-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_9662795-9893186

-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.12034_t
Valid prediction for snap_scaffold_3-snap.1950-T1
Valid prediction for snap_scaffold_3-snap.1922-T1
Valid prediction for snap_scaffold_3-snap.1927-T1
Valid prediction for snap_scaffold_3-snap.1939-T1
Valid prediction for GlimmerHMM_glimmerT_7273-T1
Valid prediction for snap_scaffold_3-snap.1962-T1
Valid prediction for GeneMark_model.12032_t
Valid prediction for GeneMark_model.12028_t
Valid prediction for GeneMark_model.12015_t
Valid prediction for pasa_asmbl_40198.p1
Valid prediction for Augustus_model.g4779.t1
Valid prediction for GeneMark_model.12030_t
Valid prediction for GeneMark_model.12049_t
Valid prediction for snap_scaffold_3-snap.1937-T1
Valid prediction for GeneMark_model.12019_t
Valid prediction for snap_scaffold_3-snap.1931-T1
Valid prediction for Augustus_model.g4768.t1
Valid prediction for snap_scaffold_3-snap.1944-T1
Valid prediction for HiQ_model.g4769.t1
Valid prediction for GeneMark_model.12042_t
Valid prediction for snap_scaffold_3-snap.1963-T1
Valid prediction for pasa_asmbl_40192.p1
Valid prediction for snap_scaffold_3-snap.1954-T1
Valid prediction for GlimmerHMM_glimmerT_7285-T1
Valid prediction for GlimmerHMM_glimmerT_7283-T1
Valid prediction for snap_scaffold_3-snap.1941-T1
Valid prediction for CodingQuarry_transcript_46130-T1
Valid prediction for GlimmerHMM_glimmerT_7266-T1
Valid prediction for Augustus_model.g4771.t1
Valid prediction for GlimmerHMM_glimmerT_7280-T1
Valid prediction for GeneMark_model.12020_t
Valid prediction for GeneMark_model.12017_t
Valid prediction for GeneMark_model.12016_t
Valid prediction for GlimmerHMM_glimmerT_7281-T1
Valid prediction for GlimmerHMM_glimmerT_7265-T1
Valid prediction for snap_scaffold_3-snap.1952-T1
Valid prediction for GeneMark_model.12045_t
Valid prediction for GeneMark_model.12024_t
Valid prediction for GlimmerHMM_glimmerT_7269-T1
Valid prediction for snap_scaffold_3-snap.1947-T1
Couldn't classify 176283, 176579
Sorry, prediction pasa_asmbl_40195.p2 fails validation.
(CGA)	 CC	176283-176579	CC	GCC
Valid prediction for snap_scaffold_3-snap.1925-T1
Valid prediction for GeneMark_model.12046_t
Valid prediction for GeneMark_model.12027_t
Valid prediction for CodingQuarry_transcript_46134-T1
Valid prediction for GeneMark_model.12058_t
Valid prediction for GlimmerHMM_glimmerT_7259-T1
Valid prediction for snap_scaffold_3-snap.1935-T1
Valid prediction for Augustus_model.g4766.t1
Valid prediction for GlimmerHMM_glimmerT_7261-T1
Valid prediction for GeneMark_model.12010_t
Valid prediction for GeneMark_model.12008_t
Valid prediction for GlimmerHMM_glimmerT_7276-T1
Valid prediction for snap_scaffold_3-snap.1951-T1
Valid prediction for Augustus_model.g4776.t1
Valid prediction for HiQ_model.g4774.t1
Valid prediction for GeneMark_model.12060_t
Valid prediction for GeneMark_model.12036_t
Valid prediction for GeneMark_model.12052_t
Valid prediction for snap_scaffold_3-snap.1926-T1
Valid prediction for GeneMark_model.12012_t
Valid prediction for GlimmerHMM_glimmerT_7279-T1
Couldn't classify 9898, 10087
Sorry, prediction pasa_asmbl_40190.p1 fails validation.
(ATG)	 TT	8321-8350	GT	TGG
(GAC)	 AG	9219-9333	GT	TGG
(GTG)	 AG	9533-9728	GT	AGG
(TTA)	 AG	9898-10087	CC	TGC
-recovered pasa_asmbl_40190.p1, initial, 8321, 8350
-recovered pasa_asmbl_40190.p1, internal, 9219, 9333
-recovered pasa_asmbl_40190.p1, internal, 9533, 9728
Valid prediction for snap_scaffold_3-snap.1957-T1
Valid prediction for snap_scaffold_3-snap.1933-T1
Valid prediction for Augustus_model.g4759.t1
Valid prediction for snap_scaffold_3-snap.1956-T1
Couldn't classify 11629, 11712
Sorry, prediction pasa_asmbl_40191.p1 fails validation.
(GTC)	 TG	11629-11712	GT	ACG
(GGC)	 AG	11845-11941	GT	AGG
(TGG)	 AG	12097-12265	GT	AGG
(TCT)	 AG	12499-12631	GT	AGG
(CTC)	 AG	12822-13000	GT	AAG
(CTC)	 AG	13102-13117	GC	GAG
-recovered pasa_asmbl_40191.p1, terminal, 13102, 13117
-recovered pasa_asmbl_40191.p1, internal, 11845, 11941
-recovered pasa_asmbl_40191.p1, internal, 12097, 12265
-recovered pasa_asmbl_40191.p1, internal, 12499, 12631
-recovered pasa_asmbl_40191.p1, internal, 12822, 13000
-recovered pasa_asmbl_40191.p1, internal, 13102, 13117
Valid prediction for GlimmerHMM_glimmerT_7277-T1
Valid prediction for GlimmerHMM_glimmerT_7284-T1
Valid prediction for GlimmerHMM_glimmerT_7263-T1
Valid prediction for GeneMark_model.12022_t
Valid prediction for GeneMark_model.12055_t
Valid prediction for GeneMark_model.12037_t
Valid prediction for GlimmerHMM_glimmerT_7256-T1
Valid prediction for Augustus_model.g4764.t1
Valid prediction for CodingQuarry_transcript_46131-T1
Valid prediction for Augustus_model.g4772.t1
Valid prediction for snap_scaffold_3-snap.1955-T1
Valid prediction for GlimmerHMM_glimmerT_7257-T1
Valid prediction for GeneMark_model.12053_t
Valid prediction for GeneMark_model.12040_t
Valid prediction for Augustus_model.g4775.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_3-snap.1948-T1
Valid prediction for snap_scaffold_3-snap.1934-T1
Valid prediction for snap_scaffold_3-snap.1949-T1
Valid prediction for GeneMark_model.12051_t
Valid prediction for GlimmerHMM_glimmerT_7267-T1
Couldn't classify 199743, 200018
Couldn't classify 204787, 204804
Sorry, prediction pasa_asmbl_39734.p1 fails validation.
(AAC)	 AG	199743-200018	GT	AGG
(GAC)	 AG	201990-202085	GT	AGG
(CTG)	 AG	204787-204804	CA	AGC
-recovered pasa_asmbl_39734.p1, internal, 199743, 200018
-recovered pasa_asmbl_39734.p1, internal, 201990, 202085
Valid prediction for HiQ_model.g4773.t1
Valid prediction for snap_scaffold_3-snap.1923-T1
Valid prediction for snap_scaffold_3-snap.1936-T1
Valid prediction for GeneMark_model.12026_t
Valid prediction for GeneMark_model.12013_t
Valid prediction for GeneMark_model.12031_t
Valid prediction for GlimmerHMM_glimmerT_7271-T1
Valid prediction for GlimmerHMM_glimmerT_7262-T1
Valid prediction for Augustus_model.g4765.t1
Valid prediction for GlimmerHMM_glimmerT_7270-T1
Valid prediction for GeneMark_model.12047_t
Valid prediction for GeneMark_model.12009_t
Valid prediction for GeneMark_model.12056_t
Valid prediction for Augustus_model.g4762.t1
Valid prediction for GlimmerHMM_glimmerT_7255-T1
Valid prediction for snap_scaffold_3-snap.1943-T1
Valid prediction for snap_scaffold_3-snap.1964-T1
Valid prediction for GlimmerHMM_glimmerT_7278-T1
Valid prediction for GeneMark_model.12044_t
Valid prediction for snap_scaffold_3-snap.1960-T1
Valid prediction for GlimmerHMM_glimmerT_7274-T1
Valid prediction for GlimmerHMM_glimmerT_7258-T1
Valid prediction for GeneMark_model.12025_t
Valid prediction for snap_scaffold_3-snap.1938-T1
Valid prediction for GeneMark_model.12011_t
Valid prediction for snap_scaffold_3-snap.1959-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for Augustus_model.g4761.t1
Valid prediction for GeneMark_model.12014_t
Valid prediction for GeneMark_model.12035_t
Valid prediction for GeneMark_model.12029_t
Valid prediction for GeneMark_model.12033_t
Valid prediction for GlimmerHMM_glimmerT_7260-T1
Valid prediction for snap_scaffold_3-snap.1928-T1
Valid prediction for GeneMark_model.12021_t
Valid prediction for snap_scaffold_3-snap.1946-T1
Valid prediction for snap_scaffold_3-snap.1945-T1
Valid prediction for Augustus_model.g4770.t1
Valid prediction for GlimmerHMM_glimmerT_7264-T1
Valid prediction for snap_scaffold_3-snap.1953-T1
Valid prediction for snap_scaffold_3-snap.1942-T1
Valid prediction for pasa_asmbl_39025.p1
Valid prediction for GeneMark_model.12023_t
Valid prediction for Augustus_model.g4760.t1
Valid prediction for Augustus_model.g4758.t1
Valid prediction for GlimmerHMM_glimmerT_7275-T1
Valid prediction for CodingQuarry_transcript_46133-T1
Valid prediction for HiQ_model.g4767.t1
Valid prediction for GeneMark_model.12018_t
Valid prediction for snap_scaffold_3-snap.1930-T1
Valid prediction for snap_scaffold_3-snap.1958-T1
Valid prediction for GlimmerHMM_glimmerT_7268-T1
Valid prediction for GlimmerHMM_glimmerT_7272-T1
Valid prediction for Augustus_model.g4763.t1
Valid prediction for snap_scaffold_3-snap.1929-T1
Valid prediction for GeneMark_model.12054_t
Valid prediction for GlimmerHMM_glimmerT_7282-T1
Valid prediction for snap_scaffold_3-snap.1932-T1
Valid prediction for Augustus_model.g4777.t1
Valid prediction for snap_scaffold_3-snap.1924-T1
Valid prediction for Augustus_model.g4778.t1
Couldn't classify 110798, 111144
Sorry, prediction pasa_asmbl_39023.p1 fails validation.
(ATG)	 CT	109565-109699	GT	AGG
(AAG)	 AG	110265-110592	GT	AGG
(ATG)	 AG	110798-111144	TC	ACT
-recovered pasa_asmbl_39023.p1, initial, 109565, 109699
-recovered pasa_asmbl_39023.p1, internal, 110265, 110592
Valid prediction for CodingQuarry_transcript_46132-T1
Valid prediction for GeneMark_model.12038_t
Valid prediction for snap_scaffold_3-snap.1921-T1
Valid prediction for GeneMark_model.12059_t
Valid prediction for GeneMark_model.12057_t
Valid prediction for GeneMark_model.12039_t
Valid prediction for GeneMark_model.12043_t
Valid prediction for GlimmerHMM_glimmerT_7286-T1
Valid prediction for snap_scaffold_3-snap.1961-T1
Valid prediction for snap_scaffold_3-snap.1940-T1
Valid prediction for GeneMark_model.12041_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 19543, rend_intergenic: 9553  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44903, rend_intergenic: 20119  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62313, rend_intergenic: 44999  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79407, rend_intergenic: 67894  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80666, rend_intergenic: 80352  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86872, rend_intergenic: 82210  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88243, rend_intergenic: 87266  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100746, rend_intergenic: 98448  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109446, rend_intergenic: 107797  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110700, rend_intergenic: 110198  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115158, rend_intergenic: 111592  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120104, rend_intergenic: 117842  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 228530, rend_intergenic: 220956  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 230392
-exon list size: 782


building trellis

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79.2    
79.3    
79.5    
79.6    
79.7    
79.8    
80.0    
80.1    
80.2    
80.4    
80.5    
80.6    
80.7    
80.9    
81.0    
81.1    
81.2    
81.4    
81.5    
81.6    
81.8    
81.9    
82.0    
82.1    
82.3    
82.4    
82.5    
82.7    
82.8    
82.9    
83.0    
83.2    
83.3    
83.4    
83.5    
83.7    
83.8    
83.9    
84.1    
84.2    
84.3    
84.4    
84.6    
84.7    
84.8    
84.9    
85.1    
85.2    
85.3    
85.5    
85.6    
85.7    
85.8    
86.0    
86.1    
86.2    
86.4    
86.5    
86.6    
86.7    
86.9    
87.0    
87.1    
87.2    
87.4    
87.5    
87.6    
87.8    
87.9    
88.0    
88.1    
88.3    
88.4    
88.5    
88.6    
88.8    
88.9    
89.0    
89.2    
89.3    
89.4    
89.5    
89.7    
89.8    
89.9    
90.1    
90.2    
90.3    
90.4    
90.6    
90.7    
90.8    
90.9    
91.1    
91.2    
91.3    
91.5    
91.6    
91.7    
91.8    
92.0    
92.1    
92.2    
92.3    
92.5    
92.6    
92.7    
92.9    
93.0    
93.1    
93.2    
93.4    
93.5    
93.6    
93.8    
93.9    
94.0    
94.1    
94.3    
94.4    
94.5    
94.6    
94.8    
94.9    
95.0    
95.2    
95.3    
95.4    
95.5    
95.7    
95.8    
95.9    
96.0    
96.2    
96.3    
96.4    
96.6    
96.7    
96.8    
96.9    
97.1    
97.2    
97.3    
97.4    
97.6    
97.7    
97.8    
98.0    
98.1    
98.2    
98.3    
98.5    
98.6    
98.7    
98.9    
99.0    
99.1    
99.2    
99.4    
99.5    
99.6    
99.7    
99.9    
-found 45 predictions from path traversal
Error with prediction: snap lend_intergenic: 19543, rend_intergenic: 9553  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44903, rend_intergenic: 20119  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62313, rend_intergenic: 44999  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79407, rend_intergenic: 67894  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80666, rend_intergenic: 80352  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86872, rend_intergenic: 82210  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88243, rend_intergenic: 87266  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100746, rend_intergenic: 98448  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109446, rend_intergenic: 107797  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110700, rend_intergenic: 110198  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115158, rend_intergenic: 111592  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120104, rend_intergenic: 117842  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 228530, rend_intergenic: 220956  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support