMM_glimmerT_50424-T1
Valid prediction for GeneMark_model.87258_t
Valid prediction for GeneMark_model.87228_t
Valid prediction for GeneMark_model.87234_t
Valid prediction for snap_scaffold_22-snap.642-T1
Valid prediction for snap_scaffold_22-snap.635-T1
Valid prediction for snap_scaffold_22-snap.637-T1
Valid prediction for GlimmerHMM_glimmerT_50429-T1
Valid prediction for snap_scaffold_22-snap.648-T1
Valid prediction for Augustus_model.g33806.t1
Valid prediction for GeneMark_model.87245_t
Valid prediction for GeneMark_model.87240_t
Valid prediction for GeneMark_model.87217_t
Valid prediction for GlimmerHMM_glimmerT_50418-T1
Valid prediction for GeneMark_model.87239_t
Valid prediction for GeneMark_model.87216_t
Valid prediction for GeneMark_model.87255_t
Valid prediction for GlimmerHMM_glimmerT_50411-T1
Valid prediction for GeneMark_model.87221_t
Valid prediction for snap_scaffold_22-snap.628-T1
Valid prediction for GeneMark_model.87219_t
Valid prediction for HiQ_model.g33808.t1
Valid prediction for GeneMark_model.87224_t
Valid prediction for GlimmerHMM_glimmerT_50422-T1
Valid prediction for snap_scaffold_22-snap.624-T1
Valid prediction for GlimmerHMM_glimmerT_50407-T1
Valid prediction for GeneMark_model.87248_t
Valid prediction for Augustus_model.g33810.t1
Valid prediction for snap_scaffold_22-snap.631-T1
Valid prediction for GeneMark_model.87251_t
Valid prediction for snap_scaffold_22-snap.646-T1
Valid prediction for snap_scaffold_22-snap.638-T1
Valid prediction for GeneMark_model.87250_t
Valid prediction for GeneMark_model.87236_t
Valid prediction for snap_scaffold_22-snap.633-T1
Valid prediction for snap_scaffold_22-snap.651-T1
Valid prediction for snap_scaffold_22-snap.620-T1
Valid prediction for snap_scaffold_22-snap.652-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.87242_t
Valid prediction for Augustus_model.g33803.t1
Valid prediction for Augustus_model.g33813.t1
Valid prediction for Augustus_model.g33797.t1
Valid prediction for snap_scaffold_22-snap.644-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 pasa_asmbl_29941.p1
Valid prediction for GeneMark_model.87256_t
Valid prediction for snap_scaffold_22-snap.627-T1
Valid prediction for snap_scaffold_22-snap.636-T1
Valid prediction for GeneMark_model.87257_t
Valid prediction for HiQ_model.g33809.t1
Valid prediction for CodingQuarry_transcript_34063-T1
Valid prediction for GeneMark_model.87237_t
Valid prediction for GlimmerHMM_glimmerT_50408-T1
Couldn't classify 133124, 133232
Sorry, prediction pasa_asmbl_29938.p1 fails validation.
(GAC)	 AG	133124-133232	GT	TGG
(CCC)	 AG	135624-135815	GT	AGG
(TGC)	 AG	137256-137281	GA	AAG
-recovered pasa_asmbl_29938.p1, terminal, 137256, 137281
-recovered pasa_asmbl_29938.p1, internal, 133124, 133232
-recovered pasa_asmbl_29938.p1, internal, 135624, 135815
Valid prediction for Augustus_model.g33800.t1
Valid prediction for GlimmerHMM_glimmerT_50417-T1
Valid prediction for GeneMark_model.87252_t
Valid prediction for GeneMark_model.87246_t
Valid prediction for snap_scaffold_22-snap.647-T1
Valid prediction for GlimmerHMM_glimmerT_50421-T1
Valid prediction for snap_scaffold_22-snap.629-T1
Valid prediction for GeneMark_model.87241_t
Valid prediction for snap_scaffold_22-snap.639-T1
Valid prediction for Augustus_model.g33802.t1
Valid prediction for GlimmerHMM_glimmerT_50430-T1
Valid prediction for snap_scaffold_22-snap.632-T1
Valid prediction for snap_scaffold_22-snap.623-T1
Valid prediction for GeneMark_model.87238_t
Valid prediction for GeneMark_model.87218_t
Valid prediction for snap_scaffold_22-snap.626-T1
Valid prediction for GeneMark_model.87227_t
Valid prediction for GlimmerHMM_glimmerT_50426-T1
Valid prediction for snap_scaffold_22-snap.641-T1
Valid prediction for GeneMark_model.87223_t
Valid prediction for snap_scaffold_22-snap.649-T1
Valid prediction for Augustus_model.g33801.t1
Valid prediction for GeneMark_model.87229_t
Valid prediction for GeneMark_model.87231_t
Valid prediction for GlimmerHMM_glimmerT_50414-T1
Valid prediction for GeneMark_model.87254_t
Valid prediction for snap_scaffold_22-snap.634-T1
Valid prediction for GeneMark_model.87235_t
Valid prediction for GeneMark_model.87253_t
Valid prediction for Augustus_model.g33814.t1
Valid prediction for Augustus_model.g33807.t1
Valid prediction for snap_scaffold_22-snap.622-T1
Valid prediction for Augustus_model.g33816.t1
Valid prediction for snap_scaffold_22-snap.653-T1
Valid prediction for GlimmerHMM_glimmerT_50413-T1
Valid prediction for GlimmerHMM_glimmerT_50416-T1
Valid prediction for snap_scaffold_22-snap.630-T1
Valid prediction for GlimmerHMM_glimmerT_50427-T1
Valid prediction for GlimmerHMM_glimmerT_50410-T1
Valid prediction for Augustus_model.g33798.t1
Valid prediction for GeneMark_model.87220_t
Couldn't classify 137686, 137754
Sorry, prediction pasa_asmbl_29937.p1 fails validation.
(ACC)	 GC	137686-137754	GT	AGG
(GTG)	 AG	138600-138769	GT	TGG
(GCT)	 AG	139046-139163	GC	GAG
-recovered pasa_asmbl_29937.p1, terminal, 139046, 139163
-recovered pasa_asmbl_29937.p1, internal, 138600, 138769
-recovered pasa_asmbl_29937.p1, internal, 139046, 139163
Valid prediction for GlimmerHMM_glimmerT_50419-T1
Couldn't classify 103938, 104191
Sorry, prediction pasa_asmbl_29939.p1 fails validation.
(TTG)	 GA	103938-104191	GT	AAG
(GAG)	 AG	104365-104494	GT	AGG
(CTG)	 AG	104569-104669	GT	TAG
(CTC)	 AG	104860-105228	GT	AAG
(TTT)	 AG	105339-105429	AA	AGA
-recovered pasa_asmbl_29939.p1, terminal, 105339, 105429
-recovered pasa_asmbl_29939.p1, internal, 104365, 104494
-recovered pasa_asmbl_29939.p1, internal, 104569, 104669
-recovered pasa_asmbl_29939.p1, internal, 104860, 105228
Valid prediction for GeneMark_model.87249_t
Valid prediction for GeneMark_model.87244_t
Valid prediction for GlimmerHMM_glimmerT_50409-T1
Valid prediction for GeneMark_model.87225_t
Valid prediction for Augustus_model.g33805.t1
Valid prediction for GlimmerHMM_glimmerT_50423-T1
Valid prediction for Augustus_model.g33799.t1
Valid prediction for snap_scaffold_22-snap.650-T1
Valid prediction for snap_scaffold_22-snap.625-T1
Valid prediction for Augustus_model.g33811.t1
Valid prediction for GlimmerHMM_glimmerT_50428-T1
Valid prediction for GlimmerHMM_glimmerT_50432-T1
Valid prediction for snap_scaffold_22-snap.643-T1
Valid prediction for Augustus_model.g33812.t1
Valid prediction for GlimmerHMM_glimmerT_50425-T1
Valid prediction for GeneMark_model.87243_t
Valid prediction for GeneMark_model.87233_t
Valid prediction for GlimmerHMM_glimmerT_50412-T1
Valid prediction for Augustus_model.g33804.t1
Valid prediction for snap_scaffold_22-snap.621-T1
Valid prediction for GeneMark_model.87222_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 29655, rend_intergenic: 24000  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43002, rend_intergenic: 40567  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60201, rend_intergenic: 57618  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86026, rend_intergenic: 76355  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96629, rend_intergenic: 92994  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103517, rend_intergenic: 101278  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105275, rend_intergenic: 104031  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109509, rend_intergenic: 107433  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113355, rend_intergenic: 110442  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123989, rend_intergenic: 123809  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132864, rend_intergenic: 126236  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136636, rend_intergenic: 133827  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142749, rend_intergenic: 137201  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 154568
-exon list size: 571


building trellis

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18.7    
18.8    
19.0    
19.2    
19.4    
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20.1    
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20.9    
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22.2    
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22.7    
22.9    
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24.1    
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24.8    
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25.1    
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25.5    
25.7    
25.8    
26.0    
26.2    
26.4    
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26.7    
26.9    
27.1    
27.2    
27.4    
27.6    
27.7    
27.9    
28.1    
28.3    
28.4    
28.6    
28.8    
29.0    
29.1    
29.3    
29.5    
29.7    
29.8    
30.0    
30.2    
30.4    
30.5    
30.7    
30.9    
31.1    
31.2    
31.4    
31.6    
31.8    
31.9    
32.1    
32.3    
32.5    
32.6    
32.8    
33.0    
33.2    
33.3    
33.5    
33.7    
33.9    
34.0    
34.2    
34.4    
34.6    
34.7    
34.9    
35.1    
35.3    
35.4    
35.6    
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36.3    
36.5    
36.6    
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37.3    
37.5    
37.7    
37.9    
38.0    
38.2    
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38.6    
38.7    
38.9    
39.1    
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40.1    
40.3    
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40.7    
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41.4    
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42.2    
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45.4    
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48.2    
48.3    
48.5    
48.7    
48.9    
49.0    
49.2    
49.4    
49.6    
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50.3    
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50.8    
51.0    
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54.3    
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54.6    
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55.0    
55.1    
55.3    
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56.7    
56.9    
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57.6    
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58.3    
58.5    
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59.2    
59.3    
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60.2    
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61.1    
61.3    
61.4    
61.6    
61.8    
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62.3    
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63.9    
64.0    
64.2    
64.4    
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65.1    
65.3    
65.4    
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65.8    
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66.3    
66.5    
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67.4    
67.5    
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68.1    
68.2    
68.4    
68.6    
68.8    
68.9    
69.1    
69.3    
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69.6    
69.8    
70.0    
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70.9    
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71.2    
71.4    
71.6    
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72.1    
72.3    
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73.1    
73.3    
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73.8    
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74.2    
74.3    
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74.7    
74.9    
75.0    
75.2    
75.4    
75.6    
75.7    
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76.3    
76.4    
76.6    
76.8    
77.0    
77.1    
77.3    
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78.2    
78.4    
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78.7    
78.9    
79.1    
79.2    
79.4    
79.6    
79.8    
79.9    
80.1    
80.3    
80.5    
80.6    
80.8    
81.0    
81.2    
81.3    
81.5    
81.7    
81.8    
82.0    
82.2    
82.4    
82.5    
82.7    
82.9    
83.1    
83.2    
83.4    
83.6    
83.8    
83.9    
84.1    
84.3    
84.5    
84.6    
84.8    
85.0    
85.2    
85.3    
85.5    
85.7    
85.9    
86.0    
86.2    
86.4    
86.6    
86.7    
86.9    
87.1    
87.3    
87.4    
87.6    
87.8    
88.0    
88.1    
88.3    
88.5    
88.7    
88.8    
89.0    
89.2    
89.4    
89.5    
89.7    
89.9    
90.1    
90.2    
90.4    
90.6    
90.8    
90.9    
91.1    
91.3    
91.4    
91.6    
91.8    
92.0    
92.1    
92.3    
92.5    
92.7    
92.8    
93.0    
93.2    
93.4    
93.5    
93.7    
93.9    
94.1    
94.2    
94.4    
94.6    
94.8    
94.9    
95.1    
95.3    
95.5    
95.6    
95.8    
96.0    
96.2    
96.3    
96.5    
96.7    
96.9    
97.0    
97.2    
97.4    
97.6    
97.7    
97.9    
98.1    
98.3    
98.4    
98.6    
98.8    
99.0    
99.1    
99.3    
99.5    
99.7    
99.8    
-found 37 predictions from path traversal
Error with prediction: snap lend_intergenic: 29655, rend_intergenic: 24000  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43002, rend_intergenic: 40567  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60201, rend_intergenic: 57618  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86026, rend_intergenic: 76355  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96629, rend_intergenic: 92994  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103517, rend_intergenic: 101278  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105275, rend_intergenic: 104031  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109509, rend_intergenic: 107433  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113355, rend_intergenic: 110442  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123989, rend_intergenic: 123809  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132864, rend_intergenic: 126236  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136636, rend_intergenic: 133827  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142749, rend_intergenic: 137201  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

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