-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_5/scaffold_5_2127845-2339807

-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 GeneMark_model.19782_t
Valid prediction for snap_scaffold_5-snap.434-T1
Valid prediction for snap_scaffold_5-snap.431-T1
Valid prediction for GeneMark_model.19818_t
Valid prediction for Augustus_model.g7771.t1
Valid prediction for GlimmerHMM_glimmerT_11804-T1
Valid prediction for Augustus_model.g7764.t1
Valid prediction for snap_scaffold_5-snap.438-T1
Valid prediction for GeneMark_model.19829_t
Valid prediction for GlimmerHMM_glimmerT_11802-T1
Valid prediction for snap_scaffold_5-snap.453-T1
Valid prediction for GeneMark_model.19813_t
Valid prediction for snap_scaffold_5-snap.456-T1
Valid prediction for GeneMark_model.19775_t
Valid prediction for Augustus_model.g7770.t1
Valid prediction for GeneMark_model.19820_t
Valid prediction for GeneMark_model.19776_t
Valid prediction for Augustus_model.g7765.t1
Valid prediction for GlimmerHMM_glimmerT_11813-T1
Valid prediction for GeneMark_model.19808_t
Valid prediction for snap_scaffold_5-snap.441-T1
Valid prediction for CodingQuarry_transcript_51868-T1
Valid prediction for GlimmerHMM_glimmerT_11798-T1
Valid prediction for GeneMark_model.19790_t
Valid prediction for GlimmerHMM_glimmerT_11803-T1
Valid prediction for GeneMark_model.19779_t
Valid prediction for GeneMark_model.19814_t
Valid prediction for GeneMark_model.19788_t
Valid prediction for GeneMark_model.19785_t
Valid prediction for snap_scaffold_5-snap.449-T1
Valid prediction for GeneMark_model.19810_t
Valid prediction for GeneMark_model.19833_t
Valid prediction for snap_scaffold_5-snap.460-T1
Valid prediction for snap_scaffold_5-snap.446-T1
Valid prediction for GeneMark_model.19822_t
Valid prediction for GeneMark_model.19806_t
Valid prediction for GeneMark_model.19791_t
Valid prediction for GeneMark_model.19802_t
Valid prediction for snap_scaffold_5-snap.450-T1
Valid prediction for GeneMark_model.19804_t
Couldn't classify 95455, 95517
Couldn't classify 97249, 97419
Sorry, prediction pasa_asmbl_43823.p1 fails validation.
(CTA)	 TC	95455-95517	GT	AGG
(GGT)	 AG	96028-96103	GT	GGG
(GAA)	 AG	96439-96584	GT	AGG
(GTT)	 AG	97249-97419	TG	AGT
-recovered pasa_asmbl_43823.p1, internal, 96028, 96103
-recovered pasa_asmbl_43823.p1, internal, 96439, 96584
Valid prediction for pasa_asmbl_43820.p1
Couldn't classify 84562, 84654
Couldn't classify 87879, 87947
Sorry, prediction pasa_asmbl_43822.p1 fails validation.
(AGC)	 GC	84562-84654	GT	AGG
(GAC)	 AG	85194-85355	GT	AGG
(GAT)	 AG	87879-87947	CT	GAC
-recovered pasa_asmbl_43822.p1, internal, 85194, 85355
Valid prediction for GeneMark_model.19795_t
Valid prediction for GlimmerHMM_glimmerT_11801-T1
Valid prediction for GeneMark_model.19827_t
Valid prediction for GeneMark_model.19799_t
Valid prediction for GlimmerHMM_glimmerT_11812-T1
Valid prediction for GeneMark_model.19831_t
Valid prediction for snap_scaffold_5-snap.426-T1
Valid prediction for GeneMark_model.19824_t
Valid prediction for GeneMark_model.19774_t
Valid prediction for GeneMark_model.19797_t
Valid prediction for GeneMark_model.19815_t
Valid prediction for snap_scaffold_5-snap.440-T1
Valid prediction for snap_scaffold_5-snap.457-T1
Valid prediction for snap_scaffold_5-snap.443-T1
Valid prediction for GeneMark_model.19777_t
Valid prediction for GlimmerHMM_glimmerT_11810-T1
Valid prediction for snap_scaffold_5-snap.430-T1
Valid prediction for GeneMark_model.19811_t
Couldn't classify 101110, 101334
Sorry, prediction pasa_asmbl_43824.p1 fails validation.
(CCT)	 CC	101110-101334	GT	AGG
(AGG)	 AG	101947-101992	GT	TGG
(ATC)	 AG	104062-104246	AA	AAA
-recovered pasa_asmbl_43824.p1, terminal, 104062, 104246
-recovered pasa_asmbl_43824.p1, internal, 101947, 101992
Valid prediction for GlimmerHMM_glimmerT_11797-T1
Valid prediction for snap_scaffold_5-snap.439-T1
Valid prediction for snap_scaffold_5-snap.432-T1
Valid prediction for snap_scaffold_5-snap.435-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_5-snap.429-T1
Valid prediction for GeneMark_model.19781_t
Valid prediction for GeneMark_model.19812_t
Valid prediction for snap_scaffold_5-snap.428-T1
Valid prediction for GeneMark_model.19803_t
Valid prediction for GeneMark_model.19826_t
Valid prediction for GeneMark_model.19784_t
Valid prediction for snap_scaffold_5-snap.455-T1
Valid prediction for CodingQuarry_transcript_51871-T1
Valid prediction for Augustus_model.g7769.t1
Valid prediction for snap_scaffold_5-snap.454-T1
Valid prediction for HiQ_model.g7773.t1
Couldn't classify 163644, 163709
Couldn't classify 173412, 173453
Sorry, prediction pasa_asmbl_45265.p1 fails validation.
(GCA)	 CA	163644-163709	GT	AGG
(GGG)	 AG	164080-164200	GT	CGG
(GAA)	 AG	166246-166353	GT	TGG
(AGA)	 AG	166762-166874	GT	AGG
(CTA)	 AG	167643-167734	GT	AAG
(GAG)	 AG	168809-168935	GT	CAG
(CTC)	 AG	170138-170291	GT	GGG
(TCT)	 AG	171000-171060	GT	AAG
(GTG)	 AG	171600-171666	GT	TGG
(GTG)	 AG	172830-173048	GT	AGG
(GGT)	 AG	173412-173453	GT	AGG
-recovered pasa_asmbl_45265.p1, internal, 164080, 164200
-recovered pasa_asmbl_45265.p1, internal, 166246, 166353
-recovered pasa_asmbl_45265.p1, internal, 166762, 166874
-recovered pasa_asmbl_45265.p1, internal, 167643, 167734
-recovered pasa_asmbl_45265.p1, internal, 168809, 168935
-recovered pasa_asmbl_45265.p1, internal, 170138, 170291
-recovered pasa_asmbl_45265.p1, internal, 171000, 171060
-recovered pasa_asmbl_45265.p1, internal, 171600, 171666
-recovered pasa_asmbl_45265.p1, internal, 172830, 173048
-recovered pasa_asmbl_45265.p1, internal, 173412, 173453
Valid prediction for GlimmerHMM_glimmerT_11806-T1
Couldn't classify 104900, 104916
Sorry, prediction pasa_asmbl_45269.p1 fails validation.
(AGT)	 AG	104900-104916	GT	AGG
(GTA)	 AG	104955-105154	GT	TGG
(TCC)	 AG	105630-105742	GC	GAG
-recovered pasa_asmbl_45269.p1, terminal, 105630, 105742
-recovered pasa_asmbl_45269.p1, internal, 104900, 104916
-recovered pasa_asmbl_45269.p1, internal, 104955, 105154
-recovered pasa_asmbl_45269.p1, internal, 105630, 105742
Valid prediction for GlimmerHMM_glimmerT_11811-T1
Valid prediction for snap_scaffold_5-snap.437-T1
Valid prediction for Augustus_model.g7767.t1
Valid prediction for Augustus_model.g7763.t1
Valid prediction for snap_scaffold_5-snap.442-T1
Valid prediction for pasa_asmbl_45273.p1
Valid prediction for GeneMark_model.19773_t
Valid prediction for GlimmerHMM_glimmerT_11799-T1
Valid prediction for GeneMark_model.19817_t
Valid prediction for GlimmerHMM_glimmerT_11808-T1
Valid prediction for GeneMark_model.19783_t
Valid prediction for snap_scaffold_5-snap.444-T1
Valid prediction for snap_scaffold_5-snap.451-T1
Valid prediction for GeneMark_model.19800_t
Valid prediction for GeneMark_model.19796_t
Valid prediction for snap_scaffold_5-snap.433-T1
Valid prediction for GeneMark_model.19809_t
Couldn't classify 177327, 177686
Sorry, prediction pasa_asmbl_45263.p1 fails validation.
(GAT)	 AA	177327-177686	CA	GAC
Valid prediction for snap_scaffold_5-snap.427-T1
Valid prediction for GeneMark_model.19819_t
Valid prediction for GlimmerHMM_glimmerT_11809-T1
Valid prediction for GeneMark_model.19798_t
Valid prediction for GlimmerHMM_glimmerT_11800-T1
Valid prediction for HiQ_model.g7766.t1
Valid prediction for GeneMark_model.19807_t
Valid prediction for Augustus_model.g7762.t1
Valid prediction for snap_scaffold_5-snap.436-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for GeneMark_model.19828_t
Valid prediction for snap_scaffold_5-snap.459-T1
Valid prediction for GeneMark_model.19821_t
Valid prediction for GeneMark_model.19778_t
Valid prediction for GeneMark_model.19786_t
Valid prediction for GeneMark_model.19825_t
Valid prediction for snap_scaffold_5-snap.458-T1
Valid prediction for CodingQuarry_transcript_51870-T1
Valid prediction for snap_scaffold_5-snap.448-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.19832_t
Valid prediction for GeneMark_model.19780_t
Valid prediction for pasa_asmbl_45275.p1
Valid prediction for GlimmerHMM_glimmerT_11814-T1
Valid prediction for GeneMark_model.19794_t
Valid prediction for GeneMark_model.19823_t
Valid prediction for CodingQuarry_transcript_51869-T1
Valid prediction for Augustus_model.g7772.t1
Valid prediction for GeneMark_model.19816_t
Valid prediction for CodingQuarry_transcript_51867-T1
Valid prediction for GeneMark_model.19787_t
Valid prediction for GeneMark_model.19805_t
Valid prediction for GlimmerHMM_glimmerT_11807-T1
Valid prediction for GlimmerHMM_glimmerT_11805-T1
Valid prediction for Augustus_model.g7768.t1
Valid prediction for GeneMark_model.19792_t
Valid prediction for snap_scaffold_5-snap.445-T1
Valid prediction for GeneMark_model.19801_t
Valid prediction for snap_scaffold_5-snap.447-T1
Valid prediction for GeneMark_model.19789_t
Valid prediction for snap_scaffold_5-snap.452-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10391, rend_intergenic: 6374  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42383, rend_intergenic: 38454  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50713, rend_intergenic: 42842  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73562, rend_intergenic: 64362  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81946, rend_intergenic: 79328  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103370, rend_intergenic: 98836  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137322, rend_intergenic: 123372  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163974, rend_intergenic: 138311  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173050, rend_intergenic: 168629  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174953, rend_intergenic: 174296  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178457, rend_intergenic: 175025  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195432, rend_intergenic: 183196  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 211963
-exon list size: 821


building trellis

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78.7    
78.9    
79.0    
79.1    
79.2    
79.3    
79.5    
79.6    
79.7    
79.8    
80.0    
80.1    
80.2    
80.3    
80.4    
80.6    
80.7    
80.8    
80.9    
81.0    
81.2    
81.3    
81.4    
81.5    
81.7    
81.8    
81.9    
82.0    
82.1    
82.3    
82.4    
82.5    
82.6    
82.7    
82.9    
83.0    
83.1    
83.2    
83.4    
83.5    
83.6    
83.7    
83.8    
84.0    
84.1    
84.2    
84.3    
84.4    
84.6    
84.7    
84.8    
84.9    
85.1    
85.2    
85.3    
85.4    
85.5    
85.7    
85.8    
85.9    
86.0    
86.1    
86.3    
86.4    
86.5    
86.6    
86.8    
86.9    
87.0    
87.1    
87.2    
87.4    
87.5    
87.6    
87.7    
87.8    
88.0    
88.1    
88.2    
88.3    
88.5    
88.6    
88.7    
88.8    
88.9    
89.1    
89.2    
89.3    
89.4    
89.6    
89.7    
89.8    
89.9    
90.0    
90.2    
90.3    
90.4    
90.5    
90.6    
90.8    
90.9    
91.0    
91.1    
91.3    
91.4    
91.5    
91.6    
91.7    
91.9    
92.0    
92.1    
92.2    
92.3    
92.5    
92.6    
92.7    
92.8    
93.0    
93.1    
93.2    
93.3    
93.4    
93.6    
93.7    
93.8    
93.9    
94.0    
94.2    
94.3    
94.4    
94.5    
94.7    
94.8    
94.9    
95.0    
95.1    
95.3    
95.4    
95.5    
95.6    
95.7    
95.9    
96.0    
96.1    
96.2    
96.4    
96.5    
96.6    
96.7    
96.8    
97.0    
97.1    
97.2    
97.3    
97.4    
97.6    
97.7    
97.8    
97.9    
98.1    
98.2    
98.3    
98.4    
98.5    
98.7    
98.8    
98.9    
99.0    
99.1    
99.3    
99.4    
99.5    
99.6    
99.8    
99.9    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 10391, rend_intergenic: 6374  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42383, rend_intergenic: 38454  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50713, rend_intergenic: 42842  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73562, rend_intergenic: 64362  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81946, rend_intergenic: 79328  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103370, rend_intergenic: 98836  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137322, rend_intergenic: 123372  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163974, rend_intergenic: 138311  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173050, rend_intergenic: 168629  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174953, rend_intergenic: 174296  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178457, rend_intergenic: 175025  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195432, rend_intergenic: 183196  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 12 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 200295 - 211963
-exon list size: 19


building trellis

4.8    
9.5    
14.3    
19.0    
23.8    
28.6    
33.3    
38.1    
42.9    
47.6    
52.4    
57.1    
61.9    
66.7    
71.4    
76.2    
81.0    
85.7    
90.5    
95.2    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support