-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_28/scaffold_28_1-221301

-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: +)Couldn't classify 81831, 82406
Sorry, prediction pasa_asmbl_37944.p1 fails validation.
(GGG)	 AG	81831-82406	CC	TGC
Valid prediction for snap_scaffold_28-snap.23-T1
Valid prediction for snap_scaffold_28-snap.19-T1
Valid prediction for snap_scaffold_28-snap.22-T1
Couldn't classify 89600, 90043
Sorry, prediction pasa_asmbl_37947.p1 fails validation.
(GGT)	 TA	89600-90043	GA	AGG
Valid prediction for GlimmerHMM_glimmerT_59324-T1
Valid prediction for GlimmerHMM_glimmerT_59329-T1
Valid prediction for snap_scaffold_28-snap.8-T1
Valid prediction for GeneMark_model.103579_t
Couldn't classify 31463, 31518
Sorry, prediction pasa_asmbl_37941.p1 fails validation.
(CAG)	 TG	31463-31518	GT	AGG
(CGA)	 AG	31627-31711	GT	AGG
(GGA)	 AG	32701-32797	GT	ACG
(AAG)	 AG	33124-33305	GT	AGG
(GGC)	 AG	35614-35662	GT	AGG
(GTT)	 AG	36084-36280	GT	AGG
(GCA)	 AG	36596-36768	GT	CGG
(GGC)	 AG	36904-37043	GT	CGG
(ACA)	 AG	37306-37361	AC	GAA
add_exon() Sorry, pasa_asmbl_37941.p1 35614-35662-terminal-3 is invalid.
-recovered pasa_asmbl_37941.p1, terminal, 35614, 35662
-recovered pasa_asmbl_37941.p1, terminal, 37306, 37361
-recovered pasa_asmbl_37941.p1, internal, 31627, 31711
-recovered pasa_asmbl_37941.p1, internal, 32701, 32797
-recovered pasa_asmbl_37941.p1, internal, 33124, 33305
-recovered pasa_asmbl_37941.p1, internal, 35614, 35662
-recovered pasa_asmbl_37941.p1, internal, 36084, 36280
-recovered pasa_asmbl_37941.p1, internal, 36596, 36768
-recovered pasa_asmbl_37941.p1, internal, 36904, 37043
Valid prediction for GeneMark_model.103585_t
Valid prediction for GlimmerHMM_glimmerT_59339-T1
Valid prediction for snap_scaffold_28-snap.41-T1
Valid prediction for GeneMark_model.103599_t
Valid prediction for snap_scaffold_28-snap.16-T1
Valid prediction for GlimmerHMM_glimmerT_59336-T1
Valid prediction for snap_scaffold_28-snap.7-T1
Valid prediction for GlimmerHMM_glimmerT_59330-T1
Valid prediction for snap_scaffold_28-snap.11-T1
Valid prediction for GeneMark_model.103594_t
Valid prediction for GeneMark_model.103573_t
Valid prediction for GlimmerHMM_glimmerT_59321-T1
Valid prediction for snap_scaffold_28-snap.33-T1
Valid prediction for snap_scaffold_28-snap.18-T1
Valid prediction for GeneMark_model.103576_t
Valid prediction for GeneMark_model.103583_t
Valid prediction for CodingQuarry_transcript_43406-T1
Valid prediction for Augustus_model.g39478.t1
Valid prediction for GlimmerHMM_glimmerT_59328-T1
Valid prediction for snap_scaffold_28-snap.40-T1
Valid prediction for GlimmerHMM_glimmerT_59320-T1
Valid prediction for snap_scaffold_28-snap.5-T1
Valid prediction for snap_scaffold_28-snap.38-T1
Valid prediction for snap_scaffold_28-snap.10-T1
Valid prediction for GeneMark_model.103587_t
Valid prediction for GeneMark_model.103592_t
Valid prediction for GlimmerHMM_glimmerT_59327-T1
Valid prediction for GeneMark_model.103570_t
Valid prediction for Augustus_model.g39470.t1
Couldn't classify 26792, 26899
Couldn't classify 28121, 28233
Sorry, prediction pasa_asmbl_38561.p1 fails validation.
(GAC)	 AG	26792-26899	GT	ATG
(GAC)	 AG	27192-27351	GT	TGG
(GTC)	 AG	28121-28233	AA	CCA
-recovered pasa_asmbl_38561.p1, internal, 26792, 26899
-recovered pasa_asmbl_38561.p1, internal, 27192, 27351
Valid prediction for GeneMark_model.103575_t
Valid prediction for GeneMark_model.103597_t
Valid prediction for snap_scaffold_28-snap.24-T1
Valid prediction for snap_scaffold_28-snap.42-T1
Valid prediction for snap_scaffold_28-snap.3-T1
Valid prediction for Augustus_model.g39468.t1
Valid prediction for GlimmerHMM_glimmerT_59340-T1
Couldn't classify 2214, 2264
Sorry, prediction snap_scaffold_28-snap.2-T1 fails validation.
(AAA)	 AG	2214-2264	GT	TGG
(GAT)	 AG	3958-4051	GT	CAG
(GCC)	 AG	4383-4439	GT	GGG
(GGG)	 AG	7293-7534	GT	GGG
(GGG)	 AG	7922-8020	GT	TGG
(GGC)	 AG	8728-8827	GT	TGG
(TCC)	 AG	10057-10074	CT	AGC
-recovered snap_scaffold_28-snap.2-T1, terminal, 10057, 10074
-recovered snap_scaffold_28-snap.2-T1, internal, 2214, 2264
-recovered snap_scaffold_28-snap.2-T1, internal, 3958, 4051
-recovered snap_scaffold_28-snap.2-T1, internal, 4383, 4439
-recovered snap_scaffold_28-snap.2-T1, internal, 7293, 7534
-recovered snap_scaffold_28-snap.2-T1, internal, 7922, 8020
-recovered snap_scaffold_28-snap.2-T1, internal, 8728, 8827
Valid prediction for snap_scaffold_28-snap.14-T1
Valid prediction for GlimmerHMM_glimmerT_59318-T1
Valid prediction for Augustus_model.g39469.t1
Valid prediction for GlimmerHMM_glimmerT_59337-T1
Valid prediction for snap_scaffold_28-snap.31-T1
Valid prediction for snap_scaffold_28-snap.28-T1
Valid prediction for Augustus_model.g39464.t1
Valid prediction for GeneMark_model.103582_t
Valid prediction for Augustus_model.g39479.t1
Valid prediction for snap_scaffold_28-snap.39-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for Augustus_model.g39462.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_59338-T1
Valid prediction for GeneMark_model.103590_t
Valid prediction for CodingQuarry_transcript_43410-T1
Valid prediction for GlimmerHMM_glimmerT_59326-T1
Valid prediction for GeneMark_model.103584_t
Valid prediction for GeneMark_model.103591_t
Valid prediction for snap_scaffold_28-snap.13-T1
Valid prediction for CodingQuarry_transcript_43407-T1
Valid prediction for GlimmerHMM_glimmerT_59322-T1
Valid prediction for GlimmerHMM_glimmerT_59325-T1
Valid prediction for pasa_asmbl_37214.p1
Valid prediction for Augustus_model.g39466.t1
Valid prediction for HiQ_model.g39472.t1
Valid prediction for snap_scaffold_28-snap.32-T1
Valid prediction for Augustus_model.g39461.t1
Valid prediction for GlimmerHMM_glimmerT_59323-T1
Valid prediction for GlimmerHMM_glimmerT_59316-T1
Couldn't classify 70455, 70508
Sorry, prediction pasa_asmbl_37219.p1 fails validation.
(ACC)	 GC	70455-70508	GT	ACG
(ACT)	 AG	73078-73204	GT	AGG
(ATG)	 AG	74130-74298	GT	AGG
(GAG)	 AG	76209-76290	TT	GAT
add_exon() Sorry, pasa_asmbl_37219.p1 74130-74298-initial-1 is invalid.
-recovered pasa_asmbl_37219.p1, initial, 74130, 74298
-recovered pasa_asmbl_37219.p1, terminal, 76209, 76290
-recovered pasa_asmbl_37219.p1, internal, 73078, 73204
-recovered pasa_asmbl_37219.p1, internal, 74130, 74298
Valid prediction for snap_scaffold_28-snap.29-T1
Valid prediction for GeneMark_model.103581_t
Valid prediction for GeneMark_model.103571_t
Valid prediction for Augustus_model.g39465.t1
Valid prediction for Augustus_model.g39471.t1
Valid prediction for GeneMark_model.103598_t
Valid prediction for GeneMark_model.103572_t
Valid prediction for GeneMark_model.103586_t
Valid prediction for snap_scaffold_28-snap.4-T1
Valid prediction for snap_scaffold_28-snap.15-T1
Valid prediction for snap_scaffold_28-snap.9-T1
Valid prediction for snap_scaffold_28-snap.30-T1
Valid prediction for Augustus_model.g39463.t1
Valid prediction for GeneMark_model.103593_t
Valid prediction for Augustus_model.g39476.t1
Valid prediction for snap_scaffold_28-snap.27-T1
Valid prediction for snap_scaffold_28-snap.34-T1
Valid prediction for Augustus_model.g39475.t1
Valid prediction for GeneMark_model.103596_t
Valid prediction for GeneMark_model.103577_t
Valid prediction for snap_scaffold_28-snap.1-T1
Valid prediction for GlimmerHMM_glimmerT_59331-T1
Valid prediction for GeneMark_model.103578_t
Valid prediction for Augustus_model.g39477.t1
Valid prediction for snap_scaffold_28-snap.26-T1
Valid prediction for GlimmerHMM_glimmerT_59332-T1
Valid prediction for GeneMark_model.103595_t
Valid prediction for snap_scaffold_28-snap.20-T1
Valid prediction for pasa_asmbl_37205.p1
Valid prediction for snap_scaffold_28-snap.25-T1
Valid prediction for GlimmerHMM_glimmerT_59333-T1
Valid prediction for snap_scaffold_28-snap.36-T1
Couldn't classify 173407, 173465
Couldn't classify 175058, 175188
Sorry, prediction pasa_asmbl_37883.p1 fails validation.
(TTC)	 TC	173407-173465	GT	TGG
(GTA)	 AG	174470-174681	GT	ACG
(TTA)	 AG	174859-174951	GT	AAG
(CGG)	 AG	175058-175188	TG	CCT
-recovered pasa_asmbl_37883.p1, internal, 174470, 174681
-recovered pasa_asmbl_37883.p1, internal, 174859, 174951
Valid prediction for GeneMark_model.103574_t
Valid prediction for snap_scaffold_28-snap.6-T1
Valid prediction for CodingQuarry_transcript_43409-T1
Valid prediction for snap_scaffold_28-snap.35-T1
Valid prediction for GeneMark_model.103580_t
Valid prediction for HiQ_model.g39467.t1
Valid prediction for GeneMark_model.103589_t
Couldn't classify 171677, 171844
Couldn't classify 172467, 172530
Sorry, prediction pasa_asmbl_37866.p1 fails validation.
(CTG)	 AG	171677-171844	GT	ACG
(ATC)	 AG	172202-172377	GT	GGG
(GTT)	 AG	172467-172530	CA	AGC
-recovered pasa_asmbl_37866.p1, internal, 171677, 171844
-recovered pasa_asmbl_37866.p1, internal, 172202, 172377
Valid prediction for Augustus_model.g39474.t1
Valid prediction for snap_scaffold_28-snap.17-T1
Couldn't classify 220971, 221075
Sorry, prediction GeneMark_model.103569_t fails validation.
(ATG)	 TG	218369-218379	GT	AGG
(GAG)	 AG	218527-219054	GT	AGG
(ACA)	 AG	219242-219265	GT	AAG
(AAG)	 AG	219575-219673	GT	GAG
(GTG)	 AG	220278-220445	GT	AGG
(ACA)	 AG	220633-220656	GT	AAG
(ACA)	 AG	220971-221075	GT	AAG
-recovered GeneMark_model.103569_t, initial, 218369, 218379
-recovered GeneMark_model.103569_t, internal, 218527, 219054
-recovered GeneMark_model.103569_t, internal, 219242, 219265
-recovered GeneMark_model.103569_t, internal, 219575, 219673
-recovered GeneMark_model.103569_t, internal, 220278, 220445
-recovered GeneMark_model.103569_t, internal, 220633, 220656
-recovered GeneMark_model.103569_t, internal, 220971, 221075
Valid prediction for GlimmerHMM_glimmerT_59317-T1
Valid prediction for GlimmerHMM_glimmerT_59319-T1
Valid prediction for GlimmerHMM_glimmerT_59335-T1
Couldn't classify 179327, 179401
Sorry, prediction pasa_asmbl_37203.p2 fails validation.
(TGC)	 TG	179327-179401	GT	AGG
(AGA)	 AG	179549-179585	GT	AGG
(ACG)	 AG	180901-181051	GT	CAG
(TTA)	 AG	181224-181368	GG	AGG
-recovered pasa_asmbl_37203.p2, terminal, 181224, 181368
-recovered pasa_asmbl_37203.p2, internal, 179549, 179585
-recovered pasa_asmbl_37203.p2, internal, 180901, 181051
Valid prediction for snap_scaffold_28-snap.37-T1
Valid prediction for snap_scaffold_28-snap.12-T1
Valid prediction for Augustus_model.g39473.t1
Valid prediction for GlimmerHMM_glimmerT_59334-T1
Valid prediction for snap_scaffold_28-snap.21-T1
Valid prediction for snap_scaffold_28-snap.43-T1
Valid prediction for CodingQuarry_transcript_43411-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9165, rend_intergenic: 2214  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50281, rend_intergenic: 47833  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78632, rend_intergenic: 76310  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80919, rend_intergenic: 79617  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91356, rend_intergenic: 83408  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113957, rend_intergenic: 112120  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135860, rend_intergenic: 133163  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143093, rend_intergenic: 136542  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150979, rend_intergenic: 146499  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 216944, rend_intergenic: 214006  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 221301
-exon list size: 533


building trellis

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96.3    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.8    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.3    
99.4    
99.6    
99.8    
-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 9165, rend_intergenic: 2214  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50281, rend_intergenic: 47833  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78632, rend_intergenic: 76310  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80919, rend_intergenic: 79617  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91356, rend_intergenic: 83408  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113957, rend_intergenic: 112120  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135860, rend_intergenic: 133163  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143093, rend_intergenic: 136542  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150979, rend_intergenic: 146499  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 216944, rend_intergenic: 214006  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

-building DP trellis

-building trellis in range 210125 - 221301
-exon list size: 10


building trellis

8.3    
16.7    
25.0    
33.3    
41.7    
50.0    
58.3    
66.7    
75.0    
83.3    
91.7    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 210660 - 221301
-exon list size: 9


building trellis

9.1    
18.2    
27.3    
36.4    
45.5    
54.5    
63.6    
72.7    
81.8    
90.9    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support