-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_1/scaffold_1_13944204-14313675

-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_1-snap.2438-T1
Couldn't classify 324416, 324468
Sorry, prediction pasa_asmbl_2362.p1 fails validation.
(CGG)	 CA	324416-324468	GT	AGG
(TTT)	 AG	324676-324805	GT	CTG
(ATG)	 AG	324878-324938	GT	AGG
(GCG)	 AG	325030-325144	GT	CAG
(GAC)	 AG	325306-325408	GT	AGG
(CTC)	 AG	325664-325855	AC	AGA
-recovered pasa_asmbl_2362.p1, initial, 324878, 324938
-recovered pasa_asmbl_2362.p1, terminal, 325664, 325855
-recovered pasa_asmbl_2362.p1, internal, 324676, 324805
-recovered pasa_asmbl_2362.p1, internal, 324878, 324938
-recovered pasa_asmbl_2362.p1, internal, 325030, 325144
-recovered pasa_asmbl_2362.p1, internal, 325306, 325408
Valid prediction for CodingQuarry_transcript_2906-T1
Valid prediction for GlimmerHMM_glimmerT_1865-T1
Valid prediction for snap_scaffold_1-snap.2423-T1
Valid prediction for pasa_asmbl_2369.p1
Valid prediction for pasa_asmbl_2363.p2
Valid prediction for Augustus_model.g1375.t1
Valid prediction for GlimmerHMM_glimmerT_1834-T1
Valid prediction for Augustus_model.g1405.t1
Couldn't classify 281806, 281829
Sorry, prediction pasa_asmbl_2358.p1 fails validation.
(TTC)	 AC	281806-281829	GT	AGG
(GTG)	 AG	282009-282404	TA	AAT
-recovered pasa_asmbl_2358.p1, terminal, 282009, 282404
Valid prediction for snap_scaffold_1-snap.2449-T1
Valid prediction for snap_scaffold_1-snap.2448-T1
Valid prediction for GlimmerHMM_glimmerT_1855-T1
Valid prediction for snap_scaffold_1-snap.2425-T1
Valid prediction for snap_scaffold_1-snap.2432-T1
Valid prediction for pasa_asmbl_2376.p1
Valid prediction for pasa_asmbl_2331.p1
Valid prediction for snap_scaffold_1-snap.2412-T1
Valid prediction for Augustus_model.g1401.t1
Valid prediction for GlimmerHMM_glimmerT_1839-T1
Valid prediction for HiQ_model.g1399.t1
Valid prediction for snap_scaffold_1-snap.2444-T1
Valid prediction for HiQ_model.g1395.t1
Valid prediction for snap_scaffold_1-snap.2427-T1
Couldn't classify 261681, 261992
Sorry, prediction pasa_asmbl_2351.p1 fails validation.
(ATG)	 AG	261681-261992	AT	AGA
Valid prediction for GlimmerHMM_glimmerT_1848-T1
Valid prediction for GlimmerHMM_glimmerT_1842-T1
Valid prediction for snap_scaffold_1-snap.2413-T1
Valid prediction for GlimmerHMM_glimmerT_1857-T1
Valid prediction for GlimmerHMM_glimmerT_1866-T1
Valid prediction for snap_scaffold_1-snap.2414-T1
Valid prediction for snap_scaffold_1-snap.2446-T1
Valid prediction for Augustus_model.g1393.t1
Valid prediction for Augustus_model.g1388.t1
Valid prediction for Augustus_model.g1409.t1
Valid prediction for HiQ_model.g1407.t1
Valid prediction for snap_scaffold_1-snap.2436-T1
Valid prediction for Augustus_model.g1380.t1
Couldn't classify 127902, 127936
Sorry, prediction pasa_asmbl_2330.p1 fails validation.
(ACC)	 TG	127902-127936	GT	AGG
(GAG)	 AG	128811-128902	GT	AGG
(ATG)	 AG	131336-131427	GT	AGG
(GAT)	 AG	131609-131716	CC	GAC
add_exon() Sorry, pasa_asmbl_2330.p1 131336-131427-initial-1 is invalid.
-recovered pasa_asmbl_2330.p1, initial, 131336, 131427
-recovered pasa_asmbl_2330.p1, terminal, 131609, 131716
-recovered pasa_asmbl_2330.p1, internal, 128811, 128902
-recovered pasa_asmbl_2330.p1, internal, 131336, 131427
Valid prediction for Augustus_model.g1379.t1
Valid prediction for pasa_asmbl_2335.p1
Valid prediction for GlimmerHMM_glimmerT_1859-T1
Valid prediction for CodingQuarry_transcript_2899-T1
Valid prediction for pasa_asmbl_2357.p1
Valid prediction for GlimmerHMM_glimmerT_1863-T1
Couldn't classify 115510, 115584
Couldn't classify 122505, 122689
Sorry, prediction pasa_asmbl_2329.p1 fails validation.
(TCT)	 AC	115510-115584	GT	AGG
(GTG)	 AG	117205-117271	GT	TGG
(AGA)	 AG	119458-119615	GT	AGG
(CTG)	 AG	120639-120831	GT	AGG
(TGT)	 AG	122505-122689	GT	TGG
-recovered pasa_asmbl_2329.p1, internal, 117205, 117271
-recovered pasa_asmbl_2329.p1, internal, 119458, 119615
-recovered pasa_asmbl_2329.p1, internal, 120639, 120831
-recovered pasa_asmbl_2329.p1, internal, 122505, 122689
Valid prediction for snap_scaffold_1-snap.2411-T1
Valid prediction for HiQ_model.g1381.t1
Couldn't classify 265527, 265883
Sorry, prediction pasa_asmbl_2352.p1 fails validation.
(GGA)	 CA	265527-265883	GA	GCG
Couldn't classify 320169, 320265
Couldn't classify 321659, 321811
Sorry, prediction pasa_asmbl_2359.p1 fails validation.
(CAC)	 GA	320169-320265	GT	ATG
(ATG)	 AG	320378-320448	GT	TGG
(CAT)	 AG	320535-320627	GT	CTG
(GTA)	 AG	320747-320844	GT	AGG
(TAC)	 AG	321062-321128	GT	AGG
(AAG)	 AG	321216-321346	GT	CAG
(GCA)	 AG	321468-321549	GT	TGG
(GCT)	 AG	321659-321811	GA	GAG
add_exon() Sorry, pasa_asmbl_2359.p1 320378-320448-initial-1 is invalid.
-recovered pasa_asmbl_2359.p1, initial, 320378, 320448
-recovered pasa_asmbl_2359.p1, internal, 320378, 320448
-recovered pasa_asmbl_2359.p1, internal, 320535, 320627
-recovered pasa_asmbl_2359.p1, internal, 320747, 320844
-recovered pasa_asmbl_2359.p1, internal, 321062, 321128
-recovered pasa_asmbl_2359.p1, internal, 321216, 321346
-recovered pasa_asmbl_2359.p1, internal, 321468, 321549
Couldn't classify 271399, 271431
Couldn't classify 271465, 271532
Sorry, prediction pasa_asmbl_2353.p1 fails validation.
(ATG)	 AG	270657-270950	GT	AGG
(GTT)	 AG	271183-271274	GT	GGG
(TAA)	 AG	271399-271431	AT	CCA
(AGG)	 AC	271465-271532	GT	GGG
(CAA)	 AG	271689-271826	GT	TGG
(GCA)	 AG	271946-272027	GT	AGG
(GTT)	 AG	272140-272254	GT	AGG
(GAA)	 AG	272429-272527	GT	AGG
(GAA)	 AG	272607-272690	TG	AAT
-recovered pasa_asmbl_2353.p1, initial, 270657, 270950
-recovered pasa_asmbl_2353.p1, terminal, 272607, 272690
-recovered pasa_asmbl_2353.p1, internal, 270657, 270950
-recovered pasa_asmbl_2353.p1, internal, 271183, 271274
-recovered pasa_asmbl_2353.p1, internal, 271689, 271826
-recovered pasa_asmbl_2353.p1, internal, 271946, 272027
-recovered pasa_asmbl_2353.p1, internal, 272140, 272254
-recovered pasa_asmbl_2353.p1, internal, 272429, 272527
Couldn't classify 322849, 322897
Couldn't classify 324102, 324284
Sorry, prediction pasa_asmbl_2361.p1 fails validation.
(CAC)	 GT	322849-322897	GT	TTG
(TGT)	 AG	323010-323170	GT	AGG
(GGG)	 AG	323261-323335	GT	CGG
(CTG)	 AG	323569-323643	GT	AGG
(GTG)	 AG	323842-324018	GT	AGG
(AAC)	 AG	324102-324284	CT	CCC
-recovered pasa_asmbl_2361.p1, internal, 323010, 323170
-recovered pasa_asmbl_2361.p1, internal, 323261, 323335
-recovered pasa_asmbl_2361.p1, internal, 323569, 323643
-recovered pasa_asmbl_2361.p1, internal, 323842, 324018
Valid prediction for GlimmerHMM_glimmerT_1867-T1
Valid prediction for snap_scaffold_1-snap.2439-T1
Valid prediction for snap_scaffold_1-snap.2437-T1
Valid prediction for GlimmerHMM_glimmerT_1850-T1
Valid prediction for CodingQuarry_transcript_2907-T1
Valid prediction for CodingQuarry_transcript_2902-T1
Valid prediction for GlimmerHMM_glimmerT_1841-T1
Valid prediction for snap_scaffold_1-snap.2443-T1
Valid prediction for CodingQuarry_transcript_2903-T1
Valid prediction for GlimmerHMM_glimmerT_1862-T1
Valid prediction for Augustus_model.g1398.t1
Valid prediction for Augustus_model.g1400.t1
Valid prediction for snap_scaffold_1-snap.2416-T1
Valid prediction for pasa_asmbl_2344.p1
Valid prediction for CodingQuarry_transcript_2901-T1
Valid prediction for HiQ_model.g1406.t1
Valid prediction for snap_scaffold_1-snap.2431-T1
Valid prediction for GlimmerHMM_glimmerT_1840-T1
Valid prediction for GlimmerHMM_glimmerT_1851-T1
Valid prediction for HiQ_model.g1392.t1
Valid prediction for GlimmerHMM_glimmerT_1856-T1
Valid prediction for HiQ_model.g1410.t1
Valid prediction for GlimmerHMM_glimmerT_1861-T1
Valid prediction for snap_scaffold_1-snap.2450-T1
Valid prediction for snap_scaffold_1-snap.2434-T1
Valid prediction for snap_scaffold_1-snap.2445-T1
Valid prediction for snap_scaffold_1-snap.2417-T1
Valid prediction for HiQ_model.g1396.t1
Couldn't classify 124004, 124112
Couldn't classify 124389, 124643
Sorry, prediction pasa_asmbl_2731.p1 fails validation.
(AAA)	 AG	124004-124112	GT	TGG
(CAA)	 AG	124238-124287	GT	TGG
(CCC)	 AG	124389-124643	GC	AGG
-recovered pasa_asmbl_2731.p1, internal, 124004, 124112
-recovered pasa_asmbl_2731.p1, internal, 124238, 124287
-recovered pasa_asmbl_2731.p1, internal, 124389, 124643

-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.g1382.t1
Valid prediction for GlimmerHMM_glimmerT_1864-T1
Valid prediction for GlimmerHMM_glimmerT_1838-T1
Valid prediction for snap_scaffold_1-snap.2418-T1
Valid prediction for snap_scaffold_1-snap.2429-T1
Valid prediction for Augustus_model.g1408.t1
Valid prediction for pasa_asmbl_884.p1
Valid prediction for GlimmerHMM_glimmerT_1844-T1
Valid prediction for CodingQuarry_transcript_2908-T1
Valid prediction for snap_scaffold_1-snap.2409-T1
Valid prediction for snap_scaffold_1-snap.2426-T1
Valid prediction for GlimmerHMM_glimmerT_1835-T1
Valid prediction for Augustus_model.g1387.t1
Couldn't classify 65627, 65663
Sorry, prediction pasa_asmbl_875.p1 fails validation.
(GGG)	 GC	65627-65663	GT	AGG
(ACG)	 AG	66307-66785	CT	GAC
-recovered pasa_asmbl_875.p1, terminal, 66307, 66785
Valid prediction for Augustus_model.g1383.t1
Valid prediction for CodingQuarry_transcript_2900-T1
Valid prediction for snap_scaffold_1-snap.2440-T1
Valid prediction for GlimmerHMM_glimmerT_1852-T1
Valid prediction for snap_scaffold_1-snap.2407-T1
Valid prediction for snap_scaffold_1-snap.2422-T1
Valid prediction for snap_scaffold_1-snap.2442-T1
Valid prediction for snap_scaffold_1-snap.2415-T1
Valid prediction for HiQ_model.g1404.t1
Valid prediction for Augustus_model.g1390.t1
Valid prediction for CodingQuarry_transcript_2905-T1
Valid prediction for GlimmerHMM_glimmerT_1860-T1
Valid prediction for snap_scaffold_1-snap.2419-T1
Valid prediction for GlimmerHMM_glimmerT_1845-T1
Valid prediction for snap_scaffold_1-snap.2421-T1
Valid prediction for Augustus_model.g1377.t1
Valid prediction for GlimmerHMM_glimmerT_1858-T1
Valid prediction for Augustus_model.g1376.t1
Valid prediction for GlimmerHMM_glimmerT_1853-T1
Valid prediction for Augustus_model.g1402.t1
Valid prediction for snap_scaffold_1-snap.2406-T1
Valid prediction for snap_scaffold_1-snap.2433-T1
Valid prediction for Augustus_model.g1384.t1
Valid prediction for snap_scaffold_1-snap.2447-T1
Valid prediction for GlimmerHMM_glimmerT_1847-T1
Valid prediction for Augustus_model.g1385.t1
Valid prediction for snap_scaffold_1-snap.2430-T1
Valid prediction for pasa_asmbl_866.p1
Valid prediction for GlimmerHMM_glimmerT_1846-T1
Valid prediction for Augustus_model.g1403.t1
Valid prediction for GlimmerHMM_glimmerT_1854-T1
Valid prediction for pasa_asmbl_878.p1
Valid prediction for HiQ_model.g1391.t1
Valid prediction for Augustus_model.g1378.t1
Valid prediction for snap_scaffold_1-snap.2408-T1
Valid prediction for snap_scaffold_1-snap.2405-T1
Valid prediction for snap_scaffold_1-snap.2435-T1
Valid prediction for snap_scaffold_1-snap.2441-T1
Valid prediction for Augustus_model.g1389.t1
Valid prediction for snap_scaffold_1-snap.2420-T1
Valid prediction for GlimmerHMM_glimmerT_1849-T1
Valid prediction for snap_scaffold_1-snap.2404-T1
Valid prediction for Augustus_model.g1386.t1
Valid prediction for HiQ_model.g1394.t1
Valid prediction for GlimmerHMM_glimmerT_1836-T1
Valid prediction for snap_scaffold_1-snap.2428-T1
Valid prediction for GlimmerHMM_glimmerT_1837-T1
Valid prediction for Augustus_model.g1411.t1
Couldn't classify 62987, 63157
Sorry, prediction pasa_asmbl_876.p1 fails validation.
(ATG)	 GC	61324-62561	GT	AGG
(GCC)	 AG	62682-62745	GT	AGG
(ATC)	 AG	62987-63157	GG	AAG
-recovered pasa_asmbl_876.p1, initial, 61324, 62561
-recovered pasa_asmbl_876.p1, internal, 62682, 62745
Valid prediction for snap_scaffold_1-snap.2410-T1
Valid prediction for GlimmerHMM_glimmerT_1843-T1
Valid prediction for snap_scaffold_1-snap.2403-T1
Valid prediction for Augustus_model.g1397.t1
Valid prediction for snap_scaffold_1-snap.2424-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 125156, rend_intergenic: 121450  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128832, rend_intergenic: 125737  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 369472
-exon list size: 557


building trellis

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82.3    
82.5    
82.6    
82.8    
83.0    
83.2    
83.4    
83.5    
83.7    
83.9    
84.1    
84.3    
84.4    
84.6    
84.8    
85.0    
85.2    
85.3    
85.5    
85.7    
85.9    
86.0    
86.2    
86.4    
86.6    
86.8    
86.9    
87.1    
87.3    
87.5    
87.7    
87.8    
88.0    
88.2    
88.4    
88.6    
88.7    
88.9    
89.1    
89.3    
89.4    
89.6    
89.8    
90.0    
90.2    
90.3    
90.5    
90.7    
90.9    
91.1    
91.2    
91.4    
91.6    
91.8    
91.9    
92.1    
92.3    
92.5    
92.7    
92.8    
93.0    
93.2    
93.4    
93.6    
93.7    
93.9    
94.1    
94.3    
94.5    
94.6    
94.8    
95.0    
95.2    
95.3    
95.5    
95.7    
95.9    
96.1    
96.2    
96.4    
96.6    
96.8    
97.0    
97.1    
97.3    
97.5    
97.7    
97.9    
98.0    
98.2    
98.4    
98.6    
98.7    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 45 predictions from path traversal
Error with prediction: snap lend_intergenic: 125156, rend_intergenic: 121450  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128832, rend_intergenic: 125737  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 40 predictions persist after filtering for low support