-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_10/scaffold_10_16344398-16541483

-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 snap_scaffold_10-snap.3335-T1
Valid prediction for snap_scaffold_10-snap.3353-T1
Valid prediction for GeneMark_model.45948_t
Valid prediction for GlimmerHMM_glimmerT_26664-T1
Valid prediction for HiQ_model.g17861.t1
Couldn't classify 190025, 190864
Sorry, prediction pasa_asmbl_4999.p1 fails validation.
(TTG)	 TT	190025-190864	GC	ATG
Valid prediction for snap_scaffold_10-snap.3333-T1
Valid prediction for GeneMark_model.45937_t
Valid prediction for GeneMark_model.45917_t
Valid prediction for snap_scaffold_10-snap.3352-T1
Valid prediction for GeneMark_model.45955_t
Valid prediction for GeneMark_model.45924_t
Valid prediction for GlimmerHMM_glimmerT_26660-T1
Valid prediction for snap_scaffold_10-snap.3369-T1
Valid prediction for snap_scaffold_10-snap.3355-T1
Valid prediction for GeneMark_model.45933_t
Valid prediction for GeneMark_model.45926_t
Valid prediction for GeneMark_model.45943_t
Valid prediction for GeneMark_model.45931_t
Valid prediction for snap_scaffold_10-snap.3361-T1
Valid prediction for GeneMark_model.45899_t
Valid prediction for GlimmerHMM_glimmerT_26652-T1
Valid prediction for GeneMark_model.45913_t
Valid prediction for GeneMark_model.45918_t
Valid prediction for snap_scaffold_10-snap.3358-T1
Valid prediction for GlimmerHMM_glimmerT_26647-T1
Valid prediction for snap_scaffold_10-snap.3375-T1
Valid prediction for Augustus_model.g17870.t1
Valid prediction for snap_scaffold_10-snap.3372-T1
Valid prediction for GeneMark_model.45940_t
Valid prediction for snap_scaffold_10-snap.3347-T1
Valid prediction for GeneMark_model.45904_t
Valid prediction for CodingQuarry_transcript_5654-T1
Valid prediction for snap_scaffold_10-snap.3350-T1
Valid prediction for GlimmerHMM_glimmerT_26648-T1
Valid prediction for GeneMark_model.45929_t
Valid prediction for GeneMark_model.45945_t
Valid prediction for GeneMark_model.45921_t
Valid prediction for GeneMark_model.45915_t
Valid prediction for GeneMark_model.45935_t
Valid prediction for GeneMark_model.45897_t
Valid prediction for snap_scaffold_10-snap.3371-T1
Valid prediction for snap_scaffold_10-snap.3365-T1
Valid prediction for snap_scaffold_10-snap.3338-T1
Valid prediction for Augustus_model.g17866.t1
Valid prediction for snap_scaffold_10-snap.3340-T1
Couldn't classify 189581, 189813
Sorry, prediction pasa_asmbl_4992.p1 fails validation.
(ATG)	 GC	186484-186536	GT	AGG
(GTT)	 AG	187080-187163	GT	AGG
(GGA)	 AG	187407-187517	GT	GGG
(TAC)	 AG	187603-187722	GT	GTG
(GAG)	 AG	188163-188466	GT	AGG
(ATG)	 AG	188912-188945	GT	AAG
(AAC)	 AG	189120-189371	GT	AAG
(AAT)	 AG	189581-189813	CT	ACC
-recovered pasa_asmbl_4992.p1, initial, 186484, 186536
-recovered pasa_asmbl_4992.p1, initial, 188912, 188945
-recovered pasa_asmbl_4992.p1, internal, 187080, 187163
-recovered pasa_asmbl_4992.p1, internal, 187407, 187517
-recovered pasa_asmbl_4992.p1, internal, 187603, 187722
-recovered pasa_asmbl_4992.p1, internal, 188163, 188466
-recovered pasa_asmbl_4992.p1, internal, 188912, 188945
-recovered pasa_asmbl_4992.p1, internal, 189120, 189371
Valid prediction for Augustus_model.g17860.t1
Valid prediction for snap_scaffold_10-snap.3341-T1
Valid prediction for GeneMark_model.45911_t
Valid prediction for snap_scaffold_10-snap.3370-T1
Valid prediction for GlimmerHMM_glimmerT_26646-T1
Valid prediction for snap_scaffold_10-snap.3344-T1
Valid prediction for GeneMark_model.45950_t
Valid prediction for GlimmerHMM_glimmerT_26649-T1
Valid prediction for GeneMark_model.45954_t
Valid prediction for GeneMark_model.45909_t
Valid prediction for GeneMark_model.45907_t
Valid prediction for GlimmerHMM_glimmerT_26651-T1
Couldn't classify 135297, 135374
Sorry, prediction pasa_asmbl_4988.p1 fails validation.
(ATG)	 CG	134127-134218	GT	AGG
(CAC)	 AG	134457-134682	GT	TGG
(ACG)	 AG	135007-135120	GT	AGG
(GAG)	 AG	135297-135374	GG	ACG
-recovered pasa_asmbl_4988.p1, initial, 134127, 134218
-recovered pasa_asmbl_4988.p1, internal, 134457, 134682
-recovered pasa_asmbl_4988.p1, internal, 135007, 135120
Valid prediction for GlimmerHMM_glimmerT_26655-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_26643-T1
Valid prediction for GlimmerHMM_glimmerT_26661-T1
Valid prediction for Augustus_model.g17859.t1
Valid prediction for snap_scaffold_10-snap.3373-T1
Valid prediction for GeneMark_model.45952_t
Valid prediction for GeneMark_model.45958_t
Valid prediction for GeneMark_model.45902_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_10-snap.3360-T1
Valid prediction for Augustus_model.g17858.t1
Valid prediction for GeneMark_model.45949_t
Valid prediction for snap_scaffold_10-snap.3356-T1
Valid prediction for GeneMark_model.45939_t
Valid prediction for GeneMark_model.45925_t
Valid prediction for GeneMark_model.45898_t
Valid prediction for snap_scaffold_10-snap.3348-T1
Valid prediction for GeneMark_model.45938_t
Valid prediction for GeneMark_model.45936_t
Valid prediction for GeneMark_model.45956_t
Valid prediction for GeneMark_model.45919_t
Valid prediction for snap_scaffold_10-snap.3359-T1
Valid prediction for snap_scaffold_10-snap.3349-T1
Valid prediction for GlimmerHMM_glimmerT_26657-T1
Valid prediction for snap_scaffold_10-snap.3336-T1
Valid prediction for GeneMark_model.45934_t
Valid prediction for GeneMark_model.45906_t
Valid prediction for GlimmerHMM_glimmerT_26656-T1
Valid prediction for pasa_asmbl_3907.p1
Valid prediction for GeneMark_model.45923_t
Valid prediction for GlimmerHMM_glimmerT_26650-T1
Valid prediction for GeneMark_model.45901_t
Valid prediction for CodingQuarry_transcript_5656-T1
Couldn't classify 157641, 158048
Sorry, prediction pasa_asmbl_3902.p1 fails validation.
(CAG)	 GC	157641-158048	GG	GAG
Valid prediction for CodingQuarry_transcript_5657-T1
Valid prediction for Augustus_model.g17869.t1
Valid prediction for snap_scaffold_10-snap.3363-T1
Valid prediction for snap_scaffold_10-snap.3334-T1
Valid prediction for snap_scaffold_10-snap.3374-T1
Valid prediction for GeneMark_model.45932_t
Valid prediction for GeneMark_model.45951_t
Valid prediction for snap_scaffold_10-snap.3351-T1
Valid prediction for GlimmerHMM_glimmerT_26658-T1
Valid prediction for Augustus_model.g17867.t1
Valid prediction for GeneMark_model.45944_t
Valid prediction for Augustus_model.g17857.t1
Valid prediction for snap_scaffold_10-snap.3362-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_10-snap.3368-T1
Valid prediction for HiQ_model.g17862.t1
Valid prediction for snap_scaffold_10-snap.3366-T1
Valid prediction for snap_scaffold_10-snap.3345-T1
Valid prediction for snap_scaffold_10-snap.3343-T1
Valid prediction for GeneMark_model.45942_t
Valid prediction for snap_scaffold_10-snap.3339-T1
Valid prediction for snap_scaffold_10-snap.3364-T1
Valid prediction for GeneMark_model.45916_t
Valid prediction for CodingQuarry_transcript_5658-T1
Valid prediction for GlimmerHMM_glimmerT_26663-T1
Valid prediction for GlimmerHMM_glimmerT_26645-T1
Valid prediction for Augustus_model.g17868.t1
Valid prediction for GlimmerHMM_glimmerT_26653-T1
Valid prediction for snap_scaffold_10-snap.3367-T1
Valid prediction for snap_scaffold_10-snap.3357-T1
Valid prediction for snap_scaffold_10-snap.3342-T1
Valid prediction for snap_scaffold_10-snap.3337-T1
Valid prediction for CodingQuarry_transcript_5660-T1
Valid prediction for GeneMark_model.45900_t
Valid prediction for GeneMark_model.45905_t
Valid prediction for HiQ_model.g17863.t1
Valid prediction for GeneMark_model.45922_t
Valid prediction for CodingQuarry_transcript_5659-T1
Couldn't classify 14017, 14559
Sorry, prediction pasa_asmbl_3914.p1 fails validation.
(ATG)	 AT	14017-14559	CA	ACC
Valid prediction for GeneMark_model.45946_t
Couldn't classify 67371, 67588
Couldn't classify 68302, 69229
Sorry, prediction pasa_asmbl_3906.p1 fails validation.
(GTG)	 TG	67371-67588	GT	AGG
(GTA)	 AG	68302-69229	GA	ACG
Couldn't classify 69500, 70441
Sorry, prediction pasa_asmbl_3905.p1 fails validation.
(GAT)	 GA	69500-70441	CG	AAC
Valid prediction for GeneMark_model.45928_t
Valid prediction for HiQ_model.g17864.t1
Valid prediction for GeneMark_model.45912_t
Valid prediction for GlimmerHMM_glimmerT_26662-T1
Valid prediction for GeneMark_model.45953_t
Valid prediction for GeneMark_model.45908_t
Valid prediction for GeneMark_model.45930_t
Valid prediction for snap_scaffold_10-snap.3354-T1
Valid prediction for GeneMark_model.45910_t
Valid prediction for GeneMark_model.45941_t
Valid prediction for GlimmerHMM_glimmerT_26644-T1
Valid prediction for GeneMark_model.45914_t
Couldn't classify 49882, 49998
Sorry, prediction pasa_asmbl_3912.p2 fails validation.
(AGA)	 TC	49882-49998	GT	AGG
(AAG)	 AG	51605-51761	GT	GGG
(AGG)	 AG	52138-52286	GA	AGG
-recovered pasa_asmbl_3912.p2, terminal, 52138, 52286
-recovered pasa_asmbl_3912.p2, internal, 51605, 51761
Valid prediction for GlimmerHMM_glimmerT_26654-T1
Valid prediction for GlimmerHMM_glimmerT_26659-T1
Valid prediction for GeneMark_model.45957_t
Valid prediction for GeneMark_model.45947_t
Couldn't classify 72040, 72191
Sorry, prediction pasa_asmbl_3904.p1 fails validation.
(ATA)	 TC	72040-72191	GT	TTG
(ATG)	 AG	73122-73544	GT	AAG
(ATT)	 AG	73660-73681	AC	GAA
add_exon() Sorry, pasa_asmbl_3904.p1 73122-73544-initial-1 is invalid.
-recovered pasa_asmbl_3904.p1, initial, 73122, 73544
-recovered pasa_asmbl_3904.p1, terminal, 73660, 73681
-recovered pasa_asmbl_3904.p1, internal, 73122, 73544
Valid prediction for GeneMark_model.45920_t
Valid prediction for snap_scaffold_10-snap.3346-T1
Valid prediction for HiQ_model.g17865.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7413, rend_intergenic: 2861  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 8637, rend_intergenic: 7634  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17767, rend_intergenic: 8735  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23706, rend_intergenic: 21122  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28677, rend_intergenic: 24600  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33326, rend_intergenic: 28756  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34749, rend_intergenic: 33466  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39594, rend_intergenic: 34758  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42932, rend_intergenic: 39619  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49060, rend_intergenic: 43234  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65058, rend_intergenic: 59273  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70383, rend_intergenic: 69646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90530, rend_intergenic: 71037  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99423, rend_intergenic: 93437  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122038, rend_intergenic: 117939  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140382, rend_intergenic: 134587  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171318, rend_intergenic: 141635  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182674, rend_intergenic: 179325  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 197086
-exon list size: 749


building trellis

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73.1    
73.2    
73.4    
73.5    
73.6    
73.8    
73.9    
74.0    
74.2    
74.3    
74.4    
74.6    
74.7    
74.8    
75.0    
75.1    
75.2    
75.4    
75.5    
75.6    
75.8    
75.9    
76.0    
76.2    
76.3    
76.4    
76.6    
76.7    
76.8    
77.0    
77.1    
77.2    
77.4    
77.5    
77.6    
77.8    
77.9    
78.0    
78.2    
78.3    
78.4    
78.6    
78.7    
78.8    
79.0    
79.1    
79.2    
79.4    
79.5    
79.6    
79.8    
79.9    
80.0    
80.2    
80.3    
80.4    
80.6    
80.7    
80.8    
81.0    
81.1    
81.2    
81.4    
81.5    
81.6    
81.8    
81.9    
82.0    
82.2    
82.3    
82.4    
82.6    
82.7    
82.8    
83.0    
83.1    
83.2    
83.4    
83.5    
83.6    
83.8    
83.9    
84.0    
84.2    
84.3    
84.4    
84.6    
84.7    
84.8    
85.0    
85.1    
85.2    
85.4    
85.5    
85.6    
85.8    
85.9    
86.0    
86.2    
86.3    
86.4    
86.6    
86.7    
86.8    
87.0    
87.1    
87.2    
87.4    
87.5    
87.6    
87.7    
87.9    
88.0    
88.1    
88.3    
88.4    
88.5    
88.7    
88.8    
88.9    
89.1    
89.2    
89.3    
89.5    
89.6    
89.7    
89.9    
90.0    
90.1    
90.3    
90.4    
90.5    
90.7    
90.8    
90.9    
91.1    
91.2    
91.3    
91.5    
91.6    
91.7    
91.9    
92.0    
92.1    
92.3    
92.4    
92.5    
92.7    
92.8    
92.9    
93.1    
93.2    
93.3    
93.5    
93.6    
93.7    
93.9    
94.0    
94.1    
94.3    
94.4    
94.5    
94.7    
94.8    
94.9    
95.1    
95.2    
95.3    
95.5    
95.6    
95.7    
95.9    
96.0    
96.1    
96.3    
96.4    
96.5    
96.7    
96.8    
96.9    
97.1    
97.2    
97.3    
97.5    
97.6    
97.7    
97.9    
98.0    
98.1    
98.3    
98.4    
98.5    
98.7    
98.8    
98.9    
99.1    
99.2    
99.3    
99.5    
99.6    
99.7    
99.9    
-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 7413, rend_intergenic: 2861  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 8637, rend_intergenic: 7634  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17767, rend_intergenic: 8735  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23706, rend_intergenic: 21122  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28677, rend_intergenic: 24600  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33326, rend_intergenic: 28756  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34749, rend_intergenic: 33466  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39594, rend_intergenic: 34758  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42932, rend_intergenic: 39619  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49060, rend_intergenic: 43234  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65058, rend_intergenic: 59273  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70383, rend_intergenic: 69646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90530, rend_intergenic: 71037  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99423, rend_intergenic: 93437  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122038, rend_intergenic: 117939  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140382, rend_intergenic: 134587  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171318, rend_intergenic: 141635  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182674, rend_intergenic: 179325  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

-building DP trellis

-building trellis in range 1 - 13969
-exon list size: 54


building trellis

1.8    
3.6    
5.4    
7.1    
8.9    
10.7    
12.5    
14.3    
16.1    
17.9    
19.6    
21.4    
23.2    
25.0    
26.8    
28.6    
30.4    
32.1    
33.9    
35.7    
37.5    
39.3    
41.1    
42.9    
44.6    
46.4    
48.2    
50.0    
51.8    
53.6    
55.4    
57.1    
58.9    
60.7    
62.5    
64.3    
66.1    
67.9    
69.6    
71.4    
73.2    
75.0    
76.8    
78.6    
80.4    
82.1    
83.9    
85.7    
87.5    
89.3    
91.1    
92.9    
94.6    
96.4    
98.2    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 13082
-exon list size: 50


building trellis

1.9    
3.8    
5.8    
7.7    
9.6    
11.5    
13.5    
15.4    
17.3    
19.2    
21.2    
23.1    
25.0    
26.9    
28.8    
30.8    
32.7    
34.6    
36.5    
38.5    
40.4    
42.3    
44.2    
46.2    
48.1    
50.0    
51.9    
53.8    
55.8    
57.7    
59.6    
61.5    
63.5    
65.4    
67.3    
69.2    
71.2    
73.1    
75.0    
76.9    
78.8    
80.8    
82.7    
84.6    
86.5    
88.5    
90.4    
92.3    
94.2    
96.2    
98.1    
-found 2 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support