-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_20/scaffold_20_8716583-8882181

-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_20-snap.1932-T1
Valid prediction for GeneMark_model.83177_t
Valid prediction for GeneMark_model.83210_t
Valid prediction for snap_scaffold_20-snap.1962-T1
Valid prediction for Augustus_model.g31804.t1
Valid prediction for GlimmerHMM_glimmerT_47666-T1
Valid prediction for GlimmerHMM_glimmerT_47660-T1
Valid prediction for GeneMark_model.83206_t
Valid prediction for snap_scaffold_20-snap.1959-T1
Valid prediction for GeneMark_model.83189_t
Valid prediction for snap_scaffold_20-snap.1926-T1
Valid prediction for Augustus_model.g31795.t1
Valid prediction for Augustus_model.g31797.t1
Valid prediction for Augustus_model.g31799.t1
Valid prediction for GlimmerHMM_glimmerT_47676-T1
Valid prediction for snap_scaffold_20-snap.1948-T1
Valid prediction for GlimmerHMM_glimmerT_47667-T1
Valid prediction for snap_scaffold_20-snap.1927-T1
Valid prediction for GlimmerHMM_glimmerT_47682-T1
Valid prediction for GlimmerHMM_glimmerT_47677-T1
Valid prediction for GeneMark_model.83178_t
Valid prediction for GeneMark_model.83179_t
Valid prediction for snap_scaffold_20-snap.1940-T1
Valid prediction for GeneMark_model.83182_t
Couldn't classify 128681, 129223
Sorry, prediction pasa_asmbl_25956.p1 fails validation.
(CAG)	 CG	128681-129223	GC	GAG
Couldn't classify 56756, 56971
Sorry, prediction GeneMark_model.83180_t fails validation.
(GCT)	 AG	56756-56971	GT	TGG
(TTC)	 AG	57086-57160	GT	TGG
(GTC)	 AG	57389-57496	GT	AGG
(AAC)	 AG	57973-58065	GT	AGG
(CTG)	 AG	59762-59959	GT	TGG
(GTC)	 AG	60384-60491	GT	AGG
(AAC)	 AG	60686-60841	GT	CGG
(AGC)	 AG	61059-61142	GT	AGG
(CCT)	 AG	63420-63494	GT	TCG
(CGA)	 AG	63799-63853	GT	CGG
(ACG)	 AG	63884-64070	GT	GGG
(GAG)	 AG	64091-64101	GT	CAG
(TTG)	 AG	65452-65482	GT	GAG
(TGA)	 AG	65512-65541	GT	GGG
(GAC)	 AG	65631-65666	GT	TGG
(CGG)	 AG	65691-65732	GT	CGG
(ACC)	 AG	66092-66097	GT	AAG
(CAG)	 AG	66206-66307	GT	ACG
(AGA)	 AG	66345-66390	GA	AGG
-recovered GeneMark_model.83180_t, terminal, 66345, 66390
-recovered GeneMark_model.83180_t, internal, 56756, 56971
-recovered GeneMark_model.83180_t, internal, 57086, 57160
-recovered GeneMark_model.83180_t, internal, 57389, 57496
-recovered GeneMark_model.83180_t, internal, 57973, 58065
-recovered GeneMark_model.83180_t, internal, 59762, 59959
-recovered GeneMark_model.83180_t, internal, 60384, 60491
-recovered GeneMark_model.83180_t, internal, 60686, 60841
-recovered GeneMark_model.83180_t, internal, 61059, 61142
-recovered GeneMark_model.83180_t, internal, 63420, 63494
-recovered GeneMark_model.83180_t, internal, 63799, 63853
-recovered GeneMark_model.83180_t, internal, 63884, 64070
-recovered GeneMark_model.83180_t, internal, 64091, 64101
-recovered GeneMark_model.83180_t, internal, 65452, 65482
-recovered GeneMark_model.83180_t, internal, 65512, 65541
-recovered GeneMark_model.83180_t, internal, 65631, 65666
-recovered GeneMark_model.83180_t, internal, 65691, 65732
-recovered GeneMark_model.83180_t, internal, 66092, 66097
-recovered GeneMark_model.83180_t, internal, 66206, 66307
Valid prediction for GeneMark_model.83184_t
Valid prediction for GlimmerHMM_glimmerT_47679-T1
Valid prediction for snap_scaffold_20-snap.1953-T1
Valid prediction for snap_scaffold_20-snap.1923-T1
Valid prediction for snap_scaffold_20-snap.1934-T1
Valid prediction for GlimmerHMM_glimmerT_47668-T1
Valid prediction for snap_scaffold_20-snap.1928-T1
Valid prediction for snap_scaffold_20-snap.1929-T1
Valid prediction for GeneMark_model.83187_t
Valid prediction for snap_scaffold_20-snap.1957-T1
Valid prediction for GeneMark_model.83208_t
Valid prediction for GeneMark_model.83169_t
Valid prediction for GeneMark_model.83200_t
Valid prediction for GeneMark_model.83193_t
Valid prediction for snap_scaffold_20-snap.1961-T1
Valid prediction for snap_scaffold_20-snap.1947-T1
Valid prediction for GeneMark_model.83195_t
Valid prediction for Augustus_model.g31802.t1
Valid prediction for GeneMark_model.83172_t
Valid prediction for Augustus_model.g31805.t1
Valid prediction for GeneMark_model.83202_t
Valid prediction for GeneMark_model.83174_t
Valid prediction for snap_scaffold_20-snap.1931-T1
Valid prediction for GlimmerHMM_glimmerT_47669-T1
Valid prediction for Augustus_model.g31800.t1
Valid prediction for snap_scaffold_20-snap.1935-T1
Valid prediction for snap_scaffold_20-snap.1941-T1
Valid prediction for snap_scaffold_20-snap.1954-T1
Valid prediction for GlimmerHMM_glimmerT_47673-T1
Valid prediction for GeneMark_model.83190_t
Valid prediction for Augustus_model.g31792.t1
Valid prediction for Augustus_model.g31803.t1
Valid prediction for GeneMark_model.83205_t
Valid prediction for snap_scaffold_20-snap.1945-T1
Valid prediction for Augustus_model.g31796.t1
Valid prediction for Augustus_model.g31798.t1
Valid prediction for GeneMark_model.83192_t
Valid prediction for GlimmerHMM_glimmerT_47662-T1
Valid prediction for snap_scaffold_20-snap.1937-T1
Valid prediction for GlimmerHMM_glimmerT_47659-T1
Valid prediction for Augustus_model.g31793.t1
Valid prediction for GeneMark_model.83185_t
Couldn't classify 151220, 151623
Couldn't classify 151818, 151986
Sorry, prediction CodingQuarry_transcript_30522-T1 fails validation.
(ATG)	 AC	151220-151623	AT	ACA
(ATG)	 AC	151818-151986	AG	GAA
Valid prediction for snap_scaffold_20-snap.1950-T1
Valid prediction for snap_scaffold_20-snap.1938-T1
Valid prediction for GeneMark_model.83168_t

-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 GeneMark_model.83191_t
Valid prediction for GeneMark_model.83196_t
Valid prediction for GlimmerHMM_glimmerT_47671-T1
Valid prediction for GlimmerHMM_glimmerT_47684-T1
Valid prediction for snap_scaffold_20-snap.1952-T1
Valid prediction for GlimmerHMM_glimmerT_47672-T1
Valid prediction for snap_scaffold_20-snap.1939-T1
Valid prediction for GlimmerHMM_glimmerT_47658-T1
Valid prediction for GeneMark_model.83194_t
Valid prediction for GlimmerHMM_glimmerT_47664-T1
Valid prediction for GeneMark_model.83204_t
Valid prediction for GeneMark_model.83175_t
Valid prediction for Augustus_model.g31794.t1
Valid prediction for GlimmerHMM_glimmerT_47685-T1
Valid prediction for snap_scaffold_20-snap.1949-T1
Valid prediction for GeneMark_model.83171_t
Valid prediction for GeneMark_model.83170_t
Valid prediction for GlimmerHMM_glimmerT_47683-T1
Couldn't classify 33787, 33898
Sorry, prediction GeneMark_model.83198_t fails validation.
(TCT)	 AG	33787-33898	GT	GAG
(GTG)	 AG	33927-34019	GT	CAG
(GTC)	 AG	34700-34773	GT	GCG
(AGA)	 AG	35620-35654	GT	GCG
(CCT)	 AG	35678-35708	GT	GCG
(TGT)	 AG	36309-36351	GT	AGG
-recovered GeneMark_model.83198_t, terminal, 36309, 36351
-recovered GeneMark_model.83198_t, internal, 33787, 33898
-recovered GeneMark_model.83198_t, internal, 33927, 34019
-recovered GeneMark_model.83198_t, internal, 34700, 34773
-recovered GeneMark_model.83198_t, internal, 35620, 35654
-recovered GeneMark_model.83198_t, internal, 35678, 35708
-recovered GeneMark_model.83198_t, internal, 36309, 36351
Valid prediction for GeneMark_model.83211_t
Valid prediction for snap_scaffold_20-snap.1942-T1
Valid prediction for GeneMark_model.83176_t
Valid prediction for snap_scaffold_20-snap.1930-T1
Valid prediction for GlimmerHMM_glimmerT_47680-T1
Valid prediction for GeneMark_model.83181_t
Valid prediction for snap_scaffold_20-snap.1925-T1
Valid prediction for GlimmerHMM_glimmerT_47670-T1
Valid prediction for GlimmerHMM_glimmerT_47674-T1
Couldn't classify 26851, 27041
Sorry, prediction GeneMark_model.83199_t fails validation.
(ATG)	 TC	26799-26803	GT	GTG
(AGG)	 AG	26851-27041	GT	ACG
-recovered GeneMark_model.83199_t, initial, 26799, 26803
-recovered GeneMark_model.83199_t, internal, 26851, 27041
Valid prediction for snap_scaffold_20-snap.1943-T1
Valid prediction for snap_scaffold_20-snap.1936-T1
Valid prediction for GlimmerHMM_glimmerT_47681-T1
Valid prediction for GlimmerHMM_glimmerT_47675-T1
Valid prediction for GeneMark_model.83186_t
Valid prediction for snap_scaffold_20-snap.1944-T1
Valid prediction for Augustus_model.g31801.t1
Valid prediction for GeneMark_model.83201_t
Valid prediction for GeneMark_model.83183_t
Valid prediction for snap_scaffold_20-snap.1924-T1
Valid prediction for snap_scaffold_20-snap.1955-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_47678-T1
Valid prediction for GeneMark_model.83173_t
Valid prediction for GeneMark_model.83207_t
Valid prediction for GeneMark_model.83166_t
Valid prediction for snap_scaffold_20-snap.1951-T1
Valid prediction for GeneMark_model.83188_t
Valid prediction for snap_scaffold_20-snap.1958-T1
Valid prediction for GlimmerHMM_glimmerT_47665-T1
Valid prediction for snap_scaffold_20-snap.1933-T1
Valid prediction for GeneMark_model.83167_t
Valid prediction for snap_scaffold_20-snap.1956-T1
Valid prediction for GlimmerHMM_glimmerT_47661-T1
Valid prediction for GlimmerHMM_glimmerT_47663-T1
Valid prediction for GeneMark_model.83203_t
Valid prediction for snap_scaffold_20-snap.1946-T1
Valid prediction for GeneMark_model.83209_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9199, rend_intergenic: 3078  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12294, rend_intergenic: 9720  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52391, rend_intergenic: 48655  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80136, rend_intergenic: 72015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95176, rend_intergenic: 92910  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99228, rend_intergenic: 95403  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112053, rend_intergenic: 109926  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138822, rend_intergenic: 128479  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143948, rend_intergenic: 139595  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152828, rend_intergenic: 144935  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156241, rend_intergenic: 152850  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 165599
-exon list size: 619


building trellis

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-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 9199, rend_intergenic: 3078  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12294, rend_intergenic: 9720  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52391, rend_intergenic: 48655  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80136, rend_intergenic: 72015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95176, rend_intergenic: 92910  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99228, rend_intergenic: 95403  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112053, rend_intergenic: 109926  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138822, rend_intergenic: 128479  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143948, rend_intergenic: 139595  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152828, rend_intergenic: 144935  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156241, rend_intergenic: 152850  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support