-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_26/scaffold_26_8252009-8409058

-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_57548-T1
Valid prediction for GlimmerHMM_glimmerT_57554-T1
Valid prediction for GeneMark_model.100344_t
Valid prediction for CodingQuarry_transcript_40316-T1
Valid prediction for GlimmerHMM_glimmerT_57556-T1
Valid prediction for Augustus_model.g38351.t1
Valid prediction for GeneMark_model.100330_t
Valid prediction for GlimmerHMM_glimmerT_57561-T1
Valid prediction for snap_scaffold_26-snap.1932-T1
Valid prediction for snap_scaffold_26-snap.1916-T1
Valid prediction for HiQ_model.g38338.t1
Valid prediction for snap_scaffold_26-snap.1934-T1
Valid prediction for HiQ_model.g38352.t1
Valid prediction for Augustus_model.g38347.t1
Valid prediction for GlimmerHMM_glimmerT_57567-T1
Valid prediction for GlimmerHMM_glimmerT_57563-T1
Valid prediction for GlimmerHMM_glimmerT_57557-T1
Couldn't classify 106971, 106994
Sorry, prediction pasa_asmbl_35692.p1 fails validation.
(ATG)	 TC	104827-104937	GT	GGG
(ATC)	 AG	105653-105795	GT	ATG
(AGA)	 AG	105888-105949	GT	CTG
(TGG)	 AG	106045-106167	GT	CAG
(GAA)	 AG	106395-106496	GT	AGG
(AGG)	 AG	106723-106799	GT	TTG
(ATT)	 AG	106971-106994	AA	TCA
-recovered pasa_asmbl_35692.p1, initial, 104827, 104937
-recovered pasa_asmbl_35692.p1, internal, 105653, 105795
-recovered pasa_asmbl_35692.p1, internal, 105888, 105949
-recovered pasa_asmbl_35692.p1, internal, 106045, 106167
-recovered pasa_asmbl_35692.p1, internal, 106395, 106496
-recovered pasa_asmbl_35692.p1, internal, 106723, 106799
Valid prediction for snap_scaffold_26-snap.1933-T1
Valid prediction for GeneMark_model.100328_t
Valid prediction for GeneMark_model.100326_t
Valid prediction for snap_scaffold_26-snap.1948-T1
Valid prediction for snap_scaffold_26-snap.1946-T1
Valid prediction for GlimmerHMM_glimmerT_57564-T1
Valid prediction for Augustus_model.g38357.t1
Valid prediction for CodingQuarry_transcript_40314-T1
Valid prediction for Augustus_model.g38340.t1
Valid prediction for GeneMark_model.100333_t
Valid prediction for GlimmerHMM_glimmerT_57568-T1
Valid prediction for GeneMark_model.100325_t
Valid prediction for GeneMark_model.100335_t
Valid prediction for snap_scaffold_26-snap.1938-T1
Valid prediction for CodingQuarry_transcript_40315-T1
Valid prediction for GlimmerHMM_glimmerT_57559-T1
Valid prediction for snap_scaffold_26-snap.1928-T1
Valid prediction for snap_scaffold_26-snap.1919-T1
Valid prediction for snap_scaffold_26-snap.1942-T1
Valid prediction for snap_scaffold_26-snap.1923-T1
Valid prediction for GeneMark_model.100320_t
Valid prediction for snap_scaffold_26-snap.1947-T1
Valid prediction for GlimmerHMM_glimmerT_57547-T1
Couldn't classify 101479, 101499
Sorry, prediction pasa_asmbl_35690.p1 fails validation.
(GCA)	 CA	101479-101499	GT	TGG
(GGT)	 AG	101659-101713	GT	AGG
(ACT)	 AG	101822-101892	GT	ATG
(TTC)	 AG	102011-102089	GT	AGG
(GAT)	 AG	102350-102378	GT	AGG
(AAC)	 AG	102468-102566	GT	GTG
(TAT)	 AG	102698-102727	AG	GAA
add_exon() Sorry, pasa_asmbl_35690.p1 102011-102089-terminal-3 is invalid.
-recovered pasa_asmbl_35690.p1, terminal, 102011, 102089
-recovered pasa_asmbl_35690.p1, terminal, 102698, 102727
-recovered pasa_asmbl_35690.p1, internal, 101659, 101713
-recovered pasa_asmbl_35690.p1, internal, 101822, 101892
-recovered pasa_asmbl_35690.p1, internal, 102011, 102089
-recovered pasa_asmbl_35690.p1, internal, 102350, 102378
-recovered pasa_asmbl_35690.p1, internal, 102468, 102566
Valid prediction for Augustus_model.g38348.t1
Valid prediction for Augustus_model.g38344.t1
Valid prediction for GlimmerHMM_glimmerT_57552-T1
Valid prediction for GlimmerHMM_glimmerT_57562-T1
Valid prediction for GeneMark_model.100341_t
Valid prediction for snap_scaffold_26-snap.1926-T1
Valid prediction for GeneMark_model.100316_t
Valid prediction for snap_scaffold_26-snap.1914-T1
Couldn't classify 110313, 110510
Sorry, prediction pasa_asmbl_35694.p1 fails validation.
(ATT)	 CC	110313-110510	GT	AGG
(ATC)	 AG	110811-110953	GT	GTG
(GGA)	 AG	111053-111120	GT	TAG
(TGA)	 AG	111223-111351	GT	CAG
(CGA)	 AG	111597-111692	GT	AGG
(ATC)	 AG	111838-111890	GG	AAG
-recovered pasa_asmbl_35694.p1, terminal, 111838, 111890
-recovered pasa_asmbl_35694.p1, internal, 110811, 110953
-recovered pasa_asmbl_35694.p1, internal, 111053, 111120
-recovered pasa_asmbl_35694.p1, internal, 111223, 111351
-recovered pasa_asmbl_35694.p1, internal, 111597, 111692
Valid prediction for snap_scaffold_26-snap.1937-T1
Couldn't classify 150998, 151372
Sorry, prediction pasa_asmbl_35697.p1 fails validation.
(ATG)	 AT	149018-149273	GT	TGG
(ATA)	 AG	149825-149882	GT	GGG
(AAA)	 AG	150000-150150	GT	TGG
(TCT)	 AG	150347-150440	GT	AGG
(GTG)	 AG	150626-150882	GT	AGG
(GTG)	 AG	150998-151372	AT	CCA
-recovered pasa_asmbl_35697.p1, initial, 149018, 149273
-recovered pasa_asmbl_35697.p1, internal, 149825, 149882
-recovered pasa_asmbl_35697.p1, internal, 150000, 150150
-recovered pasa_asmbl_35697.p1, internal, 150347, 150440
-recovered pasa_asmbl_35697.p1, internal, 150626, 150882
Valid prediction for snap_scaffold_26-snap.1936-T1
Valid prediction for GlimmerHMM_glimmerT_57549-T1
Valid prediction for Augustus_model.g38353.t1
Couldn't classify 39348, 39624
Sorry, prediction GeneMark_model.100322_t fails validation.
(GCT)	 AG	39348-39624	GT	AGG
(GGG)	 AG	39712-39735	CC	GAC
-recovered GeneMark_model.100322_t, terminal, 39712, 39735
-recovered GeneMark_model.100322_t, internal, 39348, 39624
Valid prediction for Augustus_model.g38339.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 snap_scaffold_26-snap.1935-T1
Valid prediction for GlimmerHMM_glimmerT_57550-T1
Valid prediction for GeneMark_model.100334_t
Valid prediction for snap_scaffold_26-snap.1944-T1
Valid prediction for Augustus_model.g38354.t1
Valid prediction for snap_scaffold_26-snap.1941-T1
Valid prediction for GeneMark_model.100329_t
Valid prediction for GlimmerHMM_glimmerT_57546-T1
Valid prediction for GeneMark_model.100342_t
Valid prediction for snap_scaffold_26-snap.1929-T1
Valid prediction for GlimmerHMM_glimmerT_57545-T1
Valid prediction for snap_scaffold_26-snap.1939-T1
Valid prediction for snap_scaffold_26-snap.1925-T1
Valid prediction for Augustus_model.g38343.t1
Valid prediction for GlimmerHMM_glimmerT_57555-T1
Valid prediction for snap_scaffold_26-snap.1931-T1
Valid prediction for GlimmerHMM_glimmerT_57553-T1
Valid prediction for Augustus_model.g38355.t1
Valid prediction for Augustus_model.g38350.t1
Valid prediction for GeneMark_model.100336_t
Valid prediction for snap_scaffold_26-snap.1918-T1
Valid prediction for Augustus_model.g38346.t1
Valid prediction for GeneMark_model.100315_t
Couldn't classify 26487, 26603
Couldn't classify 28180, 28275
Sorry, prediction pasa_asmbl_35118.p1 fails validation.
(AAC)	 CC	26487-26603	GT	AGG
(GCT)	 AG	26765-26848	GT	AGG
(ATC)	 AG	27001-27072	GT	ACG
(GAG)	 AG	27200-27269	GT	CAG
(CCG)	 AG	27469-27677	GT	AGG
(GAC)	 AG	27869-28012	GT	AGG
(ACC)	 AG	28180-28275	GC	ACG
-recovered pasa_asmbl_35118.p1, internal, 26765, 26848
-recovered pasa_asmbl_35118.p1, internal, 27001, 27072
-recovered pasa_asmbl_35118.p1, internal, 27200, 27269
-recovered pasa_asmbl_35118.p1, internal, 27469, 27677
-recovered pasa_asmbl_35118.p1, internal, 27869, 28012
-recovered pasa_asmbl_35118.p1, internal, 28180, 28275
Valid prediction for GeneMark_model.100338_t
Valid prediction for snap_scaffold_26-snap.1943-T1
Valid prediction for GlimmerHMM_glimmerT_57565-T1
Valid prediction for snap_scaffold_26-snap.1915-T1
Valid prediction for GeneMark_model.100340_t
Valid prediction for GeneMark_model.100337_t
Valid prediction for GeneMark_model.100317_t
Valid prediction for GeneMark_model.100331_t
Valid prediction for Augustus_model.g38345.t1
Valid prediction for GeneMark_model.100339_t
Valid prediction for GeneMark_model.100327_t
Valid prediction for snap_scaffold_26-snap.1924-T1
Valid prediction for GeneMark_model.100332_t
Couldn't classify 25058, 25066
Couldn't classify 26433, 26516
Sorry, prediction pasa_asmbl_35160.p1 fails validation.
(CTC)	 AG	25058-25066	GT	AGG
(AGC)	 AG	25547-25637	GT	CTG
(TGG)	 AG	25801-25968	GT	AGG
(CTC)	 AG	26141-26289	GT	AGG
(AGC)	 AG	26433-26516	CG	CCC
-recovered pasa_asmbl_35160.p1, internal, 25058, 25066
-recovered pasa_asmbl_35160.p1, internal, 25547, 25637
-recovered pasa_asmbl_35160.p1, internal, 25801, 25968
-recovered pasa_asmbl_35160.p1, internal, 26141, 26289
Couldn't classify 121385, 121481
Sorry, prediction GeneMark_model.100321_t fails validation.
(AGC)	 AG	121385-121481	GT	AGG
(GAG)	 AG	121950-122131	GT	AGG
(GTC)	 AG	122595-122695	GT	CCG
(TAC)	 AG	122772-122943	CA	AGC
-recovered GeneMark_model.100321_t, terminal, 122772, 122943
-recovered GeneMark_model.100321_t, internal, 121385, 121481
-recovered GeneMark_model.100321_t, internal, 121950, 122131
-recovered GeneMark_model.100321_t, internal, 122595, 122695
Couldn't classify 24174, 24379
Couldn't classify 24566, 24689
Sorry, prediction pasa_asmbl_35157.p1 fails validation.
(CAT)	 AG	24174-24379	GC	AGG
(GTA)	 AG	24566-24689	CG	AAC
-recovered pasa_asmbl_35157.p1, internal, 24174, 24379
Valid prediction for GeneMark_model.100319_t
Valid prediction for GlimmerHMM_glimmerT_57560-T1
Valid prediction for Augustus_model.g38356.t1
Valid prediction for Augustus_model.g38342.t1
Valid prediction for GlimmerHMM_glimmerT_57558-T1
Valid prediction for Augustus_model.g38341.t1
Valid prediction for snap_scaffold_26-snap.1920-T1
Valid prediction for GeneMark_model.100324_t
Valid prediction for GlimmerHMM_glimmerT_57566-T1
Valid prediction for snap_scaffold_26-snap.1922-T1
Valid prediction for snap_scaffold_26-snap.1940-T1
Valid prediction for snap_scaffold_26-snap.1930-T1
Valid prediction for snap_scaffold_26-snap.1927-T1
Valid prediction for Augustus_model.g38349.t1
Valid prediction for GlimmerHMM_glimmerT_57551-T1
Valid prediction for snap_scaffold_26-snap.1917-T1
Valid prediction for snap_scaffold_26-snap.1945-T1
Valid prediction for snap_scaffold_26-snap.1921-T1
Valid prediction for GeneMark_model.100323_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 59991, rend_intergenic: 54421  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68612, rend_intergenic: 66240  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91704, rend_intergenic: 80126  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103421, rend_intergenic: 95496  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135354, rend_intergenic: 128663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146775, rend_intergenic: 142720  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 157050
-exon list size: 524


building trellis

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-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 59991, rend_intergenic: 54421  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68612, rend_intergenic: 66240  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91704, rend_intergenic: 80126  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103421, rend_intergenic: 95496  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135354, rend_intergenic: 128663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146775, rend_intergenic: 142720  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support