-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_11/scaffold_11_16324022-16590482

-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.3358-T1
Valid prediction for GeneMark_model.50217_t
Valid prediction for Augustus_model.g19421.t1
Valid prediction for GeneMark_model.50212_t
Valid prediction for snap_scaffold_11-snap.3381-T1
Couldn't classify 184540, 184587
Couldn't classify 185303, 185405
Sorry, prediction pasa_asmbl_6137.p1 fails validation.
(GAG)	 AG	184540-184587	GT	AGG
(GAG)	 AG	184714-184830	GT	AGG
(ATA)	 AG	184961-185040	GT	GGG
(GAT)	 AG	185303-185405	GA	AGG
-recovered pasa_asmbl_6137.p1, internal, 184540, 184587
-recovered pasa_asmbl_6137.p1, internal, 184714, 184830
-recovered pasa_asmbl_6137.p1, internal, 184961, 185040
Valid prediction for snap_scaffold_11-snap.3349-T1
Valid prediction for pasa_asmbl_6134.p1
Valid prediction for GeneMark_model.50241_t
Valid prediction for GeneMark_model.50223_t
Valid prediction for snap_scaffold_11-snap.3361-T1
Valid prediction for Augustus_model.g19427.t1
Valid prediction for snap_scaffold_11-snap.3369-T1
Valid prediction for snap_scaffold_11-snap.3374-T1
Valid prediction for GeneMark_model.50225_t
Valid prediction for GlimmerHMM_glimmerT_29081-T1
Couldn't classify 186130, 186273
Couldn't classify 186928, 187024
Sorry, prediction pasa_asmbl_6336.p1 fails validation.
(AGG)	 CC	186130-186273	GT	AGG
(AAT)	 AG	186488-186604	GT	AGG
(GCT)	 AG	186749-186828	GT	CAG
(CGC)	 AG	186928-187024	GG	GGG
-recovered pasa_asmbl_6336.p1, internal, 186488, 186604
-recovered pasa_asmbl_6336.p1, internal, 186749, 186828
Valid prediction for GeneMark_model.50230_t
Valid prediction for GlimmerHMM_glimmerT_29100-T1
Valid prediction for GeneMark_model.50218_t
Valid prediction for GlimmerHMM_glimmerT_29089-T1
Valid prediction for snap_scaffold_11-snap.3386-T1
Valid prediction for GeneMark_model.50235_t
Valid prediction for GlimmerHMM_glimmerT_29094-T1
Valid prediction for GeneMark_model.50231_t
Valid prediction for GeneMark_model.50205_t
Couldn't classify 97587, 97744
Sorry, prediction pasa_asmbl_6266.p1 fails validation.
(ATG)	 CC	97001-97169	GT	AGG
(GTA)	 AG	97587-97744	CC	GGC
-recovered pasa_asmbl_6266.p1, initial, 97001, 97169
Valid prediction for snap_scaffold_11-snap.3347-T1
Valid prediction for Augustus_model.g19415.t1
Valid prediction for snap_scaffold_11-snap.3359-T1
Valid prediction for GlimmerHMM_glimmerT_29090-T1
Valid prediction for GeneMark_model.50238_t
Valid prediction for snap_scaffold_11-snap.3376-T1
Valid prediction for GeneMark_model.50250_t
Valid prediction for Augustus_model.g19430.t1
Valid prediction for snap_scaffold_11-snap.3363-T1
Valid prediction for GlimmerHMM_glimmerT_29084-T1
Valid prediction for Augustus_model.g19424.t1
Valid prediction for snap_scaffold_11-snap.3387-T1
Valid prediction for GlimmerHMM_glimmerT_29082-T1
Valid prediction for GeneMark_model.50208_t
Valid prediction for GeneMark_model.50207_t
Valid prediction for GlimmerHMM_glimmerT_29097-T1
Valid prediction for GeneMark_model.50245_t
Valid prediction for GeneMark_model.50232_t
Valid prediction for snap_scaffold_11-snap.3367-T1
Valid prediction for pasa_asmbl_6136.p1
Valid prediction for GeneMark_model.50226_t
Valid prediction for GlimmerHMM_glimmerT_29104-T1
Valid prediction for GlimmerHMM_glimmerT_29091-T1
Valid prediction for Augustus_model.g19433.t1
Valid prediction for snap_scaffold_11-snap.3353-T1
Valid prediction for snap_scaffold_11-snap.3362-T1
Valid prediction for CodingQuarry_transcript_8299-T1
Valid prediction for GlimmerHMM_glimmerT_29106-T1
Couldn't classify 205425, 205551
Sorry, prediction pasa_asmbl_6140.p1 fails validation.
(CAT)	 AC	205425-205551	GT	TGG
(GGA)	 AG	205797-205951	GT	AAG
(GTG)	 AG	206074-206200	GT	AGG
(GTT)	 AG	206374-206481	GT	AGG
(GTG)	 AG	206768-206919	CT	AGC
-recovered pasa_asmbl_6140.p1, terminal, 206768, 206919
-recovered pasa_asmbl_6140.p1, internal, 205797, 205951
-recovered pasa_asmbl_6140.p1, internal, 206074, 206200
-recovered pasa_asmbl_6140.p1, internal, 206374, 206481
Valid prediction for GeneMark_model.50248_t
Valid prediction for GeneMark_model.50247_t
Valid prediction for GeneMark_model.50240_t
Valid prediction for GlimmerHMM_glimmerT_29109-T1
Valid prediction for CodingQuarry_transcript_8308-T1
Valid prediction for snap_scaffold_11-snap.3351-T1
Valid prediction for GeneMark_model.50219_t
Valid prediction for snap_scaffold_11-snap.3375-T1
Valid prediction for GlimmerHMM_glimmerT_29088-T1
Valid prediction for GlimmerHMM_glimmerT_29102-T1
Valid prediction for GeneMark_model.50237_t
Couldn't classify 178775, 179179
Sorry, prediction pasa_asmbl_6135.p1 fails validation.
(TCA)	 CA	178775-179179	AT	CTA
Valid prediction for Augustus_model.g19432.t1
Valid prediction for snap_scaffold_11-snap.3383-T1
Couldn't classify 205409, 205412
Sorry, prediction pasa_asmbl_6139.p1 fails validation.
(ATG)	 CT	204387-204800	GT	AGG
(ATC)	 AG	205067-205215	GT	GAG
(CGT)	 AG	205409-205412	AC	TGA
-recovered pasa_asmbl_6139.p1, initial, 204387, 204800
-recovered pasa_asmbl_6139.p1, internal, 205067, 205215
Valid prediction for Augustus_model.g19420.t1
Valid prediction for snap_scaffold_11-snap.3384-T1
Valid prediction for GeneMark_model.50221_t
Valid prediction for snap_scaffold_11-snap.3377-T1
Valid prediction for GeneMark_model.50210_t
Valid prediction for snap_scaffold_11-snap.3378-T1
Valid prediction for GeneMark_model.50251_t
Valid prediction for CodingQuarry_transcript_8307-T1
Valid prediction for GlimmerHMM_glimmerT_29083-T1
Valid prediction for snap_scaffold_11-snap.3354-T1
Valid prediction for snap_scaffold_11-snap.3360-T1
Valid prediction for snap_scaffold_11-snap.3380-T1
Valid prediction for GeneMark_model.50236_t
Valid prediction for GeneMark_model.50243_t
Valid prediction for GeneMark_model.50214_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.50244_t
Valid prediction for snap_scaffold_11-snap.3372-T1
Valid prediction for snap_scaffold_11-snap.3364-T1
Valid prediction for CodingQuarry_transcript_8301-T1
Valid prediction for snap_scaffold_11-snap.3348-T1
Valid prediction for GeneMark_model.50233_t
Valid prediction for snap_scaffold_11-snap.3368-T1
Valid prediction for Augustus_model.g19419.t1
Valid prediction for snap_scaffold_11-snap.3389-T1
Valid prediction for snap_scaffold_11-snap.3356-T1
Valid prediction for snap_scaffold_11-snap.3350-T1
Valid prediction for Augustus_model.g19422.t1
Valid prediction for snap_scaffold_11-snap.3357-T1
Valid prediction for snap_scaffold_11-snap.3379-T1
Valid prediction for Augustus_model.g19423.t1
Valid prediction for GeneMark_model.50249_t
Valid prediction for pasa_asmbl_7198.p1
Valid prediction for GlimmerHMM_glimmerT_29103-T1
Valid prediction for CodingQuarry_transcript_8304-T1
Valid prediction for Augustus_model.g19431.t1
Valid prediction for snap_scaffold_11-snap.3370-T1
Valid prediction for snap_scaffold_11-snap.3385-T1
Valid prediction for Augustus_model.g19418.t1
Valid prediction for GlimmerHMM_glimmerT_29107-T1
Valid prediction for GeneMark_model.50246_t
Valid prediction for Augustus_model.g19434.t1
Valid prediction for snap_scaffold_11-snap.3388-T1
Valid prediction for GeneMark_model.50213_t
Valid prediction for GlimmerHMM_glimmerT_29101-T1
Valid prediction for GeneMark_model.50227_t
Valid prediction for GeneMark_model.50222_t
Valid prediction for snap_scaffold_11-snap.3355-T1
Valid prediction for Augustus_model.g19417.t1
Valid prediction for CodingQuarry_transcript_8302-T1
Valid prediction for GlimmerHMM_glimmerT_29087-T1
Valid prediction for snap_scaffold_11-snap.3382-T1
Valid prediction for GeneMark_model.50242_t
Valid prediction for GlimmerHMM_glimmerT_29098-T1
Valid prediction for GlimmerHMM_glimmerT_29086-T1
Valid prediction for HiQ_model.g19426.t1
Valid prediction for CodingQuarry_transcript_8306-T1
Valid prediction for snap_scaffold_11-snap.3352-T1
Valid prediction for GeneMark_model.50228_t
Valid prediction for GeneMark_model.50209_t
Valid prediction for GlimmerHMM_glimmerT_29099-T1
Valid prediction for HiQ_model.g19425.t1
Valid prediction for GeneMark_model.50206_t
Valid prediction for GeneMark_model.50215_t
Valid prediction for GeneMark_model.50220_t
Valid prediction for GlimmerHMM_glimmerT_29093-T1
Valid prediction for GeneMark_model.50252_t
Valid prediction for pasa_asmbl_7205.p1
Valid prediction for Augustus_model.g19429.t1
Valid prediction for GeneMark_model.50234_t
Valid prediction for CodingQuarry_transcript_8303-T1
Valid prediction for GlimmerHMM_glimmerT_29092-T1
Valid prediction for Augustus_model.g19435.t1
Valid prediction for GlimmerHMM_glimmerT_29105-T1
Couldn't classify 57848, 58138
Sorry, prediction pasa_asmbl_7208.p1 fails validation.
(ATG)	 CA	53641-53659	GT	AGG
(GTC)	 AG	55102-55169	GT	TGG
(GAC)	 AG	55278-55501	GT	AGG
(AGT)	 AG	56068-56150	GT	CTG
(ATG)	 AG	56421-56561	GT	AGG
(GCT)	 AG	56771-56923	GT	GGG
(GGA)	 AG	57136-57332	GT	GGG
(TTG)	 AG	57848-58138	AT	CCA
-recovered pasa_asmbl_7208.p1, initial, 53641, 53659
add_exon() Sorry, pasa_asmbl_7208.p1 56421-56561-initial-1 is invalid.
-recovered pasa_asmbl_7208.p1, initial, 56421, 56561
-recovered pasa_asmbl_7208.p1, internal, 55102, 55169
-recovered pasa_asmbl_7208.p1, internal, 55278, 55501
-recovered pasa_asmbl_7208.p1, internal, 56068, 56150
-recovered pasa_asmbl_7208.p1, internal, 56421, 56561
-recovered pasa_asmbl_7208.p1, internal, 56771, 56923
-recovered pasa_asmbl_7208.p1, internal, 57136, 57332
Valid prediction for Augustus_model.g19416.t1
Valid prediction for snap_scaffold_11-snap.3366-T1
Valid prediction for GlimmerHMM_glimmerT_29095-T1
Valid prediction for snap_scaffold_11-snap.3390-T1
Valid prediction for GlimmerHMM_glimmerT_29085-T1
Valid prediction for snap_scaffold_11-snap.3373-T1
Valid prediction for HiQ_model.g19428.t1
Valid prediction for GlimmerHMM_glimmerT_29108-T1
Valid prediction for snap_scaffold_11-snap.3365-T1
Valid prediction for GlimmerHMM_glimmerT_29096-T1
Valid prediction for CodingQuarry_transcript_8300-T1
Valid prediction for snap_scaffold_11-snap.3371-T1
Valid prediction for GeneMark_model.50216_t
Valid prediction for GeneMark_model.50229_t
Valid prediction for GeneMark_model.50224_t
Valid prediction for pasa_asmbl_7292.p1
Valid prediction for GlimmerHMM_glimmerT_29110-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 45574, rend_intergenic: 43007  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 223829, rend_intergenic: 218474  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 242300, rend_intergenic: 231178  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 266461
-exon list size: 679


building trellis

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91.5    
91.6    
91.8    
91.9    
92.1    
92.2    
92.4    
92.5    
92.7    
92.8    
93.0    
93.1    
93.2    
93.4    
93.5    
93.7    
93.8    
94.0    
94.1    
94.3    
94.4    
94.6    
94.7    
94.9    
95.0    
95.2    
95.3    
95.4    
95.6    
95.7    
95.9    
96.0    
96.2    
96.3    
96.5    
96.6    
96.8    
96.9    
97.1    
97.2    
97.4    
97.5    
97.7    
97.8    
97.9    
98.1    
98.2    
98.4    
98.5    
98.7    
98.8    
99.0    
99.1    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 45574, rend_intergenic: 43007  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 223829, rend_intergenic: 218474  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 242300, rend_intergenic: 231178  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 32 predictions persist after filtering for low support