-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_9/scaffold_9_10483354-10743499

-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 snap_scaffold_9-snap.2114-T1
Valid prediction for GlimmerHMM_glimmerT_22816-T1
Valid prediction for snap_scaffold_9-snap.2100-T1
Valid prediction for snap_scaffold_9-snap.2102-T1
Valid prediction for GlimmerHMM_glimmerT_22819-T1
Valid prediction for GlimmerHMM_glimmerT_22811-T1
Valid prediction for snap_scaffold_9-snap.2074-T1
Valid prediction for snap_scaffold_9-snap.2113-T1
Valid prediction for Augustus_model.g15166.t1
Valid prediction for GlimmerHMM_glimmerT_22818-T1
Valid prediction for snap_scaffold_9-snap.2076-T1
Valid prediction for snap_scaffold_9-snap.2081-T1
Valid prediction for snap_scaffold_9-snap.2111-T1
Valid prediction for GlimmerHMM_glimmerT_22801-T1
Valid prediction for snap_scaffold_9-snap.2106-T1
Valid prediction for snap_scaffold_9-snap.2112-T1
Valid prediction for snap_scaffold_9-snap.2067-T1
Valid prediction for GlimmerHMM_glimmerT_22803-T1
Valid prediction for snap_scaffold_9-snap.2080-T1
Valid prediction for snap_scaffold_9-snap.2087-T1
Couldn't classify 73648, 74286
Sorry, prediction pasa_asmbl_54288.p1 fails validation.
(GCC)	 TT	73648-74286	AC	CCA
Valid prediction for snap_scaffold_9-snap.2108-T1
Valid prediction for snap_scaffold_9-snap.2082-T1
Valid prediction for GlimmerHMM_glimmerT_22804-T1
Valid prediction for Augustus_model.g15168.t1
Valid prediction for GlimmerHMM_glimmerT_22805-T1
Valid prediction for Augustus_model.g15171.t1
Valid prediction for snap_scaffold_9-snap.2089-T1
Valid prediction for GlimmerHMM_glimmerT_22821-T1
Valid prediction for snap_scaffold_9-snap.2095-T1
Valid prediction for snap_scaffold_9-snap.2072-T1
Valid prediction for snap_scaffold_9-snap.2078-T1
Valid prediction for GlimmerHMM_glimmerT_22807-T1
Valid prediction for Augustus_model.g15172.t1
Valid prediction for snap_scaffold_9-snap.2083-T1
Valid prediction for snap_scaffold_9-snap.2085-T1
Valid prediction for Augustus_model.g15167.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_9-snap.2073-T1
Valid prediction for snap_scaffold_9-snap.2091-T1
Valid prediction for snap_scaffold_9-snap.2103-T1
Valid prediction for snap_scaffold_9-snap.2093-T1
Valid prediction for snap_scaffold_9-snap.2086-T1
Valid prediction for snap_scaffold_9-snap.2084-T1
Valid prediction for GlimmerHMM_glimmerT_22800-T1
Valid prediction for Augustus_model.g15180.t1
Valid prediction for Augustus_model.g15173.t1
Valid prediction for HiQ_model.g15177.t1
Valid prediction for Augustus_model.g15179.t1
Valid prediction for snap_scaffold_9-snap.2101-T1
Couldn't classify 126803, 127050
Sorry, prediction pasa_asmbl_55253.p1 fails validation.
(CCG)	 TC	126803-127050	GT	AGG
(GAG)	 AG	127911-128178	GT	TTG
(ACG)	 AG	129363-129509	GT	AGG
(ATA)	 AG	130832-130908	GT	AGG
(GAA)	 AG	131107-131276	GT	AGG
(ATG)	 AG	132074-132678	GT	AGG
(GGC)	 AG	132934-133371	TT	AAT
add_exon() Sorry, pasa_asmbl_55253.p1 132074-132678-initial-1 is invalid.
-recovered pasa_asmbl_55253.p1, initial, 132074, 132678
-recovered pasa_asmbl_55253.p1, terminal, 132934, 133371
-recovered pasa_asmbl_55253.p1, internal, 127911, 128178
-recovered pasa_asmbl_55253.p1, internal, 129363, 129509
-recovered pasa_asmbl_55253.p1, internal, 130832, 130908
-recovered pasa_asmbl_55253.p1, internal, 131107, 131276
-recovered pasa_asmbl_55253.p1, internal, 132074, 132678
Valid prediction for GlimmerHMM_glimmerT_22813-T1
Valid prediction for Augustus_model.g15176.t1
Valid prediction for Augustus_model.g15169.t1
Valid prediction for snap_scaffold_9-snap.2098-T1
Valid prediction for Augustus_model.g15178.t1
Valid prediction for snap_scaffold_9-snap.2068-T1
Valid prediction for GlimmerHMM_glimmerT_22815-T1
Valid prediction for snap_scaffold_9-snap.2109-T1
Valid prediction for snap_scaffold_9-snap.2092-T1
Valid prediction for snap_scaffold_9-snap.2094-T1
Valid prediction for snap_scaffold_9-snap.2107-T1
Valid prediction for snap_scaffold_9-snap.2099-T1
Valid prediction for snap_scaffold_9-snap.2070-T1
Valid prediction for Augustus_model.g15175.t1
Valid prediction for GlimmerHMM_glimmerT_22802-T1
Valid prediction for GlimmerHMM_glimmerT_22814-T1
Valid prediction for snap_scaffold_9-snap.2066-T1
Valid prediction for GlimmerHMM_glimmerT_22817-T1
Valid prediction for snap_scaffold_9-snap.2090-T1
Valid prediction for snap_scaffold_9-snap.2088-T1
Valid prediction for snap_scaffold_9-snap.2097-T1
Valid prediction for snap_scaffold_9-snap.2110-T1
Valid prediction for snap_scaffold_9-snap.2071-T1
Valid prediction for GlimmerHMM_glimmerT_22820-T1
Valid prediction for snap_scaffold_9-snap.2077-T1
Valid prediction for snap_scaffold_9-snap.2104-T1
Valid prediction for snap_scaffold_9-snap.2105-T1
Valid prediction for GlimmerHMM_glimmerT_22812-T1
Valid prediction for GlimmerHMM_glimmerT_22799-T1
Valid prediction for snap_scaffold_9-snap.2079-T1
Valid prediction for GlimmerHMM_glimmerT_22809-T1
Valid prediction for GlimmerHMM_glimmerT_22808-T1
Valid prediction for Augustus_model.g15170.t1
Valid prediction for Augustus_model.g15174.t1
Valid prediction for snap_scaffold_9-snap.2075-T1
Valid prediction for snap_scaffold_9-snap.2069-T1
Valid prediction for snap_scaffold_9-snap.2096-T1
Valid prediction for GlimmerHMM_glimmerT_22810-T1
Valid prediction for GlimmerHMM_glimmerT_22806-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 27224, rend_intergenic: 11438  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35299, rend_intergenic: 27225  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47220, rend_intergenic: 43921  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54488, rend_intergenic: 53441  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60455, rend_intergenic: 60090  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178094, rend_intergenic: 157642  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204860, rend_intergenic: 198580  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 207475, rend_intergenic: 205106  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 232753, rend_intergenic: 231347  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 235974, rend_intergenic: 233132  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 258881, rend_intergenic: 238976  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 260146
-exon list size: 336


building trellis

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44.7    
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97.0    
97.3    
97.6    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 39 predictions from path traversal
Error with prediction: snap lend_intergenic: 27224, rend_intergenic: 11438  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35299, rend_intergenic: 27225  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47220, rend_intergenic: 43921  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54488, rend_intergenic: 53441  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60455, rend_intergenic: 60090  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178094, rend_intergenic: 157642  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204860, rend_intergenic: 198580  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 207475, rend_intergenic: 205106  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 232753, rend_intergenic: 231347  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 235974, rend_intergenic: 233132  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 258881, rend_intergenic: 238976  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 27 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 10845
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-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