-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_9/scaffold_9_17625893-17870936

-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_9-snap.3546-T1
Valid prediction for Augustus_model.g15807.t1
Valid prediction for snap_scaffold_9-snap.3531-T1
Valid prediction for Augustus_model.g15833.t1
Valid prediction for GlimmerHMM_glimmerT_23766-T1
Valid prediction for GlimmerHMM_glimmerT_23758-T1
Valid prediction for snap_scaffold_9-snap.3566-T1
Valid prediction for GlimmerHMM_glimmerT_23763-T1
Valid prediction for pasa_asmbl_54648.p1
Valid prediction for HiQ_model.g15822.t1
Valid prediction for snap_scaffold_9-snap.3539-T1
Valid prediction for snap_scaffold_9-snap.3550-T1
Valid prediction for snap_scaffold_9-snap.3540-T1
Valid prediction for Augustus_model.g15813.t1
Valid prediction for HiQ_model.g15830.t1
Valid prediction for Augustus_model.g15817.t1
Valid prediction for Augustus_model.g15818.t1
Valid prediction for snap_scaffold_9-snap.3563-T1
Valid prediction for GlimmerHMM_glimmerT_23775-T1
Valid prediction for GlimmerHMM_glimmerT_23784-T1
Valid prediction for Augustus_model.g15805.t1
Valid prediction for snap_scaffold_9-snap.3559-T1
Valid prediction for CodingQuarry_transcript_62466-T1
Valid prediction for snap_scaffold_9-snap.3532-T1
Couldn't classify 207713, 208084
Sorry, prediction pasa_asmbl_54649.p1 fails validation.
(ATG)	 AG	207713-208084	TT	GGT
Valid prediction for GlimmerHMM_glimmerT_23767-T1
Couldn't classify 107412, 107471
Sorry, prediction pasa_asmbl_54637.p1 fails validation.
(ATG)	 AG	106788-106886	GT	AGG
(GTG)	 AG	107021-107221	GT	ACG
(GAA)	 AG	107412-107471	CG	ACC
-recovered pasa_asmbl_54637.p1, initial, 106788, 106886
-recovered pasa_asmbl_54637.p1, internal, 106788, 106886
-recovered pasa_asmbl_54637.p1, internal, 107021, 107221
Couldn't classify 132224, 132454
Couldn't classify 133565, 133597
Sorry, prediction pasa_asmbl_54647.p1 fails validation.
(CTC)	 CA	132224-132454	GT	AGG
(AAC)	 AG	132602-132670	GT	AGG
(GGC)	 AG	132770-132901	GT	AGG
(AGG)	 AG	133565-133597	GC	AGG
-recovered pasa_asmbl_54647.p1, internal, 132602, 132670
-recovered pasa_asmbl_54647.p1, internal, 132770, 132901
-recovered pasa_asmbl_54647.p1, internal, 133565, 133597
Valid prediction for GlimmerHMM_glimmerT_23754-T1
Valid prediction for Augustus_model.g15809.t1
Valid prediction for GlimmerHMM_glimmerT_23781-T1
Valid prediction for GlimmerHMM_glimmerT_23771-T1
Sorry, intron length (4) is less than minimum required (10)
Couldn't classify 208361, 208558
Sorry, prediction pasa_asmbl_54651.p1 fails validation.
(AAG)	 GG	208361-208558	GT	AGG
(GTA)	 AG	208764-208958	CC	GAC
-recovered pasa_asmbl_54651.p1, terminal, 208764, 208958
Valid prediction for snap_scaffold_9-snap.3557-T1
Valid prediction for Augustus_model.g15821.t1
Valid prediction for snap_scaffold_9-snap.3538-T1
Valid prediction for GlimmerHMM_glimmerT_23774-T1
Valid prediction for snap_scaffold_9-snap.3526-T1
Valid prediction for snap_scaffold_9-snap.3529-T1
Valid prediction for snap_scaffold_9-snap.3561-T1
Valid prediction for snap_scaffold_9-snap.3558-T1
Valid prediction for snap_scaffold_9-snap.3556-T1
Valid prediction for snap_scaffold_9-snap.3543-T1
Valid prediction for GlimmerHMM_glimmerT_23769-T1
Valid prediction for snap_scaffold_9-snap.3541-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for snap_scaffold_9-snap.3542-T1
Valid prediction for GlimmerHMM_glimmerT_23770-T1
Valid prediction for GlimmerHMM_glimmerT_23757-T1
Valid prediction for GlimmerHMM_glimmerT_23752-T1
Valid prediction for snap_scaffold_9-snap.3524-T1
Valid prediction for GlimmerHMM_glimmerT_23765-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g15816.t1
Valid prediction for snap_scaffold_9-snap.3551-T1
Valid prediction for pasa_asmbl_54643.p2
Valid prediction for Augustus_model.g15815.t1
Valid prediction for snap_scaffold_9-snap.3545-T1
Valid prediction for GlimmerHMM_glimmerT_23768-T1
Valid prediction for GlimmerHMM_glimmerT_23759-T1
Valid prediction for snap_scaffold_9-snap.3544-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_9-snap.3548-T1
Valid prediction for GlimmerHMM_glimmerT_23776-T1
Valid prediction for GlimmerHMM_glimmerT_23760-T1
Couldn't classify 4923, 5108
Couldn't classify 7520, 7546
Sorry, prediction pasa_asmbl_55694.p1 fails validation.
(CAG)	 TC	4923-5108	GT	CAG
(TTC)	 AG	5721-5837	GT	AGG
(CAA)	 AG	6682-6774	GT	AGG
(GAC)	 AG	6882-7058	GT	ATG
(ATC)	 AG	7225-7275	GT	CGG
(AAG)	 AG	7520-7546	TC	GCT
-recovered pasa_asmbl_55694.p1, internal, 5721, 5837
-recovered pasa_asmbl_55694.p1, internal, 6682, 6774
-recovered pasa_asmbl_55694.p1, internal, 6882, 7058
-recovered pasa_asmbl_55694.p1, internal, 7225, 7275
Valid prediction for Augustus_model.g15824.t1
Valid prediction for snap_scaffold_9-snap.3565-T1
Valid prediction for GlimmerHMM_glimmerT_23783-T1
Valid prediction for CodingQuarry_transcript_62470-T1
Valid prediction for CodingQuarry_transcript_62463-T1
Valid prediction for CodingQuarry_transcript_62467-T1
Valid prediction for Augustus_model.g15834.t1
Valid prediction for pasa_asmbl_55690.p1
Valid prediction for GlimmerHMM_glimmerT_23753-T1
Valid prediction for Augustus_model.g15812.t1
Couldn't classify 210075, 210167
Sorry, prediction pasa_asmbl_55669.p1 fails validation.
(AGA)	 CC	210075-210167	GT	AGG
(GCT)	 AG	211781-212390	GT	GCG
(CTC)	 AG	212513-212611	GT	AGG
(GTT)	 AG	212700-212932	GT	AGG
(AAA)	 AG	213100-213402	TA	AGT
-recovered pasa_asmbl_55669.p1, terminal, 213100, 213402
-recovered pasa_asmbl_55669.p1, internal, 211781, 212390
-recovered pasa_asmbl_55669.p1, internal, 212513, 212611
-recovered pasa_asmbl_55669.p1, internal, 212700, 212932
Valid prediction for GlimmerHMM_glimmerT_23773-T1
Valid prediction for snap_scaffold_9-snap.3530-T1
Valid prediction for snap_scaffold_9-snap.3562-T1
Valid prediction for snap_scaffold_9-snap.3537-T1
Valid prediction for Augustus_model.g15819.t1
Valid prediction for Augustus_model.g15829.t1
Valid prediction for HiQ_model.g15810.t1
Valid prediction for CodingQuarry_transcript_62468-T1
Valid prediction for Augustus_model.g15806.t1
Valid prediction for GlimmerHMM_glimmerT_23756-T1
Valid prediction for GlimmerHMM_glimmerT_23761-T1
Valid prediction for HiQ_model.g15814.t1
Valid prediction for GlimmerHMM_glimmerT_23764-T1
Valid prediction for snap_scaffold_9-snap.3564-T1
Valid prediction for GlimmerHMM_glimmerT_23772-T1
Valid prediction for snap_scaffold_9-snap.3527-T1
Valid prediction for snap_scaffold_9-snap.3552-T1
Valid prediction for pasa_asmbl_55671.p1
Couldn't classify 85135, 85140
Couldn't classify 86423, 86439
Sorry, prediction pasa_asmbl_55679.p1 fails validation.
(GAA)	 AT	85135-85140	GT	ATG
(GCC)	 AG	85237-85325	GT	AGG
(CAT)	 AG	85418-85538	GT	TGG
(GGG)	 AG	85718-85789	GT	GGG
(AGG)	 AG	86069-86243	GT	TGG
(AGG)	 AG	86423-86439	GT	CAG
-recovered pasa_asmbl_55679.p1, internal, 85237, 85325
-recovered pasa_asmbl_55679.p1, internal, 85418, 85538
-recovered pasa_asmbl_55679.p1, internal, 85718, 85789
-recovered pasa_asmbl_55679.p1, internal, 86069, 86243
-recovered pasa_asmbl_55679.p1, internal, 86423, 86439
Valid prediction for snap_scaffold_9-snap.3549-T1
Valid prediction for GlimmerHMM_glimmerT_23762-T1
Valid prediction for CodingQuarry_transcript_62464-T1
Valid prediction for GlimmerHMM_glimmerT_23782-T1
Valid prediction for GlimmerHMM_glimmerT_23785-T1
Couldn't classify 7971, 7977
Couldn't classify 10169, 10278
Sorry, prediction pasa_asmbl_55693.p1 fails validation.
(GTG)	 TG	7971-7977	GT	AAG
(ACT)	 AG	8057-8175	GT	AGG
(TCG)	 AG	8389-8596	GT	GGG
(CAA)	 AG	8730-8803	GT	AGG
(TTC)	 AG	8987-9070	GT	AGG
(GTG)	 AG	9270-9373	GT	AGG
(GGA)	 AG	9622-9743	GT	AGG
(GGG)	 AG	9867-9986	GT	GAG
(ACG)	 AG	10169-10278	GG	GAG
-recovered pasa_asmbl_55693.p1, internal, 8057, 8175
-recovered pasa_asmbl_55693.p1, internal, 8389, 8596
-recovered pasa_asmbl_55693.p1, internal, 8730, 8803
-recovered pasa_asmbl_55693.p1, internal, 8987, 9070
-recovered pasa_asmbl_55693.p1, internal, 9270, 9373
-recovered pasa_asmbl_55693.p1, internal, 9622, 9743
-recovered pasa_asmbl_55693.p1, internal, 9867, 9986
Couldn't classify 51261, 51373
Couldn't classify 64473, 64544
Sorry, prediction pasa_asmbl_55686.p1 fails validation.
(ATC)	 AC	51261-51373	GT	AAG
(GTC)	 AG	54353-54407	GT	AGG
(TTG)	 AG	54649-54777	GT	AGG
(ACA)	 AG	57483-57605	GT	GGG
(GTG)	 AG	57826-57921	GT	CGG
(AGT)	 AG	60028-60144	GT	GAG
(ACG)	 AG	60226-60330	GT	AGG
(ATT)	 AG	62246-62335	GT	AGG
(GTG)	 AG	62423-62485	GT	CGG
(GGC)	 AG	63795-63929	GT	AGG
(GCG)	 AG	64473-64544	GA	AGG
-recovered pasa_asmbl_55686.p1, internal, 54353, 54407
-recovered pasa_asmbl_55686.p1, internal, 54649, 54777
-recovered pasa_asmbl_55686.p1, internal, 57483, 57605
-recovered pasa_asmbl_55686.p1, internal, 57826, 57921
-recovered pasa_asmbl_55686.p1, internal, 60028, 60144
-recovered pasa_asmbl_55686.p1, internal, 60226, 60330
-recovered pasa_asmbl_55686.p1, internal, 62246, 62335
-recovered pasa_asmbl_55686.p1, internal, 62423, 62485
-recovered pasa_asmbl_55686.p1, internal, 63795, 63929
Valid prediction for GlimmerHMM_glimmerT_23755-T1
Valid prediction for snap_scaffold_9-snap.3534-T1
Valid prediction for snap_scaffold_9-snap.3555-T1
Valid prediction for pasa_asmbl_55681.p1
Valid prediction for GlimmerHMM_glimmerT_23777-T1
Valid prediction for GlimmerHMM_glimmerT_23780-T1
Valid prediction for CodingQuarry_transcript_62461-T1
Valid prediction for Augustus_model.g15828.t1
Couldn't classify 88834, 88968
Sorry, prediction pasa_asmbl_55676.p1 fails validation.
(TTT)	 AC	88834-88968	GT	AGG
(GTT)	 AG	89061-89204	GT	AGG
(GTG)	 AG	89333-89453	GT	GGG
(AGC)	 AG	89661-89851	GC	AGG
-recovered pasa_asmbl_55676.p1, terminal, 89661, 89851
-recovered pasa_asmbl_55676.p1, internal, 89061, 89204
-recovered pasa_asmbl_55676.p1, internal, 89333, 89453
-recovered pasa_asmbl_55676.p1, internal, 89661, 89851
Valid prediction for GlimmerHMM_glimmerT_23779-T1
Valid prediction for pasa_asmbl_55667.p1
Valid prediction for snap_scaffold_9-snap.3567-T1
Couldn't classify 86587, 86628
Couldn't classify 88370, 88393
Sorry, prediction pasa_asmbl_55677.p1 fails validation.
(CTG)	 CC	86587-86628	GT	AGG
(GAC)	 AG	86899-87041	GT	AAG
(GTG)	 AG	87153-87268	GT	CTG
(ACA)	 AG	87371-87504	GT	GGG
(CTG)	 AG	87617-87783	GT	AGG
(AGA)	 AG	87972-88065	GT	AGG
(GCC)	 AG	88173-88253	GT	AAG
(ATC)	 AG	88370-88393	GA	TGG
-recovered pasa_asmbl_55677.p1, internal, 86899, 87041
-recovered pasa_asmbl_55677.p1, internal, 87153, 87268
-recovered pasa_asmbl_55677.p1, internal, 87371, 87504
-recovered pasa_asmbl_55677.p1, internal, 87617, 87783
-recovered pasa_asmbl_55677.p1, internal, 87972, 88065
-recovered pasa_asmbl_55677.p1, internal, 88173, 88253
Valid prediction for HiQ_model.g15811.t1
Valid prediction for HiQ_model.g15825.t1
Valid prediction for pasa_asmbl_55673.p1
Valid prediction for HiQ_model.g15831.t1
Valid prediction for Augustus_model.g15827.t1
Valid prediction for snap_scaffold_9-snap.3553-T1
Valid prediction for HiQ_model.g15808.t1
Valid prediction for Augustus_model.g15820.t1
Valid prediction for snap_scaffold_9-snap.3554-T1
Valid prediction for CodingQuarry_transcript_62462-T1
Valid prediction for Augustus_model.g15823.t1
Valid prediction for Augustus_model.g15832.t1
Valid prediction for CodingQuarry_transcript_62465-T1
Valid prediction for snap_scaffold_9-snap.3536-T1
Valid prediction for snap_scaffold_9-snap.3560-T1
Valid prediction for Augustus_model.g15826.t1
Valid prediction for pasa_asmbl_55674.p1
Valid prediction for GlimmerHMM_glimmerT_23778-T1
Valid prediction for snap_scaffold_9-snap.3535-T1
Valid prediction for CodingQuarry_transcript_62469-T1
Valid prediction for snap_scaffold_9-snap.3547-T1
Valid prediction for snap_scaffold_9-snap.3533-T1
Valid prediction for snap_scaffold_9-snap.3528-T1
Valid prediction for snap_scaffold_9-snap.3525-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 191512, rend_intergenic: 172527  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197330, rend_intergenic: 193668  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 221217, rend_intergenic: 218203  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 223507, rend_intergenic: 221371  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 240253, rend_intergenic: 236496  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 101200, rend_intergenic: 101197  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 245044
-exon list size: 527


building trellis

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79.6    
79.8    
80.0    
80.2    
80.3    
80.5    
80.7    
80.9    
81.1    
81.3    
81.5    
81.7    
81.9    
82.0    
82.2    
82.4    
82.6    
82.8    
83.0    
83.2    
83.4    
83.6    
83.7    
83.9    
84.1    
84.3    
84.5    
84.7    
84.9    
85.1    
85.3    
85.4    
85.6    
85.8    
86.0    
86.2    
86.4    
86.6    
86.8    
87.0    
87.1    
87.3    
87.5    
87.7    
87.9    
88.1    
88.3    
88.5    
88.7    
88.8    
89.0    
89.2    
89.4    
89.6    
89.8    
90.0    
90.2    
90.4    
90.5    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
91.9    
92.1    
92.2    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
94.0    
94.1    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.2    
99.4    
99.6    
99.8    
-found 41 predictions from path traversal
Error with prediction: snap lend_intergenic: 191512, rend_intergenic: 172527  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197330, rend_intergenic: 193668  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 221217, rend_intergenic: 218203  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 223507, rend_intergenic: 221371  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 240253, rend_intergenic: 236496  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 101200, rend_intergenic: 101197  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 38 predictions persist after filtering for low support