-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_27/scaffold_27_9317619-9487677

-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: +)Couldn't classify 94944, 95259
Couldn't classify 96650, 96743
Sorry, prediction pasa_asmbl_36538.p1 fails validation.
(TTG)	 CG	94944-95259	GT	AGG
(AGC)	 AG	95571-95672	GT	AGG
(GTG)	 AG	95769-95910	GT	GAG
(GTC)	 AG	96650-96743	GG	CTG
-recovered pasa_asmbl_36538.p1, internal, 95571, 95672
-recovered pasa_asmbl_36538.p1, internal, 95769, 95910
Valid prediction for GlimmerHMM_glimmerT_59230-T1
Valid prediction for snap_scaffold_27-snap.2192-T1
Valid prediction for GeneMark_model.103416_t
Valid prediction for GeneMark_model.103381_t
Valid prediction for snap_scaffold_27-snap.2194-T1
Valid prediction for snap_scaffold_27-snap.2219-T1
Valid prediction for snap_scaffold_27-snap.2217-T1
Valid prediction for GeneMark_model.103394_t
Valid prediction for GeneMark_model.103403_t
Valid prediction for GlimmerHMM_glimmerT_59221-T1
Valid prediction for GeneMark_model.103418_t
Valid prediction for snap_scaffold_27-snap.2179-T1
Valid prediction for GlimmerHMM_glimmerT_59229-T1
Valid prediction for GeneMark_model.103390_t
Valid prediction for snap_scaffold_27-snap.2203-T1
Valid prediction for snap_scaffold_27-snap.2198-T1
Valid prediction for GeneMark_model.103397_t
Valid prediction for GeneMark_model.103396_t
Valid prediction for GeneMark_model.103408_t
Valid prediction for snap_scaffold_27-snap.2188-T1
Valid prediction for GeneMark_model.103391_t
Valid prediction for Augustus_model.g39420.t1
Valid prediction for snap_scaffold_27-snap.2183-T1
Valid prediction for snap_scaffold_27-snap.2184-T1
Valid prediction for GeneMark_model.103371_t
Valid prediction for GlimmerHMM_glimmerT_59223-T1
Valid prediction for GeneMark_model.103410_t
Valid prediction for GlimmerHMM_glimmerT_59228-T1
Valid prediction for GeneMark_model.103387_t
Valid prediction for GeneMark_model.103373_t
Valid prediction for GlimmerHMM_glimmerT_59222-T1
Valid prediction for snap_scaffold_27-snap.2202-T1
Valid prediction for snap_scaffold_27-snap.2215-T1
Valid prediction for snap_scaffold_27-snap.2211-T1
Valid prediction for GeneMark_model.103405_t
Valid prediction for GeneMark_model.103380_t
Valid prediction for Augustus_model.g39418.t1
Valid prediction for GeneMark_model.103382_t
Couldn't classify 87377, 87428
Couldn't classify 90641, 90760
Sorry, prediction pasa_asmbl_36534.p1 fails validation.
(AAG)	 CG	87377-87428	GT	AGG
(CTC)	 AG	90165-90322	GT	CCG
(GAA)	 AG	90641-90760	GG	TCG
-recovered pasa_asmbl_36534.p1, internal, 90165, 90322
Valid prediction for pasa_asmbl_36476.p1
Valid prediction for snap_scaffold_27-snap.2196-T1
Valid prediction for GeneMark_model.103395_t
Valid prediction for snap_scaffold_27-snap.2208-T1
Valid prediction for snap_scaffold_27-snap.2216-T1
Valid prediction for GeneMark_model.103420_t
Valid prediction for CodingQuarry_transcript_41879-T1
Valid prediction for snap_scaffold_27-snap.2181-T1
Valid prediction for GlimmerHMM_glimmerT_59232-T1
Valid prediction for snap_scaffold_27-snap.2197-T1
Valid prediction for GeneMark_model.103423_t
Valid prediction for GeneMark_model.103378_t
Valid prediction for GeneMark_model.103375_t
Valid prediction for snap_scaffold_27-snap.2191-T1
Valid prediction for GeneMark_model.103415_t
Valid prediction for snap_scaffold_27-snap.2187-T1
Valid prediction for GeneMark_model.103399_t
Valid prediction for GlimmerHMM_glimmerT_59226-T1
Valid prediction for GeneMark_model.103388_t
Valid prediction for HiQ_model.g39419.t1
Valid prediction for GeneMark_model.103385_t
Valid prediction for GeneMark_model.103413_t
Valid prediction for snap_scaffold_27-snap.2220-T1
Valid prediction for GeneMark_model.103401_t
Valid prediction for GlimmerHMM_glimmerT_59225-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 152955, 153056
Sorry, prediction pasa_asmbl_37083.p1 fails validation.
(TCA)	 CT	152955-153056	GT	AGG
(GTG)	 AG	155740-155859	GT	TGG
(CAT)	 AG	157216-157292	GT	TGG
(GTT)	 AG	157735-157913	GT	CAG
(ACT)	 AG	158142-158413	GA	AAG
-recovered pasa_asmbl_37083.p1, terminal, 158142, 158413
-recovered pasa_asmbl_37083.p1, internal, 155740, 155859
-recovered pasa_asmbl_37083.p1, internal, 157216, 157292
-recovered pasa_asmbl_37083.p1, internal, 157735, 157913
Valid prediction for snap_scaffold_27-snap.2213-T1
Valid prediction for GlimmerHMM_glimmerT_59233-T1
Valid prediction for GeneMark_model.103419_t
Valid prediction for GeneMark_model.103384_t
Valid prediction for CodingQuarry_transcript_41881-T1
Valid prediction for GeneMark_model.103393_t
Valid prediction for snap_scaffold_27-snap.2190-T1
Valid prediction for GeneMark_model.103372_t
Valid prediction for GeneMark_model.103411_t
Valid prediction for GeneMark_model.103424_t
Valid prediction for snap_scaffold_27-snap.2189-T1
Valid prediction for snap_scaffold_27-snap.2178-T1
Valid prediction for Augustus_model.g39423.t1
Valid prediction for GeneMark_model.103421_t
Valid prediction for GlimmerHMM_glimmerT_59227-T1
Valid prediction for Augustus_model.g39417.t1
Valid prediction for snap_scaffold_27-snap.2193-T1
Valid prediction for GlimmerHMM_glimmerT_59217-T1
Valid prediction for snap_scaffold_27-snap.2218-T1
Valid prediction for snap_scaffold_27-snap.2195-T1
Valid prediction for snap_scaffold_27-snap.2186-T1
Valid prediction for GlimmerHMM_glimmerT_59231-T1
Valid prediction for snap_scaffold_27-snap.2212-T1
Valid prediction for GeneMark_model.103412_t
Valid prediction for snap_scaffold_27-snap.2185-T1
Valid prediction for snap_scaffold_27-snap.2204-T1
Valid prediction for GeneMark_model.103392_t
Valid prediction for snap_scaffold_27-snap.2210-T1
Valid prediction for GeneMark_model.103402_t
Couldn't classify 46998, 47204
Couldn't classify 57231, 57382
Sorry, prediction pasa_asmbl_37093.p1 fails validation.
(GCC)	 CA	46998-47204	GT	AGG
(GAA)	 AG	49581-49662	GT	AGG
(AGA)	 AG	51733-51901	GT	AGG
(CCA)	 AG	53554-53720	GT	AGG
(ATG)	 AG	53806-53927	GT	CGG
(GTG)	 AG	54199-54415	GT	AGG
(TCC)	 AG	54836-54960	GT	GGG
(GTG)	 AG	55239-55422	GT	TAG
(AGC)	 AG	55880-56116	GT	AGG
(TTG)	 AG	56776-56815	GT	AGG
(GCC)	 AG	56917-57053	GT	CGG
(AGG)	 AG	57231-57382	CC	CCC
add_exon() Sorry, pasa_asmbl_37093.p1 53806-53927-initial-1 is invalid.
-recovered pasa_asmbl_37093.p1, initial, 53806, 53927
-recovered pasa_asmbl_37093.p1, internal, 49581, 49662
-recovered pasa_asmbl_37093.p1, internal, 51733, 51901
-recovered pasa_asmbl_37093.p1, internal, 53554, 53720
-recovered pasa_asmbl_37093.p1, internal, 53806, 53927
-recovered pasa_asmbl_37093.p1, internal, 54199, 54415
-recovered pasa_asmbl_37093.p1, internal, 54836, 54960
-recovered pasa_asmbl_37093.p1, internal, 55239, 55422
-recovered pasa_asmbl_37093.p1, internal, 55880, 56116
-recovered pasa_asmbl_37093.p1, internal, 56776, 56815
-recovered pasa_asmbl_37093.p1, internal, 56917, 57053
Valid prediction for snap_scaffold_27-snap.2182-T1
Valid prediction for GeneMark_model.103422_t
Valid prediction for GeneMark_model.103398_t
Valid prediction for Augustus_model.g39422.t1
Valid prediction for GlimmerHMM_glimmerT_59219-T1
Valid prediction for snap_scaffold_27-snap.2201-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_59218-T1
Valid prediction for CodingQuarry_transcript_41880-T1
Valid prediction for GlimmerHMM_glimmerT_59216-T1
Valid prediction for Augustus_model.g39415.t1
Valid prediction for GeneMark_model.103414_t
Couldn't classify 26611, 26766
Couldn't classify 28633, 28742
Sorry, prediction pasa_asmbl_37140.p1 fails validation.
(CTG)	 TT	26611-26766	GT	CCG
(ATC)	 AG	28212-28332	GT	TGG
(AGA)	 AG	28633-28742	AG	GGA
-recovered pasa_asmbl_37140.p1, internal, 28212, 28332
Valid prediction for snap_scaffold_27-snap.2200-T1
Valid prediction for GeneMark_model.103407_t
Valid prediction for snap_scaffold_27-snap.2206-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for HiQ_model.g39414.t1
Valid prediction for snap_scaffold_27-snap.2209-T1
Valid prediction for GeneMark_model.103417_t
Valid prediction for GlimmerHMM_glimmerT_59220-T1
Couldn't classify 46998, 47204
Sorry, prediction pasa_asmbl_37091.p1 fails validation.
(GCC)	 CA	46998-47204	GT	AGG
(GAA)	 AG	49581-49662	GT	AGG
(AGA)	 AG	51733-51905	GC	GAG
-recovered pasa_asmbl_37091.p1, terminal, 51733, 51905
-recovered pasa_asmbl_37091.p1, internal, 49581, 49662
-recovered pasa_asmbl_37091.p1, internal, 51733, 51905
Valid prediction for GeneMark_model.103400_t
Valid prediction for GeneMark_model.103376_t
Valid prediction for GeneMark_model.103379_t
Valid prediction for GeneMark_model.103386_t
Valid prediction for GeneMark_model.103383_t
Couldn't classify 58092, 58183
Sorry, prediction pasa_asmbl_37090.p1 fails validation.
(GGC)	 TG	58092-58183	GT	GGG
(GTC)	 AG	59835-60032	GT	AGG
(GAG)	 AG	61153-61319	GT	AGG
(GCC)	 AG	61543-61773	GT	AGG
(ACC)	 AG	61988-62107	GT	CGG
(AGG)	 AG	62244-62356	GT	AGG
(GAC)	 AG	63656-63667	AA	AAA
-recovered pasa_asmbl_37090.p1, terminal, 63656, 63667
-recovered pasa_asmbl_37090.p1, internal, 59835, 60032
-recovered pasa_asmbl_37090.p1, internal, 61153, 61319
-recovered pasa_asmbl_37090.p1, internal, 61543, 61773
-recovered pasa_asmbl_37090.p1, internal, 61988, 62107
-recovered pasa_asmbl_37090.p1, internal, 62244, 62356
Valid prediction for snap_scaffold_27-snap.2199-T1
Valid prediction for GlimmerHMM_glimmerT_59224-T1
Valid prediction for snap_scaffold_27-snap.2180-T1
Valid prediction for snap_scaffold_27-snap.2214-T1
Valid prediction for Augustus_model.g39413.t1
Valid prediction for GeneMark_model.103425_t
Valid prediction for HiQ_model.g39416.t1
Valid prediction for Augustus_model.g39421.t1
Valid prediction for GeneMark_model.103389_t
Valid prediction for GeneMark_model.103409_t
Valid prediction for GlimmerHMM_glimmerT_59215-T1
Valid prediction for snap_scaffold_27-snap.2207-T1
Valid prediction for GeneMark_model.103377_t
Valid prediction for GeneMark_model.103374_t
Valid prediction for GeneMark_model.103404_t
Valid prediction for snap_scaffold_27-snap.2205-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8132, rend_intergenic: 3342  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17075, rend_intergenic: 12513  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27114, rend_intergenic: 20827  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35972, rend_intergenic: 31753  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39236, rend_intergenic: 36934  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52026, rend_intergenic: 41940  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58759, rend_intergenic: 54707  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99905, rend_intergenic: 90637  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114392, rend_intergenic: 104045  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116529, rend_intergenic: 115849  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118287, rend_intergenic: 117048  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147998, rend_intergenic: 127441  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167561, rend_intergenic: 148475  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 170059
-exon list size: 692


building trellis

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78.0    
78.1    
78.2    
78.4    
78.5    
78.7    
78.8    
79.0    
79.1    
79.3    
79.4    
79.5    
79.7    
79.8    
80.0    
80.1    
80.3    
80.4    
80.5    
80.7    
80.8    
81.0    
81.1    
81.3    
81.4    
81.6    
81.7    
81.8    
82.0    
82.1    
82.3    
82.4    
82.6    
82.7    
82.9    
83.0    
83.1    
83.3    
83.4    
83.6    
83.7    
83.9    
84.0    
84.1    
84.3    
84.4    
84.6    
84.7    
84.9    
85.0    
85.2    
85.3    
85.4    
85.6    
85.7    
85.9    
86.0    
86.2    
86.3    
86.5    
86.6    
86.7    
86.9    
87.0    
87.2    
87.3    
87.5    
87.6    
87.8    
87.9    
88.0    
88.2    
88.3    
88.5    
88.6    
88.8    
88.9    
89.0    
89.2    
89.3    
89.5    
89.6    
89.8    
89.9    
90.1    
90.2    
90.3    
90.5    
90.6    
90.8    
90.9    
91.1    
91.2    
91.4    
91.5    
91.6    
91.8    
91.9    
92.1    
92.2    
92.4    
92.5    
92.7    
92.8    
92.9    
93.1    
93.2    
93.4    
93.5    
93.7    
93.8    
93.9    
94.1    
94.2    
94.4    
94.5    
94.7    
94.8    
95.0    
95.1    
95.2    
95.4    
95.5    
95.7    
95.8    
96.0    
96.1    
96.3    
96.4    
96.5    
96.7    
96.8    
97.0    
97.1    
97.3    
97.4    
97.6    
97.7    
97.8    
98.0    
98.1    
98.3    
98.4    
98.6    
98.7    
98.8    
99.0    
99.1    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 8132, rend_intergenic: 3342  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17075, rend_intergenic: 12513  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27114, rend_intergenic: 20827  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35972, rend_intergenic: 31753  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39236, rend_intergenic: 36934  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52026, rend_intergenic: 41940  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58759, rend_intergenic: 54707  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99905, rend_intergenic: 90637  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114392, rend_intergenic: 104045  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116529, rend_intergenic: 115849  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118287, rend_intergenic: 117048  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147998, rend_intergenic: 127441  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167561, rend_intergenic: 148475  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support