-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_27/scaffold_27_6190752-6351068

-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_57438-T1
Valid prediction for snap_scaffold_27-snap.1482-T1
Valid prediction for snap_scaffold_27-snap.1463-T1
Valid prediction for GlimmerHMM_glimmerT_57445-T1
Valid prediction for GlimmerHMM_glimmerT_57444-T1
Valid prediction for snap_scaffold_27-snap.1459-T1
Valid prediction for Augustus_model.g38053.t1
Valid prediction for HiQ_model.g38057.t1
Valid prediction for GlimmerHMM_glimmerT_57440-T1
Valid prediction for snap_scaffold_27-snap.1474-T1
Valid prediction for Augustus_model.g38054.t1
Valid prediction for snap_scaffold_27-snap.1449-T1
Couldn't classify 50250, 50269
Sorry, prediction pasa_asmbl_36388.p1 fails validation.
(TCC)	 GC	50250-50269	GT	CGG
(GTT)	 AG	50478-50592	GT	AGG
(ACA)	 AG	51000-51078	GT	AGG
(GTA)	 AG	51260-51415	GT	GAG
(GGT)	 AG	51593-51902	GT	TGG
(CAG)	 AG	52594-52706	GT	AGG
(CGA)	 AG	52803-52846	GT	AGG
(ATC)	 AG	53304-53402	GT	CGG
(TGT)	 AG	53641-53734	GT	AGG
(TTG)	 AG	54751-54866	GA	AAG
-recovered pasa_asmbl_36388.p1, terminal, 54751, 54866
-recovered pasa_asmbl_36388.p1, internal, 50478, 50592
-recovered pasa_asmbl_36388.p1, internal, 51000, 51078
-recovered pasa_asmbl_36388.p1, internal, 51260, 51415
-recovered pasa_asmbl_36388.p1, internal, 51593, 51902
-recovered pasa_asmbl_36388.p1, internal, 52594, 52706
-recovered pasa_asmbl_36388.p1, internal, 52803, 52846
-recovered pasa_asmbl_36388.p1, internal, 53304, 53402
-recovered pasa_asmbl_36388.p1, internal, 53641, 53734
Couldn't classify 49763, 49897
Sorry, prediction pasa_asmbl_36387.p1 fails validation.
(ATG)	 CA	46667-46669	GT	TGG
(CAA)	 AG	46902-46937	GT	AGG
(TAC)	 AG	47158-47280	GT	AGG
(AAG)	 AG	47455-47581	GT	CGG
(ACT)	 AG	47827-47930	GT	AGG
(GTG)	 AG	48102-48272	GT	AGG
(GAT)	 AG	48565-48704	GT	CGG
(GTG)	 AG	48950-49106	GT	ACG
(TGT)	 AG	49356-49412	GT	ACG
(GTG)	 AG	49519-49584	GT	AGG
(GAG)	 AG	49763-49897	GA	AGG
-recovered pasa_asmbl_36387.p1, initial, 46667, 46669
-recovered pasa_asmbl_36387.p1, internal, 46902, 46937
-recovered pasa_asmbl_36387.p1, internal, 47158, 47280
-recovered pasa_asmbl_36387.p1, internal, 47455, 47581
-recovered pasa_asmbl_36387.p1, internal, 47827, 47930
-recovered pasa_asmbl_36387.p1, internal, 48102, 48272
-recovered pasa_asmbl_36387.p1, internal, 48565, 48704
-recovered pasa_asmbl_36387.p1, internal, 48950, 49106
-recovered pasa_asmbl_36387.p1, internal, 49356, 49412
-recovered pasa_asmbl_36387.p1, internal, 49519, 49584
Valid prediction for snap_scaffold_27-snap.1464-T1
Valid prediction for snap_scaffold_27-snap.1479-T1
Valid prediction for snap_scaffold_27-snap.1477-T1
Valid prediction for HiQ_model.g38059.t1
Valid prediction for snap_scaffold_27-snap.1472-T1
Valid prediction for GlimmerHMM_glimmerT_57439-T1
Valid prediction for snap_scaffold_27-snap.1468-T1
Valid prediction for snap_scaffold_27-snap.1450-T1
Valid prediction for snap_scaffold_27-snap.1480-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_57437-T1
Valid prediction for pasa_asmbl_36391.p1
Valid prediction for snap_scaffold_27-snap.1452-T1
Valid prediction for GlimmerHMM_glimmerT_57455-T1
Valid prediction for Augustus_model.g38071.t1
Valid prediction for GlimmerHMM_glimmerT_57458-T1
Valid prediction for snap_scaffold_27-snap.1455-T1
Valid prediction for snap_scaffold_27-snap.1488-T1
Valid prediction for snap_scaffold_27-snap.1456-T1
Valid prediction for snap_scaffold_27-snap.1454-T1
Valid prediction for GlimmerHMM_glimmerT_57446-T1
Valid prediction for snap_scaffold_27-snap.1478-T1
Valid prediction for HiQ_model.g38060.t1
Valid prediction for CodingQuarry_transcript_41915-T1
Valid prediction for pasa_asmbl_36393.p1
Valid prediction for snap_scaffold_27-snap.1487-T1
Valid prediction for snap_scaffold_27-snap.1475-T1
Valid prediction for GlimmerHMM_glimmerT_57457-T1
Valid prediction for Augustus_model.g38064.t1
Valid prediction for CodingQuarry_transcript_41914-T1
Valid prediction for snap_scaffold_27-snap.1471-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_27-snap.1486-T1
Valid prediction for GlimmerHMM_glimmerT_57454-T1
Valid prediction for GlimmerHMM_glimmerT_57442-T1
Valid prediction for GlimmerHMM_glimmerT_57456-T1
Valid prediction for Augustus_model.g38072.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 HiQ_model.g38062.t1
Valid prediction for snap_scaffold_27-snap.1453-T1
Valid prediction for CodingQuarry_transcript_41913-T1
Valid prediction for Augustus_model.g38056.t1
Valid prediction for pasa_asmbl_37053.p1
Valid prediction for GlimmerHMM_glimmerT_57449-T1
Valid prediction for snap_scaffold_27-snap.1451-T1
Valid prediction for Augustus_model.g38052.t1
Valid prediction for Augustus_model.g38063.t1
Valid prediction for GlimmerHMM_glimmerT_57441-T1
Valid prediction for Augustus_model.g38051.t1
Valid prediction for snap_scaffold_27-snap.1469-T1
Valid prediction for snap_scaffold_27-snap.1476-T1
Valid prediction for snap_scaffold_27-snap.1460-T1
Valid prediction for HiQ_model.g38058.t1
Valid prediction for snap_scaffold_27-snap.1462-T1
Valid prediction for GlimmerHMM_glimmerT_57447-T1
Valid prediction for Augustus_model.g38065.t1
Valid prediction for GlimmerHMM_glimmerT_57448-T1
Valid prediction for snap_scaffold_27-snap.1483-T1
Valid prediction for snap_scaffold_27-snap.1457-T1
Valid prediction for snap_scaffold_27-snap.1466-T1
Valid prediction for snap_scaffold_27-snap.1467-T1
Valid prediction for GlimmerHMM_glimmerT_57450-T1
Valid prediction for snap_scaffold_27-snap.1485-T1
Valid prediction for snap_scaffold_27-snap.1473-T1
Valid prediction for CodingQuarry_transcript_41916-T1
Valid prediction for Augustus_model.g38069.t1
Couldn't classify 85397, 85648
Sorry, prediction pasa_asmbl_37049.p1 fails validation.
(ATG)	 TG	83611-83792	GT	AGG
(CAG)	 AG	84079-84307	GT	AAG
(GCA)	 AG	84439-84631	GT	ATG
(CAC)	 AG	84781-84909	GT	TGG
(CTC)	 AG	85182-85255	GT	AGG
(ATT)	 AG	85397-85648	GG	GGG
-recovered pasa_asmbl_37049.p1, initial, 83611, 83792
-recovered pasa_asmbl_37049.p1, internal, 84079, 84307
-recovered pasa_asmbl_37049.p1, internal, 84439, 84631
-recovered pasa_asmbl_37049.p1, internal, 84781, 84909
-recovered pasa_asmbl_37049.p1, internal, 85182, 85255
Valid prediction for snap_scaffold_27-snap.1461-T1
Valid prediction for GlimmerHMM_glimmerT_57451-T1
Valid prediction for GlimmerHMM_glimmerT_57453-T1
Valid prediction for Augustus_model.g38066.t1
Valid prediction for GlimmerHMM_glimmerT_57452-T1
Valid prediction for snap_scaffold_27-snap.1470-T1
Valid prediction for snap_scaffold_27-snap.1465-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_27-snap.1484-T1
Valid prediction for HiQ_model.g38068.t1
Valid prediction for GlimmerHMM_glimmerT_57436-T1
Sorry, intron length (7) is less than minimum required (10)
Couldn't classify 30263, 30305
Sorry, prediction pasa_asmbl_37054.p1 fails validation.
(ATG)	 AA	25620-25624	GT	AAG
(GGA)	 AG	25718-25800	GT	AGG
(GGA)	 AG	26389-26499	GT	AGG
(ACC)	 AG	26652-26692	GT	TGG
(GAT)	 AG	28302-28400	GT	AGG
(GCA)	 AG	29031-29084	GT	CGG
(CTG)	 AG	29665-29738	GT	AGG
(AGG)	 AG	30263-30305	GG	GAG
-recovered pasa_asmbl_37054.p1, initial, 25620, 25624
add_exon() Sorry, pasa_asmbl_37054.p1 26389-26499-terminal-1 is invalid.
-recovered pasa_asmbl_37054.p1, terminal, 26389, 26499
-recovered pasa_asmbl_37054.p1, internal, 25718, 25800
-recovered pasa_asmbl_37054.p1, internal, 26389, 26499
-recovered pasa_asmbl_37054.p1, internal, 26652, 26692
-recovered pasa_asmbl_37054.p1, internal, 28302, 28400
-recovered pasa_asmbl_37054.p1, internal, 29031, 29084
-recovered pasa_asmbl_37054.p1, internal, 29665, 29738
Valid prediction for Augustus_model.g38067.t1
Valid prediction for snap_scaffold_27-snap.1458-T1
Couldn't classify 101284, 101309
Sorry, prediction pasa_asmbl_37048.p1 fails validation.
(CAA)	 AT	101284-101309	GT	AAG
(GAC)	 AG	101490-101526	GT	TGG
(AAA)	 AG	101614-101677	GT	AGG
(GCT)	 AG	101823-101896	GT	CAG
(GAA)	 AG	102016-102061	GT	CGG
(TGC)	 AG	102153-102258	GT	AGG
(CTC)	 AG	102436-102481	GT	AGG
(CTG)	 AG	102662-102758	GT	CGG
(CAC)	 AG	102947-103067	GT	AAG
(CTC)	 AG	103188-103294	GT	AGG
(GAG)	 AG	104091-104209	AG	GAA
add_exon() Sorry, pasa_asmbl_37048.p1 101614-101677-terminal-3 is invalid.
-recovered pasa_asmbl_37048.p1, terminal, 101614, 101677
-recovered pasa_asmbl_37048.p1, terminal, 104091, 104209
-recovered pasa_asmbl_37048.p1, internal, 101490, 101526
-recovered pasa_asmbl_37048.p1, internal, 101614, 101677
-recovered pasa_asmbl_37048.p1, internal, 101823, 101896
-recovered pasa_asmbl_37048.p1, internal, 102016, 102061
-recovered pasa_asmbl_37048.p1, internal, 102153, 102258
-recovered pasa_asmbl_37048.p1, internal, 102436, 102481
-recovered pasa_asmbl_37048.p1, internal, 102662, 102758
-recovered pasa_asmbl_37048.p1, internal, 102947, 103067
-recovered pasa_asmbl_37048.p1, internal, 103188, 103294
Valid prediction for snap_scaffold_27-snap.1481-T1
Valid prediction for Augustus_model.g38061.t1
Valid prediction for GlimmerHMM_glimmerT_57443-T1
Valid prediction for Augustus_model.g38055.t1
Valid prediction for Augustus_model.g38070.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12108, rend_intergenic: 10421  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23812, rend_intergenic: 22462  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32097, rend_intergenic: 29475  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42419, rend_intergenic: 41411  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58212, rend_intergenic: 48529  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82255, rend_intergenic: 68419  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94597, rend_intergenic: 89770  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122729, rend_intergenic: 94754  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125327, rend_intergenic: 123611  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128445, rend_intergenic: 126866  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133574, rend_intergenic: 130576  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 160317
-exon list size: 371


building trellis

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19.3    
19.6    
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27.1    
27.3    
27.6    
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30.0    
30.3    
30.6    
30.8    
31.1    
31.4    
31.6    
31.9    
32.2    
32.4    
32.7    
33.0    
33.2    
33.5    
33.8    
34.0    
34.3    
34.6    
34.9    
35.1    
35.4    
35.7    
35.9    
36.2    
36.5    
36.7    
37.0    
37.3    
37.5    
37.8    
38.1    
38.3    
38.6    
38.9    
39.1    
39.4    
39.7    
39.9    
40.2    
40.5    
40.8    
41.0    
41.3    
41.6    
41.8    
42.1    
42.4    
42.6    
42.9    
43.2    
43.4    
43.7    
44.0    
44.2    
44.5    
44.8    
45.0    
45.3    
45.6    
45.8    
46.1    
46.4    
46.6    
46.9    
47.2    
47.5    
47.7    
48.0    
48.3    
48.5    
48.8    
49.1    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
50.9    
51.2    
51.5    
51.7    
52.0    
52.3    
52.5    
52.8    
53.1    
53.4    
53.6    
53.9    
54.2    
54.4    
54.7    
55.0    
55.2    
55.5    
55.8    
56.0    
56.3    
56.6    
56.8    
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57.6    
57.9    
58.2    
58.4    
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59.0    
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60.1    
60.3    
60.6    
60.9    
61.1    
61.4    
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66.2    
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78.0    
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80.4    
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81.8    
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82.8    
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83.4    
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85.3    
85.5    
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86.1    
86.3    
86.6    
86.9    
87.1    
87.4    
87.7    
87.9    
88.2    
88.5    
88.7    
89.0    
89.3    
89.5    
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90.1    
90.3    
90.6    
90.9    
91.2    
91.4    
91.7    
92.0    
92.2    
92.5    
92.8    
93.0    
93.3    
93.6    
93.8    
94.1    
94.4    
94.6    
94.9    
95.2    
95.4    
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96.0    
96.2    
96.5    
96.8    
97.1    
97.3    
97.6    
97.9    
98.1    
98.4    
98.7    
98.9    
99.2    
99.5    
99.7    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 12108, rend_intergenic: 10421  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23812, rend_intergenic: 22462  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32097, rend_intergenic: 29475  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42419, rend_intergenic: 41411  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58212, rend_intergenic: 48529  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82255, rend_intergenic: 68419  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94597, rend_intergenic: 89770  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122729, rend_intergenic: 94754  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125327, rend_intergenic: 123611  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128445, rend_intergenic: 126866  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133574, rend_intergenic: 130576  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 10077
-exon list size: 13


building trellis

6.7    
13.3    
20.0    
26.7    
33.3    
40.0    
46.7    
53.3    
60.0    
66.7    
73.3    
80.0    
86.7    
93.3    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support