-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_11/scaffold_11_5307539-5548475

-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_11-snap.1286-T1
Valid prediction for Augustus_model.g17951.t1
Valid prediction for pasa_asmbl_5566.p1
Valid prediction for snap_scaffold_11-snap.1306-T1
Valid prediction for snap_scaffold_11-snap.1308-T1
Valid prediction for snap_scaffold_11-snap.1291-T1
Valid prediction for snap_scaffold_11-snap.1283-T1
Valid prediction for snap_scaffold_11-snap.1295-T1
Valid prediction for snap_scaffold_11-snap.1290-T1
Valid prediction for GlimmerHMM_glimmerT_27130-T1
Couldn't classify 224435, 224524
Sorry, prediction pasa_asmbl_5568.p1 fails validation.
(ATG)	 CC	221330-221550	GT	TGG
(CCA)	 AG	221733-221790	GT	AGG
(TTC)	 AG	221953-222039	GT	AGG
(AGA)	 AG	222158-222394	GT	AAG
(GAG)	 AG	222535-222614	GT	AGG
(GTT)	 AG	222864-223008	GT	AGG
(TGT)	 AG	223301-223459	GT	AGG
(CAC)	 AG	223614-223729	GT	GGG
(AGG)	 AG	223844-223967	GT	AGG
(ACC)	 AG	224246-224326	GT	ACG
(GAG)	 AG	224435-224524	GT	AGG
-recovered pasa_asmbl_5568.p1, initial, 221330, 221550
-recovered pasa_asmbl_5568.p1, internal, 221733, 221790
-recovered pasa_asmbl_5568.p1, internal, 221953, 222039
-recovered pasa_asmbl_5568.p1, internal, 222158, 222394
-recovered pasa_asmbl_5568.p1, internal, 222535, 222614
-recovered pasa_asmbl_5568.p1, internal, 222864, 223008
-recovered pasa_asmbl_5568.p1, internal, 223301, 223459
-recovered pasa_asmbl_5568.p1, internal, 223614, 223729
-recovered pasa_asmbl_5568.p1, internal, 223844, 223967
-recovered pasa_asmbl_5568.p1, internal, 224246, 224326
-recovered pasa_asmbl_5568.p1, internal, 224435, 224524
Valid prediction for snap_scaffold_11-snap.1282-T1
Valid prediction for GlimmerHMM_glimmerT_27122-T1
Valid prediction for snap_scaffold_11-snap.1299-T1
Valid prediction for snap_scaffold_11-snap.1276-T1
Valid prediction for Augustus_model.g17942.t1
Valid prediction for snap_scaffold_11-snap.1322-T1
Valid prediction for GlimmerHMM_glimmerT_27138-T1
Valid prediction for GlimmerHMM_glimmerT_27136-T1
Valid prediction for GlimmerHMM_glimmerT_27128-T1
Valid prediction for snap_scaffold_11-snap.1304-T1
Valid prediction for GlimmerHMM_glimmerT_27118-T1
Valid prediction for HiQ_model.g17950.t1
Valid prediction for Augustus_model.g17934.t1
Valid prediction for GlimmerHMM_glimmerT_27120-T1
Valid prediction for snap_scaffold_11-snap.1309-T1
Valid prediction for GlimmerHMM_glimmerT_27137-T1
Couldn't classify 231966, 232043
Couldn't classify 233784, 233879
Sorry, prediction pasa_asmbl_6240.p1 fails validation.
(TGT)	 AG	231966-232043	GT	AGG
(TTC)	 AG	232282-232443	GT	AGG
(CCG)	 AG	233784-233879	GC	CAG
-recovered pasa_asmbl_6240.p1, internal, 231966, 232043
-recovered pasa_asmbl_6240.p1, internal, 232282, 232443
-recovered pasa_asmbl_6240.p1, internal, 233784, 233879
Valid prediction for GlimmerHMM_glimmerT_27140-T1
Valid prediction for GlimmerHMM_glimmerT_27107-T1
Valid prediction for Augustus_model.g17939.t1
Valid prediction for GlimmerHMM_glimmerT_27109-T1
Valid prediction for snap_scaffold_11-snap.1281-T1
Valid prediction for snap_scaffold_11-snap.1280-T1
Valid prediction for CodingQuarry_transcript_8075-T1
Valid prediction for snap_scaffold_11-snap.1316-T1
Valid prediction for Augustus_model.g17940.t1
Valid prediction for snap_scaffold_11-snap.1300-T1
Valid prediction for snap_scaffold_11-snap.1323-T1
Valid prediction for GlimmerHMM_glimmerT_27124-T1
Valid prediction for Augustus_model.g17954.t1
Valid prediction for GlimmerHMM_glimmerT_27121-T1
Valid prediction for snap_scaffold_11-snap.1324-T1
Valid prediction for snap_scaffold_11-snap.1287-T1
Valid prediction for GlimmerHMM_glimmerT_27141-T1
Valid prediction for Augustus_model.g17941.t1
Valid prediction for snap_scaffold_11-snap.1319-T1
Valid prediction for snap_scaffold_11-snap.1320-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 GlimmerHMM_glimmerT_27108-T1
Valid prediction for HiQ_model.g17946.t1
Couldn't classify 31246, 31429
Sorry, prediction pasa_asmbl_6671.p1 fails validation.
(ATG)	 AG	30209-30321	GT	GAG
(TGA)	 AG	31246-31429	CG	CCC
-recovered pasa_asmbl_6671.p1, initial, 30209, 30321
-recovered pasa_asmbl_6671.p1, internal, 30209, 30321
Couldn't classify 32992, 33152
Couldn't classify 35425, 35459
Sorry, prediction pasa_asmbl_6670.p1 fails validation.
(AGA)	 GC	32992-33152	GT	GGG
(TCG)	 AG	33517-33618	GT	AGG
(CCG)	 AG	33718-33805	GT	AGG
(GCC)	 AG	33946-34080	GT	AGG
(TTG)	 AG	34274-34346	GT	TGG
(TCC)	 AG	34484-34650	GT	AGG
(GAG)	 AG	34752-34847	GT	AGG
(GAG)	 AG	34946-35084	GT	AGG
(AGG)	 AG	35176-35322	GC	AGG
(ATC)	 AG	35425-35459	AC	CCA
add_exon() Sorry, pasa_asmbl_6670.p1 34946-35084-terminal-3 is invalid.
-recovered pasa_asmbl_6670.p1, terminal, 34946, 35084
-recovered pasa_asmbl_6670.p1, internal, 33517, 33618
-recovered pasa_asmbl_6670.p1, internal, 33718, 33805
-recovered pasa_asmbl_6670.p1, internal, 33946, 34080
-recovered pasa_asmbl_6670.p1, internal, 34274, 34346
-recovered pasa_asmbl_6670.p1, internal, 34484, 34650
-recovered pasa_asmbl_6670.p1, internal, 34752, 34847
-recovered pasa_asmbl_6670.p1, internal, 34946, 35084
-recovered pasa_asmbl_6670.p1, internal, 35176, 35322
Valid prediction for Augustus_model.g17953.t1
Valid prediction for HiQ_model.g17947.t1
Valid prediction for pasa_asmbl_6658.p1
Valid prediction for GlimmerHMM_glimmerT_27134-T1
Valid prediction for GlimmerHMM_glimmerT_27116-T1
Valid prediction for snap_scaffold_11-snap.1321-T1
Valid prediction for snap_scaffold_11-snap.1284-T1
Valid prediction for pasa_asmbl_6662.p1
Valid prediction for snap_scaffold_11-snap.1303-T1
Valid prediction for Augustus_model.g17935.t1
Valid prediction for GlimmerHMM_glimmerT_27123-T1
Valid prediction for snap_scaffold_11-snap.1310-T1
Valid prediction for snap_scaffold_11-snap.1292-T1
Valid prediction for CodingQuarry_transcript_8073-T1
Valid prediction for snap_scaffold_11-snap.1311-T1
Valid prediction for snap_scaffold_11-snap.1318-T1
Valid prediction for Augustus_model.g17936.t1
Valid prediction for GlimmerHMM_glimmerT_27127-T1
Valid prediction for snap_scaffold_11-snap.1307-T1
Valid prediction for snap_scaffold_11-snap.1289-T1
Valid prediction for GlimmerHMM_glimmerT_27113-T1
Valid prediction for GlimmerHMM_glimmerT_27125-T1
Valid prediction for snap_scaffold_11-snap.1305-T1
Valid prediction for GlimmerHMM_glimmerT_27135-T1
Valid prediction for GlimmerHMM_glimmerT_27106-T1
Valid prediction for snap_scaffold_11-snap.1285-T1
Valid prediction for snap_scaffold_11-snap.1313-T1
Valid prediction for Augustus_model.g17945.t1
Valid prediction for snap_scaffold_11-snap.1297-T1
Valid prediction for CodingQuarry_transcript_8074-T1
Valid prediction for snap_scaffold_11-snap.1302-T1
Valid prediction for GlimmerHMM_glimmerT_27117-T1
Valid prediction for HiQ_model.g17944.t1
Valid prediction for GlimmerHMM_glimmerT_27112-T1
Valid prediction for HiQ_model.g17949.t1
Valid prediction for pasa_asmbl_6672.p1
Valid prediction for Augustus_model.g17952.t1
Valid prediction for GlimmerHMM_glimmerT_27132-T1
Valid prediction for snap_scaffold_11-snap.1315-T1
Valid prediction for GlimmerHMM_glimmerT_27129-T1
Valid prediction for GlimmerHMM_glimmerT_27110-T1
Valid prediction for GlimmerHMM_glimmerT_27119-T1
Valid prediction for CodingQuarry_transcript_8071-T1
Valid prediction for snap_scaffold_11-snap.1317-T1
Valid prediction for snap_scaffold_11-snap.1312-T1
Valid prediction for snap_scaffold_11-snap.1294-T1
Valid prediction for GlimmerHMM_glimmerT_27115-T1
Valid prediction for Augustus_model.g17933.t1
Valid prediction for GlimmerHMM_glimmerT_27111-T1
Valid prediction for GlimmerHMM_glimmerT_27133-T1
Valid prediction for GlimmerHMM_glimmerT_27126-T1
Valid prediction for Augustus_model.g17948.t1
Valid prediction for snap_scaffold_11-snap.1296-T1
Valid prediction for snap_scaffold_11-snap.1278-T1
Couldn't classify 58510, 58652
Sorry, prediction pasa_asmbl_6661.p1 fails validation.
(TTC)	 AC	58510-58652	GT	AGG
(TTC)	 AG	58916-59097	GT	AGG
(CAG)	 AG	59226-59327	GT	AAG
(GCA)	 AG	59461-59575	GT	GGG
(GTA)	 AG	59783-59911	GT	AGG
(ACA)	 AG	60061-60373	AG	AAA
-recovered pasa_asmbl_6661.p1, terminal, 60061, 60373
-recovered pasa_asmbl_6661.p1, internal, 58916, 59097
-recovered pasa_asmbl_6661.p1, internal, 59226, 59327
-recovered pasa_asmbl_6661.p1, internal, 59461, 59575
-recovered pasa_asmbl_6661.p1, internal, 59783, 59911
Couldn't classify 35666, 35849
Couldn't classify 36036, 36202
Sorry, prediction pasa_asmbl_7306.p1 fails validation.
(TCA)	 TG	35666-35849	GT	AGG
(GTG)	 AG	36036-36202	TA	GGT
Valid prediction for snap_scaffold_11-snap.1293-T1
Valid prediction for snap_scaffold_11-snap.1279-T1
Valid prediction for GlimmerHMM_glimmerT_27142-T1
Valid prediction for snap_scaffold_11-snap.1288-T1
Valid prediction for snap_scaffold_11-snap.1277-T1
Valid prediction for Augustus_model.g17937.t1
Valid prediction for Augustus_model.g17938.t1
Valid prediction for snap_scaffold_11-snap.1314-T1
Valid prediction for snap_scaffold_11-snap.1301-T1
Couldn't classify 37970, 38357
Sorry, prediction pasa_asmbl_6668.p1 fails validation.
(GGC)	 TG	37970-38357	GT	AGG
(ACA)	 AG	38660-38829	GT	AGG
(GTG)	 AG	39073-39227	GT	AGG
(GCT)	 AG	39442-39602	GT	GGG
(GAG)	 AG	39860-39940	GT	TGG
(ACG)	 AG	40081-40328	GT	AGG
(GCG)	 AG	40583-40797	GT	AGG
(TGT)	 AG	40934-41250	GT	AGG
(AGG)	 AG	41455-41630	GT	AGG
(GTA)	 AG	42673-42760	GT	AGG
(CGG)	 AG	43016-43188	CA	AAC
-recovered pasa_asmbl_6668.p1, terminal, 43016, 43188
-recovered pasa_asmbl_6668.p1, internal, 38660, 38829
-recovered pasa_asmbl_6668.p1, internal, 39073, 39227
-recovered pasa_asmbl_6668.p1, internal, 39442, 39602
-recovered pasa_asmbl_6668.p1, internal, 39860, 39940
-recovered pasa_asmbl_6668.p1, internal, 40081, 40328
-recovered pasa_asmbl_6668.p1, internal, 40583, 40797
-recovered pasa_asmbl_6668.p1, internal, 40934, 41250
-recovered pasa_asmbl_6668.p1, internal, 41455, 41630
-recovered pasa_asmbl_6668.p1, internal, 42673, 42760
Valid prediction for GlimmerHMM_glimmerT_27139-T1
Valid prediction for GlimmerHMM_glimmerT_27131-T1
Valid prediction for GlimmerHMM_glimmerT_27114-T1
Valid prediction for snap_scaffold_11-snap.1298-T1
Valid prediction for Augustus_model.g17943.t1
Valid prediction for pasa_asmbl_6665.p1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9132, rend_intergenic: 5367  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26022, rend_intergenic: 19040  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43058, rend_intergenic: 36872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53932, rend_intergenic: 46897  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59382, rend_intergenic: 54498  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76006, rend_intergenic: 59789  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94618, rend_intergenic: 78930  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104091, rend_intergenic: 94906  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138761, rend_intergenic: 108440  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141952, rend_intergenic: 138933  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142945, rend_intergenic: 142739  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153279, rend_intergenic: 144261  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157573, rend_intergenic: 156731  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159965, rend_intergenic: 158401  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204139, rend_intergenic: 199330  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 225802, rend_intergenic: 225284  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 227976, rend_intergenic: 226198  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 240937
-exon list size: 494


building trellis

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90.1    
90.3    
90.5    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
91.9    
92.1    
92.3    
92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.8    
94.0    
94.2    
94.4    
94.6    
94.8    
95.0    
95.2    
95.4    
95.6    
95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.8    
98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 42 predictions from path traversal
Error with prediction: snap lend_intergenic: 9132, rend_intergenic: 5367  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26022, rend_intergenic: 19040  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43058, rend_intergenic: 36872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53932, rend_intergenic: 46897  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59382, rend_intergenic: 54498  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76006, rend_intergenic: 59789  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94618, rend_intergenic: 78930  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104091, rend_intergenic: 94906  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138761, rend_intergenic: 108440  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141952, rend_intergenic: 138933  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142945, rend_intergenic: 142739  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153279, rend_intergenic: 144261  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157573, rend_intergenic: 156731  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159965, rend_intergenic: 158401  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204139, rend_intergenic: 199330  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 225802, rend_intergenic: 225284  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 227976, rend_intergenic: 226198  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support