-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_25/scaffold_25_3192125-3401596

-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_53845-T1
Valid prediction for snap_scaffold_25-snap.669-T1
Valid prediction for snap_scaffold_25-snap.666-T1
Valid prediction for GlimmerHMM_glimmerT_53835-T1
Valid prediction for GlimmerHMM_glimmerT_53843-T1
Valid prediction for GlimmerHMM_glimmerT_53831-T1
Couldn't classify 77181, 77499
Sorry, prediction pasa_asmbl_33412.p1 fails validation.
(ATG)	 TT	76645-76734	GT	GGG
(ACT)	 AG	76822-76895	GT	AGG
(CCC)	 AG	77181-77499	AA	GCA
-recovered pasa_asmbl_33412.p1, initial, 76645, 76734
-recovered pasa_asmbl_33412.p1, internal, 76822, 76895
Couldn't classify 77584, 78345
Couldn't classify 78424, 78540
Sorry, prediction pasa_asmbl_33413.p1 fails validation.
(CCC)	 GC	77584-78345	GT	AGG
(ATG)	 AG	78424-78540	AC	ACA
Couldn't classify 27617, 27713
Couldn't classify 29669, 29734
Sorry, prediction pasa_asmbl_33409.p1 fails validation.
(GAT)	 GT	27617-27713	GT	AGG
(TGT)	 AG	27819-27997	GT	TGG
(GCG)	 AG	29669-29734	AC	GCA
-recovered pasa_asmbl_33409.p1, internal, 27819, 27997
Valid prediction for GlimmerHMM_glimmerT_53834-T1
Valid prediction for snap_scaffold_25-snap.676-T1
Valid prediction for snap_scaffold_25-snap.641-T1
Valid prediction for Augustus_model.g35729.t1
Valid prediction for snap_scaffold_25-snap.672-T1
Valid prediction for Augustus_model.g35733.t1
Valid prediction for GlimmerHMM_glimmerT_53830-T1
Couldn't classify 24719, 24789
Couldn't classify 25686, 25754
Sorry, prediction pasa_asmbl_33408.p1 fails validation.
(GAA)	 AT	24719-24789	GT	ATG
(CAT)	 AG	24936-25078	GT	CGG
(AGA)	 AG	25207-25262	GT	AGG
(CTA)	 AG	25686-25754	AA	ACA
-recovered pasa_asmbl_33408.p1, internal, 24936, 25078
-recovered pasa_asmbl_33408.p1, internal, 25207, 25262
Valid prediction for snap_scaffold_25-snap.661-T1
Valid prediction for snap_scaffold_25-snap.647-T1
Valid prediction for snap_scaffold_25-snap.645-T1
Valid prediction for GlimmerHMM_glimmerT_53842-T1
Valid prediction for snap_scaffold_25-snap.650-T1
Valid prediction for GlimmerHMM_glimmerT_53844-T1
Valid prediction for snap_scaffold_25-snap.663-T1
Valid prediction for snap_scaffold_25-snap.654-T1
Couldn't classify 37605, 37611
Couldn't classify 41393, 41454
Sorry, prediction pasa_asmbl_33410.p1 fails validation.
(CTA)	 TG	37605-37611	GT	CGG
(CCC)	 AG	37854-37952	GT	CCG
(AGG)	 AG	38434-38519	GT	CTG
(GAG)	 AG	41053-41245	GT	AGG
(ACG)	 AG	41393-41454	GA	GAG
-recovered pasa_asmbl_33410.p1, internal, 37854, 37952
-recovered pasa_asmbl_33410.p1, internal, 38434, 38519
-recovered pasa_asmbl_33410.p1, internal, 41053, 41245
Couldn't classify 84608, 84751
Sorry, prediction pasa_asmbl_33415.p1 fails validation.
(ATG)	 AG	82091-82262	GT	AGG
(ACG)	 AG	82369-82580	GT	AGG
(GTT)	 AG	82724-82862	GT	GGG
(GTA)	 AG	84231-84379	GT	TGG
(CCA)	 AG	84608-84751	AG	TCA
-recovered pasa_asmbl_33415.p1, initial, 82091, 82262
-recovered pasa_asmbl_33415.p1, internal, 82091, 82262
-recovered pasa_asmbl_33415.p1, internal, 82369, 82580
-recovered pasa_asmbl_33415.p1, internal, 82724, 82862
-recovered pasa_asmbl_33415.p1, internal, 84231, 84379
Valid prediction for snap_scaffold_25-snap.674-T1
Valid prediction for snap_scaffold_25-snap.671-T1
Valid prediction for snap_scaffold_25-snap.655-T1
Valid prediction for Augustus_model.g35725.t1
Valid prediction for CodingQuarry_transcript_38664-T1
Valid prediction for Augustus_model.g35732.t1
Valid prediction for GlimmerHMM_glimmerT_53838-T1
Valid prediction for snap_scaffold_25-snap.667-T1
Valid prediction for snap_scaffold_25-snap.658-T1
Valid prediction for snap_scaffold_25-snap.652-T1
Valid prediction for snap_scaffold_25-snap.664-T1
Valid prediction for GlimmerHMM_glimmerT_53840-T1
Valid prediction for Augustus_model.g35731.t1
Valid prediction for Augustus_model.g35724.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.g35728.t1
Couldn't classify 187557, 188007
Sorry, prediction pasa_asmbl_34568.p1 fails validation.
(TCA)	 TG	187557-188007	GT	GGG
(TCA)	 AG	189832-190004	GT	TGG
(GGA)	 AG	191919-192171	GT	ATG
(GTC)	 AG	192415-192671	CG	AGC
-recovered pasa_asmbl_34568.p1, terminal, 192415, 192671
-recovered pasa_asmbl_34568.p1, internal, 189832, 190004
-recovered pasa_asmbl_34568.p1, internal, 191919, 192171
Valid prediction for snap_scaffold_25-snap.649-T1
Valid prediction for snap_scaffold_25-snap.673-T1
Valid prediction for CodingQuarry_transcript_38666-T1
Valid prediction for pasa_asmbl_34117.p1
Valid prediction for GlimmerHMM_glimmerT_53839-T1
Valid prediction for GlimmerHMM_glimmerT_53841-T1
Valid prediction for snap_scaffold_25-snap.680-T1
Valid prediction for Augustus_model.g35727.t1
Valid prediction for snap_scaffold_25-snap.682-T1
Valid prediction for CodingQuarry_transcript_38667-T1
Valid prediction for GlimmerHMM_glimmerT_53833-T1
Valid prediction for snap_scaffold_25-snap.639-T1
Valid prediction for snap_scaffold_25-snap.657-T1
Valid prediction for snap_scaffold_25-snap.668-T1
Valid prediction for snap_scaffold_25-snap.665-T1
Valid prediction for GlimmerHMM_glimmerT_53836-T1
Valid prediction for GlimmerHMM_glimmerT_53837-T1
Valid prediction for snap_scaffold_25-snap.644-T1
Valid prediction for CodingQuarry_transcript_38665-T1
Valid prediction for snap_scaffold_25-snap.642-T1
Valid prediction for snap_scaffold_25-snap.675-T1
Valid prediction for snap_scaffold_25-snap.659-T1
Valid prediction for snap_scaffold_25-snap.653-T1
Valid prediction for snap_scaffold_25-snap.648-T1
Valid prediction for snap_scaffold_25-snap.640-T1
Valid prediction for snap_scaffold_25-snap.677-T1
Valid prediction for snap_scaffold_25-snap.679-T1
Valid prediction for HiQ_model.g35730.t1
Valid prediction for snap_scaffold_25-snap.643-T1
Valid prediction for snap_scaffold_25-snap.681-T1
Valid prediction for snap_scaffold_25-snap.670-T1
Couldn't classify 109127, 109159
Sorry, prediction pasa_asmbl_34122.p1 fails validation.
(CTC)	 TC	109127-109159	GT	AGG
(GTG)	 AG	109393-109500	GT	AGG
(AAG)	 AG	109789-109924	GT	CAG
(ACT)	 AG	110090-110314	GT	AGG
(GAG)	 AG	110630-110751	GT	TGG
(GGT)	 AG	110844-110970	GT	AGG
(GTG)	 AG	111081-111212	GT	CAG
(GGA)	 AG	111477-111650	GT	AGG
(GAA)	 AG	111856-112115	GA	GAG
-recovered pasa_asmbl_34122.p1, terminal, 111856, 112115
-recovered pasa_asmbl_34122.p1, internal, 109393, 109500
-recovered pasa_asmbl_34122.p1, internal, 109789, 109924
-recovered pasa_asmbl_34122.p1, internal, 110090, 110314
-recovered pasa_asmbl_34122.p1, internal, 110630, 110751
-recovered pasa_asmbl_34122.p1, internal, 110844, 110970
-recovered pasa_asmbl_34122.p1, internal, 111081, 111212
-recovered pasa_asmbl_34122.p1, internal, 111477, 111650
Valid prediction for Augustus_model.g35726.t1
Valid prediction for GlimmerHMM_glimmerT_53846-T1
Valid prediction for snap_scaffold_25-snap.646-T1
Valid prediction for HiQ_model.g35723.t1
Valid prediction for snap_scaffold_25-snap.660-T1
Valid prediction for snap_scaffold_25-snap.662-T1
Valid prediction for snap_scaffold_25-snap.651-T1
Valid prediction for snap_scaffold_25-snap.656-T1
Valid prediction for pasa_asmbl_34120.p1
Valid prediction for GlimmerHMM_glimmerT_53832-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10693, rend_intergenic: 9402  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14141, rend_intergenic: 10718  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33689, rend_intergenic: 30817  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38785, rend_intergenic: 34134  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42971, rend_intergenic: 38877  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45801, rend_intergenic: 43607  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65581, rend_intergenic: 51402  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66504, rend_intergenic: 66170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68823, rend_intergenic: 68180  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71141, rend_intergenic: 69057  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92378, rend_intergenic: 78705  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105717, rend_intergenic: 97876  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128113, rend_intergenic: 117583  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138305, rend_intergenic: 129319  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145128, rend_intergenic: 142569  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160063, rend_intergenic: 156934  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 157760, rend_intergenic: 157757  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 209472
-exon list size: 405


building trellis

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34.4    
34.6    
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35.1    
35.4    
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35.9    
36.1    
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36.6    
36.9    
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37.6    
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38.6    
38.8    
39.1    
39.3    
39.6    
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40.0    
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43.7    
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44.7    
45.0    
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45.5    
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45.9    
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48.2    
48.4    
48.6    
48.9    
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55.8    
56.0    
56.3    
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56.8    
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57.5    
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59.0    
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60.7    
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80.3    
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81.3    
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89.2    
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90.2    
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90.7    
90.9    
91.2    
91.4    
91.6    
91.9    
92.1    
92.4    
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96.1    
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96.6    
96.8    
97.1    
97.3    
97.5    
97.8    
98.0    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 22 predictions from path traversal
Error with prediction: snap lend_intergenic: 10693, rend_intergenic: 9402  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14141, rend_intergenic: 10718  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33689, rend_intergenic: 30817  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38785, rend_intergenic: 34134  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42971, rend_intergenic: 38877  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45801, rend_intergenic: 43607  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65581, rend_intergenic: 51402  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66504, rend_intergenic: 66170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68823, rend_intergenic: 68180  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71141, rend_intergenic: 69057  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92378, rend_intergenic: 78705  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105717, rend_intergenic: 97876  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128113, rend_intergenic: 117583  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138305, rend_intergenic: 129319  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145128, rend_intergenic: 142569  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160063, rend_intergenic: 156934  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 157760, rend_intergenic: 157757  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 196321 - 209472
-exon list size: 12


building trellis

7.1    
14.3    
21.4    
28.6    
35.7    
42.9    
50.0    
57.1    
64.3    
71.4    
78.6    
85.7    
92.9    
-found 1 predictions from path traversal

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