-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_23/scaffold_23_10062295-10257564

-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.g35560.t1
Valid prediction for GlimmerHMM_glimmerT_52962-T1
Valid prediction for GeneMark_model.92008_t
Valid prediction for pasa_asmbl_31126.p1
Valid prediction for GlimmerHMM_glimmerT_52967-T1
Valid prediction for Augustus_model.g35570.t1
Valid prediction for HiQ_model.g35565.t1
Valid prediction for CodingQuarry_transcript_35714-T1
Valid prediction for GeneMark_model.92022_t
Valid prediction for GlimmerHMM_glimmerT_52969-T1
Valid prediction for GeneMark_model.92020_t
Valid prediction for GeneMark_model.92003_t
Valid prediction for HiQ_model.g35576.t1
Valid prediction for GeneMark_model.92000_t
Valid prediction for GeneMark_model.91999_t
Valid prediction for snap_scaffold_23-snap.1966-T1
Valid prediction for snap_scaffold_23-snap.1957-T1
Couldn't classify 101791, 101844
Sorry, prediction pasa_asmbl_31127.p2 fails validation.
(ATG)	 CC	97889-97998	GT	ACG
(CGA)	 AG	98327-98377	GT	AGG
(GTA)	 AG	100065-100161	GT	AGG
(GAT)	 AG	100446-100581	GT	TGG
(GAA)	 AG	100839-100922	GT	AGG
(GGT)	 AG	101063-101151	GT	AGG
(GTG)	 AG	101791-101844	AG	TCA
-recovered pasa_asmbl_31127.p2, initial, 97889, 97998
-recovered pasa_asmbl_31127.p2, internal, 98327, 98377
-recovered pasa_asmbl_31127.p2, internal, 100065, 100161
-recovered pasa_asmbl_31127.p2, internal, 100446, 100581
-recovered pasa_asmbl_31127.p2, internal, 100839, 100922
-recovered pasa_asmbl_31127.p2, internal, 101063, 101151
Valid prediction for GeneMark_model.92011_t
Valid prediction for Augustus_model.g35577.t1
Valid prediction for snap_scaffold_23-snap.1947-T1
Valid prediction for pasa_asmbl_31279.p1
Valid prediction for snap_scaffold_23-snap.1967-T1
Valid prediction for GeneMark_model.92009_t
Valid prediction for snap_scaffold_23-snap.1971-T1
Valid prediction for snap_scaffold_23-snap.1974-T1
Valid prediction for GlimmerHMM_glimmerT_52959-T1
Valid prediction for GlimmerHMM_glimmerT_52968-T1
Valid prediction for snap_scaffold_23-snap.1978-T1
Valid prediction for GeneMark_model.92017_t
Valid prediction for GeneMark_model.91997_t
Valid prediction for snap_scaffold_23-snap.1964-T1
Valid prediction for GeneMark_model.91984_t
Valid prediction for GeneMark_model.92015_t
Valid prediction for CodingQuarry_transcript_35721-T1
Valid prediction for GlimmerHMM_glimmerT_52965-T1
Valid prediction for snap_scaffold_23-snap.1949-T1
Valid prediction for snap_scaffold_23-snap.1959-T1
Valid prediction for GeneMark_model.91990_t
Valid prediction for snap_scaffold_23-snap.1962-T1
Valid prediction for GeneMark_model.92006_t
Valid prediction for Augustus_model.g35569.t1
Valid prediction for snap_scaffold_23-snap.1980-T1
Valid prediction for pasa_asmbl_31129.p1
Valid prediction for snap_scaffold_23-snap.1983-T1
Valid prediction for GlimmerHMM_glimmerT_52966-T1
Valid prediction for snap_scaffold_23-snap.1977-T1
Valid prediction for GlimmerHMM_glimmerT_52956-T1
Valid prediction for snap_scaffold_23-snap.1950-T1
Valid prediction for GeneMark_model.91976_t
Valid prediction for GlimmerHMM_glimmerT_52948-T1
Valid prediction for CodingQuarry_transcript_35717-T1
Valid prediction for pasa_asmbl_31138.p1
Valid prediction for HiQ_model.g35573.t1
Valid prediction for CodingQuarry_transcript_35722-T1
Valid prediction for GeneMark_model.92005_t
Valid prediction for GeneMark_model.91973_t
Valid prediction for Augustus_model.g35562.t1
Valid prediction for HiQ_model.g35575.t1
Valid prediction for GeneMark_model.91975_t
Valid prediction for GeneMark_model.92013_t
Valid prediction for Augustus_model.g35578.t1
Valid prediction for snap_scaffold_23-snap.1961-T1
Valid prediction for GeneMark_model.91994_t
Valid prediction for snap_scaffold_23-snap.1973-T1
Valid prediction for GlimmerHMM_glimmerT_52952-T1
Valid prediction for snap_scaffold_23-snap.1951-T1
Valid prediction for GeneMark_model.91992_t
Valid prediction for GeneMark_model.91987_t
Valid prediction for GeneMark_model.91995_t
Valid prediction for snap_scaffold_23-snap.1954-T1
Valid prediction for snap_scaffold_23-snap.1985-T1
Valid prediction for CodingQuarry_transcript_35723-T1
Valid prediction for GlimmerHMM_glimmerT_52953-T1
Valid prediction for pasa_asmbl_31132.p1
Valid prediction for GeneMark_model.91978_t
Valid prediction for snap_scaffold_23-snap.1984-T1
Valid prediction for GeneMark_model.91980_t
Valid prediction for GlimmerHMM_glimmerT_52964-T1
Valid prediction for GlimmerHMM_glimmerT_52958-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: -)Couldn't classify 80333, 81751
Sorry, prediction pasa_asmbl_31921.p1 fails validation.
(CAC)	 NG	80333-81751	CG	AAC
Valid prediction for GlimmerHMM_glimmerT_52947-T1
Valid prediction for snap_scaffold_23-snap.1969-T1
Valid prediction for snap_scaffold_23-snap.1975-T1
Valid prediction for CodingQuarry_transcript_35720-T1
Valid prediction for GeneMark_model.92014_t
Valid prediction for Augustus_model.g35567.t1
Valid prediction for Augustus_model.g35559.t1
Valid prediction for CodingQuarry_transcript_35719-T1
Valid prediction for snap_scaffold_23-snap.1986-T1
Valid prediction for GeneMark_model.92016_t
Valid prediction for GeneMark_model.92010_t
Valid prediction for snap_scaffold_23-snap.1960-T1
Valid prediction for snap_scaffold_23-snap.1956-T1
Couldn't classify 55205, 55236
Sorry, prediction pasa_asmbl_31852.p1 fails validation.
(TCC)	 GA	55205-55236	GT	AGG
(TAA)	 AG	55330-55408	GT	AGG
(GCA)	 AG	55753-55851	GT	AGG
(GCC)	 AG	58064-58225	GT	AGG
(GCC)	 AG	58913-58987	GT	AGG
(ATG)	 AG	59345-59419	GT	TGG
(ATG)	 AG	60090-60308	GT	AGG
(GTG)	 AG	62001-62126	GT	AGG
(GTG)	 AG	62641-62818	GT	AGG
(CTT)	 AG	63056-63204	GT	AGG
(GTG)	 AG	64275-64493	GC	AGG
-recovered pasa_asmbl_31852.p1, initial, 59345, 59419
-recovered pasa_asmbl_31852.p1, initial, 60090, 60308
-recovered pasa_asmbl_31852.p1, terminal, 64275, 64493
-recovered pasa_asmbl_31852.p1, internal, 55330, 55408
-recovered pasa_asmbl_31852.p1, internal, 55753, 55851
-recovered pasa_asmbl_31852.p1, internal, 58064, 58225
-recovered pasa_asmbl_31852.p1, internal, 58913, 58987
-recovered pasa_asmbl_31852.p1, internal, 59345, 59419
-recovered pasa_asmbl_31852.p1, internal, 60090, 60308
-recovered pasa_asmbl_31852.p1, internal, 62001, 62126
-recovered pasa_asmbl_31852.p1, internal, 62641, 62818
-recovered pasa_asmbl_31852.p1, internal, 63056, 63204
-recovered pasa_asmbl_31852.p1, internal, 64275, 64493
Valid prediction for GlimmerHMM_glimmerT_52955-T1
Valid prediction for GeneMark_model.91989_t
Valid prediction for snap_scaffold_23-snap.1952-T1
Valid prediction for GlimmerHMM_glimmerT_52951-T1
Valid prediction for snap_scaffold_23-snap.1955-T1
Valid prediction for GlimmerHMM_glimmerT_52954-T1
Valid prediction for GeneMark_model.91972_t
Valid prediction for GeneMark_model.92004_t
Valid prediction for GeneMark_model.91988_t
Valid prediction for GeneMark_model.92021_t
Valid prediction for GlimmerHMM_glimmerT_52960-T1
Valid prediction for snap_scaffold_23-snap.1965-T1
Valid prediction for snap_scaffold_23-snap.1968-T1
Valid prediction for GeneMark_model.91974_t
Valid prediction for snap_scaffold_23-snap.1970-T1
Valid prediction for GlimmerHMM_glimmerT_52945-T1
Valid prediction for snap_scaffold_23-snap.1945-T1
Valid prediction for GeneMark_model.91986_t
Valid prediction for GlimmerHMM_glimmerT_52961-T1
Valid prediction for GlimmerHMM_glimmerT_52946-T1
Valid prediction for GeneMark_model.91998_t
Valid prediction for HiQ_model.g35572.t1
Valid prediction for GeneMark_model.91983_t
Couldn't classify 140240, 140305
Couldn't classify 144500, 144631
Sorry, prediction pasa_asmbl_31835.p1 fails validation.
(CTG)	 GT	140240-140305	GT	AGG
(TCT)	 AG	140891-141004	GT	TGG
(ATG)	 AG	142059-142194	GT	GGG
(GAG)	 AG	142401-142495	GT	GGG
(ATC)	 AG	144500-144631	GA	ACG
-recovered pasa_asmbl_31835.p1, initial, 142059, 142194
-recovered pasa_asmbl_31835.p1, internal, 140891, 141004
-recovered pasa_asmbl_31835.p1, internal, 142059, 142194
-recovered pasa_asmbl_31835.p1, internal, 142401, 142495
Valid prediction for GeneMark_model.91985_t
Couldn't classify 132650, 132853
Sorry, prediction pasa_asmbl_31837.p1 fails validation.
(GAC)	 AG	132650-132853	GT	AGG
(GCC)	 AG	133956-134088	GT	GAG
(GTG)	 AG	134488-134729	GT	AGG
(CTG)	 AG	135163-135375	GG	GAG
-recovered pasa_asmbl_31837.p1, terminal, 135163, 135375
-recovered pasa_asmbl_31837.p1, internal, 132650, 132853
-recovered pasa_asmbl_31837.p1, internal, 133956, 134088
-recovered pasa_asmbl_31837.p1, internal, 134488, 134729
Valid prediction for GeneMark_model.91977_t
Valid prediction for GeneMark_model.92007_t
Couldn't classify 131759, 131898
Sorry, prediction pasa_asmbl_31838.p1 fails validation.
(ATG)	 AC	128512-128578	GT	AGG
(ATT)	 AG	130270-130389	GT	AGG
(GCG)	 AG	130499-130616	GT	CGG
(GAC)	 AG	131089-131267	GT	CGG
(ACA)	 AG	131759-131898	AG	TCA
-recovered pasa_asmbl_31838.p1, initial, 128512, 128578
-recovered pasa_asmbl_31838.p1, internal, 130270, 130389
-recovered pasa_asmbl_31838.p1, internal, 130499, 130616
-recovered pasa_asmbl_31838.p1, internal, 131089, 131267
Valid prediction for GeneMark_model.92018_t
Valid prediction for snap_scaffold_23-snap.1972-T1
Valid prediction for pasa_asmbl_31834.p1
Valid prediction for Augustus_model.g35574.t1
Valid prediction for GeneMark_model.92001_t
Couldn't classify 55330, 55495
Sorry, prediction pasa_asmbl_31849.p1 fails validation.
(ATG)	 GA	53318-53493	GT	AGG
(TAA)	 AG	55330-55495	GA	GGG
-recovered pasa_asmbl_31849.p1, initial, 53318, 53493
Valid prediction for snap_scaffold_23-snap.1963-T1
Valid prediction for Augustus_model.g35564.t1
Valid prediction for GlimmerHMM_glimmerT_52949-T1
Valid prediction for GeneMark_model.92012_t
Valid prediction for snap_scaffold_23-snap.1958-T1
Valid prediction for GeneMark_model.91991_t
Valid prediction for GeneMark_model.91996_t
Valid prediction for Augustus_model.g35571.t1
Valid prediction for GeneMark_model.92019_t
Valid prediction for snap_scaffold_23-snap.1976-T1
Valid prediction for snap_scaffold_23-snap.1979-T1
Valid prediction for GeneMark_model.91982_t
Valid prediction for Augustus_model.g35568.t1
Valid prediction for GeneMark_model.92002_t
Valid prediction for GlimmerHMM_glimmerT_52950-T1
Valid prediction for GeneMark_model.91979_t
Valid prediction for Augustus_model.g35563.t1
Valid prediction for snap_scaffold_23-snap.1948-T1
Valid prediction for GlimmerHMM_glimmerT_52957-T1
Valid prediction for GeneMark_model.91993_t
Valid prediction for snap_scaffold_23-snap.1982-T1
Valid prediction for Augustus_model.g35566.t1
Valid prediction for Augustus_model.g35561.t1
Valid prediction for snap_scaffold_23-snap.1953-T1
Valid prediction for GlimmerHMM_glimmerT_52963-T1
Valid prediction for snap_scaffold_23-snap.1981-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.91981_t
Valid prediction for snap_scaffold_23-snap.1946-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 35338, rend_intergenic: 23662  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40666, rend_intergenic: 36410  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55151, rend_intergenic: 52725  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64584, rend_intergenic: 59939  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68747, rend_intergenic: 64651  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92938, rend_intergenic: 73774  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103633, rend_intergenic: 100278  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111437, rend_intergenic: 106603  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138079, rend_intergenic: 132464  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151338, rend_intergenic: 148963  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161750, rend_intergenic: 158781  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168492, rend_intergenic: 164532  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178730, rend_intergenic: 170114  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188941, rend_intergenic: 179749  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191669, rend_intergenic: 189556  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 195270
-exon list size: 655


building trellis

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72.9    
73.1    
73.2    
73.4    
73.5    
73.7    
73.8    
74.0    
74.1    
74.3    
74.4    
74.6    
74.7    
74.9    
75.0    
75.2    
75.3    
75.5    
75.6    
75.8    
76.0    
76.1    
76.3    
76.4    
76.6    
76.7    
76.9    
77.0    
77.2    
77.3    
77.5    
77.6    
77.8    
77.9    
78.1    
78.2    
78.4    
78.5    
78.7    
78.8    
79.0    
79.1    
79.3    
79.5    
79.6    
79.8    
79.9    
80.1    
80.2    
80.4    
80.5    
80.7    
80.8    
81.0    
81.1    
81.3    
81.4    
81.6    
81.7    
81.9    
82.0    
82.2    
82.3    
82.5    
82.6    
82.8    
83.0    
83.1    
83.3    
83.4    
83.6    
83.7    
83.9    
84.0    
84.2    
84.3    
84.5    
84.6    
84.8    
84.9    
85.1    
85.2    
85.4    
85.5    
85.7    
85.8    
86.0    
86.1    
86.3    
86.5    
86.6    
86.8    
86.9    
87.1    
87.2    
87.4    
87.5    
87.7    
87.8    
88.0    
88.1    
88.3    
88.4    
88.6    
88.7    
88.9    
89.0    
89.2    
89.3    
89.5    
89.6    
89.8    
90.0    
90.1    
90.3    
90.4    
90.6    
90.7    
90.9    
91.0    
91.2    
91.3    
91.5    
91.6    
91.8    
91.9    
92.1    
92.2    
92.4    
92.5    
92.7    
92.8    
93.0    
93.2    
93.3    
93.5    
93.6    
93.8    
93.9    
94.1    
94.2    
94.4    
94.5    
94.7    
94.8    
95.0    
95.1    
95.3    
95.4    
95.6    
95.7    
95.9    
96.0    
96.2    
96.3    
96.5    
96.7    
96.8    
97.0    
97.1    
97.3    
97.4    
97.6    
97.7    
97.9    
98.0    
98.2    
98.3    
98.5    
98.6    
98.8    
98.9    
99.1    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 35338, rend_intergenic: 23662  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40666, rend_intergenic: 36410  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55151, rend_intergenic: 52725  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64584, rend_intergenic: 59939  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68747, rend_intergenic: 64651  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92938, rend_intergenic: 73774  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103633, rend_intergenic: 100278  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111437, rend_intergenic: 106603  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138079, rend_intergenic: 132464  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151338, rend_intergenic: 148963  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161750, rend_intergenic: 158781  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168492, rend_intergenic: 164532  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178730, rend_intergenic: 170114  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188941, rend_intergenic: 179749  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191669, rend_intergenic: 189556  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support