-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_3/scaffold_3_11149627-11363649

-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_7334-T1
Valid prediction for GlimmerHMM_glimmerT_7319-T1
Valid prediction for pasa_asmbl_40342.p1
Valid prediction for GlimmerHMM_glimmerT_7336-T1
Valid prediction for Augustus_model.g4765.t1
Valid prediction for Augustus_model.g4775.t1
Valid prediction for snap_scaffold_3-snap.2234-T1
Valid prediction for GlimmerHMM_glimmerT_7343-T1
Valid prediction for GlimmerHMM_glimmerT_7329-T1
Valid prediction for snap_scaffold_3-snap.2228-T1
Valid prediction for GlimmerHMM_glimmerT_7339-T1
Valid prediction for snap_scaffold_3-snap.2221-T1
Valid prediction for Augustus_model.g4768.t1
Couldn't classify 147869, 147929
Couldn't classify 148297, 148365
Sorry, prediction pasa_asmbl_40339.p2 fails validation.
(CGC)	 AC	147869-147929	GT	ACG
(TGA)	 AG	148042-148211	GT	GAG
(CCT)	 AG	148297-148365	AC	CAA
-recovered pasa_asmbl_40339.p2, internal, 148042, 148211
Valid prediction for GlimmerHMM_glimmerT_7332-T1
Valid prediction for snap_scaffold_3-snap.2253-T1
Valid prediction for GlimmerHMM_glimmerT_7326-T1
Valid prediction for Augustus_model.g4781.t1
Valid prediction for Augustus_model.g4771.t1
Valid prediction for snap_scaffold_3-snap.2217-T1
Valid prediction for GlimmerHMM_glimmerT_7338-T1
Valid prediction for snap_scaffold_3-snap.2236-T1
Valid prediction for snap_scaffold_3-snap.2241-T1
Valid prediction for snap_scaffold_3-snap.2219-T1
Valid prediction for GlimmerHMM_glimmerT_7318-T1
Valid prediction for Augustus_model.g4769.t1
Valid prediction for Augustus_model.g4773.t1
Valid prediction for snap_scaffold_3-snap.2215-T1
Valid prediction for Augustus_model.g4779.t1
Valid prediction for snap_scaffold_3-snap.2248-T1
Valid prediction for Augustus_model.g4776.t1
Valid prediction for snap_scaffold_3-snap.2226-T1
Valid prediction for snap_scaffold_3-snap.2220-T1
Valid prediction for snap_scaffold_3-snap.2242-T1
Valid prediction for snap_scaffold_3-snap.2244-T1
Valid prediction for snap_scaffold_3-snap.2232-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_3-snap.2252-T1
Valid prediction for snap_scaffold_3-snap.2239-T1
Valid prediction for Augustus_model.g4766.t1
Couldn't classify 121134, 121218
Sorry, prediction pasa_asmbl_40337.p1 fails validation.
(TTC)	 GC	121134-121218	GT	CTG
(CTC)	 AG	121931-122260	GT	TGG
(TGC)	 AG	124726-125010	GT	GAG
(TTG)	 AG	125489-125590	GT	GGG
(ACT)	 AG	126790-126794	GT	GAG
-recovered pasa_asmbl_40337.p1, terminal, 126790, 126794
-recovered pasa_asmbl_40337.p1, internal, 121931, 122260
-recovered pasa_asmbl_40337.p1, internal, 124726, 125010
-recovered pasa_asmbl_40337.p1, internal, 125489, 125590
-recovered pasa_asmbl_40337.p1, internal, 126790, 126794
Valid prediction for snap_scaffold_3-snap.2246-T1
Valid prediction for snap_scaffold_3-snap.2237-T1
Valid prediction for snap_scaffold_3-snap.2230-T1
Valid prediction for GlimmerHMM_glimmerT_7335-T1
Valid prediction for GlimmerHMM_glimmerT_7320-T1
Valid prediction for snap_scaffold_3-snap.2223-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.2243-T1
Valid prediction for Augustus_model.g4770.t1
Valid prediction for CodingQuarry_transcript_46281-T1
Valid prediction for Augustus_model.g4778.t1
Valid prediction for GlimmerHMM_glimmerT_7325-T1
Valid prediction for GlimmerHMM_glimmerT_7327-T1
Valid prediction for GlimmerHMM_glimmerT_7345-T1
Valid prediction for Augustus_model.g4763.t1
Valid prediction for snap_scaffold_3-snap.2214-T1
Valid prediction for Augustus_model.g4774.t1
Valid prediction for snap_scaffold_3-snap.2224-T1
Couldn't classify 51666, 51749
Sorry, prediction pasa_asmbl_39142.p1 fails validation.
(GGG)	 CC	51666-51749	GT	AGG
(AAA)	 AG	54389-54499	GT	AGG
(CTC)	 AG	54721-54851	GT	AGG
(TGC)	 AG	55034-55140	GT	AGG
(ATG)	 AG	55531-55628	GT	AGG
(GTT)	 AG	55838-55933	GT	AGG
(GTG)	 AG	57122-57308	GT	GGG
(AGC)	 AG	57634-57732	GT	AGG
(ATG)	 AG	57938-58005	AC	GAA
add_exon() Sorry, pasa_asmbl_39142.p1 55531-55628-initial-1 is invalid.
-recovered pasa_asmbl_39142.p1, initial, 55531, 55628
-recovered pasa_asmbl_39142.p1, terminal, 55034, 55140
-recovered pasa_asmbl_39142.p1, terminal, 57938, 58005
-recovered pasa_asmbl_39142.p1, internal, 54389, 54499
-recovered pasa_asmbl_39142.p1, internal, 54721, 54851
-recovered pasa_asmbl_39142.p1, internal, 55034, 55140
-recovered pasa_asmbl_39142.p1, internal, 55531, 55628
-recovered pasa_asmbl_39142.p1, internal, 55838, 55933
-recovered pasa_asmbl_39142.p1, internal, 57122, 57308
-recovered pasa_asmbl_39142.p1, internal, 57634, 57732
Valid prediction for snap_scaffold_3-snap.2229-T1
Valid prediction for GlimmerHMM_glimmerT_7328-T1
Valid prediction for GlimmerHMM_glimmerT_7333-T1
Valid prediction for GlimmerHMM_glimmerT_7316-T1
Valid prediction for GlimmerHMM_glimmerT_7344-T1
Valid prediction for GlimmerHMM_glimmerT_7340-T1
Valid prediction for snap_scaffold_3-snap.2233-T1
Valid prediction for snap_scaffold_3-snap.2240-T1
Valid prediction for Augustus_model.g4783.t1
Valid prediction for snap_scaffold_3-snap.2238-T1
Valid prediction for pasa_asmbl_39139.p1
Valid prediction for GlimmerHMM_glimmerT_7330-T1
Valid prediction for GlimmerHMM_glimmerT_7323-T1
Valid prediction for pasa_asmbl_39152.p2
Valid prediction for GlimmerHMM_glimmerT_7337-T1
Valid prediction for snap_scaffold_3-snap.2227-T1
Valid prediction for CodingQuarry_transcript_46278-T1
Valid prediction for Augustus_model.g4782.t1
Couldn't classify 35387, 35452
Couldn't classify 38470, 38685
Sorry, prediction pasa_asmbl_39148.p1 fails validation.
(CCT)	 GG	35387-35452	GT	TGG
(ATC)	 AG	35533-35658	GT	AGG
(GTA)	 AG	35839-35934	GT	AGG
(GGT)	 AG	36039-36275	GT	AGG
(CTG)	 AG	37056-37111	GT	AGG
(GTA)	 AG	37368-37470	GT	AGG
(AAA)	 AG	38470-38685	CT	CAC
-recovered pasa_asmbl_39148.p1, internal, 35533, 35658
-recovered pasa_asmbl_39148.p1, internal, 35839, 35934
-recovered pasa_asmbl_39148.p1, internal, 36039, 36275
-recovered pasa_asmbl_39148.p1, internal, 37056, 37111
-recovered pasa_asmbl_39148.p1, internal, 37368, 37470
Valid prediction for snap_scaffold_3-snap.2218-T1
Valid prediction for GlimmerHMM_glimmerT_7324-T1
Valid prediction for Augustus_model.g4767.t1
Valid prediction for Augustus_model.g4780.t1
Valid prediction for snap_scaffold_3-snap.2235-T1
Valid prediction for snap_scaffold_3-snap.2245-T1
Valid prediction for snap_scaffold_3-snap.2216-T1
Valid prediction for snap_scaffold_3-snap.2231-T1
Valid prediction for snap_scaffold_3-snap.2249-T1
Valid prediction for GlimmerHMM_glimmerT_7322-T1
Valid prediction for GlimmerHMM_glimmerT_7321-T1
Valid prediction for GlimmerHMM_glimmerT_7331-T1
Valid prediction for CodingQuarry_transcript_46277-T1
Valid prediction for GlimmerHMM_glimmerT_7342-T1
Valid prediction for Augustus_model.g4777.t1
Valid prediction for GlimmerHMM_glimmerT_7341-T1
Couldn't classify 38911, 39276
Sorry, prediction pasa_asmbl_39147.p1 fails validation.
(CCC)	 TG	38911-39276	TA	CCT
Valid prediction for Augustus_model.g4764.t1
Valid prediction for snap_scaffold_3-snap.2251-T1
Valid prediction for CodingQuarry_transcript_46282-T1
Couldn't classify 8283, 8384
Sorry, prediction pasa_asmbl_39153.p1 fails validation.
(GAG)	 AG	8283-8384	GC	AGG
(AGC)	 AG	8608-8737	GT	GGG
(AAA)	 AG	9355-9387	GT	AGG
(TGG)	 AG	10996-11126	GT	AGG
(AAC)	 AG	12385-12503	GT	AGG
(GAG)	 AG	13254-13366	GT	GAG
(AGT)	 AG	14196-14306	GT	TGG
(ACA)	 AG	14445-14539	GT	AGG
(GAA)	 AG	15354-15395	AG	AAA
-recovered pasa_asmbl_39153.p1, terminal, 15354, 15395
-recovered pasa_asmbl_39153.p1, internal, 8283, 8384
-recovered pasa_asmbl_39153.p1, internal, 8608, 8737
-recovered pasa_asmbl_39153.p1, internal, 9355, 9387
-recovered pasa_asmbl_39153.p1, internal, 10996, 11126
-recovered pasa_asmbl_39153.p1, internal, 12385, 12503
-recovered pasa_asmbl_39153.p1, internal, 13254, 13366
-recovered pasa_asmbl_39153.p1, internal, 14196, 14306
-recovered pasa_asmbl_39153.p1, internal, 14445, 14539
Valid prediction for HiQ_model.g4772.t1
Valid prediction for GlimmerHMM_glimmerT_7317-T1
Valid prediction for snap_scaffold_3-snap.2250-T1
Valid prediction for snap_scaffold_3-snap.2225-T1
Valid prediction for snap_scaffold_3-snap.2222-T1
Couldn't classify 205881, 206508
Couldn't classify 206564, 206589
Sorry, prediction CodingQuarry_transcript_46276-T1 fails validation.
(ATG)	 CC	205881-206508	TC	GCT
(CAT)	 GC	206564-206589	GC	GAG
Valid prediction for snap_scaffold_3-snap.2247-T1
Valid prediction for CodingQuarry_transcript_46280-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 16208, rend_intergenic: 10750  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22138, rend_intergenic: 16380  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31689, rend_intergenic: 26028  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42697, rend_intergenic: 33594  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59237, rend_intergenic: 48660  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96570, rend_intergenic: 96537  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100637, rend_intergenic: 96583  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115932, rend_intergenic: 115237  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128419, rend_intergenic: 124460  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169600, rend_intergenic: 158442  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181933, rend_intergenic: 176545  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 213093, rend_intergenic: 200577  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 214023
-exon list size: 365


building trellis

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1.1    
1.4    
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1.9    
2.2    
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5.7    
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10.9    
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11.4    
11.7    
12.0    
12.3    
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16.9    
17.2    
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17.7    
18.0    
18.3    
18.5    
18.8    
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19.3    
19.6    
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20.7    
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22.1    
22.3    
22.6    
22.9    
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23.4    
23.7    
24.0    
24.3    
24.5    
24.8    
25.1    
25.3    
25.6    
25.9    
26.2    
26.4    
26.7    
27.0    
27.2    
27.5    
27.8    
28.1    
28.3    
28.6    
28.9    
29.2    
29.4    
29.7    
30.0    
30.2    
30.5    
30.8    
31.1    
31.3    
31.6    
31.9    
32.2    
32.4    
32.7    
33.0    
33.2    
33.5    
33.8    
34.1    
34.3    
34.6    
34.9    
35.1    
35.4    
35.7    
36.0    
36.2    
36.5    
36.8    
37.1    
37.3    
37.6    
37.9    
38.1    
38.4    
38.7    
39.0    
39.2    
39.5    
39.8    
40.1    
40.3    
40.6    
40.9    
41.1    
41.4    
41.7    
42.0    
42.2    
42.5    
42.8    
43.1    
43.3    
43.6    
43.9    
44.1    
44.4    
44.7    
45.0    
45.2    
45.5    
45.8    
46.0    
46.3    
46.6    
46.9    
47.1    
47.4    
47.7    
48.0    
48.2    
48.5    
48.8    
49.0    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
51.0    
51.2    
51.5    
51.8    
52.0    
52.3    
52.6    
52.9    
53.1    
53.4    
53.7    
54.0    
54.2    
54.5    
54.8    
55.0    
55.3    
55.6    
55.9    
56.1    
56.4    
56.7    
56.9    
57.2    
57.5    
57.8    
58.0    
58.3    
58.6    
58.9    
59.1    
59.4    
59.7    
59.9    
60.2    
60.5    
60.8    
61.0    
61.3    
61.6    
61.9    
62.1    
62.4    
62.7    
62.9    
63.2    
63.5    
63.8    
64.0    
64.3    
64.6    
64.9    
65.1    
65.4    
65.7    
65.9    
66.2    
66.5    
66.8    
67.0    
67.3    
67.6    
67.8    
68.1    
68.4    
68.7    
68.9    
69.2    
69.5    
69.8    
70.0    
70.3    
70.6    
70.8    
71.1    
71.4    
71.7    
71.9    
72.2    
72.5    
72.8    
73.0    
73.3    
73.6    
73.8    
74.1    
74.4    
74.7    
74.9    
75.2    
75.5    
75.7    
76.0    
76.3    
76.6    
76.8    
77.1    
77.4    
77.7    
77.9    
78.2    
78.5    
78.7    
79.0    
79.3    
79.6    
79.8    
80.1    
80.4    
80.7    
80.9    
81.2    
81.5    
81.7    
82.0    
82.3    
82.6    
82.8    
83.1    
83.4    
83.7    
83.9    
84.2    
84.5    
84.7    
85.0    
85.3    
85.6    
85.8    
86.1    
86.4    
86.6    
86.9    
87.2    
87.5    
87.7    
88.0    
88.3    
88.6    
88.8    
89.1    
89.4    
89.6    
89.9    
90.2    
90.5    
90.7    
91.0    
91.3    
91.6    
91.8    
92.1    
92.4    
92.6    
92.9    
93.2    
93.5    
93.7    
94.0    
94.3    
94.6    
94.8    
95.1    
95.4    
95.6    
95.9    
96.2    
96.5    
96.7    
97.0    
97.3    
97.5    
97.8    
98.1    
98.4    
98.6    
98.9    
99.2    
99.5    
99.7    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 16208, rend_intergenic: 10750  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22138, rend_intergenic: 16380  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31689, rend_intergenic: 26028  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42697, rend_intergenic: 33594  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59237, rend_intergenic: 48660  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96570, rend_intergenic: 96537  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100637, rend_intergenic: 96583  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115932, rend_intergenic: 115237  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128419, rend_intergenic: 124460  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169600, rend_intergenic: 158442  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181933, rend_intergenic: 176545  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 213093, rend_intergenic: 200577  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support