-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_21/scaffold_21_6384406-6531691

-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_21-snap.1322-T1
Valid prediction for GlimmerHMM_glimmerT_47865-T1
Valid prediction for GlimmerHMM_glimmerT_47862-T1
Valid prediction for CodingQuarry_transcript_32578-T1
Valid prediction for snap_scaffold_21-snap.1321-T1
Valid prediction for GlimmerHMM_glimmerT_47870-T1
Valid prediction for GlimmerHMM_glimmerT_47873-T1
Valid prediction for snap_scaffold_21-snap.1296-T1
Valid prediction for snap_scaffold_21-snap.1310-T1
Valid prediction for snap_scaffold_21-snap.1318-T1
Valid prediction for snap_scaffold_21-snap.1324-T1
Valid prediction for pasa_asmbl_28642.p1
Valid prediction for CodingQuarry_transcript_32577-T1
Valid prediction for CodingQuarry_transcript_32576-T1
Valid prediction for snap_scaffold_21-snap.1306-T1
Valid prediction for pasa_asmbl_28658.p1
Valid prediction for Augustus_model.g31943.t1
Valid prediction for snap_scaffold_21-snap.1302-T1
Valid prediction for snap_scaffold_21-snap.1313-T1
Valid prediction for HiQ_model.g31929.t1
Couldn't classify 64364, 64631
Sorry, prediction pasa_asmbl_28647.p1 fails validation.
(GAA)	 AT	64364-64631	GT	AGG
(CCT)	 AG	64833-64902	GT	GGG
(AAT)	 AG	65063-65168	GT	TGG
(GAC)	 AG	65356-65481	AC	GAA
-recovered pasa_asmbl_28647.p1, terminal, 65356, 65481
-recovered pasa_asmbl_28647.p1, internal, 64833, 64902
-recovered pasa_asmbl_28647.p1, internal, 65063, 65168
Valid prediction for snap_scaffold_21-snap.1303-T1
Valid prediction for GlimmerHMM_glimmerT_47867-T1
Valid prediction for snap_scaffold_21-snap.1316-T1
Valid prediction for snap_scaffold_21-snap.1304-T1
Valid prediction for snap_scaffold_21-snap.1319-T1
Valid prediction for HiQ_model.g31934.t1
Valid prediction for CodingQuarry_transcript_32579-T1
Valid prediction for snap_scaffold_21-snap.1298-T1
Valid prediction for GlimmerHMM_glimmerT_47850-T1
Valid prediction for GlimmerHMM_glimmerT_47857-T1
Valid prediction for snap_scaffold_21-snap.1301-T1
Valid prediction for pasa_asmbl_28654.p1
Valid prediction for snap_scaffold_21-snap.1315-T1
Valid prediction for GlimmerHMM_glimmerT_47849-T1
Valid prediction for snap_scaffold_21-snap.1325-T1
Valid prediction for Augustus_model.g31941.t1
Valid prediction for GlimmerHMM_glimmerT_47851-T1
Valid prediction for pasa_asmbl_28651.p1
Valid prediction for Augustus_model.g31949.t1
Valid prediction for Augustus_model.g31931.t1
Couldn't classify 6552, 6671
Couldn't classify 16638, 17046
Sorry, prediction pasa_asmbl_28635.p1 fails validation.
(CAG)	 TC	6552-6671	GT	ATG
(ACC)	 AG	7808-7837	GT	CTG
(GTC)	 AG	9003-9085	GT	AGG
(ATG)	 AG	10080-10246	GT	AGG
(GTG)	 AG	10645-10741	GT	AAG
(GTT)	 AG	12232-12345	GT	AGG
(GCA)	 AG	12439-12638	GT	CGG
(ACT)	 AG	14195-14323	GT	GGG
(AGT)	 AG	14539-14650	GT	AAG
(CTG)	 AG	15170-15365	GT	AGG
(GGT)	 AG	15474-15659	GT	TGG
(GTC)	 AG	15867-16037	GT	TGG
(GTG)	 AG	16169-16323	GT	AGG
(GCT)	 AG	16638-17046	CC	TCC
add_exon() Sorry, pasa_asmbl_28635.p1 10080-10246-initial-1 is invalid.
-recovered pasa_asmbl_28635.p1, initial, 10080, 10246
-recovered pasa_asmbl_28635.p1, internal, 7808, 7837
-recovered pasa_asmbl_28635.p1, internal, 9003, 9085
-recovered pasa_asmbl_28635.p1, internal, 10080, 10246
-recovered pasa_asmbl_28635.p1, internal, 10645, 10741
-recovered pasa_asmbl_28635.p1, internal, 12232, 12345
-recovered pasa_asmbl_28635.p1, internal, 12439, 12638
-recovered pasa_asmbl_28635.p1, internal, 14195, 14323
-recovered pasa_asmbl_28635.p1, internal, 14539, 14650
-recovered pasa_asmbl_28635.p1, internal, 15170, 15365
-recovered pasa_asmbl_28635.p1, internal, 15474, 15659
-recovered pasa_asmbl_28635.p1, internal, 15867, 16037
-recovered pasa_asmbl_28635.p1, internal, 16169, 16323
Valid prediction for Augustus_model.g31938.t1
Valid prediction for Augustus_model.g31948.t1
Valid prediction for GlimmerHMM_glimmerT_47853-T1
Valid prediction for GlimmerHMM_glimmerT_47855-T1
Couldn't classify 17155, 18300
Sorry, prediction pasa_asmbl_28638.p1 fails validation.
(TGC)	 CC	17155-18300	GT	TCG
(ACG)	 AG	18553-18663	GT	AGG
(GTC)	 AG	18835-18923	GT	AGG
(GAA)	 AG	19156-19333	GA	GAG
-recovered pasa_asmbl_28638.p1, terminal, 19156, 19333
-recovered pasa_asmbl_28638.p1, internal, 18553, 18663
-recovered pasa_asmbl_28638.p1, internal, 18835, 18923
Valid prediction for CodingQuarry_transcript_32580-T1
Valid prediction for GlimmerHMM_glimmerT_47866-T1
Valid prediction for CodingQuarry_transcript_32572-T1
Valid prediction for snap_scaffold_21-snap.1307-T1
Valid prediction for GlimmerHMM_glimmerT_47868-T1
Valid prediction for snap_scaffold_21-snap.1311-T1
Valid prediction for Augustus_model.g31946.t1
Valid prediction for snap_scaffold_21-snap.1295-T1
Valid prediction for HiQ_model.g31944.t1
Valid prediction for HiQ_model.g31942.t1
Valid prediction for snap_scaffold_21-snap.1314-T1
Couldn't classify 123116, 123331
Sorry, prediction pasa_asmbl_28655.p1 fails validation.
(CAT)	 TC	123116-123331	GT	AGG
(CCG)	 AG	123458-123652	GG	AGG
-recovered pasa_asmbl_28655.p1, terminal, 123458, 123652
Valid prediction for HiQ_model.g31932.t1
Valid prediction for Augustus_model.g31945.t1
Valid prediction for GlimmerHMM_glimmerT_47869-T1
Valid prediction for Augustus_model.g31940.t1
Couldn't classify 26322, 26367
Sorry, prediction pasa_asmbl_28640.p1 fails validation.
(GAT)	 CA	26322-26367	GT	TGG
(CAC)	 AG	26533-26697	GT	TGG
(TTC)	 AG	26782-26927	GT	AGG
(CTG)	 AG	27034-27126	GT	AGG
(GAA)	 AG	27244-27310	GT	AAG
(ATG)	 AG	27382-27545	GT	AGG
(CTG)	 AG	27727-27906	AG	AGA
add_exon() Sorry, pasa_asmbl_28640.p1 27382-27545-initial-1 is invalid.
-recovered pasa_asmbl_28640.p1, initial, 27382, 27545
-recovered pasa_asmbl_28640.p1, terminal, 27727, 27906
-recovered pasa_asmbl_28640.p1, internal, 26533, 26697
-recovered pasa_asmbl_28640.p1, internal, 26782, 26927
-recovered pasa_asmbl_28640.p1, internal, 27034, 27126
-recovered pasa_asmbl_28640.p1, internal, 27244, 27310
-recovered pasa_asmbl_28640.p1, internal, 27382, 27545
Valid prediction for CodingQuarry_transcript_32575-T1
Valid prediction for CodingQuarry_transcript_32573-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.g31935.t1
Valid prediction for Augustus_model.g31947.t1
Valid prediction for snap_scaffold_21-snap.1320-T1
Valid prediction for snap_scaffold_21-snap.1323-T1
Valid prediction for snap_scaffold_21-snap.1317-T1
Valid prediction for CodingQuarry_transcript_32574-T1
Valid prediction for Augustus_model.g31950.t1
Valid prediction for HiQ_model.g31939.t1
Couldn't classify 66966, 66996
Sorry, prediction pasa_asmbl_27723.p1 fails validation.
(TCA)	 TC	66966-66996	GT	AGG
(CCA)	 AG	67222-67334	GT	AGG
(GAC)	 AG	67663-67737	GT	AGG
(GAT)	 AG	67863-68012	GT	AGG
(ACC)	 AG	68257-68382	CC	AAC
-recovered pasa_asmbl_27723.p1, terminal, 68257, 68382
-recovered pasa_asmbl_27723.p1, internal, 67222, 67334
-recovered pasa_asmbl_27723.p1, internal, 67663, 67737
-recovered pasa_asmbl_27723.p1, internal, 67863, 68012
Valid prediction for GlimmerHMM_glimmerT_47848-T1
Couldn't classify 55149, 55190
Sorry, prediction pasa_asmbl_27724.p1 fails validation.
(CGT)	 GC	55149-55190	GT	GGG
(TCC)	 AG	55548-55644	GT	TGG
(GCA)	 AG	55902-56025	GT	GGG
(GTA)	 AG	56205-56278	GT	ACG
(ACC)	 AG	56379-56524	GT	AGG
(GAG)	 AG	56745-56888	GG	GAG
-recovered pasa_asmbl_27724.p1, terminal, 56745, 56888
-recovered pasa_asmbl_27724.p1, internal, 55548, 55644
-recovered pasa_asmbl_27724.p1, internal, 55902, 56025
-recovered pasa_asmbl_27724.p1, internal, 56205, 56278
-recovered pasa_asmbl_27724.p1, internal, 56379, 56524
Valid prediction for snap_scaffold_21-snap.1308-T1
Valid prediction for Augustus_model.g31936.t1
Valid prediction for GlimmerHMM_glimmerT_47872-T1
Valid prediction for snap_scaffold_21-snap.1309-T1
Valid prediction for snap_scaffold_21-snap.1300-T1
Valid prediction for GlimmerHMM_glimmerT_47856-T1
Valid prediction for Augustus_model.g31937.t1
Valid prediction for snap_scaffold_21-snap.1297-T1
Valid prediction for GlimmerHMM_glimmerT_47874-T1
Valid prediction for snap_scaffold_21-snap.1326-T1
Valid prediction for GlimmerHMM_glimmerT_47859-T1
Couldn't classify 2683, 2766
Sorry, prediction pasa_asmbl_27726.p1 fails validation.
(TCG)	 GC	2683-2766	GT	AGG
(GTG)	 AG	2967-3125	GT	AGG
(GTC)	 AG	3532-3785	GT	AAG
(GGT)	 AG	4103-4304	GT	AGG
(CTT)	 AG	4427-4459	GT	AGG
-recovered pasa_asmbl_27726.p1, terminal, 4427, 4459
-recovered pasa_asmbl_27726.p1, internal, 2967, 3125
-recovered pasa_asmbl_27726.p1, internal, 3532, 3785
-recovered pasa_asmbl_27726.p1, internal, 4103, 4304
-recovered pasa_asmbl_27726.p1, internal, 4427, 4459
Valid prediction for GlimmerHMM_glimmerT_47852-T1
Valid prediction for GlimmerHMM_glimmerT_47858-T1
Valid prediction for snap_scaffold_21-snap.1312-T1
Valid prediction for GlimmerHMM_glimmerT_47871-T1
Valid prediction for GlimmerHMM_glimmerT_47860-T1
Valid prediction for GlimmerHMM_glimmerT_47861-T1
Valid prediction for Augustus_model.g31930.t1
Valid prediction for snap_scaffold_21-snap.1299-T1
Sorry, intron length (3) is less than minimum required (10)
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_47864-T1
Valid prediction for HiQ_model.g31933.t1
Valid prediction for snap_scaffold_21-snap.1305-T1
Valid prediction for GlimmerHMM_glimmerT_47854-T1
Valid prediction for GlimmerHMM_glimmerT_47863-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11842, rend_intergenic: 8738  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15284, rend_intergenic: 11862  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19333, rend_intergenic: 17329  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76475, rend_intergenic: 70283  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85256, rend_intergenic: 82771  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121369, rend_intergenic: 120395  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 147286
-exon list size: 329


building trellis

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18.7    
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19.6    
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23.6    
23.9    
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25.7    
26.0    
26.3    
26.6    
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27.8    
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28.4    
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29.3    
29.6    
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30.2    
30.5    
30.8    
31.1    
31.4    
31.7    
32.0    
32.3    
32.6    
32.9    
33.2    
33.5    
33.8    
34.1    
34.4    
34.7    
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35.3    
35.6    
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36.3    
36.6    
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39.0    
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39.6    
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40.8    
41.1    
41.4    
41.7    
42.0    
42.3    
42.6    
42.9    
43.2    
43.5    
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44.1    
44.4    
44.7    
45.0    
45.3    
45.6    
45.9    
46.2    
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46.8    
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    
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54.4    
54.7    
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58.6    
58.9    
59.2    
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60.1    
60.4    
60.7    
61.0    
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61.6    
61.9    
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63.1    
63.4    
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64.0    
64.4    
64.7    
65.0    
65.3    
65.6    
65.9    
66.2    
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67.1    
67.4    
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68.0    
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68.6    
68.9    
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71.0    
71.3    
71.6    
71.9    
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73.1    
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74.6    
74.9    
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77.0    
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81.0    
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81.6    
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84.0    
84.3    
84.6    
84.9    
85.2    
85.5    
85.8    
86.1    
86.4    
86.7    
87.0    
87.3    
87.6    
87.9    
88.2    
88.5    
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    
93.1    
93.4    
93.7    
94.0    
94.3    
94.6    
94.9    
95.2    
95.5    
95.8    
96.1    
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 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 11842, rend_intergenic: 8738  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15284, rend_intergenic: 11862  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19333, rend_intergenic: 17329  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76475, rend_intergenic: 70283  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85256, rend_intergenic: 82771  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121369, rend_intergenic: 120395  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support