-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_9290594-9501922

-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_27682-T1
Valid prediction for GlimmerHMM_glimmerT_27688-T1
Couldn't classify 1741, 1796
Sorry, prediction pasa_asmbl_5887.p1 fails validation.
(GGC)	 AG	1741-1796	GT	AGG
(GCA)	 AG	2482-2773	GT	AGG
(GTC)	 AG	3037-3165	GG	AAG
-recovered pasa_asmbl_5887.p1, terminal, 1741, 1796
-recovered pasa_asmbl_5887.p1, terminal, 3037, 3165
-recovered pasa_asmbl_5887.p1, internal, 1741, 1796
-recovered pasa_asmbl_5887.p1, internal, 2482, 2773
Valid prediction for snap_scaffold_11-snap.2107-T1
Valid prediction for snap_scaffold_11-snap.2097-T1
Valid prediction for snap_scaffold_11-snap.2126-T1
Valid prediction for snap_scaffold_11-snap.2132-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_11-snap.2103-T1
Valid prediction for GlimmerHMM_glimmerT_27685-T1
Valid prediction for snap_scaffold_11-snap.2130-T1
Valid prediction for snap_scaffold_11-snap.2135-T1
Valid prediction for snap_scaffold_11-snap.2122-T1
Valid prediction for snap_scaffold_11-snap.2091-T1
Valid prediction for snap_scaffold_11-snap.2117-T1
Valid prediction for GlimmerHMM_glimmerT_27678-T1
Valid prediction for snap_scaffold_11-snap.2106-T1
Valid prediction for GlimmerHMM_glimmerT_27680-T1
Valid prediction for snap_scaffold_11-snap.2119-T1
Valid prediction for GlimmerHMM_glimmerT_27693-T1
Valid prediction for GlimmerHMM_glimmerT_27686-T1
Valid prediction for snap_scaffold_11-snap.2124-T1
Valid prediction for snap_scaffold_11-snap.2129-T1
Valid prediction for snap_scaffold_11-snap.2120-T1
Valid prediction for Augustus_model.g18330.t1
Valid prediction for snap_scaffold_11-snap.2111-T1
Valid prediction for Augustus_model.g18328.t1
Valid prediction for GlimmerHMM_glimmerT_27701-T1
Valid prediction for snap_scaffold_11-snap.2136-T1
Valid prediction for snap_scaffold_11-snap.2128-T1
Valid prediction for snap_scaffold_11-snap.2101-T1
Valid prediction for snap_scaffold_11-snap.2113-T1
Couldn't classify 704, 1090
Sorry, prediction pasa_asmbl_6925.p2 fails validation.
(CTC)	 CT	704-1090	GT	AGG
Valid prediction for GlimmerHMM_glimmerT_27691-T1
Valid prediction for GlimmerHMM_glimmerT_27676-T1
Valid prediction for HiQ_model.g18322.t1
Valid prediction for snap_scaffold_11-snap.2134-T1
Valid prediction for snap_scaffold_11-snap.2092-T1
Valid prediction for snap_scaffold_11-snap.2114-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 GlimmerHMM_glimmerT_27697-T1
Valid prediction for GlimmerHMM_glimmerT_27687-T1
Valid prediction for GlimmerHMM_glimmerT_27695-T1
Valid prediction for Augustus_model.g18327.t1
Valid prediction for snap_scaffold_11-snap.2102-T1
Valid prediction for snap_scaffold_11-snap.2138-T1
Valid prediction for GlimmerHMM_glimmerT_27702-T1
Valid prediction for Augustus_model.g18340.t1
Valid prediction for GlimmerHMM_glimmerT_27692-T1
Valid prediction for Augustus_model.g18339.t1
Valid prediction for Augustus_model.g18338.t1
Valid prediction for CodingQuarry_transcript_8210-T1
Valid prediction for GlimmerHMM_glimmerT_27694-T1
Valid prediction for Augustus_model.g18335.t1
Valid prediction for snap_scaffold_11-snap.2112-T1
Valid prediction for snap_scaffold_11-snap.2108-T1
Valid prediction for Augustus_model.g18341.t1
Valid prediction for GlimmerHMM_glimmerT_27689-T1
Valid prediction for snap_scaffold_11-snap.2123-T1
Valid prediction for Augustus_model.g18334.t1
Valid prediction for snap_scaffold_11-snap.2110-T1
Valid prediction for Augustus_model.g18331.t1
Valid prediction for GlimmerHMM_glimmerT_27690-T1
Valid prediction for CodingQuarry_transcript_8209-T1
Valid prediction for GlimmerHMM_glimmerT_27677-T1
Valid prediction for GlimmerHMM_glimmerT_27700-T1
Valid prediction for Augustus_model.g18337.t1
Valid prediction for snap_scaffold_11-snap.2100-T1
Valid prediction for Augustus_model.g18326.t1
Valid prediction for GlimmerHMM_glimmerT_27679-T1
Valid prediction for snap_scaffold_11-snap.2105-T1
Valid prediction for snap_scaffold_11-snap.2118-T1
Valid prediction for GlimmerHMM_glimmerT_27699-T1
Valid prediction for GlimmerHMM_glimmerT_27683-T1
Couldn't classify 56696, 56826
Couldn't classify 57491, 57598
Sorry, prediction pasa_asmbl_6930.p1 fails validation.
(CTG)	 AG	56696-56826	GT	AAG
(GTG)	 AG	56977-57223	GT	AGG
(TTC)	 AG	57491-57598	GA	AGG
-recovered pasa_asmbl_6930.p1, internal, 56696, 56826
-recovered pasa_asmbl_6930.p1, internal, 56977, 57223
Valid prediction for Augustus_model.g18323.t1
Valid prediction for snap_scaffold_11-snap.2096-T1
Valid prediction for Augustus_model.g18324.t1
Valid prediction for GlimmerHMM_glimmerT_27703-T1
Valid prediction for GlimmerHMM_glimmerT_27696-T1
Valid prediction for snap_scaffold_11-snap.2109-T1
Couldn't classify 81933, 81960
Couldn't classify 84417, 84593
Sorry, prediction pasa_asmbl_6928.p2 fails validation.
(CGC)	 CC	81933-81960	GT	AGG
(AGA)	 AG	82920-83104	GT	TGG
(TAC)	 AG	84417-84593	AA	ACA
-recovered pasa_asmbl_6928.p2, internal, 82920, 83104
Valid prediction for snap_scaffold_11-snap.2137-T1
Valid prediction for snap_scaffold_11-snap.2133-T1
Valid prediction for Augustus_model.g18336.t1
Valid prediction for snap_scaffold_11-snap.2127-T1
Valid prediction for Augustus_model.g18325.t1
Valid prediction for snap_scaffold_11-snap.2104-T1
Valid prediction for snap_scaffold_11-snap.2116-T1
Valid prediction for snap_scaffold_11-snap.2095-T1
Couldn't classify 84916, 84931
Couldn't classify 87305, 87462
Sorry, prediction pasa_asmbl_6927.p1 fails validation.
(CTG)	 CT	84916-84931	GT	TCG
(CTG)	 AG	85200-85445	GT	AGG
(CAT)	 AG	85657-85794	GT	ACG
(CCT)	 AG	86080-86173	GT	CTG
(GTG)	 AG	86433-86485	GT	CTG
(ACA)	 AG	86858-86952	GT	AGG
(CAA)	 AG	87065-87143	GT	AGG
(CGG)	 AG	87305-87462	GT	AAG
-recovered pasa_asmbl_6927.p1, internal, 85200, 85445
-recovered pasa_asmbl_6927.p1, internal, 85657, 85794
-recovered pasa_asmbl_6927.p1, internal, 86080, 86173
-recovered pasa_asmbl_6927.p1, internal, 86433, 86485
-recovered pasa_asmbl_6927.p1, internal, 86858, 86952
-recovered pasa_asmbl_6927.p1, internal, 87065, 87143
-recovered pasa_asmbl_6927.p1, internal, 87305, 87462
Valid prediction for snap_scaffold_11-snap.2121-T1
Valid prediction for GlimmerHMM_glimmerT_27698-T1
Valid prediction for Augustus_model.g18332.t1
Valid prediction for snap_scaffold_11-snap.2099-T1
Valid prediction for snap_scaffold_11-snap.2094-T1
Valid prediction for GlimmerHMM_glimmerT_27684-T1
Valid prediction for Augustus_model.g18329.t1
Valid prediction for snap_scaffold_11-snap.2093-T1
Valid prediction for snap_scaffold_11-snap.2115-T1
Valid prediction for snap_scaffold_11-snap.2098-T1
Valid prediction for pasa_asmbl_6931.p1
Valid prediction for snap_scaffold_11-snap.2125-T1
Valid prediction for Augustus_model.g18333.t1
Valid prediction for snap_scaffold_11-snap.2131-T1
Valid prediction for GlimmerHMM_glimmerT_27681-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12521, rend_intergenic: 6149  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30162, rend_intergenic: 28663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34350, rend_intergenic: 31808  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47888, rend_intergenic: 45691  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52243, rend_intergenic: 49363  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58695, rend_intergenic: 54752  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62808, rend_intergenic: 60452  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88367, rend_intergenic: 86634  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91690, rend_intergenic: 88367  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99130, rend_intergenic: 94501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106879, rend_intergenic: 106621  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120265, rend_intergenic: 108895  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126901, rend_intergenic: 122193  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135250, rend_intergenic: 128236  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145220, rend_intergenic: 143517  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165511, rend_intergenic: 149074  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178744, rend_intergenic: 175684  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196140, rend_intergenic: 180752  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204620, rend_intergenic: 196239  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 211329
-exon list size: 459


building trellis

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-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 12521, rend_intergenic: 6149  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30162, rend_intergenic: 28663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34350, rend_intergenic: 31808  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47888, rend_intergenic: 45691  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52243, rend_intergenic: 49363  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58695, rend_intergenic: 54752  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62808, rend_intergenic: 60452  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88367, rend_intergenic: 86634  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91690, rend_intergenic: 88367  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99130, rend_intergenic: 94501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106879, rend_intergenic: 106621  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120265, rend_intergenic: 108895  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126901, rend_intergenic: 122193  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135250, rend_intergenic: 128236  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145220, rend_intergenic: 143517  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165511, rend_intergenic: 149074  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178744, rend_intergenic: 175684  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196140, rend_intergenic: 180752  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204620, rend_intergenic: 196239  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

-building DP trellis

-building trellis in range 197853 - 211329
-exon list size: 10


building trellis

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66.7    
75.0    
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91.7    
-found 1 predictions from path traversal

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