-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_6/scaffold_6_8527903-8705865

-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_6-snap.1928-T1
Valid prediction for snap_scaffold_6-snap.1905-T1
Valid prediction for snap_scaffold_6-snap.1904-T1
Valid prediction for GeneMark_model.26124_t
Valid prediction for GlimmerHMM_glimmerT_15510-T1
Valid prediction for snap_scaffold_6-snap.1925-T1
Valid prediction for GeneMark_model.26137_t
Valid prediction for Augustus_model.g10328.t1
Valid prediction for snap_scaffold_6-snap.1899-T1
Valid prediction for CodingQuarry_transcript_54993-T1
Valid prediction for GeneMark_model.26100_t
Valid prediction for Augustus_model.g10330.t1
Valid prediction for Augustus_model.g10346.t1
Valid prediction for GeneMark_model.26112_t
Valid prediction for GlimmerHMM_glimmerT_15492-T1
Valid prediction for GlimmerHMM_glimmerT_15489-T1
Valid prediction for pasa_asmbl_47103.p1
Valid prediction for snap_scaffold_6-snap.1906-T1
Valid prediction for GeneMark_model.26131_t
Valid prediction for snap_scaffold_6-snap.1922-T1
Valid prediction for CodingQuarry_transcript_54994-T1
Valid prediction for GeneMark_model.26128_t
Valid prediction for GlimmerHMM_glimmerT_15505-T1
Valid prediction for snap_scaffold_6-snap.1902-T1
Valid prediction for pasa_asmbl_47100.p1
Valid prediction for snap_scaffold_6-snap.1926-T1
Valid prediction for GeneMark_model.26126_t
Valid prediction for CodingQuarry_transcript_54997-T1
Valid prediction for GeneMark_model.26111_t
Valid prediction for GeneMark_model.26102_t
Valid prediction for GlimmerHMM_glimmerT_15500-T1
Valid prediction for Augustus_model.g10338.t1
Valid prediction for Augustus_model.g10344.t1
Valid prediction for GlimmerHMM_glimmerT_15507-T1
Valid prediction for GeneMark_model.26103_t
Valid prediction for GeneMark_model.26105_t
Valid prediction for GeneMark_model.26129_t
Valid prediction for HiQ_model.g10327.t1
Valid prediction for snap_scaffold_6-snap.1907-T1
Valid prediction for snap_scaffold_6-snap.1903-T1
Valid prediction for snap_scaffold_6-snap.1893-T1
Valid prediction for GlimmerHMM_glimmerT_15487-T1
Valid prediction for pasa_asmbl_47088.p1
Valid prediction for pasa_asmbl_47094.p1
Valid prediction for GlimmerHMM_glimmerT_15504-T1
Valid prediction for GlimmerHMM_glimmerT_15499-T1
Valid prediction for snap_scaffold_6-snap.1912-T1
Valid prediction for GeneMark_model.26122_t
Valid prediction for snap_scaffold_6-snap.1923-T1
Valid prediction for Augustus_model.g10322.t1
Valid prediction for GlimmerHMM_glimmerT_15493-T1
Valid prediction for Augustus_model.g10343.t1
Valid prediction for HiQ_model.g10335.t1
Valid prediction for GeneMark_model.26117_t
Valid prediction for GlimmerHMM_glimmerT_15480-T1
Valid prediction for snap_scaffold_6-snap.1918-T1
Valid prediction for CodingQuarry_transcript_54998-T1
Valid prediction for GlimmerHMM_glimmerT_15490-T1
Valid prediction for Augustus_model.g10324.t1
Valid prediction for GeneMark_model.26114_t
Valid prediction for GeneMark_model.26109_t
Valid prediction for Augustus_model.g10340.t1
Valid prediction for snap_scaffold_6-snap.1894-T1
Valid prediction for GlimmerHMM_glimmerT_15514-T1
Valid prediction for GeneMark_model.26110_t
Valid prediction for GeneMark_model.26135_t
Valid prediction for Augustus_model.g10342.t1
Valid prediction for GeneMark_model.26120_t
Valid prediction for GlimmerHMM_glimmerT_15483-T1
Valid prediction for GlimmerHMM_glimmerT_15506-T1
Valid prediction for GeneMark_model.26133_t
Valid prediction for HiQ_model.g10329.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_6-snap.1895-T1
Valid prediction for HiQ_model.g10336.t1
Valid prediction for Augustus_model.g10323.t1
Couldn't classify 144284, 144524
Sorry, prediction pasa_asmbl_48501.p1 fails validation.
(GGG)	 GG	144284-144524	GT	AAG
(ATG)	 AG	144648-144778	GT	AGG
(GAT)	 AG	144937-145142	GT	CGG
(GGG)	 AG	145230-145521	GT	CGG
(ATG)	 AG	145653-145721	GG	GAG
add_exon() Sorry, pasa_asmbl_48501.p1 144648-144778-initial-1 is invalid.
-recovered pasa_asmbl_48501.p1, initial, 144648, 144778
-recovered pasa_asmbl_48501.p1, terminal, 145653, 145721
-recovered pasa_asmbl_48501.p1, internal, 144648, 144778
-recovered pasa_asmbl_48501.p1, internal, 144937, 145142
-recovered pasa_asmbl_48501.p1, internal, 145230, 145521
Valid prediction for GlimmerHMM_glimmerT_15495-T1
Valid prediction for GeneMark_model.26123_t
Valid prediction for GeneMark_model.26118_t
Couldn't classify 51338, 51486
Couldn't classify 51612, 51861
Sorry, prediction pasa_asmbl_49270.p1 fails validation.
(GAC)	 GC	51338-51486	GT	AAG
(CCC)	 AG	51612-51861	CA	GCC
Valid prediction for GlimmerHMM_glimmerT_15481-T1
Valid prediction for GeneMark_model.26113_t
Valid prediction for snap_scaffold_6-snap.1908-T1
Couldn't classify 66860, 66959
Sorry, prediction pasa_asmbl_48510.p3 fails validation.
(CCG)	 TC	66860-66959	GT	AGG
(AAC)	 AG	67292-67527	AG	AAA
-recovered pasa_asmbl_48510.p3, terminal, 67292, 67527
Valid prediction for GeneMark_model.26134_t
Valid prediction for Augustus_model.g10345.t1
Valid prediction for snap_scaffold_6-snap.1916-T1
Valid prediction for snap_scaffold_6-snap.1910-T1
Valid prediction for GlimmerHMM_glimmerT_15498-T1
Valid prediction for Augustus_model.g10326.t1
Valid prediction for snap_scaffold_6-snap.1901-T1
Valid prediction for GlimmerHMM_glimmerT_15511-T1
Valid prediction for GlimmerHMM_glimmerT_15508-T1
Couldn't classify 74165, 74208
Sorry, prediction pasa_asmbl_48508.p1 fails validation.
(CAC)	 CA	74165-74208	GT	ACG
(GGT)	 AG	74562-74621	GT	GGG
(GAA)	 AG	75081-75165	GT	AGG
(GTG)	 AG	75293-75413	GT	TGG
(GTG)	 AG	75571-75710	GT	CGG
(GTG)	 AG	75815-75978	GT	AGG
(CCC)	 AG	76080-76173	AC	GAA
-recovered pasa_asmbl_48508.p1, terminal, 76080, 76173
-recovered pasa_asmbl_48508.p1, internal, 74562, 74621
-recovered pasa_asmbl_48508.p1, internal, 75081, 75165
-recovered pasa_asmbl_48508.p1, internal, 75293, 75413
-recovered pasa_asmbl_48508.p1, internal, 75571, 75710
-recovered pasa_asmbl_48508.p1, internal, 75815, 75978
Valid prediction for GeneMark_model.26130_t
Valid prediction for snap_scaffold_6-snap.1909-T1
Valid prediction for snap_scaffold_6-snap.1896-T1
Valid prediction for pasa_asmbl_48513.p1
Couldn't classify 52083, 52209
Couldn't classify 53757, 53830
Sorry, prediction pasa_asmbl_48517.p1 fails validation.
(GAC)	 TA	52083-52209	GT	CGG
(GCG)	 AG	52335-52560	GT	AAG
(ACA)	 AG	52747-52837	GT	AGG
(GTT)	 AG	52967-53135	GT	AGG
(ACG)	 AG	53757-53830	TC	AGT
-recovered pasa_asmbl_48517.p1, internal, 52335, 52560
-recovered pasa_asmbl_48517.p1, internal, 52747, 52837
-recovered pasa_asmbl_48517.p1, internal, 52967, 53135
Valid prediction for snap_scaffold_6-snap.1897-T1
Valid prediction for Augustus_model.g10334.t1
Valid prediction for snap_scaffold_6-snap.1924-T1
Valid prediction for GlimmerHMM_glimmerT_15503-T1
Couldn't classify 54371, 54500
Couldn't classify 54920, 55888
Sorry, prediction pasa_asmbl_48516.p1 fails validation.
(GCC)	 GT	54371-54500	GT	GGG
(GTA)	 AG	54635-54732	GT	AGG
(GAA)	 AG	54920-55888	GC	TGG
-recovered pasa_asmbl_48516.p1, internal, 54635, 54732
-recovered pasa_asmbl_48516.p1, internal, 54920, 55888
Valid prediction for GlimmerHMM_glimmerT_15482-T1
Valid prediction for GeneMark_model.26132_t
Valid prediction for GlimmerHMM_glimmerT_15501-T1
Valid prediction for GlimmerHMM_glimmerT_15494-T1
Valid prediction for snap_scaffold_6-snap.1914-T1
Valid prediction for GeneMark_model.26115_t
Valid prediction for GlimmerHMM_glimmerT_15485-T1
Valid prediction for snap_scaffold_6-snap.1919-T1
Valid prediction for snap_scaffold_6-snap.1911-T1
Valid prediction for snap_scaffold_6-snap.1917-T1
Valid prediction for snap_scaffold_6-snap.1900-T1
Valid prediction for GlimmerHMM_glimmerT_15491-T1
Valid prediction for snap_scaffold_6-snap.1927-T1
Valid prediction for Augustus_model.g10339.t1
Valid prediction for GeneMark_model.26125_t
Valid prediction for Augustus_model.g10333.t1
Valid prediction for GlimmerHMM_glimmerT_15509-T1
Valid prediction for Augustus_model.g10341.t1
Valid prediction for snap_scaffold_6-snap.1915-T1
Valid prediction for GeneMark_model.26108_t
Valid prediction for GeneMark_model.26119_t
Valid prediction for GlimmerHMM_glimmerT_15496-T1
Valid prediction for GeneMark_model.26136_t
Valid prediction for GlimmerHMM_glimmerT_15488-T1
Valid prediction for GeneMark_model.26101_t
Valid prediction for GeneMark_model.26107_t
Valid prediction for snap_scaffold_6-snap.1921-T1
Valid prediction for GeneMark_model.26121_t
Valid prediction for GeneMark_model.26099_t
Valid prediction for HiQ_model.g10325.t1
Valid prediction for GlimmerHMM_glimmerT_15512-T1
Valid prediction for snap_scaffold_6-snap.1920-T1
Valid prediction for CodingQuarry_transcript_54999-T1
Valid prediction for Augustus_model.g10337.t1
Couldn't classify 151142, 151232
Sorry, prediction pasa_asmbl_48499.p1 fails validation.
(CGC)	 GG	151142-151232	GT	GGG
(GAG)	 AG	151824-152083	GT	AGG
(GAT)	 AG	152265-152357	TG	GAT
-recovered pasa_asmbl_48499.p1, terminal, 152265, 152357
-recovered pasa_asmbl_48499.p1, internal, 151824, 152083
Valid prediction for GlimmerHMM_glimmerT_15513-T1
Valid prediction for snap_scaffold_6-snap.1913-T1
Couldn't classify 55988, 56416
Sorry, prediction pasa_asmbl_48515.p1 fails validation.
(CCG)	 CC	55988-56416	AG	AAA
Valid prediction for GlimmerHMM_glimmerT_15497-T1
Couldn't classify 66613, 66711
Sorry, prediction pasa_asmbl_48512.p1 fails validation.
(ATG)	 AA	64932-64949	GT	AGG
(CTG)	 AG	65316-65451	GT	AGG
(ACC)	 AG	65590-65639	GT	AGG
(AAT)	 AG	65736-65801	GT	AGG
(GCC)	 AG	66089-66130	GT	AGG
(GAA)	 AG	66274-66429	GT	GGG
(GTA)	 AG	66613-66711	TT	TCT
-recovered pasa_asmbl_48512.p1, initial, 64932, 64949
-recovered pasa_asmbl_48512.p1, internal, 65316, 65451
-recovered pasa_asmbl_48512.p1, internal, 65590, 65639
-recovered pasa_asmbl_48512.p1, internal, 65736, 65801
-recovered pasa_asmbl_48512.p1, internal, 66089, 66130
-recovered pasa_asmbl_48512.p1, internal, 66274, 66429
Valid prediction for Augustus_model.g10331.t1
Couldn't classify 69398, 69399
Sorry, prediction CodingQuarry_transcript_54996-T1 fails validation.
(ATG)	 AA	69398-69399	GT	ATG
(GGT)	 AG	69655-69714	GT	GGG
(GGA)	 AG	70035-70116	GT	AGG
(GTG)	 AG	70269-70389	GT	TGG
(GTG)	 AG	70555-70694	GT	TGG
(GTG)	 AG	71077-71240	GT	AGG
(CCC)	 AG	71399-71492	GC	GAG
-recovered CodingQuarry_transcript_54996-T1, terminal, 71399, 71492
-recovered CodingQuarry_transcript_54996-T1, internal, 69655, 69714
-recovered CodingQuarry_transcript_54996-T1, internal, 70035, 70116
-recovered CodingQuarry_transcript_54996-T1, internal, 70269, 70389
-recovered CodingQuarry_transcript_54996-T1, internal, 70555, 70694
-recovered CodingQuarry_transcript_54996-T1, internal, 71077, 71240
-recovered CodingQuarry_transcript_54996-T1, internal, 71399, 71492
Valid prediction for HiQ_model.g10332.t1
Valid prediction for GeneMark_model.26106_t
Valid prediction for GlimmerHMM_glimmerT_15484-T1
Valid prediction for GeneMark_model.26116_t
Valid prediction for GeneMark_model.26104_t
Valid prediction for snap_scaffold_6-snap.1898-T1
Valid prediction for GeneMark_model.26127_t
Valid prediction for GlimmerHMM_glimmerT_15486-T1
Valid prediction for GlimmerHMM_glimmerT_15502-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 41563, rend_intergenic: 41560  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 167333, rend_intergenic: 167330  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23102, rend_intergenic: 14451  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35312, rend_intergenic: 32243  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138528, rend_intergenic: 134435  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141560, rend_intergenic: 138780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156196, rend_intergenic: 154309  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165849, rend_intergenic: 162924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175328, rend_intergenic: 171028  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 177963
-exon list size: 745


building trellis

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65.2    
65.3    
65.5    
65.6    
65.7    
65.9    
66.0    
66.1    
66.3    
66.4    
66.5    
66.7    
66.8    
66.9    
67.1    
67.2    
67.3    
67.5    
67.6    
67.7    
67.9    
68.0    
68.1    
68.3    
68.4    
68.5    
68.7    
68.8    
68.9    
69.1    
69.2    
69.3    
69.5    
69.6    
69.7    
69.9    
70.0    
70.1    
70.3    
70.4    
70.5    
70.7    
70.8    
71.0    
71.1    
71.2    
71.4    
71.5    
71.6    
71.8    
71.9    
72.0    
72.2    
72.3    
72.4    
72.6    
72.7    
72.8    
73.0    
73.1    
73.2    
73.4    
73.5    
73.6    
73.8    
73.9    
74.0    
74.2    
74.3    
74.4    
74.6    
74.7    
74.8    
75.0    
75.1    
75.2    
75.4    
75.5    
75.6    
75.8    
75.9    
76.0    
76.2    
76.3    
76.4    
76.6    
76.7    
76.8    
77.0    
77.1    
77.2    
77.4    
77.5    
77.6    
77.8    
77.9    
78.0    
78.2    
78.3    
78.4    
78.6    
78.7    
78.8    
79.0    
79.1    
79.3    
79.4    
79.5    
79.7    
79.8    
79.9    
80.1    
80.2    
80.3    
80.5    
80.6    
80.7    
80.9    
81.0    
81.1    
81.3    
81.4    
81.5    
81.7    
81.8    
81.9    
82.1    
82.2    
82.3    
82.5    
82.6    
82.7    
82.9    
83.0    
83.1    
83.3    
83.4    
83.5    
83.7    
83.8    
83.9    
84.1    
84.2    
84.3    
84.5    
84.6    
84.7    
84.9    
85.0    
85.1    
85.3    
85.4    
85.5    
85.7    
85.8    
85.9    
86.1    
86.2    
86.3    
86.5    
86.6    
86.7    
86.9    
87.0    
87.1    
87.3    
87.4    
87.6    
87.7    
87.8    
88.0    
88.1    
88.2    
88.4    
88.5    
88.6    
88.8    
88.9    
89.0    
89.2    
89.3    
89.4    
89.6    
89.7    
89.8    
90.0    
90.1    
90.2    
90.4    
90.5    
90.6    
90.8    
90.9    
91.0    
91.2    
91.3    
91.4    
91.6    
91.7    
91.8    
92.0    
92.1    
92.2    
92.4    
92.5    
92.6    
92.8    
92.9    
93.0    
93.2    
93.3    
93.4    
93.6    
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    
95.9    
96.0    
96.1    
96.3    
96.4    
96.5    
96.7    
96.8    
96.9    
97.1    
97.2    
97.3    
97.5    
97.6    
97.7    
97.9    
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 36 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 41563, rend_intergenic: 41560  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 167333, rend_intergenic: 167330  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23102, rend_intergenic: 14451  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35312, rend_intergenic: 32243  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138528, rend_intergenic: 134435  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141560, rend_intergenic: 138780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156196, rend_intergenic: 154309  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165849, rend_intergenic: 162924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175328, rend_intergenic: 171028  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 26 predictions persist after filtering for low support