-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_18134352-18357398

-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 CodingQuarry_transcript_2988-T1
Valid prediction for GlimmerHMM_glimmerT_2527-T1
Valid prediction for GeneMark_model.3672_t
Valid prediction for GlimmerHMM_glimmerT_2511-T1
Valid prediction for GeneMark_model.3690_t
Valid prediction for GeneMark_model.3724_t
Valid prediction for GeneMark_model.3714_t
Valid prediction for GlimmerHMM_glimmerT_2509-T1
Valid prediction for GeneMark_model.3725_t
Valid prediction for GeneMark_model.3685_t
Valid prediction for GeneMark_model.3687_t
Valid prediction for GeneMark_model.3718_t
Valid prediction for GeneMark_model.3727_t
Valid prediction for HiQ_model.g1818.t1
Valid prediction for snap_scaffold_1-snap.3330-T1
Valid prediction for GlimmerHMM_glimmerT_2512-T1
Valid prediction for GlimmerHMM_glimmerT_2498-T1
Valid prediction for Augustus_model.g1813.t1
Valid prediction for snap_scaffold_1-snap.3341-T1
Valid prediction for CodingQuarry_transcript_2985-T1
Valid prediction for pasa_asmbl_2535.p1
Valid prediction for snap_scaffold_1-snap.3339-T1
Valid prediction for GlimmerHMM_glimmerT_2508-T1
Valid prediction for GeneMark_model.3729_t
Valid prediction for pasa_asmbl_2537.p1
Valid prediction for GlimmerHMM_glimmerT_2506-T1
Valid prediction for GlimmerHMM_glimmerT_2526-T1
Valid prediction for GeneMark_model.3733_t
Valid prediction for snap_scaffold_1-snap.3332-T1
Valid prediction for GeneMark_model.3701_t
Valid prediction for GlimmerHMM_glimmerT_2518-T1
Valid prediction for Augustus_model.g1801.t1
Valid prediction for Augustus_model.g1816.t1
Valid prediction for GlimmerHMM_glimmerT_2525-T1
Valid prediction for snap_scaffold_1-snap.3338-T1
Sorry, intron length (3) is less than minimum required (10)
Couldn't classify 140696, 140905
Sorry, prediction pasa_asmbl_2530.p1 fails validation.
(GTG)	 TG	140696-140905	GT	GTG
(CTT)	 AG	141001-141112	GT	GGG
(ATC)	 AG	141214-141245	GT	AGG
(GAT)	 AG	141446-141539	GT	GGG
(TTT)	 AG	141640-141689	GT	AGG
(GAT)	 AG	141780-142043	CC	GAC
-recovered pasa_asmbl_2530.p1, terminal, 141780, 142043
-recovered pasa_asmbl_2530.p1, internal, 141001, 141112
-recovered pasa_asmbl_2530.p1, internal, 141214, 141245
-recovered pasa_asmbl_2530.p1, internal, 141446, 141539
-recovered pasa_asmbl_2530.p1, internal, 141640, 141689
Valid prediction for GeneMark_model.3709_t
Couldn't classify 202679, 202867
Couldn't classify 202919, 202920
Sorry, prediction CodingQuarry_transcript_2989-T1 fails validation.
(ATG)	 AG	202318-202456	GT	AGG
(GTT)	 AG	202679-202867	CT	TTC
(AGC)	 AC	202919-202920	CA	AGC
-recovered CodingQuarry_transcript_2989-T1, initial, 202318, 202456
-recovered CodingQuarry_transcript_2989-T1, internal, 202318, 202456
Valid prediction for GlimmerHMM_glimmerT_2504-T1
Valid prediction for GeneMark_model.3706_t
Valid prediction for snap_scaffold_1-snap.3342-T1
Valid prediction for snap_scaffold_1-snap.3359-T1
Valid prediction for snap_scaffold_1-snap.3360-T1
Valid prediction for GeneMark_model.3711_t
Valid prediction for snap_scaffold_1-snap.3347-T1
Valid prediction for CodingQuarry_transcript_2984-T1
Valid prediction for Augustus_model.g1800.t1
Valid prediction for snap_scaffold_1-snap.3362-T1
Valid prediction for snap_scaffold_1-snap.3361-T1
Valid prediction for GeneMark_model.3675_t
Valid prediction for Augustus_model.g1805.t1
Valid prediction for snap_scaffold_1-snap.3327-T1
Valid prediction for GlimmerHMM_glimmerT_2502-T1
Valid prediction for snap_scaffold_1-snap.3363-T1
Valid prediction for GeneMark_model.3704_t
Valid prediction for GlimmerHMM_glimmerT_2522-T1
Valid prediction for GeneMark_model.3702_t
Valid prediction for CodingQuarry_transcript_2990-T1
Valid prediction for snap_scaffold_1-snap.3358-T1
Valid prediction for GeneMark_model.3671_t
Valid prediction for snap_scaffold_1-snap.3335-T1
Valid prediction for HiQ_model.g1815.t1
Valid prediction for snap_scaffold_1-snap.3348-T1
Valid prediction for GlimmerHMM_glimmerT_2507-T1
Valid prediction for Augustus_model.g1808.t1
Valid prediction for GlimmerHMM_glimmerT_2497-T1
Valid prediction for GlimmerHMM_glimmerT_2524-T1
Valid prediction for HiQ_model.g1817.t1
Valid prediction for GeneMark_model.3720_t
Valid prediction for snap_scaffold_1-snap.3365-T1
Valid prediction for GlimmerHMM_glimmerT_2516-T1
Valid prediction for GeneMark_model.3680_t
Valid prediction for GeneMark_model.3731_t
Valid prediction for Augustus_model.g1806.t1
Valid prediction for GeneMark_model.3730_t
Couldn't classify 186913, 187130
Sorry, prediction pasa_asmbl_2534.p1 fails validation.
(GCA)	 GA	186913-187130	GT	TGG
(TCC)	 AG	187222-187408	GG	GAG
-recovered pasa_asmbl_2534.p1, terminal, 187222, 187408
Valid prediction for GeneMark_model.3677_t
Valid prediction for GeneMark_model.3699_t
Valid prediction for pasa_asmbl_2538.p1
Valid prediction for Augustus_model.g1803.t1
Valid prediction for GeneMark_model.3696_t
Couldn't classify 183024, 183164
Sorry, prediction pasa_asmbl_2772.p1 fails validation.
(ATG)	 TC	182434-182682	GT	CAG
(GTA)	 AG	182876-182935	GT	AAG
(GTG)	 AG	183024-183164	GT	AGG
-recovered pasa_asmbl_2772.p1, initial, 182434, 182682
-recovered pasa_asmbl_2772.p1, internal, 182876, 182935
-recovered pasa_asmbl_2772.p1, internal, 183024, 183164
Valid prediction for GeneMark_model.3734_t
Valid prediction for snap_scaffold_1-snap.3356-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GeneMark_model.3715_t
Valid prediction for CodingQuarry_transcript_2987-T1
Valid prediction for snap_scaffold_1-snap.3321-T1
Valid prediction for snap_scaffold_1-snap.3323-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_1-snap.3340-T1
Valid prediction for GeneMark_model.3682_t
Valid prediction for GeneMark_model.3683_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.3349-T1
Couldn't classify 50689, 52302
Sorry, prediction pasa_asmbl_1100.p1 fails validation.
(CCT)	 TG	50689-52302	CC	AGC
Valid prediction for snap_scaffold_1-snap.3364-T1
Valid prediction for GeneMark_model.3674_t
Valid prediction for GeneMark_model.3693_t
Valid prediction for GeneMark_model.3712_t
Valid prediction for snap_scaffold_1-snap.3331-T1
Valid prediction for snap_scaffold_1-snap.3346-T1
Valid prediction for snap_scaffold_1-snap.3329-T1
Valid prediction for GeneMark_model.3728_t
Valid prediction for GeneMark_model.3695_t
Valid prediction for GlimmerHMM_glimmerT_2523-T1
Valid prediction for GeneMark_model.3689_t
Valid prediction for snap_scaffold_1-snap.3355-T1
Valid prediction for HiQ_model.g1819.t1
Valid prediction for GeneMark_model.3684_t
Valid prediction for snap_scaffold_1-snap.3352-T1
Valid prediction for snap_scaffold_1-snap.3344-T1
Valid prediction for GlimmerHMM_glimmerT_2520-T1
Valid prediction for GeneMark_model.3679_t
Valid prediction for GeneMark_model.3703_t
Valid prediction for snap_scaffold_1-snap.3334-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_2529-T1
Valid prediction for GlimmerHMM_glimmerT_2513-T1
Valid prediction for Augustus_model.g1802.t1
Valid prediction for GlimmerHMM_glimmerT_2500-T1
Valid prediction for GeneMark_model.3692_t
Valid prediction for GeneMark_model.3694_t
Valid prediction for snap_scaffold_1-snap.3357-T1
Valid prediction for GlimmerHMM_glimmerT_2521-T1
Valid prediction for snap_scaffold_1-snap.3322-T1
Valid prediction for GeneMark_model.3732_t
Valid prediction for pasa_asmbl_1103.p1
Valid prediction for GeneMark_model.3700_t
Valid prediction for GlimmerHMM_glimmerT_2514-T1
Valid prediction for snap_scaffold_1-snap.3325-T1
Valid prediction for Augustus_model.g1807.t1
Valid prediction for snap_scaffold_1-snap.3328-T1
Valid prediction for GeneMark_model.3688_t
Valid prediction for GlimmerHMM_glimmerT_2499-T1
Valid prediction for snap_scaffold_1-snap.3345-T1
Valid prediction for CodingQuarry_transcript_2991-T1
Valid prediction for snap_scaffold_1-snap.3351-T1
Valid prediction for snap_scaffold_1-snap.3353-T1
Valid prediction for snap_scaffold_1-snap.3326-T1
Couldn't classify 74403, 74552
Sorry, prediction pasa_asmbl_1096.p2 fails validation.
(CAG)	 CC	74403-74552	GT	GGG
(TTG)	 AG	76815-77233	GT	AGG
(GTG)	 AG	77767-77770	CA	GAC
-recovered pasa_asmbl_1096.p2, terminal, 77767, 77770
-recovered pasa_asmbl_1096.p2, internal, 76815, 77233
Valid prediction for GlimmerHMM_glimmerT_2510-T1
Valid prediction for GlimmerHMM_glimmerT_2519-T1
Valid prediction for snap_scaffold_1-snap.3350-T1
Valid prediction for GeneMark_model.3678_t
Valid prediction for Augustus_model.g1810.t1
Valid prediction for GeneMark_model.3681_t
Valid prediction for snap_scaffold_1-snap.3324-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for Augustus_model.g1809.t1
Valid prediction for GeneMark_model.3726_t
Valid prediction for GlimmerHMM_glimmerT_2517-T1
Valid prediction for GeneMark_model.3721_t
Valid prediction for HiQ_model.g1814.t1
Valid prediction for GeneMark_model.3691_t
Valid prediction for Augustus_model.g1804.t1
Valid prediction for GeneMark_model.3719_t
Valid prediction for GeneMark_model.3717_t
Valid prediction for GeneMark_model.3710_t
Valid prediction for GlimmerHMM_glimmerT_2501-T1
Valid prediction for pasa_asmbl_1102.p1
Valid prediction for GeneMark_model.3686_t
Valid prediction for snap_scaffold_1-snap.3336-T1
Valid prediction for GeneMark_model.3723_t
Valid prediction for GlimmerHMM_glimmerT_2505-T1
Valid prediction for CodingQuarry_transcript_2986-T1
Valid prediction for GeneMark_model.3708_t
Valid prediction for snap_scaffold_1-snap.3337-T1
Valid prediction for GeneMark_model.3698_t
Valid prediction for GeneMark_model.3670_t
Valid prediction for snap_scaffold_1-snap.3366-T1
Valid prediction for GlimmerHMM_glimmerT_2503-T1
Valid prediction for GeneMark_model.3676_t
Couldn't classify 58989, 60422
Sorry, prediction pasa_asmbl_1099.p1 fails validation.
(CCC)	 AA	58989-60422	TT	GAT
Valid prediction for snap_scaffold_1-snap.3343-T1
Valid prediction for GeneMark_model.3697_t
Valid prediction for GlimmerHMM_glimmerT_2515-T1
Valid prediction for GeneMark_model.3673_t
Valid prediction for Augustus_model.g1812.t1
Valid prediction for snap_scaffold_1-snap.3354-T1
Valid prediction for snap_scaffold_1-snap.3333-T1
Valid prediction for GlimmerHMM_glimmerT_2528-T1
Valid prediction for Augustus_model.g1811.t1
Valid prediction for GeneMark_model.3707_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10070, rend_intergenic: 4435  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58149, rend_intergenic: 10864  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62374, rend_intergenic: 59906  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65009, rend_intergenic: 64624  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72156, rend_intergenic: 65253  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83578, rend_intergenic: 72625  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92871, rend_intergenic: 88574  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135882, rend_intergenic: 110953  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 217995, rend_intergenic: 216480  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 223047
-exon list size: 826


building trellis

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69.7    
69.8    
69.9    
70.0    
70.2    
70.3    
70.4    
70.5    
70.7    
70.8    
70.9    
71.0    
71.1    
71.3    
71.4    
71.5    
71.6    
71.7    
71.9    
72.0    
72.1    
72.2    
72.3    
72.5    
72.6    
72.7    
72.8    
72.9    
73.1    
73.2    
73.3    
73.4    
73.6    
73.7    
73.8    
73.9    
74.0    
74.2    
74.3    
74.4    
74.5    
74.6    
74.8    
74.9    
75.0    
75.1    
75.2    
75.4    
75.5    
75.6    
75.7    
75.8    
76.0    
76.1    
76.2    
76.3    
76.4    
76.6    
76.7    
76.8    
76.9    
77.1    
77.2    
77.3    
77.4    
77.5    
77.7    
77.8    
77.9    
78.0    
78.1    
78.3    
78.4    
78.5    
78.6    
78.7    
78.9    
79.0    
79.1    
79.2    
79.3    
79.5    
79.6    
79.7    
79.8    
80.0    
80.1    
80.2    
80.3    
80.4    
80.6    
80.7    
80.8    
80.9    
81.0    
81.2    
81.3    
81.4    
81.5    
81.6    
81.8    
81.9    
82.0    
82.1    
82.2    
82.4    
82.5    
82.6    
82.7    
82.9    
83.0    
83.1    
83.2    
83.3    
83.5    
83.6    
83.7    
83.8    
83.9    
84.1    
84.2    
84.3    
84.4    
84.5    
84.7    
84.8    
84.9    
85.0    
85.1    
85.3    
85.4    
85.5    
85.6    
85.7    
85.9    
86.0    
86.1    
86.2    
86.4    
86.5    
86.6    
86.7    
86.8    
87.0    
87.1    
87.2    
87.3    
87.4    
87.6    
87.7    
87.8    
87.9    
88.0    
88.2    
88.3    
88.4    
88.5    
88.6    
88.8    
88.9    
89.0    
89.1    
89.3    
89.4    
89.5    
89.6    
89.7    
89.9    
90.0    
90.1    
90.2    
90.3    
90.5    
90.6    
90.7    
90.8    
90.9    
91.1    
91.2    
91.3    
91.4    
91.5    
91.7    
91.8    
91.9    
92.0    
92.1    
92.3    
92.4    
92.5    
92.6    
92.8    
92.9    
93.0    
93.1    
93.2    
93.4    
93.5    
93.6    
93.7    
93.8    
94.0    
94.1    
94.2    
94.3    
94.4    
94.6    
94.7    
94.8    
94.9    
95.0    
95.2    
95.3    
95.4    
95.5    
95.7    
95.8    
95.9    
96.0    
96.1    
96.3    
96.4    
96.5    
96.6    
96.7    
96.9    
97.0    
97.1    
97.2    
97.3    
97.5    
97.6    
97.7    
97.8    
97.9    
98.1    
98.2    
98.3    
98.4    
98.6    
98.7    
98.8    
98.9    
99.0    
99.2    
99.3    
99.4    
99.5    
99.6    
99.8    
99.9    
-found 40 predictions from path traversal
Error with prediction: snap lend_intergenic: 10070, rend_intergenic: 4435  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58149, rend_intergenic: 10864  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62374, rend_intergenic: 59906  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65009, rend_intergenic: 64624  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72156, rend_intergenic: 65253  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83578, rend_intergenic: 72625  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92871, rend_intergenic: 88574  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135882, rend_intergenic: 110953  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 217995, rend_intergenic: 216480  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

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