-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_19451451-19629190

-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 Augustus_model.g1913.t1
Valid prediction for GeneMark_model.4081_t
Valid prediction for GlimmerHMM_glimmerT_2691-T1
Valid prediction for snap_scaffold_1-snap.3631-T1
Valid prediction for GeneMark_model.4059_t
Valid prediction for Augustus_model.g1916.t1
Valid prediction for GeneMark_model.4065_t
Valid prediction for snap_scaffold_1-snap.3625-T1
Valid prediction for GeneMark_model.4091_t
Valid prediction for GeneMark_model.4089_t
Valid prediction for GlimmerHMM_glimmerT_2685-T1
Valid prediction for snap_scaffold_1-snap.3636-T1
Valid prediction for snap_scaffold_1-snap.3632-T1
Valid prediction for GeneMark_model.4099_t
Valid prediction for GeneMark_model.4085_t
Valid prediction for snap_scaffold_1-snap.3643-T1
Valid prediction for GeneMark_model.4097_t
Valid prediction for GeneMark_model.4056_t
Valid prediction for snap_scaffold_1-snap.3646-T1
Valid prediction for GeneMark_model.4096_t
Valid prediction for snap_scaffold_1-snap.3624-T1
Valid prediction for snap_scaffold_1-snap.3638-T1
Valid prediction for GlimmerHMM_glimmerT_2687-T1
Valid prediction for snap_scaffold_1-snap.3648-T1
Valid prediction for GlimmerHMM_glimmerT_2692-T1
Valid prediction for GeneMark_model.4087_t
Valid prediction for snap_scaffold_1-snap.3626-T1
Valid prediction for GeneMark_model.4069_t
Valid prediction for GeneMark_model.4077_t
Valid prediction for snap_scaffold_1-snap.3640-T1
Valid prediction for GeneMark_model.4063_t
Valid prediction for GlimmerHMM_glimmerT_2696-T1
Valid prediction for GeneMark_model.4075_t
Valid prediction for GlimmerHMM_glimmerT_2700-T1
Valid prediction for GeneMark_model.4070_t
Valid prediction for snap_scaffold_1-snap.3629-T1
Valid prediction for GeneMark_model.4050_t
Valid prediction for Augustus_model.g1918.t1
Valid prediction for snap_scaffold_1-snap.3649-T1
Valid prediction for GeneMark_model.4095_t
Valid prediction for snap_scaffold_1-snap.3637-T1
Valid prediction for GlimmerHMM_glimmerT_2689-T1
Valid prediction for GeneMark_model.4067_t
Valid prediction for GeneMark_model.4080_t
Valid prediction for snap_scaffold_1-snap.3622-T1
Valid prediction for GeneMark_model.4093_t
Valid prediction for GeneMark_model.4053_t
Valid prediction for snap_scaffold_1-snap.3639-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 Augustus_model.g1915.t1
Valid prediction for snap_scaffold_1-snap.3644-T1
Valid prediction for GeneMark_model.4055_t
Valid prediction for GeneMark_model.4062_t
Valid prediction for GeneMark_model.4090_t
Valid prediction for GlimmerHMM_glimmerT_2690-T1
Valid prediction for GeneMark_model.4088_t
Valid prediction for snap_scaffold_1-snap.3635-T1
Valid prediction for GeneMark_model.4051_t
Valid prediction for GeneMark_model.4100_t
Valid prediction for GeneMark_model.4071_t
Couldn't classify 41531, 41911
Sorry, prediction pasa_asmbl_1146.p4 fails validation.
(ATG)	 GA	41531-41911	TC	TCT
Valid prediction for GeneMark_model.4094_t
Valid prediction for GeneMark_model.4068_t
Valid prediction for GeneMark_model.4052_t
Valid prediction for GeneMark_model.4060_t
Valid prediction for snap_scaffold_1-snap.3634-T1
Valid prediction for GlimmerHMM_glimmerT_2697-T1
Valid prediction for Augustus_model.g1912.t1
Valid prediction for GeneMark_model.4073_t
Valid prediction for GeneMark_model.4086_t
Valid prediction for GlimmerHMM_glimmerT_2695-T1
Valid prediction for GlimmerHMM_glimmerT_2701-T1
Valid prediction for snap_scaffold_1-snap.3628-T1
Valid prediction for GeneMark_model.4058_t
Valid prediction for snap_scaffold_1-snap.3645-T1
Valid prediction for GeneMark_model.4098_t
Valid prediction for GeneMark_model.4076_t
Valid prediction for GlimmerHMM_glimmerT_2699-T1
Valid prediction for GeneMark_model.4054_t
Valid prediction for snap_scaffold_1-snap.3642-T1
Valid prediction for snap_scaffold_1-snap.3627-T1
Valid prediction for snap_scaffold_1-snap.3623-T1
Valid prediction for GlimmerHMM_glimmerT_2688-T1
Valid prediction for Augustus_model.g1914.t1
Valid prediction for snap_scaffold_1-snap.3633-T1
Valid prediction for Augustus_model.g1919.t1
Couldn't classify 14394, 14452
Sorry, prediction pasa_asmbl_1147.p1 fails validation.
(GTG)	 AG	14394-14452	GT	GTG
(GTA)	 AG	14541-14652	GT	AGG
(TAC)	 AG	14841-14870	GT	GGG
(GAC)	 AG	15132-15179	GT	AGG
(ATT)	 AG	15722-15836	GT	AGG
(TGG)	 AG	16478-16549	GT	CCG
(ATA)	 AG	17369-17448	GT	AGG
(GCC)	 AG	17876-17954	GT	AGG
(CGG)	 AG	18540-18713	GT	GAG
(GGT)	 AG	19131-19198	GT	GAG
-recovered pasa_asmbl_1147.p1, terminal, 17876, 17954
-recovered pasa_asmbl_1147.p1, terminal, 19131, 19198
-recovered pasa_asmbl_1147.p1, internal, 14394, 14452
-recovered pasa_asmbl_1147.p1, internal, 14541, 14652
-recovered pasa_asmbl_1147.p1, internal, 14841, 14870
-recovered pasa_asmbl_1147.p1, internal, 15132, 15179
-recovered pasa_asmbl_1147.p1, internal, 15722, 15836
-recovered pasa_asmbl_1147.p1, internal, 16478, 16549
-recovered pasa_asmbl_1147.p1, internal, 17369, 17448
-recovered pasa_asmbl_1147.p1, internal, 17876, 17954
-recovered pasa_asmbl_1147.p1, internal, 18540, 18713
-recovered pasa_asmbl_1147.p1, internal, 19131, 19198
Valid prediction for snap_scaffold_1-snap.3630-T1
Valid prediction for GeneMark_model.4066_t
Valid prediction for snap_scaffold_1-snap.3641-T1
Valid prediction for GlimmerHMM_glimmerT_2693-T1
Valid prediction for Augustus_model.g1917.t1
Valid prediction for GeneMark_model.4074_t
Valid prediction for Augustus_model.g1911.t1
Valid prediction for snap_scaffold_1-snap.3647-T1
Valid prediction for GeneMark_model.4064_t
Valid prediction for GlimmerHMM_glimmerT_2698-T1
Valid prediction for GeneMark_model.4084_t
Valid prediction for GeneMark_model.4079_t
Valid prediction for GlimmerHMM_glimmerT_2686-T1
Valid prediction for GeneMark_model.4078_t
Valid prediction for GeneMark_model.4082_t
Valid prediction for GlimmerHMM_glimmerT_2694-T1
Valid prediction for GeneMark_model.4057_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 39215, rend_intergenic: 36328  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49519, rend_intergenic: 47935  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94974, rend_intergenic: 64936  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116510, rend_intergenic: 96661  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150101, rend_intergenic: 137294  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174424, rend_intergenic: 159951  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 177740
-exon list size: 610


building trellis

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-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 39215, rend_intergenic: 36328  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49519, rend_intergenic: 47935  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94974, rend_intergenic: 64936  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116510, rend_intergenic: 96661  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150101, rend_intergenic: 137294  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174424, rend_intergenic: 159951  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 10 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 167705 - 177740
-exon list size: 6


building trellis

12.5    
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37.5    
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62.5    
75.0    
87.5    
-found 1 predictions from path traversal

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