-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_4/scaffold_4_18998358-19212649

-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 GlimmerHMM_glimmerT_11185-T1
Valid prediction for GlimmerHMM_glimmerT_11214-T1
Valid prediction for snap_scaffold_4-snap.3945-T1
Valid prediction for pasa_asmbl_42127.p1
Valid prediction for snap_scaffold_4-snap.3942-T1
Valid prediction for pasa_asmbl_42125.p1
Valid prediction for CodingQuarry_transcript_49388-T1
Valid prediction for snap_scaffold_4-snap.3916-T1
Valid prediction for snap_scaffold_4-snap.3935-T1
Valid prediction for GlimmerHMM_glimmerT_11186-T1
Valid prediction for snap_scaffold_4-snap.3927-T1
Couldn't classify 124319, 124449
Couldn't classify 126449, 126499
Sorry, prediction pasa_asmbl_42122.p1 fails validation.
(CCC)	 CT	124319-124449	GT	AGG
(GCC)	 AG	125072-125744	GT	AGG
(GGG)	 AG	125896-126039	GT	AGG
(GTC)	 AG	126197-126310	GT	AGG
(GAG)	 AG	126449-126499	TG	GGT
-recovered pasa_asmbl_42122.p1, internal, 125072, 125744
-recovered pasa_asmbl_42122.p1, internal, 125896, 126039
-recovered pasa_asmbl_42122.p1, internal, 126197, 126310
Valid prediction for snap_scaffold_4-snap.3944-T1
Valid prediction for snap_scaffold_4-snap.3930-T1
Valid prediction for HiQ_model.g7360.t1
Valid prediction for snap_scaffold_4-snap.3904-T1
Valid prediction for Augustus_model.g7344.t1
Valid prediction for snap_scaffold_4-snap.3938-T1
Valid prediction for snap_scaffold_4-snap.3946-T1
Valid prediction for snap_scaffold_4-snap.3924-T1
Couldn't classify 16634, 16750
Sorry, prediction pasa_asmbl_42121.p1 fails validation.
(GTG)	 AG	16634-16750	GT	AGG
(AGG)	 AG	16840-16982	GT	AGG
(AGA)	 AG	17072-17208	GT	CGG
(CCG)	 AG	17344-17441	GT	CTG
(TCT)	 AG	18555-18735	GT	AGG
(GAA)	 AG	18821-18900	TT	AGT
-recovered pasa_asmbl_42121.p1, terminal, 18821, 18900
-recovered pasa_asmbl_42121.p1, internal, 16634, 16750
-recovered pasa_asmbl_42121.p1, internal, 16840, 16982
-recovered pasa_asmbl_42121.p1, internal, 17072, 17208
-recovered pasa_asmbl_42121.p1, internal, 17344, 17441
-recovered pasa_asmbl_42121.p1, internal, 18555, 18735
Valid prediction for GlimmerHMM_glimmerT_11211-T1
Valid prediction for snap_scaffold_4-snap.3921-T1
Valid prediction for snap_scaffold_4-snap.3934-T1
Valid prediction for snap_scaffold_4-snap.3943-T1
Valid prediction for GlimmerHMM_glimmerT_11203-T1
Valid prediction for GlimmerHMM_glimmerT_11201-T1
Valid prediction for GlimmerHMM_glimmerT_11208-T1
Valid prediction for CodingQuarry_transcript_49389-T1
Valid prediction for GlimmerHMM_glimmerT_11199-T1
Valid prediction for Augustus_model.g7354.t1
Valid prediction for CodingQuarry_transcript_49390-T1
Valid prediction for GlimmerHMM_glimmerT_11194-T1
Valid prediction for snap_scaffold_4-snap.3932-T1
Valid prediction for snap_scaffold_4-snap.3918-T1
Valid prediction for GlimmerHMM_glimmerT_11187-T1
Valid prediction for snap_scaffold_4-snap.3933-T1
Valid prediction for GlimmerHMM_glimmerT_11207-T1
Valid prediction for GlimmerHMM_glimmerT_11204-T1
Valid prediction for snap_scaffold_4-snap.3911-T1
Valid prediction for GlimmerHMM_glimmerT_11213-T1
Valid prediction for snap_scaffold_4-snap.3923-T1
Valid prediction for Augustus_model.g7353.t1
Valid prediction for HiQ_model.g7357.t1
Valid prediction for GlimmerHMM_glimmerT_11192-T1
Valid prediction for GlimmerHMM_glimmerT_11198-T1
Valid prediction for snap_scaffold_4-snap.3900-T1
Valid prediction for GlimmerHMM_glimmerT_11215-T1
Valid prediction for snap_scaffold_4-snap.3913-T1
Valid prediction for snap_scaffold_4-snap.3941-T1
Valid prediction for snap_scaffold_4-snap.3919-T1
Valid prediction for snap_scaffold_4-snap.3907-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 HiQ_model.g7351.t1
Valid prediction for snap_scaffold_4-snap.3922-T1
Valid prediction for snap_scaffold_4-snap.3906-T1
Valid prediction for pasa_asmbl_43410.p1
Couldn't classify 190287, 190556
Couldn't classify 191853, 192281
Sorry, prediction pasa_asmbl_43393.p1 fails validation.
(TCT)	 AG	190287-190556	GT	AGG
(GTT)	 AG	190989-191101	GT	CAG
(GTT)	 AG	191551-191638	GT	AGG
(CAA)	 AG	191853-192281	CC	ACC
-recovered pasa_asmbl_43393.p1, internal, 190287, 190556
-recovered pasa_asmbl_43393.p1, internal, 190989, 191101
-recovered pasa_asmbl_43393.p1, internal, 191551, 191638
Valid prediction for snap_scaffold_4-snap.3899-T1
Valid prediction for GlimmerHMM_glimmerT_11209-T1
Couldn't classify 169440, 169621
Couldn't classify 172668, 172740
Sorry, prediction pasa_asmbl_43404.p1 fails validation.
(CTG)	 AC	169440-169621	GT	CAG
(CAT)	 AG	170184-170267	GT	AGG
(ATT)	 AG	171284-171332	GT	GGG
(GAC)	 AG	171463-171547	GT	ATG
(TGA)	 AG	171696-171866	GT	TGG
(GTG)	 AG	172005-172137	GT	CGG
(GTC)	 AG	172233-172295	GT	AGG
(TAT)	 AG	172668-172740	AC	AGA
-recovered pasa_asmbl_43404.p1, internal, 170184, 170267
-recovered pasa_asmbl_43404.p1, internal, 171284, 171332
-recovered pasa_asmbl_43404.p1, internal, 171463, 171547
-recovered pasa_asmbl_43404.p1, internal, 171696, 171866
-recovered pasa_asmbl_43404.p1, internal, 172005, 172137
-recovered pasa_asmbl_43404.p1, internal, 172233, 172295
Valid prediction for Augustus_model.g7348.t1
Valid prediction for snap_scaffold_4-snap.3912-T1
Valid prediction for snap_scaffold_4-snap.3910-T1
Valid prediction for snap_scaffold_4-snap.3908-T1
Valid prediction for snap_scaffold_4-snap.3903-T1
Valid prediction for GlimmerHMM_glimmerT_11205-T1
Valid prediction for Augustus_model.g7359.t1
Valid prediction for HiQ_model.g7349.t1
Valid prediction for GlimmerHMM_glimmerT_11197-T1
Valid prediction for CodingQuarry_transcript_49386-T1
Valid prediction for snap_scaffold_4-snap.3925-T1
Valid prediction for Augustus_model.g7350.t1
Valid prediction for GlimmerHMM_glimmerT_11189-T1
Couldn't classify 177822, 177862
Sorry, prediction pasa_asmbl_43400.p1 fails validation.
(CAA)	 TA	177822-177862	GT	TGG
(TGT)	 AG	178518-178658	GT	AAG
(TAA)	 AG	178781-178895	GT	ATG
(CTG)	 AG	179171-179257	GT	ATG
(CTG)	 AG	179405-179473	GT	AGG
(GAG)	 AG	179738-179953	GT	TGG
(GCT)	 AG	180662-180770	GT	CGG
(AAT)	 AG	181224-181361	GT	AGG
(AGT)	 AG	181713-181771	GT	AGG
(GAC)	 AG	182523-182696	AC	AAA
-recovered pasa_asmbl_43400.p1, terminal, 182523, 182696
-recovered pasa_asmbl_43400.p1, internal, 178518, 178658
-recovered pasa_asmbl_43400.p1, internal, 178781, 178895
-recovered pasa_asmbl_43400.p1, internal, 179171, 179257
-recovered pasa_asmbl_43400.p1, internal, 179405, 179473
-recovered pasa_asmbl_43400.p1, internal, 179738, 179953
-recovered pasa_asmbl_43400.p1, internal, 180662, 180770
-recovered pasa_asmbl_43400.p1, internal, 181224, 181361
-recovered pasa_asmbl_43400.p1, internal, 181713, 181771
Valid prediction for HiQ_model.g7352.t1
Valid prediction for CodingQuarry_transcript_49387-T1
Valid prediction for Augustus_model.g7361.t1
Valid prediction for snap_scaffold_4-snap.3917-T1
Valid prediction for GlimmerHMM_glimmerT_11188-T1
Valid prediction for GlimmerHMM_glimmerT_11193-T1
Valid prediction for snap_scaffold_4-snap.3940-T1
Valid prediction for Augustus_model.g7346.t1
Valid prediction for snap_scaffold_4-snap.3914-T1
Valid prediction for GlimmerHMM_glimmerT_11212-T1
Valid prediction for Augustus_model.g7358.t1
Valid prediction for snap_scaffold_4-snap.3909-T1
Couldn't classify 184551, 185459
Sorry, prediction pasa_asmbl_43397.p1 fails validation.
(ATG)	 GA	184551-185459	CA	AGC
Valid prediction for snap_scaffold_4-snap.3901-T1
Valid prediction for pasa_asmbl_43411.p1
Valid prediction for Augustus_model.g7356.t1
Valid prediction for GlimmerHMM_glimmerT_11202-T1
Valid prediction for GlimmerHMM_glimmerT_11200-T1
Valid prediction for GlimmerHMM_glimmerT_11210-T1
Valid prediction for snap_scaffold_4-snap.3926-T1
Valid prediction for snap_scaffold_4-snap.3902-T1
Valid prediction for snap_scaffold_4-snap.3939-T1
Valid prediction for snap_scaffold_4-snap.3937-T1
Valid prediction for snap_scaffold_4-snap.3929-T1
Couldn't classify 4182, 4511
Sorry, prediction pasa_asmbl_43413.p1 fails validation.
(GTG)	 AG	4182-4511	GT	TGG
-recovered pasa_asmbl_43413.p1, internal, 4182, 4511
Valid prediction for snap_scaffold_4-snap.3915-T1
Valid prediction for Augustus_model.g7345.t1
Valid prediction for Augustus_model.g7362.t1
Valid prediction for snap_scaffold_4-snap.3931-T1
Couldn't classify 158452, 158723
Sorry, prediction pasa_asmbl_43407.p1 fails validation.
(AGG)	 AC	158452-158723	GT	AGG
(GAC)	 AG	159284-159569	GT	AGG
(TGG)	 AG	159717-159928	GT	AAG
(GCT)	 AG	160162-160249	GT	AGG
(CTT)	 AG	160421-160597	GT	GAG
-recovered pasa_asmbl_43407.p1, terminal, 160421, 160597
-recovered pasa_asmbl_43407.p1, internal, 159284, 159569
-recovered pasa_asmbl_43407.p1, internal, 159717, 159928
-recovered pasa_asmbl_43407.p1, internal, 160162, 160249
-recovered pasa_asmbl_43407.p1, internal, 160421, 160597
Valid prediction for GlimmerHMM_glimmerT_11216-T1
Couldn't classify 188387, 188487
Sorry, prediction pasa_asmbl_43394.p1 fails validation.
(CCC)	 CC	188387-188487	GT	AGG
(GTG)	 AG	188864-189040	GT	AAG
(GAT)	 AG	189348-189414	CA	GAC
-recovered pasa_asmbl_43394.p1, terminal, 189348, 189414
-recovered pasa_asmbl_43394.p1, internal, 188864, 189040
Valid prediction for snap_scaffold_4-snap.3936-T1
Valid prediction for HiQ_model.g7347.t1
Valid prediction for GlimmerHMM_glimmerT_11190-T1
Valid prediction for snap_scaffold_4-snap.3928-T1
Valid prediction for GlimmerHMM_glimmerT_11195-T1
Couldn't classify 4764, 5063
Sorry, prediction pasa_asmbl_43412.p2 fails validation.
(GAG)	 GT	4764-5063	GG	GAG
Valid prediction for snap_scaffold_4-snap.3920-T1
Valid prediction for GlimmerHMM_glimmerT_11196-T1
Couldn't classify 165699, 165769
Couldn't classify 167854, 168066
Sorry, prediction pasa_asmbl_43405.p1 fails validation.
(CTG)	 GT	165699-165769	GT	AGG
(CGA)	 AG	166846-166963	GT	TGG
(TAC)	 AG	167075-167227	GT	TGG
(AAC)	 AG	167854-168066	GA	TGG
-recovered pasa_asmbl_43405.p1, internal, 166846, 166963
-recovered pasa_asmbl_43405.p1, internal, 167075, 167227
Valid prediction for GlimmerHMM_glimmerT_11191-T1
Couldn't classify 187190, 187279
Sorry, prediction pasa_asmbl_43395.p1 fails validation.
(ATG)	 AG	186135-186878	GT	AGG
(GGT)	 AG	187190-187279	AC	TGA
-recovered pasa_asmbl_43395.p1, initial, 186135, 186878
-recovered pasa_asmbl_43395.p1, internal, 186135, 186878
Valid prediction for Augustus_model.g7355.t1
Valid prediction for snap_scaffold_4-snap.3905-T1
Valid prediction for GlimmerHMM_glimmerT_11206-T1
Valid prediction for CodingQuarry_transcript_49385-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10465, rend_intergenic: 3986  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21662, rend_intergenic: 10941  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24874, rend_intergenic: 22102  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29613, rend_intergenic: 24879  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50515, rend_intergenic: 41019  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75414, rend_intergenic: 61830  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108300, rend_intergenic: 104076  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109785, rend_intergenic: 109612  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118601, rend_intergenic: 110107  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131438, rend_intergenic: 123028  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138996, rend_intergenic: 132615  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147098, rend_intergenic: 143772  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148535, rend_intergenic: 147573  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155706, rend_intergenic: 153811  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156605, rend_intergenic: 155746  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172053, rend_intergenic: 157320  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180590, rend_intergenic: 177759  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185173, rend_intergenic: 180744  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 212957, rend_intergenic: 185244  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 214292
-exon list size: 498


building trellis

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82.4    
82.6    
82.8    
83.0    
83.2    
83.4    
83.6    
83.8    
84.0    
84.2    
84.4    
84.6    
84.8    
85.0    
85.2    
85.4    
85.6    
85.8    
86.0    
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    
91.8    
92.0    
92.2    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
94.0    
94.2    
94.4    
94.6    
94.8    
95.0    
95.2    
95.4    
95.6    
95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
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 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 10465, rend_intergenic: 3986  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21662, rend_intergenic: 10941  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24874, rend_intergenic: 22102  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29613, rend_intergenic: 24879  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50515, rend_intergenic: 41019  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75414, rend_intergenic: 61830  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108300, rend_intergenic: 104076  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109785, rend_intergenic: 109612  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118601, rend_intergenic: 110107  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131438, rend_intergenic: 123028  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138996, rend_intergenic: 132615  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147098, rend_intergenic: 143772  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148535, rend_intergenic: 147573  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155706, rend_intergenic: 153811  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156605, rend_intergenic: 155746  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172053, rend_intergenic: 157320  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180590, rend_intergenic: 177759  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185173, rend_intergenic: 180744  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 212957, rend_intergenic: 185244  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support