-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_6/scaffold_6_17392830-17539279

-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_16825-T1
Valid prediction for GlimmerHMM_glimmerT_16830-T1
Valid prediction for snap_scaffold_6-snap.3693-T1
Valid prediction for snap_scaffold_6-snap.3695-T1
Valid prediction for GeneMark_model.28180_t
Valid prediction for snap_scaffold_6-snap.3676-T1
Valid prediction for pasa_asmbl_47694.p1
Valid prediction for GeneMark_model.28171_t
Valid prediction for Augustus_model.g11310.t1
Valid prediction for snap_scaffold_6-snap.3705-T1
Valid prediction for CodingQuarry_transcript_55258-T1
Valid prediction for GeneMark_model.28193_t
Valid prediction for GeneMark_model.28181_t
Valid prediction for snap_scaffold_6-snap.3685-T1
Valid prediction for snap_scaffold_6-snap.3708-T1
Valid prediction for GlimmerHMM_glimmerT_16815-T1
Valid prediction for snap_scaffold_6-snap.3678-T1
Valid prediction for GeneMark_model.28178_t
Valid prediction for snap_scaffold_6-snap.3689-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for snap_scaffold_6-snap.3684-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_16813-T1
Valid prediction for GlimmerHMM_glimmerT_16823-T1
Valid prediction for GeneMark_model.28167_t
Valid prediction for Augustus_model.g11306.t1
Valid prediction for Augustus_model.g11309.t1
Valid prediction for GlimmerHMM_glimmerT_16826-T1
Valid prediction for CodingQuarry_transcript_55260-T1
Valid prediction for snap_scaffold_6-snap.3699-T1
Valid prediction for GeneMark_model.28165_t
Valid prediction for snap_scaffold_6-snap.3671-T1
Couldn't classify 135090, 135419
Sorry, prediction pasa_asmbl_47703.p2 fails validation.
(ATG)	 GG	135090-135419	CA	TGC
Valid prediction for GeneMark_model.28172_t
Valid prediction for Augustus_model.g11300.t1
Valid prediction for Augustus_model.g11301.t1
Valid prediction for snap_scaffold_6-snap.3692-T1
Valid prediction for snap_scaffold_6-snap.3697-T1
Valid prediction for snap_scaffold_6-snap.3694-T1
Valid prediction for snap_scaffold_6-snap.3681-T1
Valid prediction for GeneMark_model.28187_t
Couldn't classify 128197, 128674
Sorry, prediction pasa_asmbl_47698.p1 fails validation.
(ATG)	 CT	125355-127930	GT	AGG
(GCA)	 AG	128197-128674	CA	AGC
-recovered pasa_asmbl_47698.p1, initial, 125355, 127930
Valid prediction for GlimmerHMM_glimmerT_16827-T1
Valid prediction for CodingQuarry_transcript_55261-T1
Valid prediction for GlimmerHMM_glimmerT_16829-T1
Valid prediction for snap_scaffold_6-snap.3706-T1
Valid prediction for GeneMark_model.28195_t
Valid prediction for GeneMark_model.28189_t
Valid prediction for GlimmerHMM_glimmerT_16833-T1
Valid prediction for snap_scaffold_6-snap.3696-T1
Valid prediction for GlimmerHMM_glimmerT_16812-T1
Valid prediction for snap_scaffold_6-snap.3709-T1
Valid prediction for GeneMark_model.28164_t
Couldn't classify 47494, 47574
Sorry, prediction pasa_asmbl_47691.p1 fails validation.
(ACA)	 TC	47494-47574	GT	AGG
(GAC)	 AG	48291-48416	GT	AGG
(GTG)	 AG	49660-49705	GT	AAG
(ATA)	 AG	49824-49960	GT	AGG
(AGG)	 AG	50269-50354	GT	AGG
(GGA)	 AG	50648-50720	GT	AGG
(TTA)	 AG	51044-51159	GT	ATG
(TGA)	 AG	52624-52756	GT	AGG
(CTG)	 AG	53472-53619	GT	TGG
(ATC)	 AG	54365-54495	GT	TGG
(GGA)	 AG	54679-54764	GT	AGG
(GTA)	 AG	55055-55184	GT	GGG
(CAC)	 AG	55623-55765	GT	GGG
(ATA)	 AG	56116-56308	GT	AGG
(CAA)	 AG	56607-56700	GT	AGG
(ATT)	 AG	56822-56838	GA	GAG
-recovered pasa_asmbl_47691.p1, terminal, 54679, 54764
-recovered pasa_asmbl_47691.p1, terminal, 56822, 56838
-recovered pasa_asmbl_47691.p1, internal, 48291, 48416
-recovered pasa_asmbl_47691.p1, internal, 49660, 49705
-recovered pasa_asmbl_47691.p1, internal, 49824, 49960
-recovered pasa_asmbl_47691.p1, internal, 50269, 50354
-recovered pasa_asmbl_47691.p1, internal, 50648, 50720
-recovered pasa_asmbl_47691.p1, internal, 51044, 51159
-recovered pasa_asmbl_47691.p1, internal, 52624, 52756
-recovered pasa_asmbl_47691.p1, internal, 53472, 53619
-recovered pasa_asmbl_47691.p1, internal, 54365, 54495
-recovered pasa_asmbl_47691.p1, internal, 54679, 54764
-recovered pasa_asmbl_47691.p1, internal, 55055, 55184
-recovered pasa_asmbl_47691.p1, internal, 55623, 55765
-recovered pasa_asmbl_47691.p1, internal, 56116, 56308
-recovered pasa_asmbl_47691.p1, internal, 56607, 56700
Valid prediction for snap_scaffold_6-snap.3698-T1
Valid prediction for CodingQuarry_transcript_55259-T1
Valid prediction for GeneMark_model.28194_t
Valid prediction for GeneMark_model.28185_t
Valid prediction for Augustus_model.g11311.t1
Valid prediction for snap_scaffold_6-snap.3702-T1
Valid prediction for GeneMark_model.28182_t
Valid prediction for HiQ_model.g11303.t1
Valid prediction for Augustus_model.g11302.t1
Valid prediction for GlimmerHMM_glimmerT_16820-T1
Couldn't classify 79516, 81093
Couldn't classify 81326, 81382
Sorry, prediction pasa_asmbl_47693.p1 fails validation.
(AGC)	 GC	79516-81093	GT	AGG
(TTT)	 AG	81326-81382	AG	CCA
Valid prediction for GeneMark_model.28175_t
Valid prediction for Augustus_model.g11316.t1
Valid prediction for snap_scaffold_6-snap.3700-T1
Valid prediction for Augustus_model.g11313.t1
Valid prediction for Augustus_model.g11317.t1
Valid prediction for GlimmerHMM_glimmerT_16828-T1
Valid prediction for Augustus_model.g11312.t1
Valid prediction for GlimmerHMM_glimmerT_16816-T1
Valid prediction for snap_scaffold_6-snap.3683-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 GeneMark_model.28161_t
Valid prediction for snap_scaffold_6-snap.3672-T1
Valid prediction for GeneMark_model.28174_t
Valid prediction for GeneMark_model.28176_t
Valid prediction for snap_scaffold_6-snap.3679-T1
Valid prediction for snap_scaffold_6-snap.3701-T1
Valid prediction for snap_scaffold_6-snap.3704-T1
Valid prediction for Augustus_model.g11307.t1
Valid prediction for GlimmerHMM_glimmerT_16819-T1
Valid prediction for GeneMark_model.28192_t
Valid prediction for GeneMark_model.28169_t
Valid prediction for Augustus_model.g11305.t1
Valid prediction for GeneMark_model.28179_t
Valid prediction for GeneMark_model.28186_t
Valid prediction for snap_scaffold_6-snap.3703-T1
Valid prediction for snap_scaffold_6-snap.3690-T1
Valid prediction for GlimmerHMM_glimmerT_16809-T1
Valid prediction for GlimmerHMM_glimmerT_16824-T1
Valid prediction for Augustus_model.g11304.t1
Valid prediction for snap_scaffold_6-snap.3680-T1
Valid prediction for GlimmerHMM_glimmerT_16832-T1
Valid prediction for GeneMark_model.28177_t
Valid prediction for Augustus_model.g11314.t1
Couldn't classify 31145, 31231
Couldn't classify 35150, 35383
Sorry, prediction pasa_asmbl_49126.p1 fails validation.
(GTG)	 CC	31145-31231	GT	AGG
(GTT)	 AG	32291-32525	GT	TGG
(ATG)	 AG	32633-32688	GT	AGG
(GTG)	 AG	32848-32952	GT	AGG
(GTC)	 AG	33456-33603	GT	AGG
(GAT)	 AG	33991-34073	GT	AGG
(GAG)	 AG	35150-35383	GG	AGG
-recovered pasa_asmbl_49126.p1, initial, 32633, 32688
-recovered pasa_asmbl_49126.p1, internal, 32291, 32525
-recovered pasa_asmbl_49126.p1, internal, 32633, 32688
-recovered pasa_asmbl_49126.p1, internal, 32848, 32952
-recovered pasa_asmbl_49126.p1, internal, 33456, 33603
-recovered pasa_asmbl_49126.p1, internal, 33991, 34073
Valid prediction for snap_scaffold_6-snap.3677-T1
Valid prediction for snap_scaffold_6-snap.3707-T1
Valid prediction for GeneMark_model.28163_t
Valid prediction for GeneMark_model.28188_t
Valid prediction for GlimmerHMM_glimmerT_16831-T1
Valid prediction for HiQ_model.g11315.t1
Valid prediction for GlimmerHMM_glimmerT_16821-T1
Valid prediction for snap_scaffold_6-snap.3688-T1
Valid prediction for GlimmerHMM_glimmerT_16810-T1
Valid prediction for snap_scaffold_6-snap.3673-T1
Valid prediction for GeneMark_model.28184_t
Valid prediction for GeneMark_model.28191_t
Valid prediction for GlimmerHMM_glimmerT_16814-T1
Valid prediction for GeneMark_model.28183_t
Valid prediction for snap_scaffold_6-snap.3687-T1
Valid prediction for Augustus_model.g11308.t1
Valid prediction for GeneMark_model.28173_t
Valid prediction for Augustus_model.g11299.t1
Valid prediction for snap_scaffold_6-snap.3674-T1
Valid prediction for snap_scaffold_6-snap.3682-T1
Valid prediction for GlimmerHMM_glimmerT_16811-T1
Valid prediction for GeneMark_model.28190_t
Valid prediction for snap_scaffold_6-snap.3675-T1
Valid prediction for GlimmerHMM_glimmerT_16818-T1
Valid prediction for GlimmerHMM_glimmerT_16822-T1
Valid prediction for snap_scaffold_6-snap.3686-T1
Valid prediction for snap_scaffold_6-snap.3691-T1
Valid prediction for GlimmerHMM_glimmerT_16817-T1
Valid prediction for GeneMark_model.28168_t
Valid prediction for GeneMark_model.28166_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11850, rend_intergenic: 4046  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20071, rend_intergenic: 13749  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22615, rend_intergenic: 22272  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27472, rend_intergenic: 23347  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39970, rend_intergenic: 37453  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42112, rend_intergenic: 40539  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57698, rend_intergenic: 49837  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113312, rend_intergenic: 106637  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117606, rend_intergenic: 113406  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 146450
-exon list size: 471


building trellis

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3.8    
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8.9    
9.1    
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11.8    
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17.8    
18.0    
18.2    
18.4    
18.6    
18.8    
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20.7    
20.9    
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21.6    
21.8    
22.0    
22.2    
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22.6    
22.8    
23.0    
23.3    
23.5    
23.7    
23.9    
24.1    
24.3    
24.5    
24.7    
24.9    
25.2    
25.4    
25.6    
25.8    
26.0    
26.2    
26.4    
26.6    
26.8    
27.1    
27.3    
27.5    
27.7    
27.9    
28.1    
28.3    
28.5    
28.8    
29.0    
29.2    
29.4    
29.6    
29.8    
30.0    
30.2    
30.4    
30.7    
30.9    
31.1    
31.3    
31.5    
31.7    
31.9    
32.1    
32.3    
32.6    
32.8    
33.0    
33.2    
33.4    
33.6    
33.8    
34.0    
34.2    
34.5    
34.7    
34.9    
35.1    
35.3    
35.5    
35.7    
35.9    
36.2    
36.4    
36.6    
36.8    
37.0    
37.2    
37.4    
37.6    
37.8    
38.1    
38.3    
38.5    
38.7    
38.9    
39.1    
39.3    
39.5    
39.7    
40.0    
40.2    
40.4    
40.6    
40.8    
41.0    
41.2    
41.4    
41.6    
41.9    
42.1    
42.3    
42.5    
42.7    
42.9    
43.1    
43.3    
43.6    
43.8    
44.0    
44.2    
44.4    
44.6    
44.8    
45.0    
45.2    
45.5    
45.7    
45.9    
46.1    
46.3    
46.5    
46.7    
46.9    
47.1    
47.4    
47.6    
47.8    
48.0    
48.2    
48.4    
48.6    
48.8    
49.0    
49.3    
49.5    
49.7    
49.9    
50.1    
50.3    
50.5    
50.7    
51.0    
51.2    
51.4    
51.6    
51.8    
52.0    
52.2    
52.4    
52.6    
52.9    
53.1    
53.3    
53.5    
53.7    
53.9    
54.1    
54.3    
54.5    
54.8    
55.0    
55.2    
55.4    
55.6    
55.8    
56.0    
56.2    
56.4    
56.7    
56.9    
57.1    
57.3    
57.5    
57.7    
57.9    
58.1    
58.4    
58.6    
58.8    
59.0    
59.2    
59.4    
59.6    
59.8    
60.0    
60.3    
60.5    
60.7    
60.9    
61.1    
61.3    
61.5    
61.7    
61.9    
62.2    
62.4    
62.6    
62.8    
63.0    
63.2    
63.4    
63.6    
63.8    
64.1    
64.3    
64.5    
64.7    
64.9    
65.1    
65.3    
65.5    
65.8    
66.0    
66.2    
66.4    
66.6    
66.8    
67.0    
67.2    
67.4    
67.7    
67.9    
68.1    
68.3    
68.5    
68.7    
68.9    
69.1    
69.3    
69.6    
69.8    
70.0    
70.2    
70.4    
70.6    
70.8    
71.0    
71.2    
71.5    
71.7    
71.9    
72.1    
72.3    
72.5    
72.7    
72.9    
73.2    
73.4    
73.6    
73.8    
74.0    
74.2    
74.4    
74.6    
74.8    
75.1    
75.3    
75.5    
75.7    
75.9    
76.1    
76.3    
76.5    
76.7    
77.0    
77.2    
77.4    
77.6    
77.8    
78.0    
78.2    
78.4    
78.6    
78.9    
79.1    
79.3    
79.5    
79.7    
79.9    
80.1    
80.3    
80.5    
80.8    
81.0    
81.2    
81.4    
81.6    
81.8    
82.0    
82.2    
82.5    
82.7    
82.9    
83.1    
83.3    
83.5    
83.7    
83.9    
84.1    
84.4    
84.6    
84.8    
85.0    
85.2    
85.4    
85.6    
85.8    
86.0    
86.3    
86.5    
86.7    
86.9    
87.1    
87.3    
87.5    
87.7    
87.9    
88.2    
88.4    
88.6    
88.8    
89.0    
89.2    
89.4    
89.6    
89.9    
90.1    
90.3    
90.5    
90.7    
90.9    
91.1    
91.3    
91.5    
91.8    
92.0    
92.2    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.7    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.6    
95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.2    
99.4    
99.6    
99.8    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 11850, rend_intergenic: 4046  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20071, rend_intergenic: 13749  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22615, rend_intergenic: 22272  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27472, rend_intergenic: 23347  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39970, rend_intergenic: 37453  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42112, rend_intergenic: 40539  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57698, rend_intergenic: 49837  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113312, rend_intergenic: 106637  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117606, rend_intergenic: 113406  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support