-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_28/scaffold_28_5648738-5810740

-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 snap_scaffold_28-snap.1296-T1
Valid prediction for snap_scaffold_28-snap.1285-T1
Valid prediction for GlimmerHMM_glimmerT_58830-T1
Valid prediction for GlimmerHMM_glimmerT_58852-T1
Valid prediction for Augustus_model.g39011.t1
Valid prediction for snap_scaffold_28-snap.1303-T1
Valid prediction for GlimmerHMM_glimmerT_58851-T1
Valid prediction for GlimmerHMM_glimmerT_58835-T1
Valid prediction for GlimmerHMM_glimmerT_58833-T1
Valid prediction for Augustus_model.g39001.t1
Valid prediction for pasa_asmbl_37601.p1
Valid prediction for snap_scaffold_28-snap.1300-T1
Valid prediction for GlimmerHMM_glimmerT_58829-T1
Valid prediction for snap_scaffold_28-snap.1299-T1
Valid prediction for GlimmerHMM_glimmerT_58831-T1
Valid prediction for Augustus_model.g38995.t1
Valid prediction for snap_scaffold_28-snap.1292-T1
Valid prediction for snap_scaffold_28-snap.1290-T1
Valid prediction for snap_scaffold_28-snap.1308-T1
Valid prediction for pasa_asmbl_37603.p1
Valid prediction for CodingQuarry_transcript_43684-T1
Valid prediction for snap_scaffold_28-snap.1307-T1
Valid prediction for Augustus_model.g39002.t1
Valid prediction for Augustus_model.g38996.t1
Valid prediction for Augustus_model.g39006.t1
Valid prediction for snap_scaffold_28-snap.1288-T1
Valid prediction for GlimmerHMM_glimmerT_58845-T1
Valid prediction for Augustus_model.g38993.t1
Valid prediction for GlimmerHMM_glimmerT_58838-T1
Valid prediction for GlimmerHMM_glimmerT_58837-T1
Valid prediction for Augustus_model.g38997.t1
Valid prediction for GlimmerHMM_glimmerT_58840-T1
Valid prediction for snap_scaffold_28-snap.1294-T1
Valid prediction for snap_scaffold_28-snap.1311-T1
Valid prediction for snap_scaffold_28-snap.1284-T1
Valid prediction for Augustus_model.g39012.t1
Valid prediction for CodingQuarry_transcript_43683-T1
Valid prediction for HiQ_model.g39005.t1
Valid prediction for GlimmerHMM_glimmerT_58827-T1
Valid prediction for GlimmerHMM_glimmerT_58849-T1
Valid prediction for GlimmerHMM_glimmerT_58842-T1
Valid prediction for GlimmerHMM_glimmerT_58847-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 Augustus_model.g39014.t1
Couldn't classify 45770, 45880
Couldn't classify 46656, 46791
Sorry, prediction pasa_asmbl_38323.p1 fails validation.
(TTC)	 GC	45770-45880	GT	AGG
(ATA)	 AG	45973-46043	GT	AGG
(ACG)	 AG	46160-46248	GT	AGG
(ACT)	 AG	46360-46570	GT	AGG
(GTT)	 AG	46656-46791	CC	CCC
-recovered pasa_asmbl_38323.p1, internal, 45973, 46043
-recovered pasa_asmbl_38323.p1, internal, 46160, 46248
-recovered pasa_asmbl_38323.p1, internal, 46360, 46570
Valid prediction for GlimmerHMM_glimmerT_58832-T1
Valid prediction for snap_scaffold_28-snap.1293-T1
Valid prediction for GlimmerHMM_glimmerT_58834-T1
Valid prediction for snap_scaffold_28-snap.1286-T1
Valid prediction for GlimmerHMM_glimmerT_58853-T1
Valid prediction for GlimmerHMM_glimmerT_58836-T1
Valid prediction for GlimmerHMM_glimmerT_58858-T1
Valid prediction for Augustus_model.g39016.t1
Valid prediction for GlimmerHMM_glimmerT_58843-T1
Valid prediction for snap_scaffold_28-snap.1304-T1
Valid prediction for snap_scaffold_28-snap.1309-T1
Valid prediction for snap_scaffold_28-snap.1289-T1
Valid prediction for snap_scaffold_28-snap.1305-T1
Valid prediction for snap_scaffold_28-snap.1310-T1
Valid prediction for Augustus_model.g39015.t1
Valid prediction for snap_scaffold_28-snap.1297-T1
Couldn't classify 146794, 146857
Couldn't classify 152176, 152378
Sorry, prediction pasa_asmbl_38315.p1 fails validation.
(TTT)	 CA	146794-146857	GT	AGG
(TGG)	 AG	147013-147080	GT	AGG
(ATC)	 AG	147489-147670	GT	ATG
(GAC)	 AG	147953-148073	GT	CCG
(ATC)	 AG	150432-150588	GT	CTG
(TCC)	 AG	150690-150837	GT	AGG
(GGG)	 AG	150981-151086	GT	AGG
(GTG)	 AG	151189-151456	GT	TGG
(GGA)	 AG	151791-151886	GT	TGG
(GTA)	 AG	152176-152378	GA	GGG
add_exon() Sorry, pasa_asmbl_38315.p1 150690-150837-terminal-3 is invalid.
-recovered pasa_asmbl_38315.p1, terminal, 150690, 150837
-recovered pasa_asmbl_38315.p1, internal, 147013, 147080
-recovered pasa_asmbl_38315.p1, internal, 147489, 147670
-recovered pasa_asmbl_38315.p1, internal, 147953, 148073
-recovered pasa_asmbl_38315.p1, internal, 150432, 150588
-recovered pasa_asmbl_38315.p1, internal, 150690, 150837
-recovered pasa_asmbl_38315.p1, internal, 150981, 151086
-recovered pasa_asmbl_38315.p1, internal, 151189, 151456
-recovered pasa_asmbl_38315.p1, internal, 151791, 151886
Valid prediction for CodingQuarry_transcript_43685-T1
Valid prediction for snap_scaffold_28-snap.1295-T1
Valid prediction for Augustus_model.g38998.t1
Valid prediction for Augustus_model.g38994.t1
Valid prediction for pasa_asmbl_38327.p1
Valid prediction for GlimmerHMM_glimmerT_58857-T1
Valid prediction for GlimmerHMM_glimmerT_58841-T1
Valid prediction for GlimmerHMM_glimmerT_58846-T1
Valid prediction for Augustus_model.g39013.t1
Valid prediction for snap_scaffold_28-snap.1287-T1
Valid prediction for snap_scaffold_28-snap.1313-T1
Valid prediction for GlimmerHMM_glimmerT_58854-T1
Valid prediction for Augustus_model.g39004.t1
Valid prediction for Augustus_model.g38999.t1
Valid prediction for CodingQuarry_transcript_43681-T1
Valid prediction for pasa_asmbl_38318.p1
Valid prediction for snap_scaffold_28-snap.1312-T1
Valid prediction for snap_scaffold_28-snap.1306-T1
Valid prediction for GlimmerHMM_glimmerT_58839-T1
Valid prediction for Augustus_model.g39000.t1
Valid prediction for HiQ_model.g39003.t1
Valid prediction for GlimmerHMM_glimmerT_58844-T1
Valid prediction for Augustus_model.g39007.t1
Valid prediction for GlimmerHMM_glimmerT_58855-T1
Valid prediction for GlimmerHMM_glimmerT_58850-T1
Couldn't classify 121003, 121214
Sorry, prediction pasa_asmbl_38564.p1 fails validation.
(ATG)	 TT	120232-120472	GT	GGG
(ATG)	 AG	121003-121214	GT	CAG
-recovered pasa_asmbl_38564.p1, initial, 120232, 120472
add_exon() Sorry, pasa_asmbl_38564.p1 121003-121214-initial-1 is invalid.
-recovered pasa_asmbl_38564.p1, initial, 121003, 121214
-recovered pasa_asmbl_38564.p1, internal, 121003, 121214
Valid prediction for snap_scaffold_28-snap.1302-T1
Valid prediction for Augustus_model.g39010.t1
Valid prediction for GlimmerHMM_glimmerT_58848-T1
Valid prediction for GlimmerHMM_glimmerT_58828-T1
Valid prediction for Augustus_model.g39009.t1
Valid prediction for snap_scaffold_28-snap.1291-T1
Valid prediction for GlimmerHMM_glimmerT_58856-T1
Valid prediction for Augustus_model.g39008.t1
Valid prediction for snap_scaffold_28-snap.1301-T1
Valid prediction for snap_scaffold_28-snap.1298-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17709, rend_intergenic: 14337  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37785, rend_intergenic: 31010  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120981, rend_intergenic: 118944  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138275, rend_intergenic: 132624  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143448, rend_intergenic: 141897  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 162003
-exon list size: 327


building trellis

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0.6    
0.9    
1.2    
1.5    
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2.1    
2.4    
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3.6    
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7.6    
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10.9    
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11.6    
11.9    
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13.4    
13.7    
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20.4    
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21.6    
21.9    
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24.6    
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25.8    
26.1    
26.4    
26.7    
27.1    
27.4    
27.7    
28.0    
28.3    
28.6    
28.9    
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30.1    
30.4    
30.7    
31.0    
31.3    
31.6    
31.9    
32.2    
32.5    
32.8    
33.1    
33.4    
33.7    
34.0    
34.3    
34.7    
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35.6    
35.9    
36.2    
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37.4    
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38.6    
38.9    
39.2    
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40.1    
40.4    
40.7    
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41.3    
41.6    
41.9    
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42.6    
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44.1    
44.4    
44.7    
45.0    
45.3    
45.6    
45.9    
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47.1    
47.4    
47.7    
48.0    
48.3    
48.6    
48.9    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.1    
51.4    
51.7    
52.0    
52.3    
52.6    
52.9    
53.2    
53.5    
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54.4    
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55.6    
55.9    
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57.4    
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58.7    
59.0    
59.3    
59.6    
59.9    
60.2    
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62.9    
63.2    
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63.8    
64.1    
64.4    
64.7    
65.0    
65.3    
65.7    
66.0    
66.3    
66.6    
66.9    
67.2    
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68.1    
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78.7    
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81.5    
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82.7    
83.0    
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83.6    
83.9    
84.2    
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84.8    
85.1    
85.4    
85.7    
86.0    
86.3    
86.6    
86.9    
87.2    
87.5    
87.8    
88.1    
88.4    
88.8    
89.1    
89.4    
89.7    
90.0    
90.3    
90.6    
90.9    
91.2    
91.5    
91.8    
92.1    
92.4    
92.7    
93.0    
93.3    
93.6    
93.9    
94.2    
94.5    
94.8    
95.1    
95.4    
95.7    
96.0    
96.4    
96.7    
97.0    
97.3    
97.6    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 17709, rend_intergenic: 14337  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37785, rend_intergenic: 31010  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120981, rend_intergenic: 118944  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138275, rend_intergenic: 132624  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143448, rend_intergenic: 141897  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