-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_21/scaffold_21_8680663-8797452

-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_49481-T1
Valid prediction for Augustus_model.g33194.t1
Valid prediction for GeneMark_model.85644_t
Valid prediction for GeneMark_model.85646_t
Valid prediction for snap_scaffold_21-snap.1865-T1
Valid prediction for GeneMark_model.85648_t
Valid prediction for snap_scaffold_21-snap.1859-T1
Valid prediction for Augustus_model.g33200.t1
Valid prediction for GeneMark_model.85665_t
Valid prediction for GlimmerHMM_glimmerT_49484-T1
Valid prediction for snap_scaffold_21-snap.1881-T1
Valid prediction for GeneMark_model.85657_t
Valid prediction for snap_scaffold_21-snap.1879-T1
Valid prediction for GeneMark_model.85639_t
Valid prediction for snap_scaffold_21-snap.1889-T1
Valid prediction for snap_scaffold_21-snap.1875-T1
Valid prediction for GeneMark_model.85637_t
Valid prediction for snap_scaffold_21-snap.1861-T1
Valid prediction for GlimmerHMM_glimmerT_49474-T1
Valid prediction for snap_scaffold_21-snap.1858-T1
Valid prediction for GlimmerHMM_glimmerT_49473-T1
Valid prediction for GeneMark_model.85632_t
Valid prediction for Augustus_model.g33191.t1
Valid prediction for GeneMark_model.85661_t
Valid prediction for Augustus_model.g33193.t1
Valid prediction for GeneMark_model.85669_t
Valid prediction for snap_scaffold_21-snap.1887-T1
Valid prediction for Augustus_model.g33192.t1
Valid prediction for GeneMark_model.85653_t
Valid prediction for GlimmerHMM_glimmerT_49486-T1
Valid prediction for GeneMark_model.85659_t
Valid prediction for GlimmerHMM_glimmerT_49477-T1
Valid prediction for snap_scaffold_21-snap.1868-T1
Valid prediction for GeneMark_model.85650_t
Valid prediction for GeneMark_model.85636_t
Valid prediction for GeneMark_model.85663_t
Valid prediction for GlimmerHMM_glimmerT_49489-T1
Valid prediction for GlimmerHMM_glimmerT_49479-T1
Valid prediction for snap_scaffold_21-snap.1877-T1
Valid prediction for GlimmerHMM_glimmerT_49476-T1
Valid prediction for snap_scaffold_21-snap.1874-T1
Valid prediction for snap_scaffold_21-snap.1863-T1
Valid prediction for snap_scaffold_21-snap.1866-T1
Valid prediction for Augustus_model.g33199.t1
Valid prediction for snap_scaffold_21-snap.1872-T1
Valid prediction for GeneMark_model.85638_t
Valid prediction for GeneMark_model.85641_t
Valid prediction for snap_scaffold_21-snap.1882-T1
Valid prediction for GeneMark_model.85634_t
Valid prediction for snap_scaffold_21-snap.1860-T1
Valid prediction for snap_scaffold_21-snap.1880-T1
Valid prediction for snap_scaffold_21-snap.1885-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_21-snap.1886-T1
Couldn't classify 109751, 109813
Couldn't classify 111256, 111359
Sorry, prediction pasa_asmbl_27959.p1 fails validation.
(AAC)	 CC	109751-109813	GT	AGG
(CTC)	 AG	109956-110090	GT	AGG
(TGT)	 AG	110155-110343	GT	GGG
(CAT)	 AG	110621-110796	GT	AGG
(TGA)	 AG	110994-111151	GT	TGG
(TGG)	 AG	111256-111359	AA	CCA
-recovered pasa_asmbl_27959.p1, internal, 109956, 110090
-recovered pasa_asmbl_27959.p1, internal, 110155, 110343
-recovered pasa_asmbl_27959.p1, internal, 110621, 110796
-recovered pasa_asmbl_27959.p1, internal, 110994, 111151
Couldn't classify 105862, 106012
Sorry, prediction pasa_asmbl_27960.p1 fails validation.
(ATG)	 AC	104999-105082	GT	AGG
(AGG)	 AG	105319-105433	GT	AGG
(GAC)	 AG	105528-105633	GT	CGG
(AGG)	 AG	105862-106012	CA	AGC
-recovered pasa_asmbl_27960.p1, initial, 104999, 105082
-recovered pasa_asmbl_27960.p1, internal, 105319, 105433
-recovered pasa_asmbl_27960.p1, internal, 105528, 105633
Valid prediction for snap_scaffold_21-snap.1873-T1
Valid prediction for GlimmerHMM_glimmerT_49487-T1
Valid prediction for snap_scaffold_21-snap.1862-T1
Valid prediction for GlimmerHMM_glimmerT_49490-T1
Valid prediction for snap_scaffold_21-snap.1864-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.85647_t
Valid prediction for GlimmerHMM_glimmerT_49488-T1
Valid prediction for GeneMark_model.85635_t
Valid prediction for GeneMark_model.85667_t
Valid prediction for GeneMark_model.85652_t
Valid prediction for GeneMark_model.85658_t
Valid prediction for Augustus_model.g33196.t1
Valid prediction for GeneMark_model.85660_t
Valid prediction for GlimmerHMM_glimmerT_49482-T1
Valid prediction for GeneMark_model.85633_t
Valid prediction for GlimmerHMM_glimmerT_49483-T1
Valid prediction for snap_scaffold_21-snap.1867-T1
Valid prediction for GeneMark_model.85666_t
Valid prediction for GlimmerHMM_glimmerT_49485-T1
Valid prediction for GeneMark_model.85656_t
Valid prediction for Augustus_model.g33198.t1
Valid prediction for Augustus_model.g33190.t1
Valid prediction for GeneMark_model.85645_t
Valid prediction for GeneMark_model.85651_t
Valid prediction for GeneMark_model.85668_t
Valid prediction for snap_scaffold_21-snap.1883-T1
Valid prediction for GeneMark_model.85640_t
Valid prediction for Augustus_model.g33195.t1
Valid prediction for GeneMark_model.85655_t
Valid prediction for GlimmerHMM_glimmerT_49475-T1
Valid prediction for snap_scaffold_21-snap.1884-T1
Valid prediction for snap_scaffold_21-snap.1870-T1
Valid prediction for GlimmerHMM_glimmerT_49478-T1
Valid prediction for GeneMark_model.85662_t
Valid prediction for snap_scaffold_21-snap.1876-T1
Couldn't classify 31754, 31819
Sorry, prediction GeneMark_model.85664_t fails validation.
(CGG)	 AG	31754-31819	GT	CCG
(ACA)	 AG	31852-31947	GC	AAG
(AGA)	 AG	31970-32110	GT	AGG
(GAG)	 AG	33285-33479	GC	CTG
(GCT)	 AG	33868-34041	GT	AGG
(AGA)	 AG	35866-35874	GT	GAG
(GAA)	 AG	35899-35919	GT	ATG
(AAG)	 AG	36351-36449	GT	CTG
(GCA)	 AG	36652-36684	GT	CAG
(TCA)	 AG	36708-36776	GT	CAG
(GTC)	 AG	36800-36863	GT	GAG
-recovered GeneMark_model.85664_t, terminal, 36800, 36863
-recovered GeneMark_model.85664_t, internal, 31754, 31819
-recovered GeneMark_model.85664_t, internal, 31852, 31947
-recovered GeneMark_model.85664_t, internal, 31970, 32110
-recovered GeneMark_model.85664_t, internal, 33285, 33479
-recovered GeneMark_model.85664_t, internal, 33868, 34041
-recovered GeneMark_model.85664_t, internal, 35866, 35874
-recovered GeneMark_model.85664_t, internal, 35899, 35919
-recovered GeneMark_model.85664_t, internal, 36351, 36449
-recovered GeneMark_model.85664_t, internal, 36652, 36684
-recovered GeneMark_model.85664_t, internal, 36708, 36776
-recovered GeneMark_model.85664_t, internal, 36800, 36863
Valid prediction for GlimmerHMM_glimmerT_49472-T1
Valid prediction for GeneMark_model.85649_t
Valid prediction for GeneMark_model.85642_t
Couldn't classify 112292, 112467
Couldn't classify 112665, 112803
Sorry, prediction pasa_asmbl_28253.p1 fails validation.
(CAT)	 AG	112292-112467	GT	AGG
(TGA)	 AG	112665-112803	TC	GCT
-recovered pasa_asmbl_28253.p1, internal, 112292, 112467
Valid prediction for GeneMark_model.85643_t
Valid prediction for Augustus_model.g33197.t1
Valid prediction for snap_scaffold_21-snap.1890-T1
Valid prediction for snap_scaffold_21-snap.1871-T1
Valid prediction for snap_scaffold_21-snap.1888-T1
Valid prediction for snap_scaffold_21-snap.1857-T1
Valid prediction for snap_scaffold_21-snap.1878-T1
Valid prediction for CodingQuarry_transcript_32621-T1
Valid prediction for GlimmerHMM_glimmerT_49480-T1
Valid prediction for GeneMark_model.85654_t
Valid prediction for snap_scaffold_21-snap.1869-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12556, rend_intergenic: 2718  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25386, rend_intergenic: 22900  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36012, rend_intergenic: 29305  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37018, rend_intergenic: 36087  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43954, rend_intergenic: 37355  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50597, rend_intergenic: 45278  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56277, rend_intergenic: 51522  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56803, rend_intergenic: 56305  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58141, rend_intergenic: 56857  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62469, rend_intergenic: 59848  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68498, rend_intergenic: 63178  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70595, rend_intergenic: 69375  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91433, rend_intergenic: 83305  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95012, rend_intergenic: 91787  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100311, rend_intergenic: 96983  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101783, rend_intergenic: 101184  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109633, rend_intergenic: 103345  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112107, rend_intergenic: 110740  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 116790
-exon list size: 544


building trellis

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32.8    
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33.2    
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33.9    
34.1    
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34.6    
34.8    
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35.2    
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35.5    
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35.9    
36.1    
36.3    
36.4    
36.6    
36.8    
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43.6    
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44.1    
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98.2    
98.4    
98.5    
98.7    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 12556, rend_intergenic: 2718  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25386, rend_intergenic: 22900  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36012, rend_intergenic: 29305  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37018, rend_intergenic: 36087  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43954, rend_intergenic: 37355  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50597, rend_intergenic: 45278  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56277, rend_intergenic: 51522  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56803, rend_intergenic: 56305  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58141, rend_intergenic: 56857  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62469, rend_intergenic: 59848  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68498, rend_intergenic: 63178  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70595, rend_intergenic: 69375  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91433, rend_intergenic: 83305  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95012, rend_intergenic: 91787  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100311, rend_intergenic: 96983  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101783, rend_intergenic: 101184  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109633, rend_intergenic: 103345  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112107, rend_intergenic: 110740  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 12 predictions persist after filtering for low support