-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_6/scaffold_6_8028429-8165334

-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 pasa_asmbl_47028.p1
Valid prediction for snap_scaffold_6-snap.1787-T1
Valid prediction for snap_scaffold_6-snap.1799-T1
Valid prediction for GeneMark_model.25976_t
Valid prediction for GeneMark_model.25963_t
Valid prediction for pasa_asmbl_47032.p1
Valid prediction for GlimmerHMM_glimmerT_15386-T1
Valid prediction for Augustus_model.g10258.t1
Valid prediction for GeneMark_model.25968_t
Valid prediction for Augustus_model.g10259.t1
Valid prediction for snap_scaffold_6-snap.1784-T1
Valid prediction for GlimmerHMM_glimmerT_15404-T1
Couldn't classify 111855, 112696
Sorry, prediction pasa_asmbl_47036.p1 fails validation.
(ATG)	 AA	110601-110657	GT	AGG
(TTC)	 AG	111332-111440	GT	AGG
(GTG)	 AG	111561-111671	GT	TGG
(GCC)	 AG	111855-112696	AT	CCA
-recovered pasa_asmbl_47036.p1, initial, 110601, 110657
-recovered pasa_asmbl_47036.p1, internal, 111332, 111440
-recovered pasa_asmbl_47036.p1, internal, 111561, 111671
Valid prediction for snap_scaffold_6-snap.1795-T1
Valid prediction for GeneMark_model.25967_t
Valid prediction for snap_scaffold_6-snap.1792-T1
Valid prediction for HiQ_model.g10260.t1
Valid prediction for snap_scaffold_6-snap.1796-T1
Valid prediction for GlimmerHMM_glimmerT_15409-T1
Valid prediction for GlimmerHMM_glimmerT_15408-T1
Valid prediction for HiQ_model.g10274.t1
Couldn't classify 77280, 77388
Couldn't classify 78322, 78447
Sorry, prediction pasa_asmbl_47033.p1 fails validation.
(GGA)	 CA	77280-77388	GT	AGG
(TCC)	 AG	77485-77573	GT	GTG
(AAC)	 AG	77701-77807	GT	AGG
(GAA)	 AG	78013-78178	GT	AGG
(ACG)	 AG	78322-78447	AA	GGA
-recovered pasa_asmbl_47033.p1, internal, 77485, 77573
-recovered pasa_asmbl_47033.p1, internal, 77701, 77807
-recovered pasa_asmbl_47033.p1, internal, 78013, 78178
Valid prediction for snap_scaffold_6-snap.1812-T1
Valid prediction for snap_scaffold_6-snap.1802-T1
Valid prediction for GeneMark_model.25960_t
Valid prediction for snap_scaffold_6-snap.1789-T1
Valid prediction for GlimmerHMM_glimmerT_15391-T1
Valid prediction for CodingQuarry_transcript_54979-T1
Valid prediction for HiQ_model.g10262.t1
Valid prediction for pasa_asmbl_47031.p1
Valid prediction for snap_scaffold_6-snap.1782-T1
Valid prediction for snap_scaffold_6-snap.1804-T1
Valid prediction for snap_scaffold_6-snap.1806-T1
Valid prediction for CodingQuarry_transcript_54978-T1
Valid prediction for Augustus_model.g10272.t1
Valid prediction for GlimmerHMM_glimmerT_15400-T1
Valid prediction for GlimmerHMM_glimmerT_15392-T1
Valid prediction for Augustus_model.g10255.t1
Valid prediction for GeneMark_model.25964_t
Valid prediction for GeneMark_model.25983_t
Valid prediction for GeneMark_model.25970_t
Valid prediction for snap_scaffold_6-snap.1785-T1
Valid prediction for GeneMark_model.25962_t
Valid prediction for pasa_asmbl_47037.p1
Valid prediction for snap_scaffold_6-snap.1808-T1
Valid prediction for GeneMark_model.25957_t
Valid prediction for GlimmerHMM_glimmerT_15395-T1
Valid prediction for Augustus_model.g10257.t1
Valid prediction for HiQ_model.g10269.t1
Valid prediction for GlimmerHMM_glimmerT_15401-T1
Valid prediction for Augustus_model.g10267.t1
Valid prediction for snap_scaffold_6-snap.1794-T1
Valid prediction for HiQ_model.g10263.t1
Valid prediction for GeneMark_model.25974_t
Valid prediction for GeneMark_model.25988_t
Valid prediction for CodingQuarry_transcript_54977-T1
Valid prediction for snap_scaffold_6-snap.1797-T1
Valid prediction for snap_scaffold_6-snap.1809-T1
Valid prediction for Augustus_model.g10264.t1
Valid prediction for CodingQuarry_transcript_54976-T1
Valid prediction for GeneMark_model.25977_t
Couldn't classify 128648, 128710
Sorry, prediction pasa_asmbl_47039.p1 fails validation.
(GTG)	 CA	128648-128710	GT	AGG
(CAA)	 AG	129091-129219	GT	AGG
(GTG)	 AG	129311-129409	GT	AGG
(GAC)	 AG	129568-129650	GT	AGG
(CGA)	 AG	129827-129953	GT	AGG
(GTA)	 AG	130123-130218	GT	AAG
(GGT)	 AG	130766-130888	GT	AGG
(GTG)	 AG	132582-132746	GT	AGG
(GTG)	 AG	132965-133090	AC	AGA
-recovered pasa_asmbl_47039.p1, terminal, 132965, 133090
-recovered pasa_asmbl_47039.p1, internal, 129091, 129219
-recovered pasa_asmbl_47039.p1, internal, 129311, 129409
-recovered pasa_asmbl_47039.p1, internal, 129568, 129650
-recovered pasa_asmbl_47039.p1, internal, 129827, 129953
-recovered pasa_asmbl_47039.p1, internal, 130123, 130218
-recovered pasa_asmbl_47039.p1, internal, 130766, 130888
-recovered pasa_asmbl_47039.p1, internal, 132582, 132746
Valid prediction for GlimmerHMM_glimmerT_15406-T1
Valid prediction for GeneMark_model.25986_t
Valid prediction for GeneMark_model.25973_t
Valid prediction for GeneMark_model.25966_t
Valid prediction for snap_scaffold_6-snap.1813-T1
Valid prediction for GlimmerHMM_glimmerT_15389-T1
Valid prediction for HiQ_model.g10271.t1
Valid prediction for GeneMark_model.25982_t
Valid prediction for snap_scaffold_6-snap.1781-T1
Valid prediction for GeneMark_model.25978_t
Valid prediction for GlimmerHMM_glimmerT_15388-T1
Valid prediction for snap_scaffold_6-snap.1791-T1
Valid prediction for Augustus_model.g10265.t1
Valid prediction for GlimmerHMM_glimmerT_15399-T1
Valid prediction for GlimmerHMM_glimmerT_15394-T1
Valid prediction for GeneMark_model.25971_t
Valid prediction for snap_scaffold_6-snap.1786-T1
Valid prediction for GlimmerHMM_glimmerT_15413-T1
Valid prediction for CodingQuarry_transcript_54980-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_15412-T1
Valid prediction for snap_scaffold_6-snap.1788-T1
Valid prediction for HiQ_model.g10256.t1
Valid prediction for GlimmerHMM_glimmerT_15396-T1
Valid prediction for GeneMark_model.25975_t
Valid prediction for GlimmerHMM_glimmerT_15398-T1
Valid prediction for snap_scaffold_6-snap.1801-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_15397-T1
Valid prediction for snap_scaffold_6-snap.1798-T1
Couldn't classify 27639, 27707
Sorry, prediction pasa_asmbl_48467.p1 fails validation.
(TGC)	 TG	27639-27707	GT	AGG
(AAT)	 AG	27998-28093	GT	AGG
(AGT)	 AG	28167-28397	GT	AGG
(AAT)	 AG	28526-28548	GT	AGG
(AGG)	 AG	28696-28814	GT	AGG
(CCC)	 AG	28920-29467	AT	AGA
-recovered pasa_asmbl_48467.p1, terminal, 28920, 29467
-recovered pasa_asmbl_48467.p1, internal, 27998, 28093
-recovered pasa_asmbl_48467.p1, internal, 28167, 28397
-recovered pasa_asmbl_48467.p1, internal, 28526, 28548
-recovered pasa_asmbl_48467.p1, internal, 28696, 28814
Valid prediction for GeneMark_model.25984_t
Valid prediction for Augustus_model.g10270.t1
Valid prediction for snap_scaffold_6-snap.1810-T1
Valid prediction for snap_scaffold_6-snap.1783-T1
Valid prediction for GlimmerHMM_glimmerT_15407-T1
Valid prediction for snap_scaffold_6-snap.1793-T1
Valid prediction for GlimmerHMM_glimmerT_15403-T1
Valid prediction for GeneMark_model.25972_t
Valid prediction for snap_scaffold_6-snap.1805-T1
Valid prediction for GeneMark_model.25965_t
Valid prediction for GeneMark_model.25987_t
Valid prediction for GeneMark_model.25958_t
Valid prediction for Augustus_model.g10268.t1
Valid prediction for GeneMark_model.25979_t
Valid prediction for GeneMark_model.25985_t
Valid prediction for GlimmerHMM_glimmerT_15405-T1
Valid prediction for GlimmerHMM_glimmerT_15411-T1
Valid prediction for snap_scaffold_6-snap.1790-T1
Valid prediction for pasa_asmbl_48465.p1
Valid prediction for Augustus_model.g10266.t1
Valid prediction for snap_scaffold_6-snap.1803-T1
Valid prediction for snap_scaffold_6-snap.1807-T1
Valid prediction for GlimmerHMM_glimmerT_15410-T1
Valid prediction for GeneMark_model.25969_t
Valid prediction for GlimmerHMM_glimmerT_15390-T1
Valid prediction for GlimmerHMM_glimmerT_15402-T1
Valid prediction for CodingQuarry_transcript_54974-T1
Valid prediction for snap_scaffold_6-snap.1800-T1
Valid prediction for GeneMark_model.25981_t
Valid prediction for GlimmerHMM_glimmerT_15387-T1
Valid prediction for Augustus_model.g10261.t1
Valid prediction for GlimmerHMM_glimmerT_15393-T1
Valid prediction for snap_scaffold_6-snap.1811-T1
Valid prediction for Augustus_model.g10273.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 22929, rend_intergenic: 22198  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25693, rend_intergenic: 23199  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68751, rend_intergenic: 66478  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71945, rend_intergenic: 71581  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83029, rend_intergenic: 75455  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127724, rend_intergenic: 123543  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131082, rend_intergenic: 128171  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 136906
-exon list size: 394


building trellis

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10.9    
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11.9    
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14.9    
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20.7    
21.0    
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21.5    
21.7    
22.0    
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22.7    
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23.2    
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25.3    
25.5    
25.8    
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26.3    
26.5    
26.8    
27.0    
27.3    
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27.8    
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28.3    
28.5    
28.8    
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30.6    
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31.3    
31.6    
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32.3    
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33.3    
33.6    
33.8    
34.1    
34.3    
34.6    
34.8    
35.1    
35.4    
35.6    
35.9    
36.1    
36.4    
36.6    
36.9    
37.1    
37.4    
37.6    
37.9    
38.1    
38.4    
38.6    
38.9    
39.1    
39.4    
39.6    
39.9    
40.2    
40.4    
40.7    
40.9    
41.2    
41.4    
41.7    
41.9    
42.2    
42.4    
42.7    
42.9    
43.2    
43.4    
43.7    
43.9    
44.2    
44.4    
44.7    
44.9    
45.2    
45.5    
45.7    
46.0    
46.2    
46.5    
46.7    
47.0    
47.2    
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47.7    
48.0    
48.2    
48.5    
48.7    
49.0    
49.2    
49.5    
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50.3    
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53.5    
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56.1    
56.3    
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56.8    
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57.3    
57.6    
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58.1    
58.3    
58.6    
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59.3    
59.6    
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68.4    
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70.2    
70.5    
70.7    
71.0    
71.2    
71.5    
71.7    
72.0    
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72.5    
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73.2    
73.5    
73.7    
74.0    
74.2    
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75.0    
75.3    
75.5    
75.8    
76.0    
76.3    
76.5    
76.8    
77.0    
77.3    
77.5    
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78.0    
78.3    
78.5    
78.8    
79.0    
79.3    
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80.1    
80.3    
80.6    
80.8    
81.1    
81.3    
81.6    
81.8    
82.1    
82.3    
82.6    
82.8    
83.1    
83.3    
83.6    
83.8    
84.1    
84.3    
84.6    
84.8    
85.1    
85.4    
85.6    
85.9    
86.1    
86.4    
86.6    
86.9    
87.1    
87.4    
87.6    
87.9    
88.1    
88.4    
88.6    
88.9    
89.1    
89.4    
89.6    
89.9    
90.2    
90.4    
90.7    
90.9    
91.2    
91.4    
91.7    
91.9    
92.2    
92.4    
92.7    
92.9    
93.2    
93.4    
93.7    
93.9    
94.2    
94.4    
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94.9    
95.2    
95.5    
95.7    
96.0    
96.2    
96.5    
96.7    
97.0    
97.2    
97.5    
97.7    
98.0    
98.2    
98.5    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 22929, rend_intergenic: 22198  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25693, rend_intergenic: 23199  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68751, rend_intergenic: 66478  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71945, rend_intergenic: 71581  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83029, rend_intergenic: 75455  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127724, rend_intergenic: 123543  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131082, rend_intergenic: 128171  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support