-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_10/scaffold_10_10385572-10574693

-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_10-snap.2028-T1
Valid prediction for snap_scaffold_10-snap.2050-T1
Couldn't classify 37693, 37998
Sorry, prediction pasa_asmbl_4730.p1 fails validation.
(ATG)	 CG	37693-37998	AG	ATA
Valid prediction for Augustus_model.g16860.t1
Valid prediction for HiQ_model.g16862.t1
Valid prediction for Augustus_model.g16859.t1
Valid prediction for GlimmerHMM_glimmerT_25348-T1
Valid prediction for GlimmerHMM_glimmerT_25337-T1
Valid prediction for Augustus_model.g16843.t1
Valid prediction for snap_scaffold_10-snap.2057-T1
Valid prediction for snap_scaffold_10-snap.2035-T1
Valid prediction for CodingQuarry_transcript_5547-T1
Valid prediction for snap_scaffold_10-snap.2022-T1
Valid prediction for GlimmerHMM_glimmerT_25324-T1
Valid prediction for GlimmerHMM_glimmerT_25344-T1
Valid prediction for GlimmerHMM_glimmerT_25328-T1
Valid prediction for Augustus_model.g16856.t1
Valid prediction for GlimmerHMM_glimmerT_25350-T1
Valid prediction for snap_scaffold_10-snap.2038-T1
Valid prediction for snap_scaffold_10-snap.2052-T1
Valid prediction for GlimmerHMM_glimmerT_25331-T1
Valid prediction for GlimmerHMM_glimmerT_25325-T1
Valid prediction for CodingQuarry_transcript_5549-T1
Couldn't classify 155410, 155521
Couldn't classify 158715, 158770
Sorry, prediction pasa_asmbl_3417.p1 fails validation.
(AGG)	 GG	155410-155521	GT	GGG
(GGT)	 AG	157539-157604	GT	TGG
(ACT)	 AG	157775-157854	GT	GTG
(GAC)	 AG	158002-158128	GT	GGG
(ATG)	 AG	158327-158554	GT	AGG
(AGG)	 AG	158715-158770	CC	TGC
add_exon() Sorry, pasa_asmbl_3417.p1 158327-158554-initial-1 is invalid.
-recovered pasa_asmbl_3417.p1, initial, 158327, 158554
-recovered pasa_asmbl_3417.p1, internal, 157539, 157604
-recovered pasa_asmbl_3417.p1, internal, 157775, 157854
-recovered pasa_asmbl_3417.p1, internal, 158002, 158128
-recovered pasa_asmbl_3417.p1, internal, 158327, 158554
Valid prediction for snap_scaffold_10-snap.2033-T1
Valid prediction for GlimmerHMM_glimmerT_25333-T1
Valid prediction for snap_scaffold_10-snap.2058-T1
Valid prediction for pasa_asmbl_3416.p1
Valid prediction for Augustus_model.g16857.t1
Valid prediction for snap_scaffold_10-snap.2025-T1
Valid prediction for snap_scaffold_10-snap.2023-T1
Valid prediction for Augustus_model.g16844.t1
Valid prediction for GlimmerHMM_glimmerT_25339-T1
Valid prediction for snap_scaffold_10-snap.2041-T1
Valid prediction for snap_scaffold_10-snap.2054-T1
Couldn't classify 160097, 160663
Sorry, prediction pasa_asmbl_3418.p1 fails validation.
(CCC)	 AT	160097-160663	GC	AGG
Valid prediction for snap_scaffold_10-snap.2042-T1
Couldn't classify 166371, 168666
Sorry, prediction pasa_asmbl_3421.p1 fails validation.
(CTA)	 CA	166371-168666	GT	GGG
(GCA)	 AG	168765-168778	AG	GAA
-recovered pasa_asmbl_3421.p1, terminal, 168765, 168778
Valid prediction for GlimmerHMM_glimmerT_25330-T1
Valid prediction for snap_scaffold_10-snap.2026-T1
Couldn't classify 187141, 187218
Sorry, prediction pasa_asmbl_3423.p1 fails validation.
(ATG)	 TT	178069-178215	GT	AGG
(GTG)	 AG	181135-181323	GT	AGG
(GTG)	 AG	181457-182149	GT	AGG
(GAC)	 AG	182638-182773	GT	AGG
(AGG)	 AG	182987-183138	GT	AGG
(CAT)	 AG	183226-183780	GT	AGG
(GTG)	 AG	183883-183990	GT	AGG
(ATA)	 AG	184089-184387	GT	AGG
(GAT)	 AG	184466-184616	GT	AGG
(ATG)	 AG	184691-184810	GT	AGG
(GAA)	 AG	184973-185102	GT	AGG
(ATA)	 AG	185439-185569	GT	AGG
(GAC)	 AG	185680-185795	GT	AGG
(GTC)	 AG	185933-186292	GT	GAG
(ACT)	 AG	186641-186755	GT	TGG
(GAG)	 AG	186946-187053	GT	GGG
(AGG)	 AG	187141-187218	CA	CCC
-recovered pasa_asmbl_3423.p1, initial, 178069, 178215
-recovered pasa_asmbl_3423.p1, initial, 184691, 184810
-recovered pasa_asmbl_3423.p1, terminal, 184973, 185102
-recovered pasa_asmbl_3423.p1, internal, 181135, 181323
-recovered pasa_asmbl_3423.p1, internal, 181457, 182149
-recovered pasa_asmbl_3423.p1, internal, 182638, 182773
-recovered pasa_asmbl_3423.p1, internal, 182987, 183138
-recovered pasa_asmbl_3423.p1, internal, 183226, 183780
-recovered pasa_asmbl_3423.p1, internal, 183883, 183990
-recovered pasa_asmbl_3423.p1, internal, 184089, 184387
-recovered pasa_asmbl_3423.p1, internal, 184466, 184616
-recovered pasa_asmbl_3423.p1, internal, 184691, 184810
-recovered pasa_asmbl_3423.p1, internal, 184973, 185102
-recovered pasa_asmbl_3423.p1, internal, 185439, 185569
-recovered pasa_asmbl_3423.p1, internal, 185680, 185795
-recovered pasa_asmbl_3423.p1, internal, 185933, 186292
-recovered pasa_asmbl_3423.p1, internal, 186641, 186755
-recovered pasa_asmbl_3423.p1, internal, 186946, 187053
Valid prediction for CodingQuarry_transcript_5554-T1
Valid prediction for GlimmerHMM_glimmerT_25347-T1
Valid prediction for HiQ_model.g16841.t1
Valid prediction for Augustus_model.g16850.t1
Couldn't classify 164460, 165176
Sorry, prediction pasa_asmbl_3420.p1 fails validation.
(CTC)	 GT	164460-165176	AA	TCA
Valid prediction for snap_scaffold_10-snap.2051-T1
Valid prediction for Augustus_model.g16839.t1
Valid prediction for snap_scaffold_10-snap.2029-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 Augustus_model.g16855.t1
Valid prediction for GlimmerHMM_glimmerT_25342-T1
Valid prediction for snap_scaffold_10-snap.2030-T1
Valid prediction for GlimmerHMM_glimmerT_25326-T1
Valid prediction for Augustus_model.g16842.t1
Valid prediction for GlimmerHMM_glimmerT_25345-T1
Valid prediction for Augustus_model.g16854.t1
Valid prediction for snap_scaffold_10-snap.2040-T1
Couldn't classify 150601, 150735
Sorry, prediction pasa_asmbl_4732.p1 fails validation.
(ATG)	 AA	143861-144044	GT	TGG
(CCA)	 AG	144572-144685	GT	GGG
(GCG)	 AG	145108-145263	GT	TGG
(GTG)	 AG	147511-147659	GT	TGG
(TGG)	 AG	147865-148008	GT	TGG
(GCT)	 AG	148147-148300	GT	AGG
(ACT)	 AG	148903-149120	GT	AGG
(GCT)	 AG	150601-150735	AT	TCA
-recovered pasa_asmbl_4732.p1, initial, 143861, 144044
-recovered pasa_asmbl_4732.p1, internal, 144572, 144685
-recovered pasa_asmbl_4732.p1, internal, 145108, 145263
-recovered pasa_asmbl_4732.p1, internal, 147511, 147659
-recovered pasa_asmbl_4732.p1, internal, 147865, 148008
-recovered pasa_asmbl_4732.p1, internal, 148147, 148300
-recovered pasa_asmbl_4732.p1, internal, 148903, 149120
Valid prediction for Augustus_model.g16846.t1
Valid prediction for snap_scaffold_10-snap.2060-T1
Valid prediction for snap_scaffold_10-snap.2048-T1
Valid prediction for snap_scaffold_10-snap.2024-T1
Valid prediction for CodingQuarry_transcript_5551-T1
Valid prediction for Augustus_model.g16847.t1
Valid prediction for snap_scaffold_10-snap.2049-T1
Valid prediction for Augustus_model.g16838.t1
Valid prediction for snap_scaffold_10-snap.2032-T1
Couldn't classify 53024, 53149
Couldn't classify 53850, 53926
Sorry, prediction pasa_asmbl_4748.p1 fails validation.
(GGC)	 AG	53024-53149	GT	AGG
(GTG)	 AG	53436-53658	GT	AGG
(GCA)	 AG	53850-53926	GA	ACG
-recovered pasa_asmbl_4748.p1, internal, 53024, 53149
-recovered pasa_asmbl_4748.p1, internal, 53436, 53658
Valid prediction for Augustus_model.g16848.t1
Valid prediction for snap_scaffold_10-snap.2027-T1
Valid prediction for Augustus_model.g16861.t1
Couldn't classify 72438, 72492
Sorry, prediction pasa_asmbl_4742.p1 fails validation.
(ATG)	 AT	71032-71034	GT	TGG
(ATG)	 AG	71293-71412	GT	ATG
(GAA)	 AG	71600-71738	GT	GGG
(GCC)	 AG	71867-72020	GT	AGG
(GTT)	 AG	72128-72289	GT	AGG
(GAT)	 AG	72438-72492	CA	AGC
-recovered pasa_asmbl_4742.p1, initial, 71032, 71034
-recovered pasa_asmbl_4742.p1, initial, 71293, 71412
-recovered pasa_asmbl_4742.p1, internal, 71293, 71412
-recovered pasa_asmbl_4742.p1, internal, 71600, 71738
-recovered pasa_asmbl_4742.p1, internal, 71867, 72020
-recovered pasa_asmbl_4742.p1, internal, 72128, 72289
Valid prediction for snap_scaffold_10-snap.2044-T1
Valid prediction for CodingQuarry_transcript_5552-T1
Valid prediction for GlimmerHMM_glimmerT_25329-T1
Valid prediction for snap_scaffold_10-snap.2046-T1
Couldn't classify 37142, 37222
Couldn't classify 37491, 37793
Sorry, prediction pasa_asmbl_4750.p1 fails validation.
(AAC)	 AC	37142-37222	GT	AGG
(GAT)	 AG	37491-37793	AA	AGA
Valid prediction for Augustus_model.g16845.t1
Valid prediction for HiQ_model.g16852.t1
Valid prediction for GlimmerHMM_glimmerT_25343-T1
Couldn't classify 123399, 123488
Couldn't classify 125655, 126244
Sorry, prediction pasa_asmbl_4738.p1 fails validation.
(TCT)	 TG	123399-123488	GT	AGG
(GTG)	 AG	123693-123812	GT	AGG
(GGT)	 AG	123995-124131	GT	ACG
(GAA)	 AG	124270-124489	GT	TGG
(CTG)	 AG	124711-124893	GT	AGG
(CCC)	 AG	125160-125304	GT	GGG
(GTT)	 AG	125655-126244	GA	ACG
-recovered pasa_asmbl_4738.p1, internal, 123693, 123812
-recovered pasa_asmbl_4738.p1, internal, 123995, 124131
-recovered pasa_asmbl_4738.p1, internal, 124270, 124489
-recovered pasa_asmbl_4738.p1, internal, 124711, 124893
-recovered pasa_asmbl_4738.p1, internal, 125160, 125304
Valid prediction for snap_scaffold_10-snap.2043-T1
Valid prediction for snap_scaffold_10-snap.2039-T1
Valid prediction for snap_scaffold_10-snap.2021-T1
Valid prediction for snap_scaffold_10-snap.2056-T1
Valid prediction for snap_scaffold_10-snap.2031-T1
Valid prediction for snap_scaffold_10-snap.2034-T1
Valid prediction for GlimmerHMM_glimmerT_25349-T1
Valid prediction for Augustus_model.g16853.t1
Valid prediction for GlimmerHMM_glimmerT_25340-T1
Valid prediction for GlimmerHMM_glimmerT_25336-T1
Valid prediction for GlimmerHMM_glimmerT_25338-T1
Valid prediction for GlimmerHMM_glimmerT_25332-T1
Couldn't classify 126299, 126643
Sorry, prediction pasa_asmbl_4737.p1 fails validation.
(CAC)	 TT	126299-126643	GG	GCG
Valid prediction for snap_scaffold_10-snap.2020-T1
Valid prediction for snap_scaffold_10-snap.2036-T1
Couldn't classify 126695, 126995
Sorry, prediction pasa_asmbl_4736.p1 fails validation.
(CTC)	 AC	126695-126995	GT	AGG
(ATT)	 AG	127303-127646	GT	AGG
(AAC)	 AG	127785-131102	AT	GAA
-recovered pasa_asmbl_4736.p1, terminal, 127785, 131102
-recovered pasa_asmbl_4736.p1, internal, 127303, 127646
Valid prediction for snap_scaffold_10-snap.2055-T1
Valid prediction for GlimmerHMM_glimmerT_25346-T1
Valid prediction for CodingQuarry_transcript_5553-T1
Valid prediction for snap_scaffold_10-snap.2053-T1
Valid prediction for pasa_asmbl_4728.p1
Couldn't classify 12787, 12861
Couldn't classify 12998, 13219
Sorry, prediction pasa_asmbl_5121.p1 fails validation.
(GCG)	 AG	12787-12861	GT	AGG
(TTG)	 AG	12998-13219	GT	GGG
-recovered pasa_asmbl_5121.p1, internal, 12787, 12861
-recovered pasa_asmbl_5121.p1, internal, 12998, 13219
Valid prediction for GlimmerHMM_glimmerT_25341-T1
Valid prediction for GlimmerHMM_glimmerT_25327-T1
Valid prediction for snap_scaffold_10-snap.2059-T1
Valid prediction for Augustus_model.g16851.t1
Valid prediction for snap_scaffold_10-snap.2045-T1
Valid prediction for HiQ_model.g16840.t1
Valid prediction for snap_scaffold_10-snap.2037-T1
Valid prediction for GlimmerHMM_glimmerT_25334-T1
Valid prediction for CodingQuarry_transcript_5550-T1
Valid prediction for CodingQuarry_transcript_5548-T1
Valid prediction for Augustus_model.g16858.t1
Couldn't classify 73052, 73138
Sorry, prediction pasa_asmbl_4741.p1 fails validation.
(ACA)	 AC	73052-73138	GT	TAG
(ATC)	 AG	73387-73569	GT	TGG
(TCG)	 AG	73763-74036	GT	CAG
(GCT)	 AG	74166-74284	GT	GGG
(GCT)	 AG	74362-74484	GT	AGG
(GTC)	 AG	74649-74873	CT	AGC
-recovered pasa_asmbl_4741.p1, terminal, 74649, 74873
-recovered pasa_asmbl_4741.p1, internal, 73387, 73569
-recovered pasa_asmbl_4741.p1, internal, 73763, 74036
-recovered pasa_asmbl_4741.p1, internal, 74166, 74284
-recovered pasa_asmbl_4741.p1, internal, 74362, 74484
Couldn't classify 109976, 109988
Sorry, prediction pasa_asmbl_4740.p1 fails validation.
(GAA)	 CT	109976-109988	GT	AGG
(CTA)	 AG	110096-110244	GT	AGG
(AGT)	 AG	110332-110441	GT	AAG
(ATT)	 AG	110554-110701	AT	AAA
-recovered pasa_asmbl_4740.p1, terminal, 110554, 110701
-recovered pasa_asmbl_4740.p1, internal, 110096, 110244
-recovered pasa_asmbl_4740.p1, internal, 110332, 110441
Valid prediction for GlimmerHMM_glimmerT_25335-T1
Valid prediction for snap_scaffold_10-snap.2047-T1
Couldn't classify 36146, 36829
Sorry, prediction pasa_asmbl_4751.p1 fails validation.
(TAC)	 CG	36146-36829	AA	CTA
Valid prediction for Augustus_model.g16849.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14581, rend_intergenic: 2587  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24498, rend_intergenic: 19325  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67114, rend_intergenic: 61118  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92551, rend_intergenic: 87212  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95053, rend_intergenic: 94166  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117848, rend_intergenic: 114250  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141194, rend_intergenic: 137011  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176369, rend_intergenic: 173020  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188408, rend_intergenic: 179687  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 189122
-exon list size: 417


building trellis

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85.0    
85.2    
85.4    
85.7    
85.9    
86.2    
86.4    
86.6    
86.9    
87.1    
87.4    
87.6    
87.8    
88.1    
88.3    
88.5    
88.8    
89.0    
89.3    
89.5    
89.7    
90.0    
90.2    
90.5    
90.7    
90.9    
91.2    
91.4    
91.6    
91.9    
92.1    
92.4    
92.6    
92.8    
93.1    
93.3    
93.6    
93.8    
94.0    
94.3    
94.5    
94.7    
95.0    
95.2    
95.5    
95.7    
95.9    
96.2    
96.4    
96.7    
96.9    
97.1    
97.4    
97.6    
97.9    
98.1    
98.3    
98.6    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 14581, rend_intergenic: 2587  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24498, rend_intergenic: 19325  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67114, rend_intergenic: 61118  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92551, rend_intergenic: 87212  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95053, rend_intergenic: 94166  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117848, rend_intergenic: 114250  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141194, rend_intergenic: 137011  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176369, rend_intergenic: 173020  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188408, rend_intergenic: 179687  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 29 predictions persist after filtering for low support