-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_11/scaffold_11_4352978-4515671

-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.1103-T1
Valid prediction for GlimmerHMM_glimmerT_27546-T1
Valid prediction for GlimmerHMM_glimmerT_27550-T1
Valid prediction for Augustus_model.g18361.t1
Valid prediction for snap_scaffold_11-snap.1090-T1
Valid prediction for GlimmerHMM_glimmerT_27540-T1
Valid prediction for snap_scaffold_11-snap.1075-T1
Valid prediction for GeneMark_model.47556_t
Valid prediction for GeneMark_model.47564_t
Valid prediction for pasa_asmbl_5433.p1
Valid prediction for GeneMark_model.47573_t
Valid prediction for Augustus_model.g18370.t1
Couldn't classify 43709, 43852
Sorry, prediction pasa_asmbl_5438.p1 fails validation.
(GTC)	 AC	43709-43852	GT	AGG
(CCA)	 AG	44042-44183	GT	AGG
(GCC)	 AG	44490-44639	GT	CGG
(TGA)	 AG	45310-45461	AC	AAA
-recovered pasa_asmbl_5438.p1, terminal, 45310, 45461
-recovered pasa_asmbl_5438.p1, internal, 44042, 44183
-recovered pasa_asmbl_5438.p1, internal, 44490, 44639
Couldn't classify 78815, 79204
Sorry, prediction pasa_asmbl_5447.p1 fails validation.
(CGC)	 TG	78815-79204	GT	AGG
(GTG)	 AG	80746-80910	GT	AGG
(GAG)	 AG	81818-82375	TC	AGT
-recovered pasa_asmbl_5447.p1, terminal, 81818, 82375
-recovered pasa_asmbl_5447.p1, internal, 80746, 80910
Valid prediction for snap_scaffold_11-snap.1085-T1
Valid prediction for snap_scaffold_11-snap.1081-T1
Valid prediction for Augustus_model.g18369.t1
Valid prediction for snap_scaffold_11-snap.1102-T1
Valid prediction for snap_scaffold_11-snap.1097-T1
Valid prediction for HiQ_model.g18357.t1
Valid prediction for GeneMark_model.47560_t
Valid prediction for Augustus_model.g18364.t1
Valid prediction for GeneMark_model.47578_t
Valid prediction for GeneMark_model.47554_t
Couldn't classify 64209, 64348
Couldn't classify 67624, 67646
Sorry, prediction pasa_asmbl_5444.p1 fails validation.
(CAC)	 CC	64209-64348	GT	AGG
(CAA)	 AG	64746-64797	GT	AGG
(ATC)	 AG	64984-65088	GT	TGG
(GAC)	 AG	65338-65502	GT	AGG
(AAA)	 AG	65598-65678	GT	AGG
(CTG)	 AG	65882-65956	GT	AGG
(GGT)	 AG	66107-66199	GT	AGG
(GTG)	 AG	66449-66589	GT	AGG
(AAG)	 AG	66804-66987	GT	AGG
(AGT)	 AG	67624-67646	GA	ACG
add_exon() Sorry, pasa_asmbl_5444.p1 66804-66987-terminal-3 is invalid.
-recovered pasa_asmbl_5444.p1, terminal, 66804, 66987
-recovered pasa_asmbl_5444.p1, internal, 64746, 64797
-recovered pasa_asmbl_5444.p1, internal, 64984, 65088
-recovered pasa_asmbl_5444.p1, internal, 65338, 65502
-recovered pasa_asmbl_5444.p1, internal, 65598, 65678
-recovered pasa_asmbl_5444.p1, internal, 65882, 65956
-recovered pasa_asmbl_5444.p1, internal, 66107, 66199
-recovered pasa_asmbl_5444.p1, internal, 66449, 66589
-recovered pasa_asmbl_5444.p1, internal, 66804, 66987
Valid prediction for Augustus_model.g18366.t1
Valid prediction for GlimmerHMM_glimmerT_27533-T1
Valid prediction for snap_scaffold_11-snap.1079-T1
Valid prediction for GlimmerHMM_glimmerT_27548-T1
Valid prediction for GlimmerHMM_glimmerT_27549-T1
Valid prediction for GeneMark_model.47552_t
Valid prediction for GlimmerHMM_glimmerT_27537-T1
Valid prediction for Augustus_model.g18360.t1
Couldn't classify 55977, 56024
Sorry, prediction pasa_asmbl_5442.p1 fails validation.
(CCG)	 AC	55977-56024	GT	AGG
(GTG)	 AG	56228-56332	GT	AGG
(CCT)	 AG	56548-56751	GT	AGG
(ATC)	 AG	56899-56976	GT	AGG
(GTG)	 AG	57066-57123	GT	AGG
(CCA)	 AG	57239-57504	GT	AGG
(GAG)	 AG	57764-57805	GC	GAG
-recovered pasa_asmbl_5442.p1, terminal, 57764, 57805
-recovered pasa_asmbl_5442.p1, internal, 56228, 56332
-recovered pasa_asmbl_5442.p1, internal, 56548, 56751
-recovered pasa_asmbl_5442.p1, internal, 56899, 56976
-recovered pasa_asmbl_5442.p1, internal, 57066, 57123
-recovered pasa_asmbl_5442.p1, internal, 57239, 57504
-recovered pasa_asmbl_5442.p1, internal, 57764, 57805
Valid prediction for GeneMark_model.47580_t
Valid prediction for snap_scaffold_11-snap.1095-T1
Valid prediction for snap_scaffold_11-snap.1105-T1
Valid prediction for snap_scaffold_11-snap.1098-T1
Couldn't classify 55098, 55226
Sorry, prediction pasa_asmbl_5441.p1 fails validation.
(ATG)	 AG	53816-53972	GT	TGG
(GTG)	 AG	54075-54134	GT	TGG
(AGG)	 AG	54670-54750	GT	ACG
(TTG)	 AG	54875-54927	GT	AGG
(GCG)	 AG	55098-55226	CA	TCC
-recovered pasa_asmbl_5441.p1, initial, 53816, 53972
-recovered pasa_asmbl_5441.p1, internal, 53816, 53972
-recovered pasa_asmbl_5441.p1, internal, 54075, 54134
-recovered pasa_asmbl_5441.p1, internal, 54670, 54750
-recovered pasa_asmbl_5441.p1, internal, 54875, 54927
Valid prediction for GlimmerHMM_glimmerT_27535-T1
Valid prediction for snap_scaffold_11-snap.1093-T1
Couldn't classify 35136, 35251
Couldn't classify 35656, 35856
Sorry, prediction pasa_asmbl_6311.p2 fails validation.
(GTG)	 AG	35136-35251	GT	AGG
(CGA)	 AG	35376-35517	GT	AGG
(GTC)	 AG	35656-35856	GG	CCG
-recovered pasa_asmbl_6311.p2, internal, 35136, 35251
-recovered pasa_asmbl_6311.p2, internal, 35376, 35517
Valid prediction for HiQ_model.g18365.t1
Valid prediction for GeneMark_model.47557_t
Couldn't classify 29979, 30194
Couldn't classify 30890, 31104
Sorry, prediction pasa_asmbl_5436.p1 fails validation.
(CGG)	 GG	29979-30194	GT	AGG
(GTG)	 AG	30452-30584	GT	CGG
(TGT)	 AG	30890-31104	CA	CCC
-recovered pasa_asmbl_5436.p1, internal, 30452, 30584
Valid prediction for Augustus_model.g18355.t1
Valid prediction for GlimmerHMM_glimmerT_27547-T1
Valid prediction for GeneMark_model.47566_t
Valid prediction for Augustus_model.g18359.t1
Valid prediction for CodingQuarry_transcript_8008-T1
Valid prediction for snap_scaffold_11-snap.1089-T1
Valid prediction for GlimmerHMM_glimmerT_27545-T1
Valid prediction for GeneMark_model.47569_t
Couldn't classify 75890, 75974
Sorry, prediction pasa_asmbl_5446.p1 fails validation.
(ATG)	 TC	71830-72059	GT	AGG
(GTA)	 AG	74429-74605	GT	AGG
(GTT)	 AG	75890-75974	AG	AGA
-recovered pasa_asmbl_5446.p1, initial, 71830, 72059
-recovered pasa_asmbl_5446.p1, internal, 74429, 74605
Valid prediction for GlimmerHMM_glimmerT_27538-T1
Valid prediction for GeneMark_model.47571_t
Valid prediction for snap_scaffold_11-snap.1088-T1
Couldn't classify 32545, 32946
Couldn't classify 33669, 33769
Sorry, prediction pasa_asmbl_5437.p1 fails validation.
(CCA)	 CT	32545-32946	GT	AGG
(CTG)	 AG	33119-33302	GT	AGG
(GCT)	 AG	33669-33769	AC	AGA
-recovered pasa_asmbl_5437.p1, internal, 33119, 33302
Valid prediction for snap_scaffold_11-snap.1077-T1
Valid prediction for snap_scaffold_11-snap.1082-T1
Valid prediction for Augustus_model.g18368.t1
Valid prediction for GeneMark_model.47568_t
Valid prediction for GlimmerHMM_glimmerT_27544-T1
Valid prediction for GeneMark_model.47583_t
Valid prediction for GeneMark_model.47575_t
Valid prediction for GeneMark_model.47559_t
Valid prediction for snap_scaffold_11-snap.1078-T1
Couldn't classify 28470, 28544
Couldn't classify 29441, 29509
Sorry, prediction pasa_asmbl_5435.p1 fails validation.
(GCC)	 TC	28470-28544	GT	AGG
(GGT)	 AG	28693-28821	GT	AGG
(CTG)	 AG	29013-29144	GT	AGG
(GGC)	 AG	29441-29509	AT	AGA
-recovered pasa_asmbl_5435.p1, internal, 28693, 28821
-recovered pasa_asmbl_5435.p1, internal, 29013, 29144
Valid prediction for GeneMark_model.47562_t

-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 GeneMark_model.47570_t
Valid prediction for GeneMark_model.47553_t
Valid prediction for GeneMark_model.47579_t
Valid prediction for GeneMark_model.47577_t
Valid prediction for Augustus_model.g18363.t1
Couldn't classify 135709, 136545
Sorry, prediction pasa_asmbl_6577.p1 fails validation.
(GAG)	 AC	135709-136545	GT	AGG
(CCA)	 AG	136667-137626	GT	AAG
(GTA)	 AG	137957-138196	GT	AGG
(GTG)	 AG	138471-138563	GT	AGG
(GTG)	 AG	138914-139060	GT	AAG
(GTT)	 AG	139236-139346	GT	AGG
(AAC)	 AG	139497-139611	GT	AGG
(AGC)	 AG	139872-140572	TC	GAT
-recovered pasa_asmbl_6577.p1, terminal, 139872, 140572
-recovered pasa_asmbl_6577.p1, internal, 136667, 137626
-recovered pasa_asmbl_6577.p1, internal, 137957, 138196
-recovered pasa_asmbl_6577.p1, internal, 138471, 138563
-recovered pasa_asmbl_6577.p1, internal, 138914, 139060
-recovered pasa_asmbl_6577.p1, internal, 139236, 139346
-recovered pasa_asmbl_6577.p1, internal, 139497, 139611
Valid prediction for snap_scaffold_11-snap.1101-T1
Valid prediction for GeneMark_model.47565_t
Valid prediction for GlimmerHMM_glimmerT_27541-T1
Valid prediction for GeneMark_model.47567_t
Valid prediction for GeneMark_model.47576_t
Valid prediction for snap_scaffold_11-snap.1087-T1
Valid prediction for snap_scaffold_11-snap.1092-T1
Valid prediction for snap_scaffold_11-snap.1086-T1
Valid prediction for GeneMark_model.47572_t
Valid prediction for snap_scaffold_11-snap.1084-T1
Valid prediction for GeneMark_model.47581_t
Valid prediction for GlimmerHMM_glimmerT_27534-T1
Valid prediction for GeneMark_model.47563_t
Valid prediction for GlimmerHMM_glimmerT_27536-T1
Valid prediction for GeneMark_model.47555_t
Valid prediction for GlimmerHMM_glimmerT_27539-T1
Valid prediction for GeneMark_model.47582_t
Valid prediction for GeneMark_model.47574_t
Valid prediction for GeneMark_model.47551_t
Valid prediction for snap_scaffold_11-snap.1094-T1
Valid prediction for GlimmerHMM_glimmerT_27543-T1
Valid prediction for snap_scaffold_11-snap.1083-T1
Valid prediction for snap_scaffold_11-snap.1100-T1
Valid prediction for GeneMark_model.47561_t
Valid prediction for Augustus_model.g18362.t1
Valid prediction for Augustus_model.g18367.t1
Valid prediction for GlimmerHMM_glimmerT_27542-T1
Valid prediction for pasa_asmbl_5445.p1
Valid prediction for snap_scaffold_11-snap.1080-T1
Valid prediction for snap_scaffold_11-snap.1104-T1
Valid prediction for HiQ_model.g18358.t1
Valid prediction for snap_scaffold_11-snap.1074-T1
Valid prediction for snap_scaffold_11-snap.1091-T1
Valid prediction for snap_scaffold_11-snap.1076-T1
Valid prediction for Augustus_model.g18354.t1
Valid prediction for snap_scaffold_11-snap.1096-T1
Valid prediction for Augustus_model.g18356.t1
Valid prediction for snap_scaffold_11-snap.1099-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 18959, rend_intergenic: 14159  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36767, rend_intergenic: 33709  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44316, rend_intergenic: 40113  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45461, rend_intergenic: 44432  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68186, rend_intergenic: 61296  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76570, rend_intergenic: 73525  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77435, rend_intergenic: 77159  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101241, rend_intergenic: 88307  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120515, rend_intergenic: 108181  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159161, rend_intergenic: 150207  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 162694
-exon list size: 574


building trellis

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93.1    
93.2    
93.4    
93.6    
93.8    
93.9    
94.1    
94.3    
94.4    
94.6    
94.8    
95.0    
95.1    
95.3    
95.5    
95.7    
95.8    
96.0    
96.2    
96.4    
96.5    
96.7    
96.9    
97.0    
97.2    
97.4    
97.6    
97.7    
97.9    
98.1    
98.3    
98.4    
98.6    
98.8    
99.0    
99.1    
99.3    
99.5    
99.7    
99.8    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 18959, rend_intergenic: 14159  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36767, rend_intergenic: 33709  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44316, rend_intergenic: 40113  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45461, rend_intergenic: 44432  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68186, rend_intergenic: 61296  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76570, rend_intergenic: 73525  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77435, rend_intergenic: 77159  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101241, rend_intergenic: 88307  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120515, rend_intergenic: 108181  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159161, rend_intergenic: 150207  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support