-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_22129868-22326581

-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_1-snap.4250-T1
Valid prediction for snap_scaffold_1-snap.4248-T1
Valid prediction for GeneMark_model.4848_t
Valid prediction for GlimmerHMM_glimmerT_3028-T1
Valid prediction for pasa_asmbl_2673.p1
Valid prediction for GeneMark_model.4889_t
Valid prediction for GeneMark_model.4874_t
Valid prediction for snap_scaffold_1-snap.4218-T1
Valid prediction for CodingQuarry_transcript_3052-T1
Valid prediction for GeneMark_model.4838_t
Valid prediction for snap_scaffold_1-snap.4246-T1
Valid prediction for snap_scaffold_1-snap.4249-T1
Valid prediction for GlimmerHMM_glimmerT_3023-T1
Valid prediction for snap_scaffold_1-snap.4219-T1
Valid prediction for snap_scaffold_1-snap.4213-T1
Valid prediction for snap_scaffold_1-snap.4215-T1
Valid prediction for GeneMark_model.4834_t
Valid prediction for GeneMark_model.4857_t
Valid prediction for snap_scaffold_1-snap.4227-T1
Valid prediction for GeneMark_model.4872_t
Valid prediction for GeneMark_model.4836_t
Valid prediction for GeneMark_model.4844_t
Valid prediction for GeneMark_model.4870_t
Valid prediction for GeneMark_model.4852_t
Valid prediction for GlimmerHMM_glimmerT_3030-T1
Valid prediction for GeneMark_model.4881_t
Valid prediction for snap_scaffold_1-snap.4251-T1
Valid prediction for GeneMark_model.4867_t
Valid prediction for GlimmerHMM_glimmerT_3033-T1
Valid prediction for CodingQuarry_transcript_3053-T1
Valid prediction for GeneMark_model.4860_t
Valid prediction for snap_scaffold_1-snap.4247-T1
Valid prediction for GeneMark_model.4886_t
Valid prediction for GlimmerHMM_glimmerT_3044-T1
Valid prediction for GeneMark_model.4880_t
Valid prediction for snap_scaffold_1-snap.4236-T1
Valid prediction for snap_scaffold_1-snap.4209-T1
Valid prediction for snap_scaffold_1-snap.4233-T1
Sorry, intron length (8) is less than minimum required (10)
Couldn't classify 146721, 146729
Sorry, prediction GeneMark_model.4876_t fails validation.
(AGG)	 AG	146721-146729	GT	GAG
(AGT)	 AG	146791-146948	GT	TAG
(CTC)	 AG	147803-147809	GT	CAG
(GGT)	 AG	147840-147992	GT	GGG
(TGT)	 AG	148106-148151	GT	GAG
-recovered GeneMark_model.4876_t, terminal, 148106, 148151
-recovered GeneMark_model.4876_t, internal, 146721, 146729
-recovered GeneMark_model.4876_t, internal, 146791, 146948
-recovered GeneMark_model.4876_t, internal, 147803, 147809
-recovered GeneMark_model.4876_t, internal, 147840, 147992
-recovered GeneMark_model.4876_t, internal, 148106, 148151
Valid prediction for snap_scaffold_1-snap.4240-T1
Valid prediction for snap_scaffold_1-snap.4231-T1
Valid prediction for snap_scaffold_1-snap.4222-T1
Valid prediction for snap_scaffold_1-snap.4244-T1
Valid prediction for GeneMark_model.4890_t
Valid prediction for GeneMark_model.4839_t
Valid prediction for GeneMark_model.4883_t
Valid prediction for GeneMark_model.4863_t
Valid prediction for GeneMark_model.4837_t
Valid prediction for GeneMark_model.4885_t
Valid prediction for snap_scaffold_1-snap.4237-T1
Valid prediction for GeneMark_model.4868_t
Valid prediction for GeneMark_model.4845_t
Valid prediction for snap_scaffold_1-snap.4229-T1
Valid prediction for GeneMark_model.4849_t
Valid prediction for GlimmerHMM_glimmerT_3032-T1
Valid prediction for GeneMark_model.4840_t
Valid prediction for GeneMark_model.4861_t
Valid prediction for GeneMark_model.4855_t
Valid prediction for snap_scaffold_1-snap.4239-T1
Valid prediction for GlimmerHMM_glimmerT_3027-T1
Valid prediction for snap_scaffold_1-snap.4242-T1
Couldn't classify 140105, 140110
Sorry, prediction GeneMark_model.4875_t fails validation.
(ATG)	 GG	139400-139491	GT	GAG
(CCA)	 AG	139530-139577	GT	GAG
(AAG)	 AG	139608-139769	GT	AGG
(AAA)	 AG	139797-139814	GT	GAG
(AAA)	 AG	139840-139860	GT	CAG
(GAA)	 AG	139971-139982	GT	AGG
(GGG)	 AG	140105-140110	GT	GAG
-recovered GeneMark_model.4875_t, initial, 139400, 139491
-recovered GeneMark_model.4875_t, internal, 139530, 139577
-recovered GeneMark_model.4875_t, internal, 139608, 139769
-recovered GeneMark_model.4875_t, internal, 139797, 139814
-recovered GeneMark_model.4875_t, internal, 139840, 139860
-recovered GeneMark_model.4875_t, internal, 139971, 139982
-recovered GeneMark_model.4875_t, internal, 140105, 140110
Valid prediction for GlimmerHMM_glimmerT_3026-T1
Valid prediction for snap_scaffold_1-snap.4214-T1
Valid prediction for snap_scaffold_1-snap.4225-T1
Valid prediction for GlimmerHMM_glimmerT_3041-T1
Valid prediction for GlimmerHMM_glimmerT_3037-T1
Valid prediction for snap_scaffold_1-snap.4245-T1
Valid prediction for GlimmerHMM_glimmerT_3025-T1
Valid prediction for GeneMark_model.4878_t
Valid prediction for GeneMark_model.4864_t

-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_3043-T1
Valid prediction for snap_scaffold_1-snap.4221-T1
Valid prediction for snap_scaffold_1-snap.4217-T1
Sorry, intron length (9) is less than minimum required (10)
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GeneMark_model.4887_t
Valid prediction for GeneMark_model.4873_t
Valid prediction for GlimmerHMM_glimmerT_3036-T1
Valid prediction for GeneMark_model.4843_t
Valid prediction for snap_scaffold_1-snap.4235-T1
Valid prediction for GlimmerHMM_glimmerT_3031-T1
Valid prediction for GlimmerHMM_glimmerT_3039-T1
Valid prediction for snap_scaffold_1-snap.4223-T1
Valid prediction for snap_scaffold_1-snap.4228-T1
Valid prediction for GlimmerHMM_glimmerT_3024-T1
Valid prediction for snap_scaffold_1-snap.4241-T1
Valid prediction for GeneMark_model.4882_t
Valid prediction for GeneMark_model.4871_t
Valid prediction for GeneMark_model.4856_t
Valid prediction for GeneMark_model.4879_t
Valid prediction for GeneMark_model.4862_t
Valid prediction for GeneMark_model.4841_t
Valid prediction for GeneMark_model.4850_t
Valid prediction for snap_scaffold_1-snap.4224-T1
Valid prediction for GeneMark_model.4846_t
Valid prediction for GlimmerHMM_glimmerT_3035-T1
Valid prediction for GeneMark_model.4884_t
Valid prediction for snap_scaffold_1-snap.4210-T1
Valid prediction for snap_scaffold_1-snap.4226-T1
Valid prediction for GeneMark_model.4851_t
Valid prediction for snap_scaffold_1-snap.4232-T1
Valid prediction for GlimmerHMM_glimmerT_3042-T1
Valid prediction for GlimmerHMM_glimmerT_3034-T1
Valid prediction for GeneMark_model.4866_t
Valid prediction for GeneMark_model.4853_t
Valid prediction for GeneMark_model.4858_t
Valid prediction for snap_scaffold_1-snap.4212-T1
Valid prediction for GeneMark_model.4854_t
Couldn't classify 175416, 175459
Couldn't classify 182698, 182893
Sorry, prediction pasa_asmbl_1229.p1 fails validation.
(NNN)	 NN	175416-175459	GT	ATG
(TCT)	 AG	175724-175840	GT	AGG
(GTA)	 AG	176258-176461	GT	GAG
(GGT)	 AG	177075-177276	GT	GGG
(AAC)	 AG	177796-177870	GT	AGG
(TTG)	 AG	178191-178361	GT	AGG
(GTG)	 AG	180262-180357	GT	AGG
(GTG)	 AG	180485-180602	GT	GGG
(AGT)	 AG	180945-181158	GT	AGG
(GGC)	 AG	181622-181753	GT	AGG
(GAT)	 AG	182278-182382	GT	AAG
(GGA)	 AG	182698-182893	GT	CGG
-recovered pasa_asmbl_1229.p1, internal, 175724, 175840
-recovered pasa_asmbl_1229.p1, internal, 176258, 176461
-recovered pasa_asmbl_1229.p1, internal, 177075, 177276
-recovered pasa_asmbl_1229.p1, internal, 177796, 177870
-recovered pasa_asmbl_1229.p1, internal, 178191, 178361
-recovered pasa_asmbl_1229.p1, internal, 180262, 180357
-recovered pasa_asmbl_1229.p1, internal, 180485, 180602
-recovered pasa_asmbl_1229.p1, internal, 180945, 181158
-recovered pasa_asmbl_1229.p1, internal, 181622, 181753
-recovered pasa_asmbl_1229.p1, internal, 182278, 182382
-recovered pasa_asmbl_1229.p1, internal, 182698, 182893
Valid prediction for snap_scaffold_1-snap.4230-T1
Valid prediction for GlimmerHMM_glimmerT_3040-T1
Valid prediction for GeneMark_model.4835_t
Valid prediction for snap_scaffold_1-snap.4238-T1
Valid prediction for GlimmerHMM_glimmerT_3029-T1
Valid prediction for snap_scaffold_1-snap.4243-T1
Valid prediction for GlimmerHMM_glimmerT_3038-T1
Valid prediction for snap_scaffold_1-snap.4220-T1
Valid prediction for GeneMark_model.4847_t
Valid prediction for GeneMark_model.4859_t
Valid prediction for GeneMark_model.4888_t
Valid prediction for GeneMark_model.4891_t
Valid prediction for snap_scaffold_1-snap.4216-T1
Valid prediction for GeneMark_model.4877_t
Valid prediction for snap_scaffold_1-snap.4234-T1
Valid prediction for snap_scaffold_1-snap.4211-T1
Valid prediction for GeneMark_model.4842_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 111192, rend_intergenic: 111189  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 6885, rend_intergenic: 5997  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21543, rend_intergenic: 12924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47680, rend_intergenic: 33820  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59177, rend_intergenic: 49646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66452, rend_intergenic: 60877  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70375, rend_intergenic: 66502  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79308, rend_intergenic: 70843  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89733, rend_intergenic: 83917  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98086, rend_intergenic: 90890  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105158, rend_intergenic: 102826  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111555, rend_intergenic: 106193  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131814, rend_intergenic: 122354  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149317, rend_intergenic: 132389  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156676, rend_intergenic: 150540  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158992, rend_intergenic: 156976  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163395, rend_intergenic: 161974  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 196714
-exon list size: 742


building trellis

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83.1    
83.2    
83.3    
83.5    
83.6    
83.7    
83.9    
84.0    
84.1    
84.3    
84.4    
84.5    
84.7    
84.8    
84.9    
85.1    
85.2    
85.3    
85.5    
85.6    
85.8    
85.9    
86.0    
86.2    
86.3    
86.4    
86.6    
86.7    
86.8    
87.0    
87.1    
87.2    
87.4    
87.5    
87.6    
87.8    
87.9    
88.0    
88.2    
88.3    
88.4    
88.6    
88.7    
88.8    
89.0    
89.1    
89.2    
89.4    
89.5    
89.7    
89.8    
89.9    
90.1    
90.2    
90.3    
90.5    
90.6    
90.7    
90.9    
91.0    
91.1    
91.3    
91.4    
91.5    
91.7    
91.8    
91.9    
92.1    
92.2    
92.3    
92.5    
92.6    
92.7    
92.9    
93.0    
93.1    
93.3    
93.4    
93.5    
93.7    
93.8    
94.0    
94.1    
94.2    
94.4    
94.5    
94.6    
94.8    
94.9    
95.0    
95.2    
95.3    
95.4    
95.6    
95.7    
95.8    
96.0    
96.1    
96.2    
96.4    
96.5    
96.6    
96.8    
96.9    
97.0    
97.2    
97.3    
97.4    
97.6    
97.7    
97.8    
98.0    
98.1    
98.3    
98.4    
98.5    
98.7    
98.8    
98.9    
99.1    
99.2    
99.3    
99.5    
99.6    
99.7    
99.9    
-found 38 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 111192, rend_intergenic: 111189  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 6885, rend_intergenic: 5997  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21543, rend_intergenic: 12924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47680, rend_intergenic: 33820  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59177, rend_intergenic: 49646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66452, rend_intergenic: 60877  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70375, rend_intergenic: 66502  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79308, rend_intergenic: 70843  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89733, rend_intergenic: 83917  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98086, rend_intergenic: 90890  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105158, rend_intergenic: 102826  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111555, rend_intergenic: 106193  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131814, rend_intergenic: 122354  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149317, rend_intergenic: 132389  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156676, rend_intergenic: 150540  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158992, rend_intergenic: 156976  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163395, rend_intergenic: 161974  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support