-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_7/scaffold_7_9816470-10037028

-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.30813_t
Valid prediction for GeneMark_model.30812_t
Valid prediction for GeneMark_model.30816_t
Valid prediction for GlimmerHMM_glimmerT_18380-T1
Valid prediction for CodingQuarry_transcript_57458-T1
Couldn't classify 109062, 109245
Sorry, prediction pasa_asmbl_50984.p1 fails validation.
(GCA)	 TC	109062-109245	GT	ATG
(ATG)	 AG	109373-109512	GT	GTG
(GTT)	 AG	109839-109949	GT	GTG
(GAC)	 AG	110077-110100	AC	GAA
add_exon() Sorry, pasa_asmbl_50984.p1 109373-109512-initial-1 is invalid.
-recovered pasa_asmbl_50984.p1, initial, 109373, 109512
-recovered pasa_asmbl_50984.p1, terminal, 110077, 110100
-recovered pasa_asmbl_50984.p1, internal, 109373, 109512
-recovered pasa_asmbl_50984.p1, internal, 109839, 109949
Valid prediction for GeneMark_model.30804_t
Valid prediction for GlimmerHMM_glimmerT_18378-T1
Valid prediction for GlimmerHMM_glimmerT_18374-T1
Valid prediction for GeneMark_model.30791_t
Valid prediction for GlimmerHMM_glimmerT_18369-T1
Valid prediction for snap_scaffold_7-snap.1914-T1
Valid prediction for Augustus_model.g12383.t1
Valid prediction for GeneMark_model.30807_t
Valid prediction for pasa_asmbl_50980.p1
Valid prediction for snap_scaffold_7-snap.1937-T1
Valid prediction for GeneMark_model.30788_t
Valid prediction for snap_scaffold_7-snap.1924-T1
Valid prediction for GlimmerHMM_glimmerT_18376-T1
Valid prediction for CodingQuarry_transcript_57456-T1
Valid prediction for snap_scaffold_7-snap.1927-T1
Valid prediction for Augustus_model.g12381.t1
Valid prediction for pasa_asmbl_50982.p1
Valid prediction for snap_scaffold_7-snap.1931-T1
Valid prediction for snap_scaffold_7-snap.1938-T1
Valid prediction for GeneMark_model.30817_t
Valid prediction for GlimmerHMM_glimmerT_18370-T1
Valid prediction for Augustus_model.g12385.t1
Valid prediction for GlimmerHMM_glimmerT_18383-T1
Valid prediction for snap_scaffold_7-snap.1939-T1
Valid prediction for GeneMark_model.30803_t
Valid prediction for Augustus_model.g12382.t1
Valid prediction for Augustus_model.g12380.t1
Valid prediction for GlimmerHMM_glimmerT_18372-T1
Valid prediction for snap_scaffold_7-snap.1922-T1
Valid prediction for GeneMark_model.30792_t
Valid prediction for GeneMark_model.30795_t
Valid prediction for GlimmerHMM_glimmerT_18364-T1
Valid prediction for GeneMark_model.30819_t
Valid prediction for snap_scaffold_7-snap.1934-T1
Valid prediction for snap_scaffold_7-snap.1933-T1
Valid prediction for snap_scaffold_7-snap.1930-T1
Valid prediction for snap_scaffold_7-snap.1925-T1
Valid prediction for Augustus_model.g12375.t1
Valid prediction for GeneMark_model.30782_t
Valid prediction for HiQ_model.g12376.t1
Valid prediction for GeneMark_model.30785_t
Valid prediction for snap_scaffold_7-snap.1932-T1
Valid prediction for snap_scaffold_7-snap.1941-T1
Valid prediction for GeneMark_model.30801_t
Valid prediction for CodingQuarry_transcript_57454-T1
Valid prediction for GeneMark_model.30797_t
Valid prediction for HiQ_model.g12378.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_7-snap.1942-T1
Valid prediction for GlimmerHMM_glimmerT_18379-T1
Valid prediction for GlimmerHMM_glimmerT_18365-T1
Valid prediction for GlimmerHMM_glimmerT_18375-T1
Valid prediction for GeneMark_model.30780_t
Valid prediction for GeneMark_model.30794_t
Valid prediction for snap_scaffold_7-snap.1923-T1
Valid prediction for GlimmerHMM_glimmerT_18362-T1
Couldn't classify 40218, 40273
Sorry, prediction pasa_asmbl_49917.p1 fails validation.
(ATG)	 GA	38258-38299	GT	AGG
(GGC)	 AG	39316-39471	GT	TGG
(CTG)	 AG	39673-39854	GT	AAG
(TGA)	 AG	39970-40061	GT	AGG
(GTG)	 AG	40218-40273	GC	AGG
-recovered pasa_asmbl_49917.p1, initial, 38258, 38299
-recovered pasa_asmbl_49917.p1, internal, 39316, 39471
-recovered pasa_asmbl_49917.p1, internal, 39673, 39854
-recovered pasa_asmbl_49917.p1, internal, 39970, 40061
-recovered pasa_asmbl_49917.p1, internal, 40218, 40273
Valid prediction for Augustus_model.g12386.t1
Valid prediction for snap_scaffold_7-snap.1929-T1
Couldn't classify 197557, 197728
Couldn't classify 198064, 198123
Sorry, prediction pasa_asmbl_49894.p1 fails validation.
(CCT)	 CC	197557-197728	GT	AGG
(GGA)	 AG	197873-197958	GT	AGG
(GTG)	 AG	198064-198123	TA	AGT
-recovered pasa_asmbl_49894.p1, internal, 197873, 197958
Valid prediction for GeneMark_model.30784_t
Couldn't classify 214572, 214772
Couldn't classify 217529, 217556
Sorry, prediction pasa_asmbl_50378.p1 fails validation.
(GAT)	 CA	214572-214772	GT	TGG
(TTC)	 AG	216164-216274	GT	AGG
(CTG)	 AG	216386-216478	GT	CTG
(CTG)	 AG	217213-217343	GT	AGG
(GTT)	 AG	217529-217556	GG	ACG
-recovered pasa_asmbl_50378.p1, internal, 216164, 216274
-recovered pasa_asmbl_50378.p1, internal, 216386, 216478
-recovered pasa_asmbl_50378.p1, internal, 217213, 217343
Valid prediction for pasa_asmbl_49907.p1
Valid prediction for snap_scaffold_7-snap.1916-T1
Valid prediction for GeneMark_model.30798_t
Valid prediction for snap_scaffold_7-snap.1917-T1
Valid prediction for GeneMark_model.30800_t
Valid prediction for Augustus_model.g12370.t1
Valid prediction for GlimmerHMM_glimmerT_18371-T1
Valid prediction for HiQ_model.g12377.t1
Valid prediction for GeneMark_model.30787_t
Valid prediction for snap_scaffold_7-snap.1918-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for snap_scaffold_7-snap.1928-T1
Valid prediction for GeneMark_model.30783_t
Valid prediction for snap_scaffold_7-snap.1913-T1
Valid prediction for GlimmerHMM_glimmerT_18361-T1
Valid prediction for HiQ_model.g12374.t1
Valid prediction for GlimmerHMM_glimmerT_18382-T1
Valid prediction for Augustus_model.g12384.t1
Valid prediction for snap_scaffold_7-snap.1926-T1
Valid prediction for snap_scaffold_7-snap.1920-T1
Valid prediction for GlimmerHMM_glimmerT_18373-T1
Couldn't classify 188135, 188941
Sorry, prediction pasa_asmbl_49898.p1 fails validation.
(GAC)	 AT	188135-188941	CC	TAC
Valid prediction for pasa_asmbl_49913.p1
Valid prediction for GlimmerHMM_glimmerT_18381-T1
Couldn't classify 187604, 188110
Sorry, prediction pasa_asmbl_49899.p1 fails validation.
(GCT)	 CT	187604-188110	GT	ACG
Couldn't classify 68350, 68579
Couldn't classify 69490, 69566
Sorry, prediction pasa_asmbl_50347.p1 fails validation.
(CTC)	 TC	68350-68579	GT	AGG
(GTT)	 AG	68935-69026	GT	AGG
(ACC)	 AG	69490-69566	AG	AGA
-recovered pasa_asmbl_50347.p1, internal, 68935, 69026
Valid prediction for pasa_asmbl_49910.p1
Valid prediction for snap_scaffold_7-snap.1935-T1
Couldn't classify 169037, 169137
Couldn't classify 170807, 170958
Sorry, prediction pasa_asmbl_49908.p1 fails validation.
(CTG)	 TG	169037-169137	GT	GGG
(GTG)	 AG	169340-169536	GT	AGG
(AGT)	 AG	169635-169872	GT	AGG
(GAT)	 AG	169975-170080	GT	AGG
(GTG)	 AG	170178-170405	GT	AGG
(ATG)	 AG	170560-170650	GT	AGG
(GGT)	 AG	170807-170958	CA	TGC
-recovered pasa_asmbl_49908.p1, initial, 170560, 170650
-recovered pasa_asmbl_49908.p1, internal, 169340, 169536
-recovered pasa_asmbl_49908.p1, internal, 169635, 169872
-recovered pasa_asmbl_49908.p1, internal, 169975, 170080
-recovered pasa_asmbl_49908.p1, internal, 170178, 170405
-recovered pasa_asmbl_49908.p1, internal, 170560, 170650
Valid prediction for GlimmerHMM_glimmerT_18363-T1
Valid prediction for GlimmerHMM_glimmerT_18377-T1
Valid prediction for snap_scaffold_7-snap.1915-T1
Valid prediction for GeneMark_model.30806_t
Valid prediction for GeneMark_model.30796_t
Valid prediction for GlimmerHMM_glimmerT_18367-T1
Valid prediction for Augustus_model.g12371.t1
Couldn't classify 34964, 35011
Sorry, prediction GeneMark_model.30815_t fails validation.
(ATG)	 GG	31570-31592	GT	GTG
(GAT)	 AG	31686-31709	GT	GTG
(AAA)	 AG	31735-31746	GT	AGG
(GAG)	 AG	32006-32026	GT	TTG
(AGA)	 AG	34964-35011	GT	ATG
-recovered GeneMark_model.30815_t, initial, 31570, 31592
-recovered GeneMark_model.30815_t, internal, 31686, 31709
-recovered GeneMark_model.30815_t, internal, 31735, 31746
-recovered GeneMark_model.30815_t, internal, 32006, 32026
-recovered GeneMark_model.30815_t, internal, 34964, 35011
Valid prediction for GeneMark_model.30810_t
Valid prediction for GlimmerHMM_glimmerT_18368-T1
Valid prediction for GeneMark_model.30818_t
Valid prediction for GeneMark_model.30790_t
Valid prediction for GeneMark_model.30802_t
Valid prediction for snap_scaffold_7-snap.1936-T1
Valid prediction for GeneMark_model.30781_t
Couldn't classify 189038, 189406
Sorry, prediction pasa_asmbl_49896.p1 fails validation.
(TAT)	 AT	189038-189406	GT	GGG
(CTG)	 AG	189574-189694	GT	AGG
(GCA)	 AG	192183-192793	AG	AAA
-recovered pasa_asmbl_49896.p1, terminal, 192183, 192793
-recovered pasa_asmbl_49896.p1, internal, 189574, 189694
Valid prediction for snap_scaffold_7-snap.1921-T1
Valid prediction for HiQ_model.g12379.t1
Couldn't classify 164049, 164190
Couldn't classify 165691, 165834
Sorry, prediction pasa_asmbl_50404.p1 fails validation.
(TAC)	 CC	164049-164190	GT	AGG
(GGA)	 AG	165388-165542	GT	AGG
(ATC)	 AG	165691-165834	GA	CAG
-recovered pasa_asmbl_50404.p1, internal, 165388, 165542
Couldn't classify 198586, 198666
Sorry, prediction pasa_asmbl_49890.p1 fails validation.
(AGG)	 GC	198586-198666	GT	AGG
(ATG)	 AG	199830-200015	GT	AGG
(ACA)	 AG	200275-200368	GT	AGG
(GGT)	 AG	200772-200890	GT	AGG
(AAT)	 AG	201019-203115	AA	GAA
-recovered pasa_asmbl_49890.p1, initial, 199830, 200015
-recovered pasa_asmbl_49890.p1, terminal, 201019, 203115
-recovered pasa_asmbl_49890.p1, internal, 199830, 200015
-recovered pasa_asmbl_49890.p1, internal, 200275, 200368
-recovered pasa_asmbl_49890.p1, internal, 200772, 200890
Valid prediction for GeneMark_model.30814_t
Valid prediction for snap_scaffold_7-snap.1919-T1
Valid prediction for GeneMark_model.30808_t
Valid prediction for snap_scaffold_7-snap.1940-T1
Couldn't classify 166267, 166281
Couldn't classify 168255, 168418
Sorry, prediction pasa_asmbl_49909.p1 fails validation.
(TCT)	 GA	166267-166281	GT	AGG
(GTG)	 AG	166698-166839	GT	AGG
(TGA)	 AG	167252-167442	GC	AGG
(ATA)	 AG	167738-168152	GT	AGG
(TGT)	 AG	168255-168418	CT	GCC
-recovered pasa_asmbl_49909.p1, internal, 166698, 166839
-recovered pasa_asmbl_49909.p1, internal, 167252, 167442
-recovered pasa_asmbl_49909.p1, internal, 167738, 168152
Valid prediction for Augustus_model.g12372.t1
Couldn't classify 171216, 171323
Sorry, prediction pasa_asmbl_49902.p1 fails validation.
(AGG)	 CC	171216-171323	GT	CAG
(GTC)	 AG	171410-171505	GC	AGG
(GGT)	 AG	171638-171813	GT	AAG
(ACT)	 AG	171953-172086	GT	CCG
(GAA)	 AG	172202-172387	GT	CAG
(AAG)	 AG	172704-172733	GT	GAG
(ATG)	 AG	173030-173166	GT	AGG
(GTA)	 AG	173421-173603	GT	ATG
(GTG)	 AG	173774-173931	GT	AGG
(GTA)	 AG	174038-174239	GT	AGG
(ATG)	 AG	174417-174588	GT	CAG
(GTC)	 AG	174703-174848	GT	AGG
(GAT)	 AG	174947-175076	GT	GGG
(GTG)	 AG	175232-175431	GT	AAG
(GTG)	 AG	175567-175848	CC	GAC
add_exon() Sorry, pasa_asmbl_49902.p1 173030-173166-initial-1 is invalid.
-recovered pasa_asmbl_49902.p1, initial, 173030, 173166
-recovered pasa_asmbl_49902.p1, initial, 174417, 174588
-recovered pasa_asmbl_49902.p1, terminal, 175567, 175848
-recovered pasa_asmbl_49902.p1, internal, 171410, 171505
-recovered pasa_asmbl_49902.p1, internal, 171638, 171813
-recovered pasa_asmbl_49902.p1, internal, 171953, 172086
-recovered pasa_asmbl_49902.p1, internal, 172202, 172387
-recovered pasa_asmbl_49902.p1, internal, 172704, 172733
-recovered pasa_asmbl_49902.p1, internal, 173030, 173166
-recovered pasa_asmbl_49902.p1, internal, 173421, 173603
-recovered pasa_asmbl_49902.p1, internal, 173774, 173931
-recovered pasa_asmbl_49902.p1, internal, 174038, 174239
-recovered pasa_asmbl_49902.p1, internal, 174417, 174588
-recovered pasa_asmbl_49902.p1, internal, 174703, 174848
-recovered pasa_asmbl_49902.p1, internal, 174947, 175076
-recovered pasa_asmbl_49902.p1, internal, 175232, 175431
Valid prediction for GeneMark_model.30805_t
Valid prediction for GeneMark_model.30793_t
Couldn't classify 186160, 186249
Couldn't classify 186519, 186903
Sorry, prediction pasa_asmbl_49900.p1 fails validation.
(GGG)	 GT	186160-186249	GT	AGG
(AAG)	 AG	186356-186405	GT	AAG
(CAA)	 AG	186519-186903	AG	GCA
-recovered pasa_asmbl_49900.p1, terminal, 186356, 186405
-recovered pasa_asmbl_49900.p1, internal, 186356, 186405
Valid prediction for GlimmerHMM_glimmerT_18366-T1
Valid prediction for CodingQuarry_transcript_57455-T1
Valid prediction for Augustus_model.g12373.t1
Valid prediction for GeneMark_model.30799_t
Valid prediction for CodingQuarry_transcript_57457-T1
Valid prediction for GeneMark_model.30789_t
Couldn't classify 184705, 184716
Couldn't classify 185555, 185605
Sorry, prediction pasa_asmbl_49901.p1 fails validation.
(ACT)	 TC	184705-184716	GT	CAG
(GTT)	 AG	184844-184990	GT	AGG
(TGG)	 AG	185221-185340	GT	CGG
(GCA)	 AG	185555-185605	GA	GTG
-recovered pasa_asmbl_49901.p1, internal, 184844, 184990
-recovered pasa_asmbl_49901.p1, internal, 185221, 185340

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 40567, rend_intergenic: 40564  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 7533, rend_intergenic: 4976  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10584, rend_intergenic: 7759  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153756, rend_intergenic: 150154  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 217135, rend_intergenic: 213098  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 220559
-exon list size: 489


building trellis

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75.2    
75.4    
75.6    
75.8    
76.0    
76.2    
76.4    
76.6    
76.8    
77.0    
77.2    
77.4    
77.6    
77.8    
78.0    
78.2    
78.4    
78.6    
78.8    
79.0    
79.2    
79.4    
79.6    
79.8    
80.0    
80.2    
80.4    
80.7    
80.9    
81.1    
81.3    
81.5    
81.7    
81.9    
82.1    
82.3    
82.5    
82.7    
82.9    
83.1    
83.3    
83.5    
83.7    
83.9    
84.1    
84.3    
84.5    
84.7    
84.9    
85.1    
85.3    
85.5    
85.7    
85.9    
86.2    
86.4    
86.6    
86.8    
87.0    
87.2    
87.4    
87.6    
87.8    
88.0    
88.2    
88.4    
88.6    
88.8    
89.0    
89.2    
89.4    
89.6    
89.8    
90.0    
90.2    
90.4    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.9    
92.1    
92.3    
92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.7    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.4    
97.6    
97.8    
98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 20 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 40567, rend_intergenic: 40564  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 7533, rend_intergenic: 4976  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10584, rend_intergenic: 7759  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153756, rend_intergenic: 150154  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 217135, rend_intergenic: 213098  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support