-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_11/scaffold_11_8394561-8595733

-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_27536-T1
Valid prediction for snap_scaffold_11-snap.1911-T1
Valid prediction for Augustus_model.g18224.t1
Valid prediction for Augustus_model.g18229.t1
Valid prediction for GlimmerHMM_glimmerT_27526-T1
Couldn't classify 187305, 187509
Couldn't classify 188754, 188762
Sorry, prediction pasa_asmbl_6302.p1 fails validation.
(TCC)	 CC	187305-187509	GT	TGG
(GGA)	 AG	187983-188076	GT	TGG
(GGA)	 AG	188210-188267	GT	TGG
(ATC)	 AG	188754-188762	AA	TGA
-recovered pasa_asmbl_6302.p1, internal, 187983, 188076
-recovered pasa_asmbl_6302.p1, internal, 188210, 188267
Valid prediction for Augustus_model.g18226.t1
Valid prediction for Augustus_model.g18231.t1
Valid prediction for pasa_asmbl_5805.p2
Valid prediction for pasa_asmbl_5790.p1
Valid prediction for snap_scaffold_11-snap.1941-T1
Valid prediction for GlimmerHMM_glimmerT_27554-T1
Valid prediction for snap_scaffold_11-snap.1918-T1
Valid prediction for HiQ_model.g18227.t1
Valid prediction for GlimmerHMM_glimmerT_27532-T1
Valid prediction for pasa_asmbl_5764.p1
Valid prediction for pasa_asmbl_5783.p1
Valid prediction for HiQ_model.g18236.t1
Couldn't classify 49673, 50347
Sorry, prediction pasa_asmbl_5780.p1 fails validation.
(CCT)	 GG	49673-50347	TG	GAT
Valid prediction for Augustus_model.g18232.t1
Valid prediction for Augustus_model.g18237.t1
Valid prediction for GlimmerHMM_glimmerT_27553-T1
Valid prediction for Augustus_model.g18234.t1
Valid prediction for pasa_asmbl_5771.p1
Valid prediction for snap_scaffold_11-snap.1916-T1
Couldn't classify 36353, 36395
Sorry, prediction pasa_asmbl_5776.p1 fails validation.
(ATG)	 AC	27131-27139	GT	AGG
(GTG)	 AG	28516-28675	GT	TGG
(ATA)	 AG	29059-29132	GT	AGG
(GAC)	 AG	29593-29673	GT	GGG
(CAG)	 AG	30269-30328	GT	AGG
(GTG)	 AG	30785-30930	GT	AAG
(GCC)	 AG	31092-31182	GT	CAG
(ATG)	 AG	31428-31499	GT	TTG
(GAG)	 AG	31611-31735	GC	AGG
(GCA)	 AG	31904-32036	GT	AGG
(ATC)	 AG	32459-32563	GT	AGG
(TAT)	 AG	32961-33067	GT	TTG
(CTG)	 AG	33289-33443	GT	GGG
(GAT)	 AG	33736-33846	GT	GGG
(GAC)	 AG	34216-34324	GT	AGG
(GAA)	 AG	34768-34800	GT	AGG
(TCT)	 AG	36353-36395	AG	AAA
-recovered pasa_asmbl_5776.p1, initial, 27131, 27139
-recovered pasa_asmbl_5776.p1, initial, 31428, 31499
add_exon() Sorry, pasa_asmbl_5776.p1 30785-30930-terminal-2 is invalid.
-recovered pasa_asmbl_5776.p1, terminal, 30785, 30930
-recovered pasa_asmbl_5776.p1, internal, 28516, 28675
-recovered pasa_asmbl_5776.p1, internal, 29059, 29132
-recovered pasa_asmbl_5776.p1, internal, 29593, 29673
-recovered pasa_asmbl_5776.p1, internal, 30269, 30328
-recovered pasa_asmbl_5776.p1, internal, 30785, 30930
-recovered pasa_asmbl_5776.p1, internal, 31092, 31182
-recovered pasa_asmbl_5776.p1, internal, 31428, 31499
-recovered pasa_asmbl_5776.p1, internal, 31611, 31735
-recovered pasa_asmbl_5776.p1, internal, 31904, 32036
-recovered pasa_asmbl_5776.p1, internal, 32459, 32563
-recovered pasa_asmbl_5776.p1, internal, 32961, 33067
-recovered pasa_asmbl_5776.p1, internal, 33289, 33443
-recovered pasa_asmbl_5776.p1, internal, 33736, 33846
-recovered pasa_asmbl_5776.p1, internal, 34216, 34324
-recovered pasa_asmbl_5776.p1, internal, 34768, 34800
Valid prediction for GlimmerHMM_glimmerT_27525-T1
Valid prediction for snap_scaffold_11-snap.1929-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_27551-T1
Couldn't classify 68095, 68209
Couldn't classify 74193, 74278
Sorry, prediction pasa_asmbl_5782.p1 fails validation.
(ACC)	 AG	68095-68209	GT	AGG
(GAG)	 AG	69239-69358	GT	GGG
(AGA)	 AG	71810-71896	GT	AGG
(AAA)	 AG	72134-72221	GT	AGG
(CTG)	 AG	73301-73379	GT	AGG
(GAT)	 AG	73629-73710	GT	GGG
(ACA)	 AG	74193-74278	GT	AGG
-recovered pasa_asmbl_5782.p1, internal, 68095, 68209
-recovered pasa_asmbl_5782.p1, internal, 69239, 69358
-recovered pasa_asmbl_5782.p1, internal, 71810, 71896
-recovered pasa_asmbl_5782.p1, internal, 72134, 72221
-recovered pasa_asmbl_5782.p1, internal, 73301, 73379
-recovered pasa_asmbl_5782.p1, internal, 73629, 73710
-recovered pasa_asmbl_5782.p1, internal, 74193, 74278
Valid prediction for GlimmerHMM_glimmerT_27533-T1
Valid prediction for snap_scaffold_11-snap.1926-T1
Valid prediction for snap_scaffold_11-snap.1907-T1
Valid prediction for GlimmerHMM_glimmerT_27549-T1
Valid prediction for GlimmerHMM_glimmerT_27529-T1
Valid prediction for GlimmerHMM_glimmerT_27542-T1
Valid prediction for GlimmerHMM_glimmerT_27530-T1
Valid prediction for CodingQuarry_transcript_8168-T1
Valid prediction for CodingQuarry_transcript_8171-T1
Valid prediction for snap_scaffold_11-snap.1928-T1
Valid prediction for snap_scaffold_11-snap.1914-T1
Valid prediction for snap_scaffold_11-snap.1919-T1
Valid prediction for snap_scaffold_11-snap.1909-T1
Valid prediction for Augustus_model.g18228.t1
Couldn't classify 172161, 172197
Sorry, prediction pasa_asmbl_5800.p1 fails validation.
(ACC)	 CG	172161-172197	GT	AGG
(ACA)	 AG	172435-172594	GT	AAG
(TCA)	 AG	172714-172805	GT	AGG
(TGA)	 AG	173046-173128	GT	TGG
(CTG)	 AG	173942-174050	GT	AGG
(AGA)	 AG	174159-174274	GT	AGG
(CCC)	 AG	174582-174609	GT	AGG
(TGG)	 AG	174714-174844	TG	GAT
-recovered pasa_asmbl_5800.p1, terminal, 174714, 174844
-recovered pasa_asmbl_5800.p1, internal, 172435, 172594
-recovered pasa_asmbl_5800.p1, internal, 172714, 172805
-recovered pasa_asmbl_5800.p1, internal, 173046, 173128
-recovered pasa_asmbl_5800.p1, internal, 173942, 174050
-recovered pasa_asmbl_5800.p1, internal, 174159, 174274
-recovered pasa_asmbl_5800.p1, internal, 174582, 174609
Valid prediction for GlimmerHMM_glimmerT_27528-T1
Valid prediction for snap_scaffold_11-snap.1913-T1
Valid prediction for HiQ_model.g18223.t1
Valid prediction for Augustus_model.g18230.t1
Valid prediction for CodingQuarry_transcript_8169-T1
Valid prediction for Augustus_model.g18225.t1
Valid prediction for HiQ_model.g18233.t1
Valid prediction for GlimmerHMM_glimmerT_27544-T1
Valid prediction for snap_scaffold_11-snap.1921-T1
Valid prediction for snap_scaffold_11-snap.1943-T1
Valid prediction for GlimmerHMM_glimmerT_27547-T1
Valid prediction for snap_scaffold_11-snap.1940-T1
Couldn't classify 196304, 196438
Couldn't classify 198395, 198564
Sorry, prediction pasa_asmbl_5804.p1 fails validation.
(CTG)	 TC	196304-196438	GT	AGG
(GAT)	 AG	196720-196950	GT	AGG
(GTA)	 AG	197432-197706	GT	AGG
(GCT)	 AG	198028-198209	GT	GGG
(GCA)	 AG	198395-198564	CT	AGC
-recovered pasa_asmbl_5804.p1, internal, 196720, 196950
-recovered pasa_asmbl_5804.p1, internal, 197432, 197706
-recovered pasa_asmbl_5804.p1, internal, 198028, 198209
Valid prediction for GlimmerHMM_glimmerT_27534-T1
Valid prediction for snap_scaffold_11-snap.1937-T1
Valid prediction for CodingQuarry_transcript_8167-T1
Couldn't classify 101295, 102140
Sorry, prediction pasa_asmbl_5794.p2 fails validation.
(GAA)	 AG	101295-102140	AC	AGA
Valid prediction for CodingQuarry_transcript_8170-T1
Valid prediction for GlimmerHMM_glimmerT_27548-T1
Valid prediction for snap_scaffold_11-snap.1936-T1
Valid prediction for GlimmerHMM_glimmerT_27537-T1
Couldn't classify 194599, 194659
Sorry, prediction pasa_asmbl_5803.p1 fails validation.
(AGC)	 TC	194599-194659	GT	AGG
(GCT)	 AG	194816-195031	GT	GGG
(GTA)	 AG	195211-195464	GT	AGG
(GGC)	 AG	195587-195847	TG	GAT
-recovered pasa_asmbl_5803.p1, terminal, 195587, 195847
-recovered pasa_asmbl_5803.p1, internal, 194816, 195031
-recovered pasa_asmbl_5803.p1, internal, 195211, 195464
Valid prediction for HiQ_model.g18220.t1
Valid prediction for GlimmerHMM_glimmerT_27555-T1
Valid prediction for snap_scaffold_11-snap.1908-T1
Valid prediction for CodingQuarry_transcript_8172-T1
Valid prediction for Augustus_model.g18221.t1
Valid prediction for snap_scaffold_11-snap.1934-T1
Valid prediction for snap_scaffold_11-snap.1942-T1
Valid prediction for pasa_asmbl_5798.p1
Couldn't classify 100365, 100907
Sorry, prediction pasa_asmbl_5793.p1 fails validation.
(ATG)	 GG	100365-100907	CT	GCC
Valid prediction for snap_scaffold_11-snap.1922-T1
Valid prediction for snap_scaffold_11-snap.1924-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_11-snap.1930-T1
Valid prediction for snap_scaffold_11-snap.1917-T1
Valid prediction for snap_scaffold_11-snap.1927-T1
Valid prediction for snap_scaffold_11-snap.1933-T1
Valid prediction for GlimmerHMM_glimmerT_27546-T1
Valid prediction for GlimmerHMM_glimmerT_27543-T1
Valid prediction for GlimmerHMM_glimmerT_27540-T1
Valid prediction for snap_scaffold_11-snap.1915-T1
Sorry, intron length (7) is less than minimum required (10)
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_27538-T1
Valid prediction for snap_scaffold_11-snap.1932-T1
Valid prediction for snap_scaffold_11-snap.1938-T1
Valid prediction for snap_scaffold_11-snap.1912-T1
Valid prediction for GlimmerHMM_glimmerT_27531-T1
Valid prediction for snap_scaffold_11-snap.1923-T1
Valid prediction for Augustus_model.g18222.t1
Valid prediction for snap_scaffold_11-snap.1935-T1
Valid prediction for GlimmerHMM_glimmerT_27545-T1
Valid prediction for snap_scaffold_11-snap.1910-T1
Valid prediction for GlimmerHMM_glimmerT_27541-T1
Valid prediction for GlimmerHMM_glimmerT_27539-T1
Valid prediction for snap_scaffold_11-snap.1925-T1
Valid prediction for GlimmerHMM_glimmerT_27535-T1
Valid prediction for GlimmerHMM_glimmerT_27552-T1
Valid prediction for snap_scaffold_11-snap.1931-T1
Valid prediction for snap_scaffold_11-snap.1920-T1
Valid prediction for GlimmerHMM_glimmerT_27550-T1
Valid prediction for GlimmerHMM_glimmerT_27527-T1
Valid prediction for Augustus_model.g18235.t1
Valid prediction for snap_scaffold_11-snap.1939-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 20060, rend_intergenic: 14262  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26561, rend_intergenic: 22249  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28791, rend_intergenic: 26972  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29666, rend_intergenic: 29004  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50347, rend_intergenic: 45601  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61291, rend_intergenic: 59576  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67784, rend_intergenic: 61650  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74475, rend_intergenic: 67823  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89204, rend_intergenic: 87752  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109330, rend_intergenic: 104882  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138923, rend_intergenic: 112388  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142969, rend_intergenic: 140077  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147832, rend_intergenic: 145929  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165666, rend_intergenic: 160136  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 201173
-exon list size: 465


building trellis

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-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 20060, rend_intergenic: 14262  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26561, rend_intergenic: 22249  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28791, rend_intergenic: 26972  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29666, rend_intergenic: 29004  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50347, rend_intergenic: 45601  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61291, rend_intergenic: 59576  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67784, rend_intergenic: 61650  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74475, rend_intergenic: 67823  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89204, rend_intergenic: 87752  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109330, rend_intergenic: 104882  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138923, rend_intergenic: 112388  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142969, rend_intergenic: 140077  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147832, rend_intergenic: 145929  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165666, rend_intergenic: 160136  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support