-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_7/scaffold_7_8537019-8736065

-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 GlimmerHMM_glimmerT_17803-T1
Valid prediction for snap_scaffold_7-snap.1706-T1
Sorry, intron length (4) is less than minimum required (10)
Couldn't classify 72865, 72871
Sorry, prediction pasa_asmbl_50027.p1 fails validation.
(CCA)	 CA	72865-72871	GT	TGG
(TTC)	 AG	73033-73227	GT	AGG
(AAT)	 AG	73415-73561	GT	AGG
(ACG)	 AG	73696-73899	GT	AGG
(GTG)	 AG	74128-74365	GT	AGG
(GCC)	 AG	74573-74688	GT	TGG
(CTC)	 AG	74903-75078	AC	GAA
-recovered pasa_asmbl_50027.p1, terminal, 74903, 75078
-recovered pasa_asmbl_50027.p1, internal, 73033, 73227
-recovered pasa_asmbl_50027.p1, internal, 73415, 73561
-recovered pasa_asmbl_50027.p1, internal, 73696, 73899
-recovered pasa_asmbl_50027.p1, internal, 74128, 74365
-recovered pasa_asmbl_50027.p1, internal, 74573, 74688
Valid prediction for GlimmerHMM_glimmerT_17789-T1
Valid prediction for Augustus_model.g11951.t1
Couldn't classify 72364, 72634
Couldn't classify 72764, 72840
Sorry, prediction pasa_asmbl_50026.p1 fails validation.
(GAA)	 CT	72364-72634	GT	TGG
(GTG)	 AG	72764-72840	GG	TGG
Valid prediction for snap_scaffold_7-snap.1691-T1
Valid prediction for GlimmerHMM_glimmerT_17808-T1
Valid prediction for snap_scaffold_7-snap.1703-T1
Valid prediction for CodingQuarry_transcript_57572-T1
Valid prediction for snap_scaffold_7-snap.1717-T1
Valid prediction for snap_scaffold_7-snap.1723-T1
Valid prediction for snap_scaffold_7-snap.1694-T1
Valid prediction for snap_scaffold_7-snap.1718-T1
Valid prediction for GlimmerHMM_glimmerT_17790-T1
Valid prediction for pasa_asmbl_50024.p3
Valid prediction for Augustus_model.g11946.t1
Couldn't classify 16629, 16733
Sorry, prediction pasa_asmbl_50015.p1 fails validation.
(CGC)	 GC	16629-16733	GT	TGG
(GTC)	 AG	17076-17268	GT	GGG
(GCT)	 AG	17612-17909	GT	AGG
(TGA)	 AG	18026-18201	GT	AGG
(GCA)	 AG	18451-18581	GT	AGG
(TGT)	 AG	18734-18859	CC	GAC
-recovered pasa_asmbl_50015.p1, terminal, 18734, 18859
-recovered pasa_asmbl_50015.p1, internal, 17076, 17268
-recovered pasa_asmbl_50015.p1, internal, 17612, 17909
-recovered pasa_asmbl_50015.p1, internal, 18026, 18201
-recovered pasa_asmbl_50015.p1, internal, 18451, 18581
Valid prediction for snap_scaffold_7-snap.1707-T1
Valid prediction for Augustus_model.g11936.t1
Valid prediction for HiQ_model.g11953.t1
Valid prediction for snap_scaffold_7-snap.1702-T1
Valid prediction for snap_scaffold_7-snap.1713-T1
Valid prediction for GlimmerHMM_glimmerT_17796-T1
Couldn't classify 138406, 138538
Couldn't classify 139254, 139385
Sorry, prediction pasa_asmbl_50034.p1 fails validation.
(AAT)	 GG	138406-138538	GT	AGG
(ATG)	 AG	138784-138852	GT	TGG
(GCT)	 AG	138945-139069	GT	AGG
(GTG)	 AG	139254-139385	AA	TGA
add_exon() Sorry, pasa_asmbl_50034.p1 138784-138852-initial-1 is invalid.
-recovered pasa_asmbl_50034.p1, initial, 138784, 138852
-recovered pasa_asmbl_50034.p1, internal, 138784, 138852
-recovered pasa_asmbl_50034.p1, internal, 138945, 139069
Valid prediction for snap_scaffold_7-snap.1700-T1
Valid prediction for Augustus_model.g11940.t1
Valid prediction for snap_scaffold_7-snap.1719-T1
Valid prediction for GlimmerHMM_glimmerT_17792-T1
Valid prediction for pasa_asmbl_50030.p1
Valid prediction for GlimmerHMM_glimmerT_17785-T1
Valid prediction for snap_scaffold_7-snap.1692-T1
Valid prediction for GlimmerHMM_glimmerT_17781-T1
Valid prediction for snap_scaffold_7-snap.1705-T1
Valid prediction for snap_scaffold_7-snap.1698-T1
Couldn't classify 48466, 48568
Sorry, prediction pasa_asmbl_50021.p1 fails validation.
(CTC)	 AG	48466-48568	GT	AGG
(TGG)	 AG	48734-48861	GT	CGG
(GAG)	 AG	49133-49159	GT	AGG
(GCT)	 AG	50794-50841	GT	AGG
-recovered pasa_asmbl_50021.p1, terminal, 50794, 50841
-recovered pasa_asmbl_50021.p1, internal, 48466, 48568
-recovered pasa_asmbl_50021.p1, internal, 48734, 48861
-recovered pasa_asmbl_50021.p1, internal, 49133, 49159
-recovered pasa_asmbl_50021.p1, internal, 50794, 50841
Couldn't classify 142399, 142677
Sorry, prediction pasa_asmbl_50600.p2 fails validation.
(ATG)	 AA	142196-142249	GT	AGG
(AAC)	 AG	142399-142677	GA	GGG
-recovered pasa_asmbl_50600.p2, initial, 142196, 142249
Valid prediction for snap_scaffold_7-snap.1714-T1
Valid prediction for GlimmerHMM_glimmerT_17812-T1
Valid prediction for HiQ_model.g11938.t1
Valid prediction for Augustus_model.g11937.t1
Valid prediction for GlimmerHMM_glimmerT_17807-T1
Valid prediction for Augustus_model.g11934.t1
Valid prediction for GlimmerHMM_glimmerT_17810-T1
Valid prediction for Augustus_model.g11948.t1
Couldn't classify 71335, 71802
Sorry, prediction pasa_asmbl_50025.p1 fails validation.
(AAA)	 CC	71335-71802	AC	CCA
Valid prediction for CodingQuarry_transcript_57568-T1
Valid prediction for HiQ_model.g11941.t1
Valid prediction for GlimmerHMM_glimmerT_17804-T1
Valid prediction for GlimmerHMM_glimmerT_17800-T1
Valid prediction for GlimmerHMM_glimmerT_17794-T1
Valid prediction for GlimmerHMM_glimmerT_17782-T1
Valid prediction for snap_scaffold_7-snap.1721-T1
Couldn't classify 156184, 156287
Sorry, prediction pasa_asmbl_50038.p1 fails validation.
(CAT)	 CC	156184-156287	GT	AGG
(AGG)	 AG	156486-156516	GT	AAG
(GTT)	 AG	156661-156706	GT	AGG
(GTT)	 AG	156810-156939	GT	GGG
(AGT)	 AG	157140-157177	GT	AGG
(GAA)	 AG	157565-157644	GT	TGG
(GTG)	 AG	157732-157814	GT	AAG
(TGT)	 AG	158426-158504	GT	AGG
(CTC)	 AG	159061-159188	GT	AGG
(TGA)	 AG	159602-159635	CA	AGC
-recovered pasa_asmbl_50038.p1, terminal, 159602, 159635
-recovered pasa_asmbl_50038.p1, internal, 156486, 156516
-recovered pasa_asmbl_50038.p1, internal, 156661, 156706
-recovered pasa_asmbl_50038.p1, internal, 156810, 156939
-recovered pasa_asmbl_50038.p1, internal, 157140, 157177
-recovered pasa_asmbl_50038.p1, internal, 157565, 157644
-recovered pasa_asmbl_50038.p1, internal, 157732, 157814
-recovered pasa_asmbl_50038.p1, internal, 158426, 158504
-recovered pasa_asmbl_50038.p1, internal, 159061, 159188
Valid prediction for GlimmerHMM_glimmerT_17805-T1
Valid prediction for GlimmerHMM_glimmerT_17779-T1
Couldn't classify 15258, 15418
Couldn't classify 15984, 16079
Sorry, prediction pasa_asmbl_50014.p1 fails validation.
(GCA)	 CA	15258-15418	GT	GAG
(GAC)	 AG	15646-15748	GT	AGG
(GAT)	 AG	15984-16079	CC	AAC
-recovered pasa_asmbl_50014.p1, internal, 15646, 15748
Valid prediction for Augustus_model.g11932.t1
Valid prediction for HiQ_model.g11950.t1
Valid prediction for snap_scaffold_7-snap.1710-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 pasa_asmbl_51015.p1
Valid prediction for snap_scaffold_7-snap.1725-T1
Valid prediction for snap_scaffold_7-snap.1693-T1
Valid prediction for snap_scaffold_7-snap.1708-T1
Valid prediction for Augustus_model.g11945.t1
Valid prediction for GlimmerHMM_glimmerT_17791-T1
Valid prediction for Augustus_model.g11930.t1
Valid prediction for CodingQuarry_transcript_57573-T1
Valid prediction for snap_scaffold_7-snap.1715-T1
Valid prediction for pasa_asmbl_51019.p1
Valid prediction for pasa_asmbl_51029.p1
Valid prediction for Augustus_model.g11952.t1
Valid prediction for GlimmerHMM_glimmerT_17797-T1
Valid prediction for GlimmerHMM_glimmerT_17799-T1
Valid prediction for Augustus_model.g11935.t1
Valid prediction for CodingQuarry_transcript_57569-T1
Valid prediction for snap_scaffold_7-snap.1696-T1
Couldn't classify 106542, 106585
Sorry, prediction pasa_asmbl_51020.p1 fails validation.
(GCC)	 AG	106542-106585	GT	ATG
(TGA)	 AG	109495-109685	GT	AAG
(CTC)	 AG	109818-109888	GT	AGG
(GGC)	 AG	109980-110137	GT	CCG
(TAA)	 AG	110371-110515	GT	AGG
(GAG)	 AG	110779-110922	GT	AGG
(AAA)	 AG	111206-111499	GA	AAG
-recovered pasa_asmbl_51020.p1, terminal, 111206, 111499
-recovered pasa_asmbl_51020.p1, internal, 106542, 106585
-recovered pasa_asmbl_51020.p1, internal, 109495, 109685
-recovered pasa_asmbl_51020.p1, internal, 109818, 109888
-recovered pasa_asmbl_51020.p1, internal, 109980, 110137
-recovered pasa_asmbl_51020.p1, internal, 110371, 110515
-recovered pasa_asmbl_51020.p1, internal, 110779, 110922
Valid prediction for snap_scaffold_7-snap.1711-T1
Valid prediction for Augustus_model.g11944.t1
Valid prediction for GlimmerHMM_glimmerT_17798-T1
Valid prediction for GlimmerHMM_glimmerT_17787-T1
Valid prediction for snap_scaffold_7-snap.1720-T1
Valid prediction for snap_scaffold_7-snap.1695-T1
Valid prediction for GlimmerHMM_glimmerT_17809-T1
Valid prediction for pasa_asmbl_51025.p1
Valid prediction for HiQ_model.g11947.t1
Valid prediction for pasa_asmbl_51034.p1
Valid prediction for CodingQuarry_transcript_57570-T1
Valid prediction for snap_scaffold_7-snap.1716-T1
Valid prediction for snap_scaffold_7-snap.1699-T1
Valid prediction for Augustus_model.g11931.t1
Valid prediction for snap_scaffold_7-snap.1704-T1
Valid prediction for GlimmerHMM_glimmerT_17811-T1
Valid prediction for snap_scaffold_7-snap.1697-T1
Valid prediction for GlimmerHMM_glimmerT_17793-T1
Valid prediction for GlimmerHMM_glimmerT_17801-T1
Valid prediction for GlimmerHMM_glimmerT_17783-T1
Valid prediction for HiQ_model.g11954.t1
Valid prediction for GlimmerHMM_glimmerT_17780-T1
Valid prediction for HiQ_model.g11949.t1
Valid prediction for pasa_asmbl_51016.p1
Valid prediction for GlimmerHMM_glimmerT_17786-T1
Valid prediction for Augustus_model.g11933.t1
Valid prediction for Augustus_model.g11942.t1
Valid prediction for snap_scaffold_7-snap.1712-T1
Valid prediction for CodingQuarry_transcript_57571-T1
Valid prediction for snap_scaffold_7-snap.1724-T1
Valid prediction for GlimmerHMM_glimmerT_17802-T1
Valid prediction for GlimmerHMM_glimmerT_17795-T1
Couldn't classify 101599, 101661
Sorry, prediction pasa_asmbl_51022.p1 fails validation.
(ATG)	 AC	97215-97297	GT	CGG
(GGA)	 AG	100272-100463	GT	AAG
(TAA)	 AG	100672-100752	GT	AGG
(AGC)	 AG	100849-100961	GT	AGG
(ACA)	 AG	101180-101238	GT	ATG
(AAC)	 AG	101599-101661	AA	GCA
-recovered pasa_asmbl_51022.p1, initial, 97215, 97297
-recovered pasa_asmbl_51022.p1, internal, 100272, 100463
-recovered pasa_asmbl_51022.p1, internal, 100672, 100752
-recovered pasa_asmbl_51022.p1, internal, 100849, 100961
-recovered pasa_asmbl_51022.p1, internal, 101180, 101238
Valid prediction for GlimmerHMM_glimmerT_17806-T1
Couldn't classify 29713, 29766
Sorry, prediction pasa_asmbl_51030.p1 fails validation.
(TTT)	 AC	29713-29766	GT	AGG
(GTC)	 AG	29865-29976	GT	GTG
(TCA)	 AG	30805-30887	GT	ACG
(TTC)	 AG	31552-31695	GT	AAG
(GTG)	 AG	31821-31913	GT	AGG
(GCG)	 AG	32204-32350	GT	AGG
(AGG)	 AG	32650-32813	GT	GTG
(TTT)	 AG	32950-33064	GT	AGG
(AAA)	 AG	33211-33312	GT	AGG
(GAG)	 AG	33406-33553	GT	CAG
(GGA)	 AG	33944-34002	GT	AGG
(GCT)	 AG	34114-34255	GT	AGG
(TGA)	 AG	34484-34691	GT	GGG
(GTA)	 AG	34994-35128	GT	AGG
(GTT)	 AG	35240-35306	GT	AGG
(AAC)	 AG	35858-36022	GA	GAG
-recovered pasa_asmbl_51030.p1, terminal, 35858, 36022
-recovered pasa_asmbl_51030.p1, internal, 29865, 29976
-recovered pasa_asmbl_51030.p1, internal, 30805, 30887
-recovered pasa_asmbl_51030.p1, internal, 31552, 31695
-recovered pasa_asmbl_51030.p1, internal, 31821, 31913
-recovered pasa_asmbl_51030.p1, internal, 32204, 32350
-recovered pasa_asmbl_51030.p1, internal, 32650, 32813
-recovered pasa_asmbl_51030.p1, internal, 32950, 33064
-recovered pasa_asmbl_51030.p1, internal, 33211, 33312
-recovered pasa_asmbl_51030.p1, internal, 33406, 33553
-recovered pasa_asmbl_51030.p1, internal, 33944, 34002
-recovered pasa_asmbl_51030.p1, internal, 34114, 34255
-recovered pasa_asmbl_51030.p1, internal, 34484, 34691
-recovered pasa_asmbl_51030.p1, internal, 34994, 35128
-recovered pasa_asmbl_51030.p1, internal, 35240, 35306
Couldn't classify 163840, 164160
Sorry, prediction pasa_asmbl_51018.p2 fails validation.
(ATG)	 TC	163840-164160	TG	GGT
Valid prediction for GlimmerHMM_glimmerT_17788-T1
Valid prediction for snap_scaffold_7-snap.1722-T1
Valid prediction for GlimmerHMM_glimmerT_17784-T1
Valid prediction for Augustus_model.g11943.t1
Valid prediction for snap_scaffold_7-snap.1701-T1
Valid prediction for HiQ_model.g11939.t1
Valid prediction for snap_scaffold_7-snap.1709-T1
Couldn't classify 27045, 27263
Couldn't classify 28585, 28674
Sorry, prediction pasa_asmbl_51031.p1 fails validation.
(GAA)	 AC	27045-27263	GT	AGG
(AGG)	 AG	28585-28674	GC	AGG
-recovered pasa_asmbl_51031.p1, internal, 28585, 28674

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11389, rend_intergenic: 7248  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31920, rend_intergenic: 26659  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55312, rend_intergenic: 42867  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62253, rend_intergenic: 58486  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84750, rend_intergenic: 80950  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98851, rend_intergenic: 88992  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 199047
-exon list size: 458


building trellis

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82.0    
82.2    
82.4    
82.6    
82.8    
83.0    
83.3    
83.5    
83.7    
83.9    
84.1    
84.3    
84.6    
84.8    
85.0    
85.2    
85.4    
85.7    
85.9    
86.1    
86.3    
86.5    
86.7    
87.0    
87.2    
87.4    
87.6    
87.8    
88.0    
88.3    
88.5    
88.7    
88.9    
89.1    
89.3    
89.6    
89.8    
90.0    
90.2    
90.4    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
92.0    
92.2    
92.4    
92.6    
92.8    
93.0    
93.3    
93.5    
93.7    
93.9    
94.1    
94.3    
94.6    
94.8    
95.0    
95.2    
95.4    
95.7    
95.9    
96.1    
96.3    
96.5    
96.7    
97.0    
97.2    
97.4    
97.6    
97.8    
98.0    
98.3    
98.5    
98.7    
98.9    
99.1    
99.3    
99.6    
99.8    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 11389, rend_intergenic: 7248  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31920, rend_intergenic: 26659  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55312, rend_intergenic: 42867  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62253, rend_intergenic: 58486  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84750, rend_intergenic: 80950  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98851, rend_intergenic: 88992  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 27 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 181814 - 199047
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-found 1 predictions from path traversal

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

-building DP trellis

-building trellis in range 184154 - 199047
-exon list size: 1


building trellis

33.3    
66.7    
-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