-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_28/scaffold_28_7842327-8032551

-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_28-snap.1775-T1
Valid prediction for GlimmerHMM_glimmerT_59176-T1
Valid prediction for snap_scaffold_28-snap.1796-T1
Valid prediction for GlimmerHMM_glimmerT_59202-T1
Valid prediction for GlimmerHMM_glimmerT_59198-T1
Valid prediction for pasa_asmbl_37716.p1
Valid prediction for snap_scaffold_28-snap.1799-T1
Valid prediction for GlimmerHMM_glimmerT_59196-T1
Valid prediction for GlimmerHMM_glimmerT_59179-T1
Valid prediction for snap_scaffold_28-snap.1794-T1
Valid prediction for snap_scaffold_28-snap.1788-T1
Valid prediction for GlimmerHMM_glimmerT_59199-T1
Valid prediction for snap_scaffold_28-snap.1793-T1
Valid prediction for snap_scaffold_28-snap.1774-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for Augustus_model.g39225.t1
Valid prediction for snap_scaffold_28-snap.1772-T1
Valid prediction for Augustus_model.g39230.t1
Valid prediction for GlimmerHMM_glimmerT_59189-T1
Valid prediction for GlimmerHMM_glimmerT_59182-T1
Couldn't classify 40788, 41088
Couldn't classify 42038, 42110
Sorry, prediction pasa_asmbl_37712.p1 fails validation.
(CAG)	 GT	40788-41088	GT	CTG
(ATC)	 AG	41438-41564	GT	AGG
(ATC)	 AG	42038-42110	CC	CCC
-recovered pasa_asmbl_37712.p1, internal, 41438, 41564
Valid prediction for snap_scaffold_28-snap.1800-T1
Valid prediction for GlimmerHMM_glimmerT_59185-T1
Valid prediction for snap_scaffold_28-snap.1790-T1
Valid prediction for CodingQuarry_transcript_43730-T1
Valid prediction for snap_scaffold_28-snap.1795-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_59203-T1
Valid prediction for GlimmerHMM_glimmerT_59200-T1
Valid prediction for snap_scaffold_28-snap.1784-T1
Valid prediction for snap_scaffold_28-snap.1778-T1
Valid prediction for snap_scaffold_28-snap.1798-T1
Valid prediction for Augustus_model.g39220.t1
Valid prediction for HiQ_model.g39232.t1
Valid prediction for snap_scaffold_28-snap.1783-T1
Valid prediction for snap_scaffold_28-snap.1802-T1
Valid prediction for GlimmerHMM_glimmerT_59184-T1
Valid prediction for snap_scaffold_28-snap.1807-T1
Valid prediction for GlimmerHMM_glimmerT_59188-T1
Valid prediction for snap_scaffold_28-snap.1779-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.g39221.t1
Valid prediction for snap_scaffold_28-snap.1806-T1
Couldn't classify 32802, 32849
Couldn't classify 34954, 34991
Sorry, prediction pasa_asmbl_38610.p1 fails validation.
(ACT)	 GG	32802-32849	GT	CTG
(GTA)	 AG	33799-34011	GT	CGG
(AGG)	 AG	34682-34832	GT	AAG
(CCC)	 AG	34954-34991	GT	CGG
-recovered pasa_asmbl_38610.p1, internal, 33799, 34011
-recovered pasa_asmbl_38610.p1, internal, 34682, 34832
-recovered pasa_asmbl_38610.p1, internal, 34954, 34991
Couldn't classify 35549, 35631
Couldn't classify 36489, 36591
Sorry, prediction pasa_asmbl_38598.p2 fails validation.
(TAT)	 TC	35549-35631	GT	TCG
(GGA)	 AG	36027-36117	GT	CGG
(ATC)	 AG	36263-36381	GT	CTG
(GCA)	 AG	36489-36591	CT	GGC
-recovered pasa_asmbl_38598.p2, internal, 36027, 36117
-recovered pasa_asmbl_38598.p2, internal, 36263, 36381
Valid prediction for snap_scaffold_28-snap.1781-T1
Valid prediction for snap_scaffold_28-snap.1791-T1
Valid prediction for GlimmerHMM_glimmerT_59177-T1
Couldn't classify 26434, 26536
Sorry, prediction pasa_asmbl_38566.p1 fails validation.
(TTC)	 AC	26434-26536	GT	AGG
(GTG)	 AG	26635-26727	GT	AGG
(GTG)	 AG	26879-27001	GT	CGG
(TGG)	 AG	27099-27173	GT	AGG
(GAT)	 AG	27375-27473	GT	AGG
(TGA)	 AG	27598-27715	GT	AGG
(AGA)	 AG	27804-27907	GT	ATG
(TTT)	 AG	28171-28318	GT	AGG
(TTA)	 AG	28430-28573	GT	AGG
(GTT)	 AG	28693-28781	GT	AGG
(GAG)	 AG	28865-28986	AA	AGA
add_exon() Sorry, pasa_asmbl_38566.p1 27598-27715-terminal-3 is invalid.
-recovered pasa_asmbl_38566.p1, terminal, 27598, 27715
-recovered pasa_asmbl_38566.p1, terminal, 28865, 28986
-recovered pasa_asmbl_38566.p1, internal, 26635, 26727
-recovered pasa_asmbl_38566.p1, internal, 26879, 27001
-recovered pasa_asmbl_38566.p1, internal, 27099, 27173
-recovered pasa_asmbl_38566.p1, internal, 27375, 27473
-recovered pasa_asmbl_38566.p1, internal, 27598, 27715
-recovered pasa_asmbl_38566.p1, internal, 27804, 27907
-recovered pasa_asmbl_38566.p1, internal, 28171, 28318
-recovered pasa_asmbl_38566.p1, internal, 28430, 28573
-recovered pasa_asmbl_38566.p1, internal, 28693, 28781
Valid prediction for Augustus_model.g39227.t1
Valid prediction for snap_scaffold_28-snap.1797-T1
Valid prediction for snap_scaffold_28-snap.1792-T1
Valid prediction for Augustus_model.g39218.t1
Valid prediction for snap_scaffold_28-snap.1780-T1
Couldn't classify 185539, 186027
Sorry, prediction pasa_asmbl_38424.p1 fails validation.
(GAG)	 GA	185539-186027	CA	AAC
Valid prediction for snap_scaffold_28-snap.1776-T1
Valid prediction for snap_scaffold_28-snap.1782-T1
Valid prediction for snap_scaffold_28-snap.1787-T1
Valid prediction for snap_scaffold_28-snap.1803-T1
Valid prediction for Augustus_model.g39223.t1
Valid prediction for snap_scaffold_28-snap.1785-T1
Valid prediction for GlimmerHMM_glimmerT_59180-T1
Valid prediction for Augustus_model.g39228.t1
Valid prediction for GlimmerHMM_glimmerT_59192-T1
Valid prediction for snap_scaffold_28-snap.1789-T1
Valid prediction for Augustus_model.g39229.t1
Valid prediction for GlimmerHMM_glimmerT_59194-T1
Valid prediction for GlimmerHMM_glimmerT_59201-T1
Valid prediction for GlimmerHMM_glimmerT_59191-T1
Valid prediction for snap_scaffold_28-snap.1805-T1
Valid prediction for Augustus_model.g39216.t1
Valid prediction for Augustus_model.g39231.t1
Valid prediction for GlimmerHMM_glimmerT_59195-T1
Valid prediction for Augustus_model.g39217.t1
Valid prediction for Augustus_model.g39226.t1
Valid prediction for GlimmerHMM_glimmerT_59197-T1
Couldn't classify 184335, 184745
Sorry, prediction pasa_asmbl_38425.p1 fails validation.
(GGA)	 AA	184335-184745	GC	CCG
Valid prediction for snap_scaffold_28-snap.1804-T1
Valid prediction for snap_scaffold_28-snap.1801-T1
Valid prediction for GlimmerHMM_glimmerT_59183-T1
Valid prediction for HiQ_model.g39219.t1
Valid prediction for snap_scaffold_28-snap.1808-T1
Valid prediction for Augustus_model.g39224.t1
Couldn't classify 150352, 150382
Couldn't classify 158250, 158353
Sorry, prediction pasa_asmbl_38429.p1 fails validation.
(CGA)	 AC	150352-150382	GT	GGG
(ATT)	 AG	151136-151172	GT	GGG
(CTA)	 AG	151280-151331	GT	AGG
(CAG)	 AG	151489-151639	GT	AGG
(CGG)	 AG	151858-151872	GT	AGG
(CCG)	 AG	152188-152386	GT	AGG
(CTA)	 AG	152795-153066	GT	CAG
(ACA)	 AG	153329-153494	GT	AGG
(CAT)	 AG	155960-155997	GT	TGG
(GAC)	 AG	156772-156804	GT	GGG
(GGC)	 AG	156927-157042	GT	GGG
(ATG)	 AG	157206-157335	GT	TGG
(GTA)	 AG	157441-157551	GT	AGG
(GTA)	 AG	157674-157800	GT	CCG
(GGG)	 AG	157918-158018	GT	TGG
(GAG)	 AG	158250-158353	GG	GAG
-recovered pasa_asmbl_38429.p1, initial, 157206, 157335
-recovered pasa_asmbl_38429.p1, internal, 151136, 151172
-recovered pasa_asmbl_38429.p1, internal, 151280, 151331
-recovered pasa_asmbl_38429.p1, internal, 151489, 151639
-recovered pasa_asmbl_38429.p1, internal, 151858, 151872
-recovered pasa_asmbl_38429.p1, internal, 152188, 152386
-recovered pasa_asmbl_38429.p1, internal, 152795, 153066
-recovered pasa_asmbl_38429.p1, internal, 153329, 153494
-recovered pasa_asmbl_38429.p1, internal, 155960, 155997
-recovered pasa_asmbl_38429.p1, internal, 156772, 156804
-recovered pasa_asmbl_38429.p1, internal, 156927, 157042
-recovered pasa_asmbl_38429.p1, internal, 157206, 157335
-recovered pasa_asmbl_38429.p1, internal, 157441, 157551
-recovered pasa_asmbl_38429.p1, internal, 157674, 157800
-recovered pasa_asmbl_38429.p1, internal, 157918, 158018
Couldn't classify 158250, 158353
Sorry, prediction pasa_asmbl_38431.p1 fails validation.
(ATG)	 CC	156777-156804	GT	GGG
(GGC)	 AG	156927-157042	GT	GGG
(ATG)	 AG	157206-157335	GT	TGG
(GTA)	 AG	157441-157551	GT	AGG
(GTA)	 AG	157674-157800	GT	CCG
(GGG)	 AG	157918-158018	GT	TGG
(GAG)	 AG	158250-158353	GG	GAG
-recovered pasa_asmbl_38431.p1, initial, 156777, 156804
-recovered pasa_asmbl_38431.p1, initial, 157206, 157335
-recovered pasa_asmbl_38431.p1, internal, 156927, 157042
-recovered pasa_asmbl_38431.p1, internal, 157206, 157335
-recovered pasa_asmbl_38431.p1, internal, 157441, 157551
-recovered pasa_asmbl_38431.p1, internal, 157674, 157800
-recovered pasa_asmbl_38431.p1, internal, 157918, 158018
Valid prediction for GlimmerHMM_glimmerT_59190-T1
Valid prediction for GlimmerHMM_glimmerT_59175-T1
Valid prediction for Augustus_model.g39222.t1
Valid prediction for GlimmerHMM_glimmerT_59193-T1
Valid prediction for snap_scaffold_28-snap.1773-T1
Valid prediction for GlimmerHMM_glimmerT_59178-T1
Valid prediction for GlimmerHMM_glimmerT_59186-T1
Valid prediction for snap_scaffold_28-snap.1786-T1
Valid prediction for GlimmerHMM_glimmerT_59174-T1
Valid prediction for GlimmerHMM_glimmerT_59181-T1
Valid prediction for CodingQuarry_transcript_43729-T1
Valid prediction for GlimmerHMM_glimmerT_59187-T1
Valid prediction for snap_scaffold_28-snap.1777-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 5780, rend_intergenic: 5349  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13825, rend_intergenic: 7123  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19036, rend_intergenic: 14233  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23961, rend_intergenic: 19977  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27512, rend_intergenic: 26079  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59874, rend_intergenic: 43697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81239, rend_intergenic: 60083  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105383, rend_intergenic: 82613  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117042, rend_intergenic: 107048  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147555, rend_intergenic: 120310  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159892, rend_intergenic: 151619  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178474, rend_intergenic: 166532  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187532, rend_intergenic: 182240  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 190225
-exon list size: 611


building trellis

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91.0    
91.2    
91.4    
91.5    
91.7    
91.8    
92.0    
92.2    
92.3    
92.5    
92.7    
92.8    
93.0    
93.1    
93.3    
93.5    
93.6    
93.8    
94.0    
94.1    
94.3    
94.5    
94.6    
94.8    
94.9    
95.1    
95.3    
95.4    
95.6    
95.8    
95.9    
96.1    
96.2    
96.4    
96.6    
96.7    
96.9    
97.1    
97.2    
97.4    
97.6    
97.7    
97.9    
98.0    
98.2    
98.4    
98.5    
98.7    
98.9    
99.0    
99.2    
99.3    
99.5    
99.7    
99.8    
-found 22 predictions from path traversal
Error with prediction: snap lend_intergenic: 5780, rend_intergenic: 5349  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13825, rend_intergenic: 7123  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19036, rend_intergenic: 14233  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23961, rend_intergenic: 19977  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27512, rend_intergenic: 26079  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59874, rend_intergenic: 43697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81239, rend_intergenic: 60083  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105383, rend_intergenic: 82613  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117042, rend_intergenic: 107048  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147555, rend_intergenic: 120310  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159892, rend_intergenic: 151619  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178474, rend_intergenic: 166532  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187532, rend_intergenic: 182240  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support