-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_23/scaffold_23_9690272-9962662

-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 Augustus_model.g34519.t1
Couldn't classify 202172, 202180
Couldn't classify 206973, 207040
Sorry, prediction pasa_asmbl_31940.p1 fails validation.
(ATC)	 TC	202172-202180	GT	AGG
(GCG)	 AG	202406-202531	GT	TGG
(GTG)	 AG	203561-203610	GT	AGG
(GTA)	 AG	205249-205449	GT	AGG
(ACT)	 AG	205713-205847	GT	AAG
(GAT)	 AG	206421-206584	GC	AGG
(AGG)	 AG	206973-207040	GG	AGG
-recovered pasa_asmbl_31940.p1, internal, 202406, 202531
-recovered pasa_asmbl_31940.p1, internal, 203561, 203610
-recovered pasa_asmbl_31940.p1, internal, 205249, 205449
-recovered pasa_asmbl_31940.p1, internal, 205713, 205847
-recovered pasa_asmbl_31940.p1, internal, 206421, 206584
Valid prediction for GlimmerHMM_glimmerT_51640-T1
Valid prediction for GlimmerHMM_glimmerT_51651-T1
Valid prediction for GlimmerHMM_glimmerT_51637-T1
Valid prediction for snap_scaffold_23-snap.1891-T1
Valid prediction for GlimmerHMM_glimmerT_51628-T1
Valid prediction for snap_scaffold_23-snap.1865-T1
Valid prediction for GlimmerHMM_glimmerT_51648-T1
Couldn't classify 250772, 250987
Sorry, prediction pasa_asmbl_31811.p1 fails validation.
(GCC)	 CA	250772-250987	GT	AGG
(ATG)	 AG	251531-251636	GT	AGG
(ATC)	 AG	252015-252088	GT	CTG
(GAG)	 AG	252382-252477	GT	AGG
(AAG)	 AG	253286-253402	GT	TGG
(ATG)	 AG	253645-253742	GT	AAG
(GCA)	 AG	254400-254607	CC	AAC
-recovered pasa_asmbl_31811.p1, initial, 251531, 251636
-recovered pasa_asmbl_31811.p1, initial, 253645, 253742
-recovered pasa_asmbl_31811.p1, terminal, 254400, 254607
-recovered pasa_asmbl_31811.p1, internal, 251531, 251636
-recovered pasa_asmbl_31811.p1, internal, 252015, 252088
-recovered pasa_asmbl_31811.p1, internal, 252382, 252477
-recovered pasa_asmbl_31811.p1, internal, 253286, 253402
-recovered pasa_asmbl_31811.p1, internal, 253645, 253742
Valid prediction for GlimmerHMM_glimmerT_51653-T1
Valid prediction for snap_scaffold_23-snap.1876-T1
Valid prediction for Augustus_model.g34520.t1
Valid prediction for GlimmerHMM_glimmerT_51638-T1
Valid prediction for GlimmerHMM_glimmerT_51633-T1
Valid prediction for Augustus_model.g34518.t1
Valid prediction for snap_scaffold_23-snap.1875-T1
Valid prediction for snap_scaffold_23-snap.1864-T1
Valid prediction for Augustus_model.g34515.t1
Couldn't classify 194336, 194409
Sorry, prediction pasa_asmbl_31804.p1 fails validation.
(CAG)	 TG	194336-194409	GT	AGG
(TGT)	 AG	194922-195049	GT	CAG
(AGA)	 AG	195828-195886	GT	AGG
(TAC)	 AG	195998-196066	GT	AGG
(GGC)	 AG	196175-196318	GT	CGG
(CTC)	 AG	196706-196786	GC	AGG
-recovered pasa_asmbl_31804.p1, terminal, 196706, 196786
-recovered pasa_asmbl_31804.p1, internal, 194922, 195049
-recovered pasa_asmbl_31804.p1, internal, 195828, 195886
-recovered pasa_asmbl_31804.p1, internal, 195998, 196066
-recovered pasa_asmbl_31804.p1, internal, 196175, 196318
-recovered pasa_asmbl_31804.p1, internal, 196706, 196786
Valid prediction for snap_scaffold_23-snap.1886-T1
Valid prediction for snap_scaffold_23-snap.1873-T1
Couldn't classify 139070, 139217
Couldn't classify 139806, 139838
Sorry, prediction pasa_asmbl_31798.p1 fails validation.
(AGT)	 CC	139070-139217	GT	CAG
(AGG)	 AG	139455-139600	GT	AGG
(GTA)	 AG	139806-139838	AT	GGA
-recovered pasa_asmbl_31798.p1, internal, 139455, 139600
Valid prediction for Augustus_model.g34514.t1
Valid prediction for GlimmerHMM_glimmerT_51652-T1
Valid prediction for snap_scaffold_23-snap.1867-T1
Valid prediction for GlimmerHMM_glimmerT_51643-T1
Valid prediction for snap_scaffold_23-snap.1902-T1
Valid prediction for GlimmerHMM_glimmerT_51646-T1
Valid prediction for GlimmerHMM_glimmerT_51649-T1
Couldn't classify 233344, 233584
Couldn't classify 233824, 233933
Sorry, prediction pasa_asmbl_31810.p1 fails validation.
(CCT)	 CT	233344-233584	GT	AGG
(GAC)	 AG	233824-233933	TG	ACT
Valid prediction for snap_scaffold_23-snap.1866-T1
Valid prediction for snap_scaffold_23-snap.1888-T1
Valid prediction for GlimmerHMM_glimmerT_51631-T1
Valid prediction for GlimmerHMM_glimmerT_51645-T1
Valid prediction for CodingQuarry_transcript_35775-T1
Couldn't classify 225543, 225752
Sorry, prediction pasa_asmbl_31809.p1 fails validation.
(ATG)	 AC	221582-223168	GT	TGG
(AAG)	 AG	225543-225752	CA	GCC
-recovered pasa_asmbl_31809.p1, initial, 221582, 223168
Valid prediction for snap_scaffold_23-snap.1877-T1
Valid prediction for GlimmerHMM_glimmerT_51634-T1
Valid prediction for snap_scaffold_23-snap.1879-T1
Valid prediction for Augustus_model.g34516.t1
Valid prediction for snap_scaffold_23-snap.1901-T1
Valid prediction for snap_scaffold_23-snap.1889-T1
Valid prediction for Augustus_model.g34511.t1
Valid prediction for snap_scaffold_23-snap.1863-T1
Valid prediction for GlimmerHMM_glimmerT_51629-T1
Valid prediction for GlimmerHMM_glimmerT_51647-T1
Valid prediction for snap_scaffold_23-snap.1883-T1
Valid prediction for snap_scaffold_23-snap.1894-T1
Valid prediction for Augustus_model.g34509.t1
Valid prediction for Augustus_model.g34517.t1
Valid prediction for GlimmerHMM_glimmerT_51650-T1
Valid prediction for GlimmerHMM_glimmerT_51639-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 snap_scaffold_23-snap.1896-T1
Valid prediction for GlimmerHMM_glimmerT_51627-T1
Valid prediction for snap_scaffold_23-snap.1890-T1
Valid prediction for GlimmerHMM_glimmerT_51644-T1
Couldn't classify 5151, 5162
Sorry, prediction pasa_asmbl_31117.p1 fails validation.
(CTT)	 TG	5151-5162	GT	CTG
(GGT)	 AG	5269-5385	GT	AGG
(GTG)	 AG	5934-6133	GT	GGG
(GGA)	 AG	6346-6490	GC	AGG
(AAC)	 AG	6794-6911	GT	AGG
(TGC)	 AG	9011-9108	GT	AGG
(GAG)	 AG	9416-9475	GT	AGG
(ATG)	 AG	9712-9857	GT	AGG
(AGT)	 AG	10078-10237	GT	AGG
(GCG)	 AG	10331-10456	GT	AGG
(TTC)	 AG	10745-10836	GT	TGG
(GAC)	 AG	11048-11243	TC	GAT
-recovered pasa_asmbl_31117.p1, initial, 9712, 9857
-recovered pasa_asmbl_31117.p1, terminal, 11048, 11243
-recovered pasa_asmbl_31117.p1, internal, 5269, 5385
-recovered pasa_asmbl_31117.p1, internal, 5934, 6133
-recovered pasa_asmbl_31117.p1, internal, 6346, 6490
-recovered pasa_asmbl_31117.p1, internal, 6794, 6911
-recovered pasa_asmbl_31117.p1, internal, 9011, 9108
-recovered pasa_asmbl_31117.p1, internal, 9416, 9475
-recovered pasa_asmbl_31117.p1, internal, 9712, 9857
-recovered pasa_asmbl_31117.p1, internal, 10078, 10237
-recovered pasa_asmbl_31117.p1, internal, 10331, 10456
-recovered pasa_asmbl_31117.p1, internal, 10745, 10836
Valid prediction for snap_scaffold_23-snap.1881-T1
Valid prediction for GlimmerHMM_glimmerT_51642-T1
Valid prediction for snap_scaffold_23-snap.1874-T1
Valid prediction for snap_scaffold_23-snap.1893-T1
Valid prediction for CodingQuarry_transcript_35777-T1
Valid prediction for GlimmerHMM_glimmerT_51636-T1
Valid prediction for snap_scaffold_23-snap.1871-T1
Valid prediction for GlimmerHMM_glimmerT_51655-T1
Valid prediction for CodingQuarry_transcript_35778-T1
Valid prediction for HiQ_model.g34512.t1
Valid prediction for snap_scaffold_23-snap.1898-T1
Valid prediction for CodingQuarry_transcript_35776-T1
Valid prediction for snap_scaffold_23-snap.1880-T1
Valid prediction for GlimmerHMM_glimmerT_51630-T1
Valid prediction for Augustus_model.g34513.t1
Valid prediction for GlimmerHMM_glimmerT_51635-T1
Valid prediction for snap_scaffold_23-snap.1868-T1
Valid prediction for CodingQuarry_transcript_35774-T1
Valid prediction for Augustus_model.g34521.t1
Valid prediction for snap_scaffold_23-snap.1887-T1
Valid prediction for GlimmerHMM_glimmerT_51632-T1
Valid prediction for snap_scaffold_23-snap.1884-T1
Valid prediction for snap_scaffold_23-snap.1878-T1
Valid prediction for snap_scaffold_23-snap.1895-T1
Couldn't classify 126127, 126217
Sorry, prediction pasa_asmbl_31113.p1 fails validation.
(GGG)	 TA	126127-126217	GT	AGG
(AGG)	 AG	126320-126409	GT	TTG
(ACA)	 AG	127742-127837	GT	TGG
(GAA)	 AG	128730-128866	GT	AGG
(GAA)	 AG	129627-129733	GT	AAG
(TTA)	 AG	129822-129948	GG	AAG
-recovered pasa_asmbl_31113.p1, terminal, 129822, 129948
-recovered pasa_asmbl_31113.p1, internal, 126320, 126409
-recovered pasa_asmbl_31113.p1, internal, 127742, 127837
-recovered pasa_asmbl_31113.p1, internal, 128730, 128866
-recovered pasa_asmbl_31113.p1, internal, 129627, 129733
Valid prediction for snap_scaffold_23-snap.1885-T1
Valid prediction for snap_scaffold_23-snap.1900-T1
Valid prediction for GlimmerHMM_glimmerT_51654-T1
Valid prediction for snap_scaffold_23-snap.1869-T1
Valid prediction for GlimmerHMM_glimmerT_51641-T1
Valid prediction for snap_scaffold_23-snap.1897-T1
Valid prediction for snap_scaffold_23-snap.1899-T1
Valid prediction for Augustus_model.g34510.t1
Valid prediction for snap_scaffold_23-snap.1870-T1
Valid prediction for snap_scaffold_23-snap.1872-T1
Valid prediction for snap_scaffold_23-snap.1892-T1
Valid prediction for snap_scaffold_23-snap.1882-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 121578, rend_intergenic: 72692  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130559, rend_intergenic: 125681  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144673, rend_intergenic: 142544  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155389, rend_intergenic: 146526  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171734, rend_intergenic: 162503  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178279, rend_intergenic: 171962  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185592, rend_intergenic: 180272  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196786, rend_intergenic: 191615  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 207428, rend_intergenic: 198440  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 220450, rend_intergenic: 209521  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 257909, rend_intergenic: 221371  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 271302, rend_intergenic: 262030  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 272391
-exon list size: 413


building trellis

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35.9    
36.1    
36.4    
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38.1    
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38.6    
38.8    
39.0    
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40.7    
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41.9    
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42.9    
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43.4    
43.6    
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45.5    
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91.6    
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93.3    
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97.6    
97.8    
98.1    
98.3    
98.6    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 121578, rend_intergenic: 72692  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130559, rend_intergenic: 125681  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144673, rend_intergenic: 142544  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155389, rend_intergenic: 146526  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171734, rend_intergenic: 162503  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178279, rend_intergenic: 171962  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185592, rend_intergenic: 180272  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196786, rend_intergenic: 191615  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 207428, rend_intergenic: 198440  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 220450, rend_intergenic: 209521  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 257909, rend_intergenic: 221371  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 271302, rend_intergenic: 262030  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 12826
-exon list size: 5


building trellis

14.3    
28.6    
42.9    
57.1    
71.4    
85.7    
-found 1 predictions from path traversal

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