-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_18681672-18839101

-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.3849_t
Valid prediction for Augustus_model.g1855.t1
Valid prediction for GlimmerHMM_glimmerT_2595-T1
Valid prediction for GlimmerHMM_glimmerT_2597-T1
Valid prediction for GlimmerHMM_glimmerT_2591-T1
Valid prediction for snap_scaffold_1-snap.3471-T1
Valid prediction for snap_scaffold_1-snap.3477-T1
Valid prediction for GeneMark_model.3856_t
Valid prediction for CodingQuarry_transcript_2995-T1
Valid prediction for snap_scaffold_1-snap.3454-T1
Valid prediction for GeneMark_model.3839_t
Valid prediction for GlimmerHMM_glimmerT_2578-T1
Valid prediction for Augustus_model.g1851.t1
Valid prediction for snap_scaffold_1-snap.3455-T1
Valid prediction for snap_scaffold_1-snap.3466-T1
Valid prediction for GlimmerHMM_glimmerT_2590-T1
Valid prediction for GlimmerHMM_glimmerT_2584-T1
Valid prediction for Augustus_model.g1850.t1
Valid prediction for GeneMark_model.3854_t
Valid prediction for GeneMark_model.3868_t
Valid prediction for GeneMark_model.3872_t
Valid prediction for snap_scaffold_1-snap.3480-T1
Valid prediction for CodingQuarry_transcript_2994-T1
Valid prediction for snap_scaffold_1-snap.3485-T1
Couldn't classify 81015, 81080
Couldn't classify 84460, 84562
Sorry, prediction pasa_asmbl_2557.p1 fails validation.
(CGA)	 AA	81015-81080	GT	ATG
(TTA)	 AG	81478-81592	GT	CGG
(ATA)	 AG	81748-81820	GT	AAG
(GTT)	 AG	84460-84562	GT	AGG
-recovered pasa_asmbl_2557.p1, terminal, 81748, 81820
-recovered pasa_asmbl_2557.p1, internal, 81478, 81592
-recovered pasa_asmbl_2557.p1, internal, 81748, 81820
-recovered pasa_asmbl_2557.p1, internal, 84460, 84562
Valid prediction for GeneMark_model.3878_t
Valid prediction for GlimmerHMM_glimmerT_2575-T1
Couldn't classify 76157, 76174
Sorry, prediction pasa_asmbl_2555.p1 fails validation.
(ATT)	 TA	76157-76174	GT	TGG
(ATA)	 AG	76640-76799	GT	AGG
(AGT)	 AG	77061-77115	GT	AGG
(GTA)	 AG	77394-77509	GT	AGG
(TGA)	 AG	79812-79894	GT	AGG
-recovered pasa_asmbl_2555.p1, terminal, 79812, 79894
-recovered pasa_asmbl_2555.p1, internal, 76640, 76799
-recovered pasa_asmbl_2555.p1, internal, 77061, 77115
-recovered pasa_asmbl_2555.p1, internal, 77394, 77509
-recovered pasa_asmbl_2555.p1, internal, 79812, 79894
Valid prediction for GlimmerHMM_glimmerT_2577-T1
Valid prediction for snap_scaffold_1-snap.3457-T1
Valid prediction for GlimmerHMM_glimmerT_2588-T1
Valid prediction for Augustus_model.g1852.t1
Valid prediction for GeneMark_model.3840_t
Valid prediction for GlimmerHMM_glimmerT_2583-T1
Valid prediction for snap_scaffold_1-snap.3452-T1
Valid prediction for snap_scaffold_1-snap.3483-T1
Valid prediction for snap_scaffold_1-snap.3475-T1
Valid prediction for GeneMark_model.3866_t
Valid prediction for snap_scaffold_1-snap.3458-T1
Valid prediction for GeneMark_model.3861_t
Valid prediction for GeneMark_model.3844_t
Valid prediction for GeneMark_model.3870_t
Valid prediction for GlimmerHMM_glimmerT_2593-T1
Valid prediction for GeneMark_model.3851_t
Valid prediction for GlimmerHMM_glimmerT_2574-T1
Valid prediction for GeneMark_model.3865_t
Valid prediction for snap_scaffold_1-snap.3461-T1
Valid prediction for GeneMark_model.3887_t
Valid prediction for GeneMark_model.3889_t
Valid prediction for GeneMark_model.3885_t
Valid prediction for GlimmerHMM_glimmerT_2573-T1
Valid prediction for Augustus_model.g1858.t1
Valid prediction for GeneMark_model.3837_t
Valid prediction for snap_scaffold_1-snap.3464-T1
Valid prediction for GeneMark_model.3881_t
Valid prediction for snap_scaffold_1-snap.3449-T1
Valid prediction for snap_scaffold_1-snap.3447-T1
Valid prediction for GeneMark_model.3863_t
Valid prediction for GeneMark_model.3859_t
Valid prediction for snap_scaffold_1-snap.3469-T1
Valid prediction for snap_scaffold_1-snap.3478-T1
Valid prediction for GeneMark_model.3847_t
Couldn't classify 40988, 41108
Sorry, prediction pasa_asmbl_2816.p1 fails validation.
(GTG)	 AG	40988-41108	GT	AGG
(AGA)	 AG	42155-42285	GT	AGG
(GAG)	 AG	43392-43565	GG	GAG
-recovered pasa_asmbl_2816.p1, terminal, 40988, 41108
-recovered pasa_asmbl_2816.p1, terminal, 43392, 43565
-recovered pasa_asmbl_2816.p1, internal, 40988, 41108
-recovered pasa_asmbl_2816.p1, internal, 42155, 42285
Valid prediction for GlimmerHMM_glimmerT_2585-T1
Valid prediction for snap_scaffold_1-snap.3474-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for GeneMark_model.3842_t
Valid prediction for GeneMark_model.3876_t

-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_1-snap.3462-T1
Valid prediction for GeneMark_model.3857_t
Valid prediction for GeneMark_model.3841_t
Valid prediction for GeneMark_model.3843_t
Valid prediction for GeneMark_model.3886_t
Valid prediction for GeneMark_model.3853_t
Valid prediction for GlimmerHMM_glimmerT_2592-T1
Valid prediction for GeneMark_model.3846_t
Couldn't classify 101916, 101961
Sorry, prediction pasa_asmbl_1120.p1 fails validation.
(GAG)	 AT	101916-101961	GT	AGG
(GTC)	 AG	102876-102974	GT	GGG
(GCT)	 AG	105385-105493	GT	AGG
(GTC)	 AG	105713-105830	GT	AGG
(GGC)	 AG	106100-106291	GT	AGG
(GTA)	 AG	106438-106509	GT	AGG
(GTG)	 AG	106673-106798	GT	AGG
(AGG)	 AG	107072-107160	GT	AAG
(GTT)	 AG	107415-107548	GT	CTG
(GTG)	 AG	108096-108157	CC	AGC
-recovered pasa_asmbl_1120.p1, terminal, 108096, 108157
-recovered pasa_asmbl_1120.p1, internal, 102876, 102974
-recovered pasa_asmbl_1120.p1, internal, 105385, 105493
-recovered pasa_asmbl_1120.p1, internal, 105713, 105830
-recovered pasa_asmbl_1120.p1, internal, 106100, 106291
-recovered pasa_asmbl_1120.p1, internal, 106438, 106509
-recovered pasa_asmbl_1120.p1, internal, 106673, 106798
-recovered pasa_asmbl_1120.p1, internal, 107072, 107160
-recovered pasa_asmbl_1120.p1, internal, 107415, 107548
Valid prediction for Augustus_model.g1857.t1
Valid prediction for snap_scaffold_1-snap.3481-T1
Valid prediction for snap_scaffold_1-snap.3476-T1
Valid prediction for GeneMark_model.3864_t
Valid prediction for GeneMark_model.3860_t
Valid prediction for GlimmerHMM_glimmerT_2581-T1
Valid prediction for Augustus_model.g1853.t1
Valid prediction for snap_scaffold_1-snap.3467-T1
Valid prediction for GeneMark_model.3888_t
Valid prediction for GeneMark_model.3867_t
Valid prediction for GeneMark_model.3845_t
Valid prediction for GeneMark_model.3875_t
Valid prediction for GeneMark_model.3869_t
Valid prediction for snap_scaffold_1-snap.3470-T1
Couldn't classify 85337, 85543
Sorry, prediction pasa_asmbl_1125.p1 fails validation.
(ATT)	 AG	85337-85543	GT	CTG
(GTT)	 AG	86136-86215	GT	TGG
(GAA)	 AG	86503-86581	GT	AGG
(GTG)	 AG	87114-87185	GT	ACG
(AAT)	 AG	87295-87357	GT	AGG
(ACG)	 AG	87883-88023	AG	AGA
-recovered pasa_asmbl_1125.p1, terminal, 87883, 88023
-recovered pasa_asmbl_1125.p1, internal, 85337, 85543
-recovered pasa_asmbl_1125.p1, internal, 86136, 86215
-recovered pasa_asmbl_1125.p1, internal, 86503, 86581
-recovered pasa_asmbl_1125.p1, internal, 87114, 87185
-recovered pasa_asmbl_1125.p1, internal, 87295, 87357
Valid prediction for snap_scaffold_1-snap.3450-T1
Valid prediction for GeneMark_model.3871_t
Valid prediction for GeneMark_model.3873_t
Valid prediction for snap_scaffold_1-snap.3456-T1
Valid prediction for GeneMark_model.3883_t
Valid prediction for GeneMark_model.3879_t
Valid prediction for GeneMark_model.3855_t
Valid prediction for GlimmerHMM_glimmerT_2589-T1
Valid prediction for snap_scaffold_1-snap.3473-T1
Valid prediction for snap_scaffold_1-snap.3448-T1
Valid prediction for GeneMark_model.3890_t
Valid prediction for snap_scaffold_1-snap.3463-T1
Couldn't classify 95972, 96136
Couldn't classify 99966, 100031
Sorry, prediction pasa_asmbl_1121.p1 fails validation.
(AGA)	 AC	95972-96136	GT	AGG
(GTG)	 AG	96387-96538	GT	AGG
(GAT)	 AG	97825-97972	GT	AGG
(GTG)	 AG	99966-100031	CT	TGC
-recovered pasa_asmbl_1121.p1, internal, 96387, 96538
-recovered pasa_asmbl_1121.p1, internal, 97825, 97972
Valid prediction for snap_scaffold_1-snap.3484-T1
Valid prediction for GlimmerHMM_glimmerT_2587-T1
Valid prediction for GlimmerHMM_glimmerT_2582-T1
Valid prediction for GeneMark_model.3838_t
Valid prediction for Augustus_model.g1856.t1
Valid prediction for GlimmerHMM_glimmerT_2586-T1
Valid prediction for GlimmerHMM_glimmerT_2598-T1
Valid prediction for snap_scaffold_1-snap.3465-T1
Valid prediction for snap_scaffold_1-snap.3472-T1
Valid prediction for GeneMark_model.3874_t
Valid prediction for GeneMark_model.3884_t
Valid prediction for GeneMark_model.3882_t
Valid prediction for GlimmerHMM_glimmerT_2596-T1
Couldn't classify 95966, 96136
Couldn't classify 96895, 96961
Sorry, prediction pasa_asmbl_1123.p1 fails validation.
(TCC)	 TG	95966-96136	GT	AGG
(GTG)	 AG	96387-96538	GT	AGG
(ACT)	 AG	96895-96961	AA	TGA
-recovered pasa_asmbl_1123.p1, internal, 96387, 96538
Couldn't classify 50848, 50928
Sorry, prediction pasa_asmbl_1127.p2 fails validation.
(GCG)	 AG	50848-50928	GT	TGG
(GCG)	 AG	51377-51641	GT	TGG
(GCT)	 AG	53879-54108	TG	GAT
-recovered pasa_asmbl_1127.p2, terminal, 53879, 54108
-recovered pasa_asmbl_1127.p2, internal, 50848, 50928
-recovered pasa_asmbl_1127.p2, internal, 51377, 51641
Valid prediction for GeneMark_model.3852_t
Valid prediction for GlimmerHMM_glimmerT_2576-T1
Valid prediction for snap_scaffold_1-snap.3460-T1
Valid prediction for GeneMark_model.3862_t
Valid prediction for GeneMark_model.3877_t
Valid prediction for GlimmerHMM_glimmerT_2594-T1
Valid prediction for GlimmerHMM_glimmerT_2579-T1
Valid prediction for GeneMark_model.3848_t
Valid prediction for snap_scaffold_1-snap.3482-T1
Valid prediction for GeneMark_model.3850_t
Valid prediction for snap_scaffold_1-snap.3479-T1
Valid prediction for snap_scaffold_1-snap.3453-T1
Valid prediction for snap_scaffold_1-snap.3459-T1
Valid prediction for snap_scaffold_1-snap.3468-T1
Valid prediction for GeneMark_model.3880_t
Valid prediction for GlimmerHMM_glimmerT_2580-T1
Valid prediction for snap_scaffold_1-snap.3451-T1
Valid prediction for Augustus_model.g1854.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 29769, rend_intergenic: 18069  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35511, rend_intergenic: 35151  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38808, rend_intergenic: 35664  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43565, rend_intergenic: 40929  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51355, rend_intergenic: 49274  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66378, rend_intergenic: 63222  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80783, rend_intergenic: 76275  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86550, rend_intergenic: 83986  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88506, rend_intergenic: 87320  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92442, rend_intergenic: 88586  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95978, rend_intergenic: 95141  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111643, rend_intergenic: 105327  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114429, rend_intergenic: 111698  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118834, rend_intergenic: 115939  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123622, rend_intergenic: 121065  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127477, rend_intergenic: 124487  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137781, rend_intergenic: 131533  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145179, rend_intergenic: 139032  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151616, rend_intergenic: 150320  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 157430
-exon list size: 617


building trellis

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76.1    
76.3    
76.4    
76.6    
76.7    
76.9    
77.1    
77.2    
77.4    
77.5    
77.7    
77.9    
78.0    
78.2    
78.4    
78.5    
78.7    
78.8    
79.0    
79.2    
79.3    
79.5    
79.6    
79.8    
80.0    
80.1    
80.3    
80.5    
80.6    
80.8    
80.9    
81.1    
81.3    
81.4    
81.6    
81.7    
81.9    
82.1    
82.2    
82.4    
82.6    
82.7    
82.9    
83.0    
83.2    
83.4    
83.5    
83.7    
83.8    
84.0    
84.2    
84.3    
84.5    
84.7    
84.8    
85.0    
85.1    
85.3    
85.5    
85.6    
85.8    
85.9    
86.1    
86.3    
86.4    
86.6    
86.8    
86.9    
87.1    
87.2    
87.4    
87.6    
87.7    
87.9    
88.0    
88.2    
88.4    
88.5    
88.7    
88.9    
89.0    
89.2    
89.3    
89.5    
89.7    
89.8    
90.0    
90.1    
90.3    
90.5    
90.6    
90.8    
91.0    
91.1    
91.3    
91.4    
91.6    
91.8    
91.9    
92.1    
92.2    
92.4    
92.6    
92.7    
92.9    
93.1    
93.2    
93.4    
93.5    
93.7    
93.9    
94.0    
94.2    
94.3    
94.5    
94.7    
94.8    
95.0    
95.2    
95.3    
95.5    
95.6    
95.8    
96.0    
96.1    
96.3    
96.4    
96.6    
96.8    
96.9    
97.1    
97.3    
97.4    
97.6    
97.7    
97.9    
98.1    
98.2    
98.4    
98.5    
98.7    
98.9    
99.0    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 29769, rend_intergenic: 18069  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35511, rend_intergenic: 35151  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38808, rend_intergenic: 35664  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43565, rend_intergenic: 40929  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51355, rend_intergenic: 49274  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66378, rend_intergenic: 63222  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80783, rend_intergenic: 76275  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86550, rend_intergenic: 83986  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88506, rend_intergenic: 87320  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92442, rend_intergenic: 88586  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95978, rend_intergenic: 95141  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111643, rend_intergenic: 105327  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114429, rend_intergenic: 111698  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118834, rend_intergenic: 115939  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123622, rend_intergenic: 121065  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127477, rend_intergenic: 124487  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137781, rend_intergenic: 131533  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145179, rend_intergenic: 139032  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151616, rend_intergenic: 150320  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support