-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_18772680-18981050

-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_8595-T1
Valid prediction for snap_scaffold_3-snap.3735-T1
Valid prediction for snap_scaffold_3-snap.3740-T1
Valid prediction for GeneMark_model.13956_t
Valid prediction for snap_scaffold_3-snap.3732-T1
Valid prediction for GeneMark_model.13964_t
Valid prediction for GeneMark_model.13946_t
Valid prediction for GlimmerHMM_glimmerT_8590-T1
Valid prediction for GlimmerHMM_glimmerT_8592-T1
Valid prediction for GeneMark_model.13943_t
Valid prediction for Augustus_model.g5700.t1
Valid prediction for snap_scaffold_3-snap.3727-T1
Valid prediction for GeneMark_model.13932_t
Valid prediction for snap_scaffold_3-snap.3725-T1
Valid prediction for snap_scaffold_3-snap.3724-T1
Valid prediction for snap_scaffold_3-snap.3720-T1
Valid prediction for GeneMark_model.13944_t
Valid prediction for GeneMark_model.13933_t
Valid prediction for GeneMark_model.13953_t
Valid prediction for GeneMark_model.13954_t
Valid prediction for snap_scaffold_3-snap.3716-T1
Valid prediction for GeneMark_model.13940_t
Valid prediction for snap_scaffold_3-snap.3700-T1
Valid prediction for GlimmerHMM_glimmerT_8583-T1
Valid prediction for GeneMark_model.13962_t
Valid prediction for GeneMark_model.13959_t
Valid prediction for snap_scaffold_3-snap.3708-T1
Valid prediction for GlimmerHMM_glimmerT_8594-T1
Valid prediction for GeneMark_model.13965_t
Valid prediction for GeneMark_model.13957_t
Valid prediction for snap_scaffold_3-snap.3729-T1
Valid prediction for GeneMark_model.13949_t
Valid prediction for snap_scaffold_3-snap.3712-T1
Valid prediction for GeneMark_model.13937_t
Valid prediction for GeneMark_model.13936_t
Valid prediction for Augustus_model.g5705.t1
Valid prediction for snap_scaffold_3-snap.3739-T1
Valid prediction for snap_scaffold_3-snap.3707-T1
Valid prediction for Augustus_model.g5701.t1
Valid prediction for Augustus_model.g5694.t1
Couldn't classify 171124, 171219
Sorry, prediction pasa_asmbl_40712.p1 fails validation.
(TAT)	 CC	171124-171219	GT	AGG
(TCC)	 AG	171499-171596	GT	AGG
(CGA)	 AG	171706-171835	GT	AGG
(AAA)	 AG	171956-171994	GT	ATG
(TAT)	 AG	172297-172395	GT	ATG
(GGA)	 AG	172548-172618	GT	ATG
(ATA)	 AG	172718-172771	GT	AAG
(GCT)	 AG	173097-173221	GT	CGG
(GAC)	 AG	173405-173455	GT	AGG
(AAC)	 AG	173703-173801	GT	TGG
(ATC)	 AG	174316-174385	GT	GTG
(GTA)	 AG	174485-174679	GT	AGG
(AGA)	 AG	174843-174897	GT	GGG
(TCA)	 AG	175041-175140	GT	TGG
(ATG)	 AG	175227-175285	GT	TGG
(AAT)	 AG	175403-175475	GT	CGG
(ACA)	 AG	175644-175717	GT	TGG
(TGG)	 AG	176019-176120	AA	AAA
add_exon() Sorry, pasa_asmbl_40712.p1 175227-175285-initial-1 is invalid.
-recovered pasa_asmbl_40712.p1, initial, 175227, 175285
-recovered pasa_asmbl_40712.p1, terminal, 176019, 176120
-recovered pasa_asmbl_40712.p1, internal, 171499, 171596
-recovered pasa_asmbl_40712.p1, internal, 171706, 171835
-recovered pasa_asmbl_40712.p1, internal, 171956, 171994
-recovered pasa_asmbl_40712.p1, internal, 172297, 172395
-recovered pasa_asmbl_40712.p1, internal, 172548, 172618
-recovered pasa_asmbl_40712.p1, internal, 172718, 172771
-recovered pasa_asmbl_40712.p1, internal, 173097, 173221
-recovered pasa_asmbl_40712.p1, internal, 173405, 173455
-recovered pasa_asmbl_40712.p1, internal, 173703, 173801
-recovered pasa_asmbl_40712.p1, internal, 174316, 174385
-recovered pasa_asmbl_40712.p1, internal, 174485, 174679
-recovered pasa_asmbl_40712.p1, internal, 174843, 174897
-recovered pasa_asmbl_40712.p1, internal, 175041, 175140
-recovered pasa_asmbl_40712.p1, internal, 175227, 175285
-recovered pasa_asmbl_40712.p1, internal, 175403, 175475
-recovered pasa_asmbl_40712.p1, internal, 175644, 175717
Valid prediction for snap_scaffold_3-snap.3743-T1
Valid prediction for GeneMark_model.13948_t
Valid prediction for Augustus_model.g5698.t1
Valid prediction for HiQ_model.g5703.t1
Valid prediction for GlimmerHMM_glimmerT_8588-T1
Valid prediction for CodingQuarry_transcript_46372-T1
Valid prediction for GeneMark_model.13950_t
Valid prediction for GlimmerHMM_glimmerT_8586-T1
Valid prediction for GlimmerHMM_glimmerT_8578-T1
Valid prediction for Augustus_model.g5695.t1
Valid prediction for Augustus_model.g5693.t1
Valid prediction for Augustus_model.g5702.t1
Valid prediction for GeneMark_model.13952_t
Valid prediction for snap_scaffold_3-snap.3730-T1
Valid prediction for snap_scaffold_3-snap.3744-T1
Valid prediction for snap_scaffold_3-snap.3733-T1
Valid prediction for GlimmerHMM_glimmerT_8579-T1
Valid prediction for snap_scaffold_3-snap.3737-T1
Valid prediction for snap_scaffold_3-snap.3701-T1
Couldn't classify 153611, 154144
Sorry, prediction pasa_asmbl_40709.p1 fails validation.
(AAA)	 GG	153611-154144	GT	TTG
(ATT)	 AG	154875-155037	GT	CGG
(AGC)	 AG	155465-155671	GT	AGG
(ATC)	 AG	156000-156056	GT	AGG
(ACG)	 AG	157623-157849	GT	AGG
(GTG)	 AG	158797-159007	GT	AGG
(ATT)	 AG	160070-160287	GT	GAG
(ATC)	 AG	160736-160837	GT	AGG
(GAT)	 AG	161207-161330	GT	CGG
(CTG)	 AG	161478-161693	GT	AGG
(AAA)	 AG	162058-162314	GT	TTG
(GCT)	 AG	162516-162665	GT	AGG
(GCG)	 AG	162959-163120	GT	GGG
(ATT)	 AG	163275-163468	GT	CAG
(TGA)	 AG	163565-163658	GT	AGG
(GAG)	 AG	164283-164480	GG	AGG
add_exon() Sorry, pasa_asmbl_40709.p1 156000-156056-terminal-1 is invalid.
-recovered pasa_asmbl_40709.p1, terminal, 156000, 156056
-recovered pasa_asmbl_40709.p1, terminal, 164283, 164480
-recovered pasa_asmbl_40709.p1, internal, 154875, 155037
-recovered pasa_asmbl_40709.p1, internal, 155465, 155671
-recovered pasa_asmbl_40709.p1, internal, 156000, 156056
-recovered pasa_asmbl_40709.p1, internal, 157623, 157849
-recovered pasa_asmbl_40709.p1, internal, 158797, 159007
-recovered pasa_asmbl_40709.p1, internal, 160070, 160287
-recovered pasa_asmbl_40709.p1, internal, 160736, 160837
-recovered pasa_asmbl_40709.p1, internal, 161207, 161330
-recovered pasa_asmbl_40709.p1, internal, 161478, 161693
-recovered pasa_asmbl_40709.p1, internal, 162058, 162314
-recovered pasa_asmbl_40709.p1, internal, 162516, 162665
-recovered pasa_asmbl_40709.p1, internal, 162959, 163120
-recovered pasa_asmbl_40709.p1, internal, 163275, 163468
-recovered pasa_asmbl_40709.p1, internal, 163565, 163658
Valid prediction for snap_scaffold_3-snap.3728-T1
Valid prediction for GeneMark_model.13951_t
Valid prediction for HiQ_model.g5704.t1
Valid prediction for snap_scaffold_3-snap.3721-T1
Valid prediction for GeneMark_model.13935_t
Valid prediction for snap_scaffold_3-snap.3714-T1
Valid prediction for snap_scaffold_3-snap.3734-T1
Valid prediction for snap_scaffold_3-snap.3711-T1
Valid prediction for GlimmerHMM_glimmerT_8589-T1
Valid prediction for Augustus_model.g5699.t1
Valid prediction for snap_scaffold_3-snap.3736-T1
Valid prediction for GlimmerHMM_glimmerT_8593-T1
Valid prediction for snap_scaffold_3-snap.3703-T1
Valid prediction for GlimmerHMM_glimmerT_8591-T1
Valid prediction for snap_scaffold_3-snap.3706-T1
Valid prediction for CodingQuarry_transcript_46371-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.3722-T1
Valid prediction for Augustus_model.g5706.t1
Valid prediction for snap_scaffold_3-snap.3704-T1
Valid prediction for GlimmerHMM_glimmerT_8596-T1
Valid prediction for GeneMark_model.13961_t
Valid prediction for Augustus_model.g5692.t1
Valid prediction for snap_scaffold_3-snap.3718-T1
Valid prediction for GeneMark_model.13938_t
Valid prediction for snap_scaffold_3-snap.3742-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_8584-T1
Valid prediction for snap_scaffold_3-snap.3715-T1
Valid prediction for GlimmerHMM_glimmerT_8574-T1
Valid prediction for snap_scaffold_3-snap.3709-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_8587-T1
Valid prediction for snap_scaffold_3-snap.3741-T1
Valid prediction for GlimmerHMM_glimmerT_8580-T1
Valid prediction for snap_scaffold_3-snap.3705-T1
Valid prediction for GeneMark_model.13958_t
Valid prediction for GeneMark_model.13955_t
Valid prediction for snap_scaffold_3-snap.3710-T1
Valid prediction for GlimmerHMM_glimmerT_8577-T1
Valid prediction for GlimmerHMM_glimmerT_8585-T1
Valid prediction for GlimmerHMM_glimmerT_8575-T1
Valid prediction for snap_scaffold_3-snap.3713-T1
Valid prediction for GlimmerHMM_glimmerT_8581-T1
Valid prediction for Augustus_model.g5707.t1
Valid prediction for snap_scaffold_3-snap.3731-T1
Valid prediction for GlimmerHMM_glimmerT_8582-T1
Valid prediction for snap_scaffold_3-snap.3717-T1
Valid prediction for GlimmerHMM_glimmerT_8576-T1
Valid prediction for GeneMark_model.13931_t
Valid prediction for snap_scaffold_3-snap.3726-T1
Valid prediction for GeneMark_model.13947_t
Valid prediction for GlimmerHMM_glimmerT_8597-T1
Valid prediction for GeneMark_model.13928_t
Valid prediction for GeneMark_model.13929_t
Valid prediction for GeneMark_model.13934_t
Valid prediction for GeneMark_model.13960_t
Valid prediction for snap_scaffold_3-snap.3738-T1
Valid prediction for GeneMark_model.13945_t
Valid prediction for Augustus_model.g5697.t1
Valid prediction for GeneMark_model.13941_t
Valid prediction for snap_scaffold_3-snap.3723-T1
Valid prediction for snap_scaffold_3-snap.3719-T1
Valid prediction for GeneMark_model.13942_t
Valid prediction for Augustus_model.g5696.t1
Valid prediction for GeneMark_model.13930_t
Valid prediction for snap_scaffold_3-snap.3702-T1
Valid prediction for GeneMark_model.13939_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17029, rend_intergenic: 14333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20214, rend_intergenic: 17863  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26448, rend_intergenic: 23437  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66612, rend_intergenic: 62214  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82337, rend_intergenic: 79319  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86573, rend_intergenic: 82355  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91568, rend_intergenic: 89315  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131856, rend_intergenic: 129694  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151134, rend_intergenic: 146822  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190488, rend_intergenic: 184100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192214, rend_intergenic: 190681  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 205833, rend_intergenic: 196012  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 208371
-exon list size: 628


building trellis

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89.5    
89.7    
89.8    
90.0    
90.2    
90.3    
90.5    
90.6    
90.8    
91.0    
91.1    
91.3    
91.4    
91.6    
91.7    
91.9    
92.1    
92.2    
92.4    
92.5    
92.7    
92.9    
93.0    
93.2    
93.3    
93.5    
93.7    
93.8    
94.0    
94.1    
94.3    
94.4    
94.6    
94.8    
94.9    
95.1    
95.2    
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    
97.5    
97.6    
97.8    
97.9    
98.1    
98.3    
98.4    
98.6    
98.7    
98.9    
99.0    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 17029, rend_intergenic: 14333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20214, rend_intergenic: 17863  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26448, rend_intergenic: 23437  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66612, rend_intergenic: 62214  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82337, rend_intergenic: 79319  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86573, rend_intergenic: 82355  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91568, rend_intergenic: 89315  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131856, rend_intergenic: 129694  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151134, rend_intergenic: 146822  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190488, rend_intergenic: 184100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192214, rend_intergenic: 190681  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 205833, rend_intergenic: 196012  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 16636
-exon list size: 68


building trellis

1.4    
2.9    
4.3    
5.7    
7.1    
8.6    
10.0    
11.4    
12.9    
14.3    
15.7    
17.1    
18.6    
20.0    
21.4    
22.9    
24.3    
25.7    
27.1    
28.6    
30.0    
31.4    
32.9    
34.3    
35.7    
37.1    
38.6    
40.0    
41.4    
42.9    
44.3    
45.7    
47.1    
48.6    
50.0    
51.4    
52.9    
54.3    
55.7    
57.1    
58.6    
60.0    
61.4    
62.9    
64.3    
65.7    
67.1    
68.6    
70.0    
71.4    
72.9    
74.3    
75.7    
77.1    
78.6    
80.0    
81.4    
82.9    
84.3    
85.7    
87.1    
88.6    
90.0    
91.4    
92.9    
94.3    
95.7    
97.1    
98.6    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support