-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_10/scaffold_10_9838001-10041924

-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 GeneMark_model.44062_t
Valid prediction for snap_scaffold_10-snap.1930-T1
Valid prediction for snap_scaffold_10-snap.1939-T1
Valid prediction for GeneMark_model.44064_t
Valid prediction for GlimmerHMM_glimmerT_25762-T1
Valid prediction for GeneMark_model.44050_t
Valid prediction for GeneMark_model.44093_t
Valid prediction for GlimmerHMM_glimmerT_25766-T1
Valid prediction for CodingQuarry_transcript_5531-T1
Valid prediction for pasa_asmbl_4685.p1
Valid prediction for snap_scaffold_10-snap.1917-T1
Valid prediction for GeneMark_model.44049_t
Valid prediction for GlimmerHMM_glimmerT_25750-T1
Valid prediction for GeneMark_model.44079_t
Valid prediction for GeneMark_model.44096_t
Valid prediction for GeneMark_model.44083_t
Valid prediction for snap_scaffold_10-snap.1940-T1
Valid prediction for GeneMark_model.44087_t
Valid prediction for GeneMark_model.44070_t
Valid prediction for GlimmerHMM_glimmerT_25764-T1
Valid prediction for GeneMark_model.44058_t
Valid prediction for snap_scaffold_10-snap.1921-T1
Valid prediction for GeneMark_model.44053_t
Valid prediction for GlimmerHMM_glimmerT_25751-T1
Valid prediction for snap_scaffold_10-snap.1919-T1
Valid prediction for snap_scaffold_10-snap.1936-T1
Valid prediction for snap_scaffold_10-snap.1920-T1
Valid prediction for GeneMark_model.44082_t
Valid prediction for snap_scaffold_10-snap.1909-T1
Valid prediction for GeneMark_model.44072_t
Valid prediction for GeneMark_model.44071_t
Valid prediction for Augustus_model.g17291.t1
Valid prediction for GlimmerHMM_glimmerT_25761-T1
Valid prediction for GeneMark_model.44094_t
Valid prediction for GeneMark_model.44073_t
Valid prediction for snap_scaffold_10-snap.1908-T1
Valid prediction for GeneMark_model.44060_t
Valid prediction for snap_scaffold_10-snap.1914-T1
Valid prediction for GeneMark_model.44065_t
Valid prediction for snap_scaffold_10-snap.1927-T1
Valid prediction for GlimmerHMM_glimmerT_25757-T1
Valid prediction for snap_scaffold_10-snap.1922-T1
Valid prediction for GeneMark_model.44054_t
Valid prediction for snap_scaffold_10-snap.1910-T1
Valid prediction for GeneMark_model.44066_t
Valid prediction for GeneMark_model.44067_t
Valid prediction for Augustus_model.g17289.t1
Valid prediction for GlimmerHMM_glimmerT_25758-T1
Valid prediction for snap_scaffold_10-snap.1912-T1
Valid prediction for GeneMark_model.44089_t
Valid prediction for GeneMark_model.44084_t
Valid prediction for GeneMark_model.44078_t
Valid prediction for GlimmerHMM_glimmerT_25763-T1
Valid prediction for GeneMark_model.44046_t
Valid prediction for snap_scaffold_10-snap.1938-T1
Valid prediction for GeneMark_model.44091_t
Valid prediction for snap_scaffold_10-snap.1942-T1
Valid prediction for snap_scaffold_10-snap.1924-T1
Valid prediction for HiQ_model.g17284.t1
Valid prediction for GlimmerHMM_glimmerT_25748-T1
Valid prediction for snap_scaffold_10-snap.1926-T1
Valid prediction for snap_scaffold_10-snap.1944-T1
Valid prediction for snap_scaffold_10-snap.1933-T1
Valid prediction for GlimmerHMM_glimmerT_25755-T1
Valid prediction for snap_scaffold_10-snap.1929-T1
Valid prediction for Augustus_model.g17287.t1
Valid prediction for snap_scaffold_10-snap.1931-T1
Valid prediction for GeneMark_model.44076_t
Valid prediction for Augustus_model.g17288.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 GeneMark_model.44068_t
Couldn't classify 196293, 196414
Sorry, prediction pasa_asmbl_3610.p1 fails validation.
(GAG)	 GA	196293-196414	GT	GAG
(GTA)	 AG	196659-196851	GT	AGG
(GTG)	 AG	196962-197158	GT	AGG
(GGC)	 AG	197366-197444	GT	AGG
(TAC)	 AG	197613-197708	GT	AAG
(TTG)	 AG	197863-197925	CC	GAC
-recovered pasa_asmbl_3610.p1, terminal, 197863, 197925
-recovered pasa_asmbl_3610.p1, internal, 196659, 196851
-recovered pasa_asmbl_3610.p1, internal, 196962, 197158
-recovered pasa_asmbl_3610.p1, internal, 197366, 197444
-recovered pasa_asmbl_3610.p1, internal, 197613, 197708
Valid prediction for snap_scaffold_10-snap.1918-T1
Valid prediction for Augustus_model.g17283.t1
Valid prediction for snap_scaffold_10-snap.1916-T1
Valid prediction for GeneMark_model.44061_t
Valid prediction for GeneMark_model.44069_t
Valid prediction for snap_scaffold_10-snap.1935-T1
Valid prediction for snap_scaffold_10-snap.1928-T1
Valid prediction for GeneMark_model.44055_t
Valid prediction for GeneMark_model.44088_t
Valid prediction for GlimmerHMM_glimmerT_25749-T1
Valid prediction for GlimmerHMM_glimmerT_25767-T1
Valid prediction for GeneMark_model.44092_t
Valid prediction for GlimmerHMM_glimmerT_25747-T1
Valid prediction for snap_scaffold_10-snap.1932-T1
Valid prediction for snap_scaffold_10-snap.1934-T1
Valid prediction for GeneMark_model.44090_t
Valid prediction for GlimmerHMM_glimmerT_25765-T1
Valid prediction for GeneMark_model.44051_t
Couldn't classify 194983, 195147
Couldn't classify 196093, 196158
Sorry, prediction pasa_asmbl_3611.p1 fails validation.
(TCC)	 CC	194983-195147	GT	AGG
(GCC)	 AG	195303-195401	GC	AGG
(GTG)	 AG	195914-195985	GT	TGG
(GAG)	 AG	196093-196158	CT	AGC
-recovered pasa_asmbl_3611.p1, internal, 195303, 195401
-recovered pasa_asmbl_3611.p1, internal, 195914, 195985
Valid prediction for GlimmerHMM_glimmerT_25759-T1
Valid prediction for GeneMark_model.44047_t
Valid prediction for GlimmerHMM_glimmerT_25752-T1
Valid prediction for GeneMark_model.44057_t
Valid prediction for GlimmerHMM_glimmerT_25760-T1
Valid prediction for snap_scaffold_10-snap.1915-T1
Valid prediction for snap_scaffold_10-snap.1906-T1
Valid prediction for GlimmerHMM_glimmerT_25746-T1
Valid prediction for GlimmerHMM_glimmerT_25753-T1
Valid prediction for snap_scaffold_10-snap.1907-T1
Valid prediction for Augustus_model.g17286.t1
Valid prediction for snap_scaffold_10-snap.1925-T1
Valid prediction for GeneMark_model.44080_t
Couldn't classify 42275, 42313
Sorry, prediction GeneMark_model.44085_t fails validation.
(AGA)	 AG	42275-42313	GT	GGG
(TGA)	 AG	43527-43544	GT	CAG
(GGA)	 AG	43599-43677	GC	GAG
-recovered GeneMark_model.44085_t, terminal, 43599, 43677
-recovered GeneMark_model.44085_t, internal, 42275, 42313
-recovered GeneMark_model.44085_t, internal, 43527, 43544
-recovered GeneMark_model.44085_t, internal, 43599, 43677
Valid prediction for GeneMark_model.44059_t
Valid prediction for snap_scaffold_10-snap.1943-T1
Valid prediction for GeneMark_model.44045_t
Valid prediction for GeneMark_model.44095_t
Valid prediction for GeneMark_model.44048_t
Valid prediction for Augustus_model.g17285.t1
Valid prediction for snap_scaffold_10-snap.1923-T1
Valid prediction for snap_scaffold_10-snap.1941-T1
Valid prediction for Augustus_model.g17290.t1
Valid prediction for GeneMark_model.44052_t
Valid prediction for snap_scaffold_10-snap.1937-T1
Valid prediction for snap_scaffold_10-snap.1911-T1
Valid prediction for GeneMark_model.44075_t
Valid prediction for GeneMark_model.44074_t
Valid prediction for GlimmerHMM_glimmerT_25754-T1
Valid prediction for GeneMark_model.44056_t
Valid prediction for GeneMark_model.44086_t
Valid prediction for GlimmerHMM_glimmerT_25756-T1
Valid prediction for GeneMark_model.44077_t
Valid prediction for snap_scaffold_10-snap.1913-T1
Valid prediction for GeneMark_model.44063_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 25852, rend_intergenic: 23977  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37516, rend_intergenic: 31145  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47230, rend_intergenic: 46682  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63503, rend_intergenic: 56185  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93818, rend_intergenic: 89131  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98934, rend_intergenic: 98339  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108265, rend_intergenic: 102551  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131783, rend_intergenic: 131135  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142556, rend_intergenic: 139480  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154642, rend_intergenic: 148667  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155307, rend_intergenic: 154719  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160661, rend_intergenic: 156026  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193989, rend_intergenic: 187149  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 203924
-exon list size: 538


building trellis

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-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 25852, rend_intergenic: 23977  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37516, rend_intergenic: 31145  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47230, rend_intergenic: 46682  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63503, rend_intergenic: 56185  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93818, rend_intergenic: 89131  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98934, rend_intergenic: 98339  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108265, rend_intergenic: 102551  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131783, rend_intergenic: 131135  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142556, rend_intergenic: 139480  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154642, rend_intergenic: 148667  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155307, rend_intergenic: 154719  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160661, rend_intergenic: 156026  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193989, rend_intergenic: 187149  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 9 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 193512 - 203924
-exon list size: 20


building trellis

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59.1    
63.6    
68.2    
72.7    
77.3    
81.8    
86.4    
90.9    
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-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support