-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_2/scaffold_2_9460497-9659623

-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_4417-T1
Valid prediction for snap_scaffold_2-snap.1916-T1
Valid prediction for GeneMark_model.7065_t
Couldn't classify 20217, 20267
Couldn't classify 31907, 31963
Sorry, prediction pasa_asmbl_24717.p1 fails validation.
(GCC)	 CG	20217-20267	GT	TGG
(AGG)	 AG	23194-23313	GT	AGG
(GAC)	 AG	24006-24096	GT	TGG
(ACG)	 AG	24965-25084	GT	CGG
(ACC)	 AG	25501-25643	GT	AGG
(AAC)	 AG	26683-26797	GT	GCG
(AGG)	 AG	26888-26957	GT	AGG
(TAA)	 AG	27201-27345	GT	CGG
(TGC)	 AG	27447-27666	GT	AGG
(ATG)	 AG	27781-27872	GT	GAG
(GAA)	 AG	27958-27999	GT	AGG
(CAA)	 AG	28930-29087	GT	AGG
(GAG)	 AG	30298-30365	GT	TGG
(AGG)	 AG	31641-31786	GT	AGG
(ATC)	 AG	31907-31963	AC	TGA
add_exon() Sorry, pasa_asmbl_24717.p1 27781-27872-initial-1 is invalid.
-recovered pasa_asmbl_24717.p1, initial, 27781, 27872
-recovered pasa_asmbl_24717.p1, internal, 23194, 23313
-recovered pasa_asmbl_24717.p1, internal, 24006, 24096
-recovered pasa_asmbl_24717.p1, internal, 24965, 25084
-recovered pasa_asmbl_24717.p1, internal, 25501, 25643
-recovered pasa_asmbl_24717.p1, internal, 26683, 26797
-recovered pasa_asmbl_24717.p1, internal, 26888, 26957
-recovered pasa_asmbl_24717.p1, internal, 27201, 27345
-recovered pasa_asmbl_24717.p1, internal, 27447, 27666
-recovered pasa_asmbl_24717.p1, internal, 27781, 27872
-recovered pasa_asmbl_24717.p1, internal, 27958, 27999
-recovered pasa_asmbl_24717.p1, internal, 28930, 29087
-recovered pasa_asmbl_24717.p1, internal, 30298, 30365
-recovered pasa_asmbl_24717.p1, internal, 31641, 31786
Valid prediction for GlimmerHMM_glimmerT_4421-T1
Valid prediction for GlimmerHMM_glimmerT_4422-T1
Valid prediction for Augustus_model.g2968.t1
Valid prediction for snap_scaffold_2-snap.1903-T1
Valid prediction for GeneMark_model.7083_t
Valid prediction for GeneMark_model.7074_t
Valid prediction for Augustus_model.g2970.t1
Valid prediction for snap_scaffold_2-snap.1926-T1
Valid prediction for snap_scaffold_2-snap.1925-T1
Valid prediction for Augustus_model.g2967.t1
Valid prediction for GeneMark_model.7077_t
Valid prediction for GeneMark_model.7078_t
Valid prediction for GeneMark_model.7103_t
Valid prediction for GeneMark_model.7085_t
Valid prediction for snap_scaffold_2-snap.1942-T1
Valid prediction for GlimmerHMM_glimmerT_4426-T1
Valid prediction for GeneMark_model.7098_t
Valid prediction for GlimmerHMM_glimmerT_4418-T1
Valid prediction for snap_scaffold_2-snap.1924-T1
Valid prediction for GeneMark_model.7084_t
Valid prediction for snap_scaffold_2-snap.1929-T1
Valid prediction for snap_scaffold_2-snap.1920-T1
Valid prediction for GeneMark_model.7112_t
Valid prediction for snap_scaffold_2-snap.1933-T1
Valid prediction for snap_scaffold_2-snap.1922-T1
Valid prediction for snap_scaffold_2-snap.1928-T1
Valid prediction for GeneMark_model.7089_t
Valid prediction for Augustus_model.g2975.t1
Valid prediction for GeneMark_model.7060_t
Valid prediction for snap_scaffold_2-snap.1904-T1
Valid prediction for snap_scaffold_2-snap.1935-T1
Valid prediction for GlimmerHMM_glimmerT_4427-T1
Valid prediction for snap_scaffold_2-snap.1910-T1
Couldn't classify 32569, 32877
Sorry, prediction pasa_asmbl_24719.p1 fails validation.
(CCT)	 CT	32569-32877	CT	AGC
Valid prediction for GeneMark_model.7107_t
Valid prediction for Augustus_model.g2972.t1
Valid prediction for Augustus_model.g2969.t1
Valid prediction for GlimmerHMM_glimmerT_4419-T1
Valid prediction for Augustus_model.g2974.t1
Valid prediction for snap_scaffold_2-snap.1931-T1
Valid prediction for snap_scaffold_2-snap.1914-T1
Valid prediction for GeneMark_model.7067_t
Valid prediction for Augustus_model.g2977.t1
Valid prediction for GlimmerHMM_glimmerT_4423-T1
Valid prediction for snap_scaffold_2-snap.1923-T1
Valid prediction for Augustus_model.g2973.t1
Valid prediction for GeneMark_model.7058_t
Valid prediction for GeneMark_model.7097_t
Valid prediction for Augustus_model.g2971.t1
Valid prediction for GeneMark_model.7105_t
Valid prediction for snap_scaffold_2-snap.1908-T1
Valid prediction for GeneMark_model.7114_t
Valid prediction for snap_scaffold_2-snap.1919-T1
Valid prediction for GeneMark_model.7109_t
Valid prediction for snap_scaffold_2-snap.1921-T1
Valid prediction for snap_scaffold_2-snap.1936-T1
Valid prediction for GlimmerHMM_glimmerT_4415-T1
Valid prediction for snap_scaffold_2-snap.1912-T1
Valid prediction for GeneMark_model.7079_t
Valid prediction for GeneMark_model.7082_t
Valid prediction for GeneMark_model.7075_t
Valid prediction for snap_scaffold_2-snap.1918-T1
Valid prediction for snap_scaffold_2-snap.1930-T1
Valid prediction for GeneMark_model.7056_t
Valid prediction for GlimmerHMM_glimmerT_4416-T1
Valid prediction for GeneMark_model.7062_t
Valid prediction for GeneMark_model.7070_t
Valid prediction for snap_scaffold_2-snap.1906-T1
Valid prediction for GlimmerHMM_glimmerT_4413-T1
Valid prediction for GeneMark_model.7100_t
Valid prediction for GeneMark_model.7069_t
Valid prediction for GeneMark_model.7081_t
Valid prediction for GeneMark_model.7087_t
Valid prediction for GeneMark_model.7080_t
Valid prediction for GeneMark_model.7091_t
Valid prediction for Augustus_model.g2976.t1
Valid prediction for GeneMark_model.7072_t
Valid prediction for GeneMark_model.7063_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.7068_t
Valid prediction for GlimmerHMM_glimmerT_4424-T1
Valid prediction for GeneMark_model.7057_t
Valid prediction for GlimmerHMM_glimmerT_4420-T1
Valid prediction for snap_scaffold_2-snap.1915-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_2-snap.1938-T1
Valid prediction for snap_scaffold_2-snap.1940-T1
Valid prediction for snap_scaffold_2-snap.1934-T1
Valid prediction for GeneMark_model.7102_t
Valid prediction for Augustus_model.g2966.t1
Valid prediction for Augustus_model.g2978.t1
Valid prediction for snap_scaffold_2-snap.1943-T1
Valid prediction for GeneMark_model.7101_t
Valid prediction for snap_scaffold_2-snap.1941-T1
Valid prediction for snap_scaffold_2-snap.1932-T1
Valid prediction for GeneMark_model.7071_t
Valid prediction for GeneMark_model.7111_t
Valid prediction for snap_scaffold_2-snap.1907-T1
Valid prediction for GeneMark_model.7113_t
Valid prediction for snap_scaffold_2-snap.1927-T1
Valid prediction for snap_scaffold_2-snap.1937-T1
Valid prediction for GeneMark_model.7106_t
Valid prediction for GeneMark_model.7096_t
Valid prediction for snap_scaffold_2-snap.1917-T1
Valid prediction for GeneMark_model.7076_t
Valid prediction for GeneMark_model.7104_t
Valid prediction for snap_scaffold_2-snap.1913-T1
Valid prediction for GeneMark_model.7094_t
Valid prediction for snap_scaffold_2-snap.1939-T1
Valid prediction for GeneMark_model.7110_t
Valid prediction for GeneMark_model.7059_t
Valid prediction for snap_scaffold_2-snap.1905-T1
Valid prediction for GeneMark_model.7092_t
Valid prediction for GlimmerHMM_glimmerT_4414-T1
Valid prediction for GeneMark_model.7064_t
Valid prediction for GeneMark_model.7090_t
Valid prediction for GeneMark_model.7055_t
Valid prediction for GeneMark_model.7088_t
Valid prediction for GlimmerHMM_glimmerT_4411-T1
Valid prediction for GeneMark_model.7093_t
Valid prediction for GeneMark_model.7095_t
Valid prediction for GlimmerHMM_glimmerT_4425-T1
Valid prediction for snap_scaffold_2-snap.1909-T1
Valid prediction for GeneMark_model.7086_t
Valid prediction for snap_scaffold_2-snap.1911-T1
Valid prediction for GeneMark_model.7099_t
Valid prediction for GeneMark_model.7108_t
Valid prediction for GlimmerHMM_glimmerT_4412-T1
Valid prediction for GeneMark_model.7066_t
Valid prediction for GeneMark_model.7061_t
Valid prediction for GeneMark_model.7073_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12268, rend_intergenic: 8129  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17576, rend_intergenic: 13926  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31591, rend_intergenic: 21612  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37256, rend_intergenic: 35342  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48572, rend_intergenic: 42456  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65116, rend_intergenic: 51369  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71721, rend_intergenic: 65889  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109215, rend_intergenic: 105322  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145312, rend_intergenic: 142046  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149321, rend_intergenic: 146187  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182808, rend_intergenic: 153499  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187278, rend_intergenic: 184880  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 199127
-exon list size: 674


building trellis

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-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 12268, rend_intergenic: 8129  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17576, rend_intergenic: 13926  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31591, rend_intergenic: 21612  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37256, rend_intergenic: 35342  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48572, rend_intergenic: 42456  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65116, rend_intergenic: 51369  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71721, rend_intergenic: 65889  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109215, rend_intergenic: 105322  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145312, rend_intergenic: 142046  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149321, rend_intergenic: 146187  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182808, rend_intergenic: 153499  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187278, rend_intergenic: 184880  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support