-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_26/scaffold_26_8303900-8496410

-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 CodingQuarry_transcript_40410-T1
Valid prediction for snap_scaffold_26-snap.1942-T1
Valid prediction for CodingQuarry_transcript_40409-T1
Valid prediction for snap_scaffold_26-snap.1930-T1
Valid prediction for snap_scaffold_26-snap.1936-T1
Valid prediction for snap_scaffold_26-snap.1950-T1
Couldn't classify 49588, 49608
Sorry, prediction pasa_asmbl_35166.p1 fails validation.
(GCA)	 CA	49588-49608	GT	TGG
(GGT)	 AG	49768-49822	GT	AGG
(ACT)	 AG	49931-50001	GT	ATG
(TTC)	 AG	50120-50198	GT	AGG
(GAT)	 AG	50459-50487	GT	AGG
(AAC)	 AG	50577-50675	GT	GTG
(TAT)	 AG	50807-50836	AG	GAA
add_exon() Sorry, pasa_asmbl_35166.p1 50120-50198-terminal-3 is invalid.
-recovered pasa_asmbl_35166.p1, terminal, 50120, 50198
-recovered pasa_asmbl_35166.p1, terminal, 50807, 50836
-recovered pasa_asmbl_35166.p1, internal, 49768, 49822
-recovered pasa_asmbl_35166.p1, internal, 49931, 50001
-recovered pasa_asmbl_35166.p1, internal, 50120, 50198
-recovered pasa_asmbl_35166.p1, internal, 50459, 50487
-recovered pasa_asmbl_35166.p1, internal, 50577, 50675
Valid prediction for snap_scaffold_26-snap.1944-T1
Valid prediction for GlimmerHMM_glimmerT_56237-T1
Valid prediction for GlimmerHMM_glimmerT_56225-T1
Valid prediction for GlimmerHMM_glimmerT_56223-T1
Valid prediction for GlimmerHMM_glimmerT_56236-T1
Valid prediction for Augustus_model.g37247.t1
Valid prediction for Augustus_model.g37252.t1
Couldn't classify 58443, 58619
Sorry, prediction pasa_asmbl_35170.p1 fails validation.
(GGG)	 CT	58443-58619	GT	AGG
(ATC)	 AG	58920-59062	GT	GTG
(GGA)	 AG	59162-59229	GT	TAG
(TGA)	 AG	59332-59460	GT	CAG
(CGA)	 AG	59706-59801	GT	AGG
(ATC)	 AG	59947-59999	GG	AAG
-recovered pasa_asmbl_35170.p1, terminal, 59947, 59999
-recovered pasa_asmbl_35170.p1, internal, 58920, 59062
-recovered pasa_asmbl_35170.p1, internal, 59162, 59229
-recovered pasa_asmbl_35170.p1, internal, 59332, 59460
-recovered pasa_asmbl_35170.p1, internal, 59706, 59801
Valid prediction for snap_scaffold_26-snap.1954-T1
Valid prediction for GlimmerHMM_glimmerT_56220-T1
Valid prediction for GlimmerHMM_glimmerT_56232-T1
Valid prediction for snap_scaffold_26-snap.1921-T1
Valid prediction for Augustus_model.g37256.t1
Valid prediction for GlimmerHMM_glimmerT_56240-T1
Valid prediction for GlimmerHMM_glimmerT_56238-T1
Valid prediction for GlimmerHMM_glimmerT_56230-T1
Valid prediction for HiQ_model.g37251.t1
Valid prediction for GlimmerHMM_glimmerT_56224-T1
Valid prediction for snap_scaffold_26-snap.1945-T1
Valid prediction for snap_scaffold_26-snap.1934-T1
Valid prediction for snap_scaffold_26-snap.1952-T1
Valid prediction for snap_scaffold_26-snap.1929-T1
Valid prediction for snap_scaffold_26-snap.1925-T1
Valid prediction for snap_scaffold_26-snap.1913-T1
Valid prediction for Augustus_model.g37246.t1
Valid prediction for snap_scaffold_26-snap.1924-T1
Valid prediction for GlimmerHMM_glimmerT_56221-T1
Valid prediction for Augustus_model.g37264.t1
Valid prediction for GlimmerHMM_glimmerT_56228-T1
Valid prediction for Augustus_model.g37250.t1
Valid prediction for snap_scaffold_26-snap.1920-T1
Valid prediction for GlimmerHMM_glimmerT_56217-T1
Couldn't classify 99107, 99481
Sorry, prediction pasa_asmbl_35172.p1 fails validation.
(ATG)	 AT	97127-97382	GT	TGG
(ATA)	 AG	97934-97991	GT	GGG
(AAA)	 AG	98109-98259	GT	TGG
(TCT)	 AG	98456-98549	GT	AGG
(GTG)	 AG	98735-98991	GT	AGG
(GTG)	 AG	99107-99481	AT	CCA
-recovered pasa_asmbl_35172.p1, initial, 97127, 97382
-recovered pasa_asmbl_35172.p1, internal, 97934, 97991
-recovered pasa_asmbl_35172.p1, internal, 98109, 98259
-recovered pasa_asmbl_35172.p1, internal, 98456, 98549
-recovered pasa_asmbl_35172.p1, internal, 98735, 98991
Valid prediction for snap_scaffold_26-snap.1923-T1
Valid prediction for CodingQuarry_transcript_40413-T1
Valid prediction for GlimmerHMM_glimmerT_56218-T1
Couldn't classify 55080, 55103
Sorry, prediction pasa_asmbl_35168.p1 fails validation.
(ATG)	 TC	52936-53046	GT	GGG
(ATC)	 AG	53762-53904	GT	ATG
(AGA)	 AG	53997-54058	GT	CTG
(TGG)	 AG	54154-54276	GT	CAG
(GAA)	 AG	54504-54605	GT	AGG
(AGG)	 AG	54832-54908	GT	TTG
(ATT)	 AG	55080-55103	AA	TCA
-recovered pasa_asmbl_35168.p1, initial, 52936, 53046
-recovered pasa_asmbl_35168.p1, internal, 53762, 53904
-recovered pasa_asmbl_35168.p1, internal, 53997, 54058
-recovered pasa_asmbl_35168.p1, internal, 54154, 54276
-recovered pasa_asmbl_35168.p1, internal, 54504, 54605
-recovered pasa_asmbl_35168.p1, internal, 54832, 54908
Valid prediction for snap_scaffold_26-snap.1941-T1
Valid prediction for Augustus_model.g37259.t1
Valid prediction for Augustus_model.g37261.t1
Valid prediction for snap_scaffold_26-snap.1919-T1
Valid prediction for snap_scaffold_26-snap.1935-T1
Valid prediction for snap_scaffold_26-snap.1916-T1
Valid prediction for snap_scaffold_26-snap.1947-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: -)Couldn't classify 111526, 111731
Couldn't classify 111918, 112041
Sorry, prediction pasa_asmbl_35843.p1 fails validation.
(CAT)	 AG	111526-111731	GC	AGG
(GTA)	 AG	111918-112041	CG	AAC
-recovered pasa_asmbl_35843.p1, internal, 111526, 111731
Valid prediction for CodingQuarry_transcript_40412-T1
Valid prediction for snap_scaffold_26-snap.1951-T1
Valid prediction for snap_scaffold_26-snap.1917-T1
Valid prediction for Augustus_model.g37249.t1
Valid prediction for Augustus_model.g37254.t1
Valid prediction for snap_scaffold_26-snap.1932-T1
Valid prediction for snap_scaffold_26-snap.1928-T1
Couldn't classify 113839, 113955
Couldn't classify 115532, 115627
Sorry, prediction pasa_asmbl_35872.p1 fails validation.
(AAC)	 CC	113839-113955	GT	AGG
(GCT)	 AG	114117-114200	GT	AGG
(ATC)	 AG	114353-114424	GT	ACG
(GAG)	 AG	114552-114621	GT	CAG
(CCG)	 AG	114821-115029	GT	AGG
(GAC)	 AG	115221-115364	GT	AGG
(ACC)	 AG	115532-115627	GC	ACG
-recovered pasa_asmbl_35872.p1, internal, 114117, 114200
-recovered pasa_asmbl_35872.p1, internal, 114353, 114424
-recovered pasa_asmbl_35872.p1, internal, 114552, 114621
-recovered pasa_asmbl_35872.p1, internal, 114821, 115029
-recovered pasa_asmbl_35872.p1, internal, 115221, 115364
-recovered pasa_asmbl_35872.p1, internal, 115532, 115627
Valid prediction for GlimmerHMM_glimmerT_56234-T1
Valid prediction for GlimmerHMM_glimmerT_56233-T1
Valid prediction for GlimmerHMM_glimmerT_56222-T1
Valid prediction for GlimmerHMM_glimmerT_56219-T1
Valid prediction for Augustus_model.g37245.t1
Valid prediction for GlimmerHMM_glimmerT_56227-T1
Valid prediction for Augustus_model.g37248.t1
Valid prediction for snap_scaffold_26-snap.1940-T1
Valid prediction for snap_scaffold_26-snap.1948-T1
Valid prediction for snap_scaffold_26-snap.1914-T1
Valid prediction for snap_scaffold_26-snap.1953-T1
Valid prediction for GlimmerHMM_glimmerT_56226-T1
Valid prediction for snap_scaffold_26-snap.1949-T1
Valid prediction for snap_scaffold_26-snap.1926-T1
Valid prediction for Augustus_model.g37258.t1
Valid prediction for Augustus_model.g37257.t1
Valid prediction for GlimmerHMM_glimmerT_56231-T1
Valid prediction for Augustus_model.g37263.t1
Valid prediction for HiQ_model.g37260.t1
Valid prediction for Augustus_model.g37255.t1
Valid prediction for Augustus_model.g37265.t1
Valid prediction for snap_scaffold_26-snap.1922-T1
Valid prediction for snap_scaffold_26-snap.1938-T1
Valid prediction for snap_scaffold_26-snap.1943-T1
Valid prediction for snap_scaffold_26-snap.1939-T1
Valid prediction for pasa_asmbl_35731.p1
Valid prediction for snap_scaffold_26-snap.1931-T1
Couldn't classify 112410, 112418
Couldn't classify 113785, 113868
Sorry, prediction pasa_asmbl_35863.p1 fails validation.
(CTC)	 AG	112410-112418	GT	AGG
(AGC)	 AG	112899-112989	GT	CTG
(TGG)	 AG	113153-113320	GT	AGG
(CTC)	 AG	113493-113641	GT	AGG
(AGC)	 AG	113785-113868	CG	CCC
-recovered pasa_asmbl_35863.p1, internal, 112410, 112418
-recovered pasa_asmbl_35863.p1, internal, 112899, 112989
-recovered pasa_asmbl_35863.p1, internal, 113153, 113320
-recovered pasa_asmbl_35863.p1, internal, 113493, 113641
Valid prediction for Augustus_model.g37262.t1
Valid prediction for Augustus_model.g37253.t1
Valid prediction for snap_scaffold_26-snap.1933-T1
Valid prediction for CodingQuarry_transcript_40411-T1
Valid prediction for snap_scaffold_26-snap.1918-T1
Valid prediction for snap_scaffold_26-snap.1927-T1
Couldn't classify 67976, 68042
Sorry, prediction pasa_asmbl_35729.p1 fails validation.
(CAT)	 TT	67976-68042	GT	TGG
(CGA)	 AG	68145-68266	GT	AGG
(ATG)	 AG	70127-70216	GT	AGG
(GTG)	 AG	70321-70521	GT	GAG
(GAC)	 AG	71805-71906	GT	AGG
(ACG)	 AG	72053-72202	AT	AGA
-recovered pasa_asmbl_35729.p1, initial, 70127, 70216
-recovered pasa_asmbl_35729.p1, terminal, 72053, 72202
-recovered pasa_asmbl_35729.p1, internal, 68145, 68266
-recovered pasa_asmbl_35729.p1, internal, 70127, 70216
-recovered pasa_asmbl_35729.p1, internal, 70321, 70521
-recovered pasa_asmbl_35729.p1, internal, 71805, 71906
Valid prediction for snap_scaffold_26-snap.1912-T1
Valid prediction for snap_scaffold_26-snap.1937-T1
Valid prediction for GlimmerHMM_glimmerT_56216-T1
Valid prediction for GlimmerHMM_glimmerT_56235-T1
Valid prediction for snap_scaffold_26-snap.1946-T1
Valid prediction for snap_scaffold_26-snap.1915-T1
Valid prediction for GlimmerHMM_glimmerT_56229-T1
Couldn't classify 80177, 80243
Sorry, prediction pasa_asmbl_35728.p1 fails validation.
(CTC)	 TC	80177-80243	GT	AGG
(GTG)	 AG	80455-80592	GT	CGG
(ATG)	 AG	80730-80845	GT	AGG
(ATG)	 AG	80975-81192	GT	AGG
(TGC)	 AG	81323-81527	AT	GAA
add_exon() Sorry, pasa_asmbl_35728.p1 80730-80845-initial-1 is invalid.
-recovered pasa_asmbl_35728.p1, initial, 80730, 80845
-recovered pasa_asmbl_35728.p1, initial, 80975, 81192
-recovered pasa_asmbl_35728.p1, terminal, 81323, 81527
-recovered pasa_asmbl_35728.p1, internal, 80455, 80592
-recovered pasa_asmbl_35728.p1, internal, 80730, 80845
-recovered pasa_asmbl_35728.p1, internal, 80975, 81192
Valid prediction for GlimmerHMM_glimmerT_56239-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8100, rend_intergenic: 2530  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20751, rend_intergenic: 16787  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39813, rend_intergenic: 28235  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51530, rend_intergenic: 43605  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83463, rend_intergenic: 74257  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94884, rend_intergenic: 90829  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171784, rend_intergenic: 168972  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179888, rend_intergenic: 176584  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180970, rend_intergenic: 180659  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192029, rend_intergenic: 184560  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 192511
-exon list size: 435


building trellis

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-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 8100, rend_intergenic: 2530  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20751, rend_intergenic: 16787  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39813, rend_intergenic: 28235  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51530, rend_intergenic: 43605  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83463, rend_intergenic: 74257  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94884, rend_intergenic: 90829  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171784, rend_intergenic: 168972  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179888, rend_intergenic: 176584  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180970, rend_intergenic: 180659  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192029, rend_intergenic: 184560  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support