-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_2/scaffold_2_6138022-6408908

-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_2-snap.1374-T1
Couldn't classify 161172, 161436
Sorry, prediction pasa_asmbl_24457.p1 fails validation.
(CTG)	 GC	161172-161436	GT	TGG
(GGG)	 AG	161615-162540	GA	AAG
-recovered pasa_asmbl_24457.p1, terminal, 161615, 162540
Valid prediction for GlimmerHMM_glimmerT_3913-T1
Valid prediction for snap_scaffold_2-snap.1377-T1
Valid prediction for GlimmerHMM_glimmerT_3918-T1
Valid prediction for GlimmerHMM_glimmerT_3930-T1
Couldn't classify 47622, 47717
Couldn't classify 50565, 50659
Sorry, prediction pasa_asmbl_25408.p1 fails validation.
(GGG)	 CC	47622-47717	GT	GGG
(CAA)	 AG	47978-48095	GT	TGG
(GGT)	 AG	50565-50659	GG	TCG
-recovered pasa_asmbl_25408.p1, internal, 47978, 48095
Valid prediction for snap_scaffold_2-snap.1397-T1
Valid prediction for snap_scaffold_2-snap.1394-T1
Valid prediction for snap_scaffold_2-snap.1389-T1
Valid prediction for snap_scaffold_2-snap.1380-T1
Couldn't classify 216717, 216725
Sorry, prediction pasa_asmbl_24461.p1 fails validation.
(TAC)	 CC	216717-216725	GT	GGG
(GAC)	 AG	216855-217073	GT	TTG
(GAA)	 AG	217300-217512	GT	AGG
(GTG)	 AG	217763-217980	GT	AGG
(GTC)	 AG	219103-219271	TT	GAT
-recovered pasa_asmbl_24461.p1, terminal, 219103, 219271
-recovered pasa_asmbl_24461.p1, internal, 216855, 217073
-recovered pasa_asmbl_24461.p1, internal, 217300, 217512
-recovered pasa_asmbl_24461.p1, internal, 217763, 217980
Valid prediction for GlimmerHMM_glimmerT_3923-T1
Couldn't classify 204182, 204187
Sorry, prediction pasa_asmbl_24460.p1 fails validation.
(GAC)	 TT	204182-204187	GT	GGG
(ACC)	 AG	204410-204509	GT	GAG
(AGC)	 AG	205128-205280	GT	AGG
(CCA)	 AG	205716-207154	TG	AGT
-recovered pasa_asmbl_24460.p1, terminal, 205716, 207154
-recovered pasa_asmbl_24460.p1, internal, 204410, 204509
-recovered pasa_asmbl_24460.p1, internal, 205128, 205280
Valid prediction for GlimmerHMM_glimmerT_3932-T1
Valid prediction for snap_scaffold_2-snap.1395-T1
Valid prediction for GlimmerHMM_glimmerT_3938-T1
Couldn't classify 198748, 198821
Couldn't classify 200059, 200070
Sorry, prediction pasa_asmbl_24459.p1 fails validation.
(GGC)	 AA	198748-198821	GT	CAG
(CGA)	 AG	199150-199189	GT	AGG
(CAT)	 AG	199357-199437	GT	AGG
(ATG)	 AG	199779-199886	GT	AGG
(AAA)	 AG	200059-200070	CA	GGC
-recovered pasa_asmbl_24459.p1, initial, 199779, 199886
-recovered pasa_asmbl_24459.p1, internal, 199150, 199189
-recovered pasa_asmbl_24459.p1, internal, 199357, 199437
-recovered pasa_asmbl_24459.p1, internal, 199779, 199886
Valid prediction for snap_scaffold_2-snap.1383-T1
Valid prediction for Augustus_model.g2623.t1
Valid prediction for Augustus_model.g2625.t1
Valid prediction for pasa_asmbl_24458.p1
Valid prediction for Augustus_model.g2618.t1
Valid prediction for Augustus_model.g2613.t1
Valid prediction for snap_scaffold_2-snap.1393-T1
Valid prediction for GlimmerHMM_glimmerT_3916-T1
Valid prediction for GlimmerHMM_glimmerT_3912-T1
Valid prediction for snap_scaffold_2-snap.1368-T1
Valid prediction for snap_scaffold_2-snap.1370-T1
Valid prediction for Augustus_model.g2617.t1
Valid prediction for Augustus_model.g2614.t1
Valid prediction for GlimmerHMM_glimmerT_3914-T1
Valid prediction for GlimmerHMM_glimmerT_3911-T1
Valid prediction for HiQ_model.g2621.t1
Valid prediction for snap_scaffold_2-snap.1387-T1
Valid prediction for snap_scaffold_2-snap.1376-T1
Valid prediction for Augustus_model.g2616.t1
Valid prediction for snap_scaffold_2-snap.1365-T1
Valid prediction for snap_scaffold_2-snap.1379-T1
Valid prediction for GlimmerHMM_glimmerT_3917-T1
Valid prediction for snap_scaffold_2-snap.1386-T1
Valid prediction for snap_scaffold_2-snap.1404-T1
Valid prediction for GlimmerHMM_glimmerT_3921-T1
Valid prediction for GlimmerHMM_glimmerT_3919-T1
Valid prediction for GlimmerHMM_glimmerT_3935-T1
Valid prediction for GlimmerHMM_glimmerT_3934-T1
Couldn't classify 160812, 161114
Sorry, prediction pasa_asmbl_24456.p1 fails validation.
(CGC)	 GC	160812-161114	GT	AGG
Valid prediction for GlimmerHMM_glimmerT_3928-T1
Valid prediction for snap_scaffold_2-snap.1367-T1
Valid prediction for GlimmerHMM_glimmerT_3937-T1
Valid prediction for GlimmerHMM_glimmerT_3933-T1
Valid prediction for snap_scaffold_2-snap.1373-T1
Valid prediction for CodingQuarry_transcript_28571-T1
Valid prediction for GlimmerHMM_glimmerT_3924-T1
Valid prediction for Augustus_model.g2622.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_3926-T1
Valid prediction for snap_scaffold_2-snap.1398-T1
Valid prediction for snap_scaffold_2-snap.1392-T1
Valid prediction for snap_scaffold_2-snap.1381-T1
Valid prediction for CodingQuarry_transcript_28573-T1
Valid prediction for snap_scaffold_2-snap.1366-T1
Valid prediction for Augustus_model.g2628.t1
Valid prediction for snap_scaffold_2-snap.1407-T1
Valid prediction for CodingQuarry_transcript_28574-T1
Valid prediction for GlimmerHMM_glimmerT_3936-T1
Valid prediction for snap_scaffold_2-snap.1391-T1
Valid prediction for HiQ_model.g2619.t1
Valid prediction for HiQ_model.g2624.t1
Valid prediction for snap_scaffold_2-snap.1364-T1
Valid prediction for snap_scaffold_2-snap.1369-T1
Valid prediction for HiQ_model.g2627.t1
Valid prediction for GlimmerHMM_glimmerT_3927-T1
Valid prediction for snap_scaffold_2-snap.1384-T1
Valid prediction for GlimmerHMM_glimmerT_3920-T1
Valid prediction for snap_scaffold_2-snap.1388-T1
Valid prediction for GlimmerHMM_glimmerT_3929-T1
Valid prediction for snap_scaffold_2-snap.1390-T1
Valid prediction for CodingQuarry_transcript_28575-T1
Valid prediction for snap_scaffold_2-snap.1371-T1
Valid prediction for snap_scaffold_2-snap.1406-T1
Valid prediction for GlimmerHMM_glimmerT_3941-T1
Valid prediction for snap_scaffold_2-snap.1399-T1
Couldn't classify 30042, 30144
Sorry, prediction pasa_asmbl_23200.p2 fails validation.
(CCG)	 CA	30042-30144	GT	ATG
(TGC)	 AG	30252-30299	GC	AGG
(AAA)	 AG	30415-30459	GT	GGG
(TGT)	 AG	30736-30851	CC	GAC
-recovered pasa_asmbl_23200.p2, terminal, 30736, 30851
-recovered pasa_asmbl_23200.p2, internal, 30252, 30299
-recovered pasa_asmbl_23200.p2, internal, 30415, 30459
Valid prediction for GlimmerHMM_glimmerT_3939-T1
Valid prediction for snap_scaffold_2-snap.1396-T1
Valid prediction for Augustus_model.g2620.t1
Valid prediction for snap_scaffold_2-snap.1405-T1
Valid prediction for snap_scaffold_2-snap.1403-T1
Valid prediction for GlimmerHMM_glimmerT_3931-T1
Valid prediction for snap_scaffold_2-snap.1372-T1
Valid prediction for GlimmerHMM_glimmerT_3922-T1
Valid prediction for pasa_asmbl_23197.p1
Valid prediction for HiQ_model.g2626.t1
Valid prediction for GlimmerHMM_glimmerT_3915-T1
Valid prediction for snap_scaffold_2-snap.1375-T1
Valid prediction for pasa_asmbl_23193.p1
Valid prediction for snap_scaffold_2-snap.1401-T1
Valid prediction for snap_scaffold_2-snap.1400-T1
Valid prediction for snap_scaffold_2-snap.1382-T1
Valid prediction for Augustus_model.g2615.t1
Valid prediction for CodingQuarry_transcript_28572-T1
Valid prediction for CodingQuarry_transcript_28570-T1
Valid prediction for snap_scaffold_2-snap.1378-T1
Valid prediction for snap_scaffold_2-snap.1402-T1
Valid prediction for Augustus_model.g2629.t1
Valid prediction for GlimmerHMM_glimmerT_3940-T1
Valid prediction for GlimmerHMM_glimmerT_3942-T1
Couldn't classify 92907, 92907
Couldn't classify 101933, 102067
Sorry, prediction pasa_asmbl_23191.p1 fails validation.
(AGT)	 AC	92907-92907	GT	CAG
(TGT)	 AG	93197-93258	GT	AGG
(GTA)	 AG	93375-93602	GT	AGG
(GAT)	 AG	93806-93870	GT	AGG
(GAG)	 AG	94246-94476	GT	CAG
(CGG)	 AG	97240-97359	GT	GGG
(AGA)	 AG	98137-98249	GT	GAG
(GGT)	 AG	98657-98692	GT	CGG
(ACA)	 AG	101002-101048	GT	AGG
(GAG)	 AG	101933-102067	GT	AGG
-recovered pasa_asmbl_23191.p1, internal, 93197, 93258
-recovered pasa_asmbl_23191.p1, internal, 93375, 93602
-recovered pasa_asmbl_23191.p1, internal, 93806, 93870
-recovered pasa_asmbl_23191.p1, internal, 94246, 94476
-recovered pasa_asmbl_23191.p1, internal, 97240, 97359
-recovered pasa_asmbl_23191.p1, internal, 98137, 98249
-recovered pasa_asmbl_23191.p1, internal, 98657, 98692
-recovered pasa_asmbl_23191.p1, internal, 101002, 101048
-recovered pasa_asmbl_23191.p1, internal, 101933, 102067
Couldn't classify 40965, 41104
Sorry, prediction pasa_asmbl_23198.p1 fails validation.
(ATG)	 GG	34852-34929	GT	AGG
(AAA)	 AG	35532-35572	GT	GGG
(TTG)	 AG	35687-35759	GT	CGG
(AAT)	 AG	36413-36463	GT	CGG
(GGT)	 AG	36665-36834	GT	GAG
(GGC)	 AG	37473-37572	GT	AGG
(ATT)	 AG	37724-37875	GT	GTG
(GAC)	 AG	38081-38159	GT	AGG
(GAT)	 AG	39377-39427	GT	AGG
(AAC)	 AG	39597-39719	GT	AGG
(GAC)	 AG	39854-39976	GT	CTG
(AAC)	 AG	40180-40284	GT	GGG
(TTT)	 AG	40470-40578	GT	CCG
(CGT)	 AG	40965-41104	CC	TGC
-recovered pasa_asmbl_23198.p1, initial, 34852, 34929
add_exon() Sorry, pasa_asmbl_23198.p1 36665-36834-terminal-2 is invalid.
-recovered pasa_asmbl_23198.p1, terminal, 36665, 36834
-recovered pasa_asmbl_23198.p1, internal, 35532, 35572
-recovered pasa_asmbl_23198.p1, internal, 35687, 35759
-recovered pasa_asmbl_23198.p1, internal, 36413, 36463
-recovered pasa_asmbl_23198.p1, internal, 36665, 36834
-recovered pasa_asmbl_23198.p1, internal, 37473, 37572
-recovered pasa_asmbl_23198.p1, internal, 37724, 37875
-recovered pasa_asmbl_23198.p1, internal, 38081, 38159
-recovered pasa_asmbl_23198.p1, internal, 39377, 39427
-recovered pasa_asmbl_23198.p1, internal, 39597, 39719
-recovered pasa_asmbl_23198.p1, internal, 39854, 39976
-recovered pasa_asmbl_23198.p1, internal, 40180, 40284
-recovered pasa_asmbl_23198.p1, internal, 40470, 40578
Valid prediction for snap_scaffold_2-snap.1385-T1
Valid prediction for GlimmerHMM_glimmerT_3925-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 25550, rend_intergenic: 22471  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33423, rend_intergenic: 31663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34467, rend_intergenic: 34139  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45927, rend_intergenic: 37602  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80088, rend_intergenic: 72719  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158341, rend_intergenic: 153292  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 207154, rend_intergenic: 194408  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 227953, rend_intergenic: 225416  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 259019, rend_intergenic: 252151  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 270887
-exon list size: 429


building trellis

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98.8    
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99.3    
99.5    
99.8    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 25550, rend_intergenic: 22471  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33423, rend_intergenic: 31663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34467, rend_intergenic: 34139  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45927, rend_intergenic: 37602  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80088, rend_intergenic: 72719  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158341, rend_intergenic: 153292  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 207154, rend_intergenic: 194408  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 227953, rend_intergenic: 225416  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 259019, rend_intergenic: 252151  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 24454
-exon list size: 16


building trellis

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50.0    
55.6    
61.1    
66.7    
72.2    
77.8    
83.3    
88.9    
94.4    
-found 2 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support