-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_19244286-19455863

-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_2654-T1
Valid prediction for GeneMark_model.4028_t
Valid prediction for GlimmerHMM_glimmerT_2659-T1
Valid prediction for snap_scaffold_1-snap.3608-T1
Valid prediction for GlimmerHMM_glimmerT_2669-T1
Valid prediction for GeneMark_model.4044_t
Valid prediction for GeneMark_model.4033_t
Valid prediction for GlimmerHMM_glimmerT_2665-T1
Valid prediction for GlimmerHMM_glimmerT_2668-T1
Valid prediction for CodingQuarry_transcript_3003-T1
Valid prediction for GeneMark_model.4023_t
Valid prediction for GeneMark_model.4012_t
Valid prediction for snap_scaffold_1-snap.3586-T1
Valid prediction for CodingQuarry_transcript_3005-T1
Valid prediction for GeneMark_model.4047_t
Valid prediction for GlimmerHMM_glimmerT_2683-T1
Valid prediction for GlimmerHMM_glimmerT_2666-T1
Valid prediction for Augustus_model.g1907.t1
Valid prediction for snap_scaffold_1-snap.3609-T1
Valid prediction for snap_scaffold_1-snap.3590-T1
Valid prediction for snap_scaffold_1-snap.3612-T1
Sorry, intron length (4) is less than minimum required (10)
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.4006_t
Valid prediction for snap_scaffold_1-snap.3605-T1
Valid prediction for GlimmerHMM_glimmerT_2681-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.4005_t
Valid prediction for GeneMark_model.4042_t
Valid prediction for GeneMark_model.4048_t
Valid prediction for Augustus_model.g1902.t1
Valid prediction for GeneMark_model.4021_t
Valid prediction for snap_scaffold_1-snap.3610-T1
Couldn't classify 133340, 133561
Couldn't classify 137128, 137184
Sorry, prediction pasa_asmbl_2579.p1 fails validation.
(CAC)	 CC	133340-133561	GT	AGG
(GTG)	 AG	133657-133848	GT	AGG
(GTG)	 AG	134002-134183	GT	AGG
(AGC)	 AG	134277-134400	GT	AGG
(ATC)	 AG	134622-134741	GT	AGG
(ACT)	 AG	135689-135775	GT	AGG
(GTC)	 AG	136410-136594	GT	CAG
(TGT)	 AG	136891-137044	GC	AGG
(GTG)	 AG	137128-137184	CA	AGC
-recovered pasa_asmbl_2579.p1, internal, 133657, 133848
-recovered pasa_asmbl_2579.p1, internal, 134002, 134183
-recovered pasa_asmbl_2579.p1, internal, 134277, 134400
-recovered pasa_asmbl_2579.p1, internal, 134622, 134741
-recovered pasa_asmbl_2579.p1, internal, 135689, 135775
-recovered pasa_asmbl_2579.p1, internal, 136410, 136594
-recovered pasa_asmbl_2579.p1, internal, 136891, 137044
Valid prediction for GlimmerHMM_glimmerT_2673-T1
Valid prediction for GeneMark_model.4036_t
Valid prediction for GlimmerHMM_glimmerT_2672-T1
Valid prediction for pasa_asmbl_2577.p1
Valid prediction for Augustus_model.g1905.t1
Valid prediction for GlimmerHMM_glimmerT_2678-T1
Valid prediction for GlimmerHMM_glimmerT_2656-T1
Valid prediction for GeneMark_model.4039_t
Valid prediction for snap_scaffold_1-snap.3600-T1
Valid prediction for GeneMark_model.4035_t
Valid prediction for Augustus_model.g1899.t1
Valid prediction for CodingQuarry_transcript_3006-T1
Valid prediction for snap_scaffold_1-snap.3591-T1
Valid prediction for snap_scaffold_1-snap.3607-T1
Valid prediction for Augustus_model.g1901.t1
Valid prediction for GeneMark_model.4010_t
Valid prediction for GeneMark_model.4032_t
Valid prediction for Augustus_model.g1904.t1
Valid prediction for Augustus_model.g1903.t1
Valid prediction for Augustus_model.g1900.t1
Valid prediction for GlimmerHMM_glimmerT_2657-T1
Valid prediction for GlimmerHMM_glimmerT_2660-T1
Valid prediction for GlimmerHMM_glimmerT_2674-T1
Valid prediction for Augustus_model.g1894.t1
Valid prediction for CodingQuarry_transcript_3007-T1
Valid prediction for HiQ_model.g1896.t1
Valid prediction for Augustus_model.g1895.t1
Valid prediction for snap_scaffold_1-snap.3618-T1
Valid prediction for GeneMark_model.4015_t
Valid prediction for CodingQuarry_transcript_3004-T1
Couldn't classify 141857, 141914
Sorry, prediction pasa_asmbl_2581.p1 fails validation.
(CTG)	 CG	141857-141914	GT	AGG
(GAT)	 AG	142163-142266	GT	AGG
(GTG)	 AG	142533-142904	GG	AAG
-recovered pasa_asmbl_2581.p1, terminal, 142533, 142904
-recovered pasa_asmbl_2581.p1, internal, 142163, 142266
Valid prediction for GeneMark_model.4046_t
Valid prediction for GlimmerHMM_glimmerT_2680-T1
Valid prediction for GlimmerHMM_glimmerT_2671-T1
Valid prediction for snap_scaffold_1-snap.3593-T1
Valid prediction for snap_scaffold_1-snap.3606-T1
Valid prediction for snap_scaffold_1-snap.3620-T1
Valid prediction for GeneMark_model.4041_t
Valid prediction for GeneMark_model.4027_t
Valid prediction for Augustus_model.g1898.t1
Valid prediction for GeneMark_model.4034_t
Valid prediction for snap_scaffold_1-snap.3579-T1
Valid prediction for GlimmerHMM_glimmerT_2662-T1
Valid prediction for snap_scaffold_1-snap.3604-T1
Valid prediction for GeneMark_model.4018_t
Couldn't classify 141645, 141753
Sorry, prediction pasa_asmbl_2580.p1 fails validation.
(ATG)	 AC	140915-140964	GT	AGG
(AGG)	 AG	141180-141251	GT	AGG
(AAA)	 AG	141373-141543	GT	AGG
(CTA)	 AG	141645-141753	CT	ACC
-recovered pasa_asmbl_2580.p1, initial, 140915, 140964
-recovered pasa_asmbl_2580.p1, internal, 141180, 141251
-recovered pasa_asmbl_2580.p1, internal, 141373, 141543
Couldn't classify 149195, 149743
Sorry, prediction pasa_asmbl_2583.p1 fails validation.
(AGG)	 AC	149195-149743	CC	GAC
Valid prediction for GeneMark_model.4025_t
Valid prediction for snap_scaffold_1-snap.3619-T1
Valid prediction for snap_scaffold_1-snap.3595-T1
Valid prediction for snap_scaffold_1-snap.3615-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_1-snap.3582-T1
Valid prediction for GlimmerHMM_glimmerT_2676-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_2664-T1
Valid prediction for GlimmerHMM_glimmerT_2658-T1
Valid prediction for Augustus_model.g1909.t1
Valid prediction for GeneMark_model.4049_t
Valid prediction for Augustus_model.g1897.t1
Valid prediction for snap_scaffold_1-snap.3601-T1
Valid prediction for GeneMark_model.4026_t
Valid prediction for snap_scaffold_1-snap.3581-T1
Valid prediction for snap_scaffold_1-snap.3597-T1
Valid prediction for GlimmerHMM_glimmerT_2670-T1
Valid prediction for snap_scaffold_1-snap.3613-T1
Valid prediction for snap_scaffold_1-snap.3592-T1
Valid prediction for snap_scaffold_1-snap.3611-T1
Valid prediction for GeneMark_model.4045_t
Valid prediction for snap_scaffold_1-snap.3602-T1
Valid prediction for GlimmerHMM_glimmerT_2675-T1
Valid prediction for GeneMark_model.4038_t
Valid prediction for snap_scaffold_1-snap.3589-T1
Valid prediction for snap_scaffold_1-snap.3588-T1
Valid prediction for GlimmerHMM_glimmerT_2684-T1
Valid prediction for GlimmerHMM_glimmerT_2651-T1
Valid prediction for snap_scaffold_1-snap.3584-T1
Valid prediction for GeneMark_model.4031_t
Valid prediction for snap_scaffold_1-snap.3621-T1
Valid prediction for snap_scaffold_1-snap.3614-T1
Valid prediction for GlimmerHMM_glimmerT_2653-T1
Valid prediction for GeneMark_model.4016_t
Valid prediction for snap_scaffold_1-snap.3599-T1
Valid prediction for GeneMark_model.4004_t
Valid prediction for GlimmerHMM_glimmerT_2682-T1
Valid prediction for GeneMark_model.4030_t
Valid prediction for GeneMark_model.4043_t
Valid prediction for GlimmerHMM_glimmerT_2663-T1
Valid prediction for GeneMark_model.4003_t
Valid prediction for snap_scaffold_1-snap.3596-T1
Valid prediction for snap_scaffold_1-snap.3585-T1
Valid prediction for snap_scaffold_1-snap.3594-T1
Valid prediction for GlimmerHMM_glimmerT_2679-T1
Valid prediction for GeneMark_model.4011_t
Valid prediction for snap_scaffold_1-snap.3598-T1
Valid prediction for Augustus_model.g1908.t1
Valid prediction for GlimmerHMM_glimmerT_2677-T1
Valid prediction for GlimmerHMM_glimmerT_2655-T1
Valid prediction for GeneMark_model.4022_t
Valid prediction for GeneMark_model.4024_t
Valid prediction for GeneMark_model.4014_t
Valid prediction for snap_scaffold_1-snap.3617-T1
Valid prediction for Augustus_model.g1892.t1
Valid prediction for GeneMark_model.4013_t
Couldn't classify 167288, 167319
Sorry, prediction pasa_asmbl_1144.p1 fails validation.
(ATG)	 CC	163190-163287	GT	ACG
(GGA)	 AG	165157-165327	GT	AGG
(AAA)	 AG	166576-166630	GT	AGG
(GTG)	 AG	166849-167011	GT	AGG
(ATC)	 AG	167288-167319	CT	ACC
-recovered pasa_asmbl_1144.p1, initial, 163190, 163287
-recovered pasa_asmbl_1144.p1, internal, 165157, 165327
-recovered pasa_asmbl_1144.p1, internal, 166576, 166630
-recovered pasa_asmbl_1144.p1, internal, 166849, 167011
Valid prediction for GeneMark_model.4037_t
Valid prediction for Augustus_model.g1906.t1
Valid prediction for GeneMark_model.4029_t
Valid prediction for GeneMark_model.4040_t
Valid prediction for snap_scaffold_1-snap.3580-T1
Valid prediction for snap_scaffold_1-snap.3616-T1
Valid prediction for Augustus_model.g1910.t1
Valid prediction for snap_scaffold_1-snap.3587-T1
Valid prediction for GeneMark_model.4017_t
Valid prediction for GlimmerHMM_glimmerT_2661-T1
Valid prediction for snap_scaffold_1-snap.3603-T1
Valid prediction for Augustus_model.g1893.t1
Valid prediction for GeneMark_model.4009_t
Valid prediction for GlimmerHMM_glimmerT_2667-T1
Valid prediction for GlimmerHMM_glimmerT_2652-T1
Valid prediction for snap_scaffold_1-snap.3583-T1
Valid prediction for snap_scaffold_1-snap.3578-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13249, rend_intergenic: 6741  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23344, rend_intergenic: 20915  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41915, rend_intergenic: 38237  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51023, rend_intergenic: 46996  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55671, rend_intergenic: 52636  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57349, rend_intergenic: 56069  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58547, rend_intergenic: 58341  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71767, rend_intergenic: 60662  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90995, rend_intergenic: 72017  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108902, rend_intergenic: 92200  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142904, rend_intergenic: 137098  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155606, rend_intergenic: 149066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169822, rend_intergenic: 163901  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203096, rend_intergenic: 187206  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 208568, rend_intergenic: 203392  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 211578
-exon list size: 687


building trellis

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84.3    
84.5    
84.6    
84.8    
84.9    
85.1    
85.2    
85.3    
85.5    
85.6    
85.8    
85.9    
86.1    
86.2    
86.4    
86.5    
86.6    
86.8    
86.9    
87.1    
87.2    
87.4    
87.5    
87.7    
87.8    
88.0    
88.1    
88.2    
88.4    
88.5    
88.7    
88.8    
89.0    
89.1    
89.3    
89.4    
89.6    
89.7    
89.8    
90.0    
90.1    
90.3    
90.4    
90.6    
90.7    
90.9    
91.0    
91.1    
91.3    
91.4    
91.6    
91.7    
91.9    
92.0    
92.2    
92.3    
92.5    
92.6    
92.7    
92.9    
93.0    
93.2    
93.3    
93.5    
93.6    
93.8    
93.9    
94.0    
94.2    
94.3    
94.5    
94.6    
94.8    
94.9    
95.1    
95.2    
95.4    
95.5    
95.6    
95.8    
95.9    
96.1    
96.2    
96.4    
96.5    
96.7    
96.8    
97.0    
97.1    
97.2    
97.4    
97.5    
97.7    
97.8    
98.0    
98.1    
98.3    
98.4    
98.5    
98.7    
98.8    
99.0    
99.1    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 13249, rend_intergenic: 6741  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23344, rend_intergenic: 20915  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41915, rend_intergenic: 38237  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51023, rend_intergenic: 46996  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55671, rend_intergenic: 52636  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57349, rend_intergenic: 56069  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58547, rend_intergenic: 58341  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71767, rend_intergenic: 60662  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90995, rend_intergenic: 72017  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108902, rend_intergenic: 92200  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142904, rend_intergenic: 137098  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155606, rend_intergenic: 149066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169822, rend_intergenic: 163901  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203096, rend_intergenic: 187206  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 208568, rend_intergenic: 203392  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support