-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_2/scaffold_2_1991402-2157424

-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_2-snap.491-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_2-snap.484-T1
Valid prediction for Augustus_model.g2221.t1
Valid prediction for Augustus_model.g2231.t1
Couldn't classify 78890, 78969
Couldn't classify 80123, 80225
Sorry, prediction pasa_asmbl_24231.p2 fails validation.
(AAG)	 AT	78890-78969	GT	AAG
(AGT)	 AG	79228-79395	GT	CGG
(GTA)	 AG	80123-80225	GC	CCG
-recovered pasa_asmbl_24231.p2, internal, 79228, 79395
-recovered pasa_asmbl_24231.p2, internal, 80123, 80225
Valid prediction for snap_scaffold_2-snap.498-T1
Valid prediction for snap_scaffold_2-snap.480-T1
Valid prediction for snap_scaffold_2-snap.477-T1
Valid prediction for CodingQuarry_transcript_28469-T1
Valid prediction for Augustus_model.g2227.t1
Valid prediction for snap_scaffold_2-snap.478-T1
Valid prediction for snap_scaffold_2-snap.487-T1
Valid prediction for snap_scaffold_2-snap.507-T1
Valid prediction for snap_scaffold_2-snap.500-T1
Valid prediction for GlimmerHMM_glimmerT_3316-T1
Valid prediction for Augustus_model.g2224.t1
Valid prediction for snap_scaffold_2-snap.482-T1
Valid prediction for Augustus_model.g2223.t1
Valid prediction for Augustus_model.g2226.t1
Valid prediction for Augustus_model.g2225.t1
Valid prediction for snap_scaffold_2-snap.495-T1
Valid prediction for snap_scaffold_2-snap.506-T1
Valid prediction for snap_scaffold_2-snap.501-T1
Valid prediction for GlimmerHMM_glimmerT_3324-T1
Valid prediction for GlimmerHMM_glimmerT_3317-T1
Valid prediction for GlimmerHMM_glimmerT_3322-T1
Valid prediction for snap_scaffold_2-snap.509-T1
Valid prediction for snap_scaffold_2-snap.503-T1
Valid prediction for GlimmerHMM_glimmerT_3319-T1
Valid prediction for GlimmerHMM_glimmerT_3312-T1
Valid prediction for GlimmerHMM_glimmerT_3321-T1
Valid prediction for snap_scaffold_2-snap.502-T1
Valid prediction for snap_scaffold_2-snap.479-T1
Valid prediction for snap_scaffold_2-snap.485-T1
Couldn't classify 72441, 72750
Sorry, prediction pasa_asmbl_24229.p1 fails validation.
(GTC)	 CG	72441-72750	GT	AGG
(ACC)	 AG	73029-73273	GC	GAG
-recovered pasa_asmbl_24229.p1, terminal, 73029, 73273
-recovered pasa_asmbl_24229.p1, internal, 73029, 73273
Valid prediction for GlimmerHMM_glimmerT_3311-T1
Valid prediction for snap_scaffold_2-snap.493-T1
Valid prediction for snap_scaffold_2-snap.508-T1
Valid prediction for GlimmerHMM_glimmerT_3310-T1
Valid prediction for snap_scaffold_2-snap.494-T1
Valid prediction for snap_scaffold_2-snap.489-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_2-snap.499-T1
Valid prediction for GlimmerHMM_glimmerT_3318-T1
Valid prediction for Augustus_model.g2230.t1
Valid prediction for snap_scaffold_2-snap.505-T1
Valid prediction for GlimmerHMM_glimmerT_3308-T1
Valid prediction for snap_scaffold_2-snap.481-T1
Valid prediction for GlimmerHMM_glimmerT_3306-T1
Valid prediction for snap_scaffold_2-snap.496-T1
Valid prediction for snap_scaffold_2-snap.486-T1
Valid prediction for GlimmerHMM_glimmerT_3323-T1
Valid prediction for GlimmerHMM_glimmerT_3309-T1
Valid prediction for Augustus_model.g2222.t1
Valid prediction for GlimmerHMM_glimmerT_3305-T1
Valid prediction for snap_scaffold_2-snap.510-T1
Valid prediction for Augustus_model.g2228.t1
Valid prediction for GlimmerHMM_glimmerT_3307-T1
Valid prediction for GlimmerHMM_glimmerT_3320-T1
Valid prediction for GlimmerHMM_glimmerT_3326-T1
Valid prediction for snap_scaffold_2-snap.483-T1
Valid prediction for snap_scaffold_2-snap.490-T1
Valid prediction for GlimmerHMM_glimmerT_3315-T1
Valid prediction for snap_scaffold_2-snap.488-T1
Valid prediction for Augustus_model.g2232.t1
Valid prediction for GlimmerHMM_glimmerT_3314-T1
Valid prediction for GlimmerHMM_glimmerT_3313-T1
Valid prediction for Augustus_model.g2229.t1
Valid prediction for GlimmerHMM_glimmerT_3304-T1
Valid prediction for snap_scaffold_2-snap.492-T1
Valid prediction for GlimmerHMM_glimmerT_3325-T1
Valid prediction for Augustus_model.g2220.t1
Valid prediction for snap_scaffold_2-snap.497-T1
Valid prediction for snap_scaffold_2-snap.504-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 29747, rend_intergenic: 27905  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47002, rend_intergenic: 36562  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60526, rend_intergenic: 59539  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71185, rend_intergenic: 60576  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81434, rend_intergenic: 79211  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98180, rend_intergenic: 90948  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101564, rend_intergenic: 99628  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119575, rend_intergenic: 101589  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134317, rend_intergenic: 119620  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151299, rend_intergenic: 134617  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162602, rend_intergenic: 151624  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 166023
-exon list size: 269


building trellis

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96.7    
97.0    
97.4    
97.8    
98.2    
98.5    
98.9    
99.3    
99.6    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 29747, rend_intergenic: 27905  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47002, rend_intergenic: 36562  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60526, rend_intergenic: 59539  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71185, rend_intergenic: 60576  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81434, rend_intergenic: 79211  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98180, rend_intergenic: 90948  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101564, rend_intergenic: 99628  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119575, rend_intergenic: 101589  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134317, rend_intergenic: 119620  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151299, rend_intergenic: 134617  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162602, rend_intergenic: 151624  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 7 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 13923
-exon list size: 8


building trellis

10.0    
20.0    
30.0    
40.0    
50.0    
60.0    
70.0    
80.0    
90.0    
-found 1 predictions from path traversal

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