-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_11/scaffold_11_16517053-16753653

-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_28530-T1
Valid prediction for snap_scaffold_11-snap.3403-T1
Valid prediction for GlimmerHMM_glimmerT_28518-T1
Valid prediction for snap_scaffold_11-snap.3374-T1
Valid prediction for snap_scaffold_11-snap.3394-T1
Valid prediction for GlimmerHMM_glimmerT_28525-T1
Valid prediction for pasa_asmbl_6167.p1
Valid prediction for CodingQuarry_transcript_8341-T1
Couldn't classify 127274, 127333
Sorry, prediction pasa_asmbl_6165.p1 fails validation.
(CAG)	 AC	127274-127333	GT	CGG
(CTG)	 AG	127482-127568	GT	AGG
(ATC)	 AG	127684-127800	GT	AGG
(ACA)	 AG	128083-128235	GT	TGG
(GTG)	 AG	128413-128554	GT	AGG
(GTT)	 AG	128759-128934	GT	AGG
(AAT)	 AG	129213-129317	GT	AGG
(ATG)	 AG	129452-129595	GT	AGG
(CTC)	 AG	129715-129936	CG	GAC
-recovered pasa_asmbl_6165.p1, initial, 129452, 129595
-recovered pasa_asmbl_6165.p1, terminal, 129715, 129936
-recovered pasa_asmbl_6165.p1, internal, 127482, 127568
-recovered pasa_asmbl_6165.p1, internal, 127684, 127800
-recovered pasa_asmbl_6165.p1, internal, 128083, 128235
-recovered pasa_asmbl_6165.p1, internal, 128413, 128554
-recovered pasa_asmbl_6165.p1, internal, 128759, 128934
-recovered pasa_asmbl_6165.p1, internal, 129213, 129317
-recovered pasa_asmbl_6165.p1, internal, 129452, 129595
Valid prediction for snap_scaffold_11-snap.3377-T1
Valid prediction for snap_scaffold_11-snap.3387-T1
Valid prediction for snap_scaffold_11-snap.3388-T1
Valid prediction for snap_scaffold_11-snap.3398-T1
Valid prediction for CodingQuarry_transcript_8350-T1
Couldn't classify 121305, 123575
Sorry, prediction pasa_asmbl_6164.p1 fails validation.
(TTT)	 CA	121305-123575	TT	AGT
Valid prediction for CodingQuarry_transcript_8345-T1
Valid prediction for GlimmerHMM_glimmerT_28529-T1
Valid prediction for GlimmerHMM_glimmerT_28512-T1
Valid prediction for GlimmerHMM_glimmerT_28505-T1
Valid prediction for snap_scaffold_11-snap.3386-T1
Valid prediction for pasa_asmbl_6171.p1
Valid prediction for pasa_asmbl_6168.p1
Valid prediction for snap_scaffold_11-snap.3383-T1
Valid prediction for snap_scaffold_11-snap.3409-T1
Valid prediction for GlimmerHMM_glimmerT_28531-T1
Valid prediction for GlimmerHMM_glimmerT_28509-T1
Valid prediction for GlimmerHMM_glimmerT_28514-T1
Valid prediction for GlimmerHMM_glimmerT_28520-T1
Valid prediction for CodingQuarry_transcript_8342-T1
Valid prediction for Augustus_model.g18890.t1
Valid prediction for Augustus_model.g18877.t1
Valid prediction for Augustus_model.g18892.t1
Valid prediction for snap_scaffold_11-snap.3368-T1
Valid prediction for GlimmerHMM_glimmerT_28527-T1
Valid prediction for snap_scaffold_11-snap.3376-T1
Valid prediction for Augustus_model.g18879.t1
Couldn't classify 116032, 116154
Sorry, prediction pasa_asmbl_6162.p1 fails validation.
(ATG)	 AG	114590-114769	GT	AGG
(GCG)	 AG	116032-116154	AA	ACA
-recovered pasa_asmbl_6162.p1, initial, 114590, 114769
-recovered pasa_asmbl_6162.p1, internal, 114590, 114769
Valid prediction for CodingQuarry_transcript_8351-T1
Valid prediction for Augustus_model.g18880.t1
Valid prediction for HiQ_model.g18891.t1
Valid prediction for snap_scaffold_11-snap.3363-T1
Valid prediction for snap_scaffold_11-snap.3385-T1
Valid prediction for snap_scaffold_11-snap.3382-T1
Valid prediction for snap_scaffold_11-snap.3384-T1
Valid prediction for snap_scaffold_11-snap.3391-T1
Couldn't classify 12378, 12381
Sorry, prediction pasa_asmbl_6157.p1 fails validation.
(ATG)	 CT	11356-11769	GT	AGG
(ATC)	 AG	12036-12184	GT	GAG
(CGT)	 AG	12378-12381	AC	TGA
-recovered pasa_asmbl_6157.p1, initial, 11356, 11769
-recovered pasa_asmbl_6157.p1, internal, 12036, 12184
Valid prediction for GlimmerHMM_glimmerT_28535-T1
Valid prediction for Augustus_model.g18889.t1
Valid prediction for snap_scaffold_11-snap.3402-T1
Valid prediction for GlimmerHMM_glimmerT_28517-T1
Valid prediction for snap_scaffold_11-snap.3366-T1
Valid prediction for snap_scaffold_11-snap.3392-T1
Valid prediction for GlimmerHMM_glimmerT_28508-T1
Couldn't classify 12394, 12520
Sorry, prediction pasa_asmbl_6158.p1 fails validation.
(CAT)	 AC	12394-12520	GT	TGG
(GGA)	 AG	12766-12920	GT	AAG
(GTG)	 AG	13043-13169	GT	AGG
(GTT)	 AG	13343-13450	GT	AGG
(GTG)	 AG	13737-13888	CT	AGC
-recovered pasa_asmbl_6158.p1, terminal, 13737, 13888
-recovered pasa_asmbl_6158.p1, internal, 12766, 12920
-recovered pasa_asmbl_6158.p1, internal, 13043, 13169
-recovered pasa_asmbl_6158.p1, internal, 13343, 13450
Valid prediction for Augustus_model.g18885.t1
Valid prediction for GlimmerHMM_glimmerT_28528-T1
Valid prediction for pasa_asmbl_6172.p1
Valid prediction for CodingQuarry_transcript_8352-T1
Couldn't classify 120525, 120872
Sorry, prediction pasa_asmbl_6163.p1 fails validation.
(TCT)	 CA	120525-120872	AA	CCA
Valid prediction for pasa_asmbl_6161.p1
Valid prediction for GlimmerHMM_glimmerT_28526-T1
Valid prediction for snap_scaffold_11-snap.3362-T1
Valid prediction for CodingQuarry_transcript_8349-T1
Valid prediction for Augustus_model.g18894.t1
Valid prediction for snap_scaffold_11-snap.3390-T1
Valid prediction for snap_scaffold_11-snap.3381-T1
Valid prediction for snap_scaffold_11-snap.3369-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_11-snap.3389-T1
Valid prediction for CodingQuarry_transcript_8348-T1
Valid prediction for Augustus_model.g18882.t1
Valid prediction for GlimmerHMM_glimmerT_28533-T1
Valid prediction for snap_scaffold_11-snap.3395-T1
Valid prediction for GlimmerHMM_glimmerT_28510-T1
Valid prediction for snap_scaffold_11-snap.3396-T1
Valid prediction for GlimmerHMM_glimmerT_28522-T1
Valid prediction for snap_scaffold_11-snap.3372-T1
Valid prediction for GlimmerHMM_glimmerT_28524-T1
Valid prediction for snap_scaffold_11-snap.3379-T1
Valid prediction for snap_scaffold_11-snap.3365-T1
Valid prediction for GlimmerHMM_glimmerT_28537-T1
Valid prediction for snap_scaffold_11-snap.3406-T1
Valid prediction for snap_scaffold_11-snap.3371-T1
Valid prediction for snap_scaffold_11-snap.3399-T1
Valid prediction for CodingQuarry_transcript_8346-T1
Couldn't classify 221019, 221309
Sorry, prediction pasa_asmbl_7228.p1 fails validation.
(ATG)	 CA	216812-216830	GT	AGG
(GTC)	 AG	218273-218340	GT	TGG
(GAC)	 AG	218449-218672	GT	AGG
(AGT)	 AG	219239-219321	GT	CTG
(ATG)	 AG	219592-219732	GT	AGG
(GCT)	 AG	219942-220094	GT	GGG
(GGA)	 AG	220307-220503	GT	GGG
(TTG)	 AG	221019-221309	AT	CCA
-recovered pasa_asmbl_7228.p1, initial, 216812, 216830
add_exon() Sorry, pasa_asmbl_7228.p1 219592-219732-initial-1 is invalid.
-recovered pasa_asmbl_7228.p1, initial, 219592, 219732
-recovered pasa_asmbl_7228.p1, internal, 218273, 218340
-recovered pasa_asmbl_7228.p1, internal, 218449, 218672
-recovered pasa_asmbl_7228.p1, internal, 219239, 219321
-recovered pasa_asmbl_7228.p1, internal, 219592, 219732
-recovered pasa_asmbl_7228.p1, internal, 219942, 220094
-recovered pasa_asmbl_7228.p1, internal, 220307, 220503
Valid prediction for snap_scaffold_11-snap.3364-T1
Valid prediction for Augustus_model.g18897.t1
Valid prediction for GlimmerHMM_glimmerT_28536-T1
Valid prediction for snap_scaffold_11-snap.3378-T1
Valid prediction for GlimmerHMM_glimmerT_28538-T1
Valid prediction for Augustus_model.g18878.t1
Valid prediction for snap_scaffold_11-snap.3401-T1
Valid prediction for pasa_asmbl_7233.p1
Valid prediction for CodingQuarry_transcript_8343-T1
Valid prediction for Augustus_model.g18896.t1
Valid prediction for Augustus_model.g18887.t1
Valid prediction for Augustus_model.g18886.t1
Valid prediction for GlimmerHMM_glimmerT_28507-T1
Valid prediction for snap_scaffold_11-snap.3367-T1
Valid prediction for GlimmerHMM_glimmerT_28521-T1
Valid prediction for GlimmerHMM_glimmerT_28515-T1
Valid prediction for snap_scaffold_11-snap.3408-T1
Valid prediction for Augustus_model.g18883.t1
Valid prediction for GlimmerHMM_glimmerT_28516-T1
Valid prediction for snap_scaffold_11-snap.3407-T1
Valid prediction for snap_scaffold_11-snap.3404-T1
Valid prediction for GlimmerHMM_glimmerT_28532-T1
Valid prediction for snap_scaffold_11-snap.3380-T1
Valid prediction for snap_scaffold_11-snap.3373-T1
Valid prediction for snap_scaffold_11-snap.3400-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for Augustus_model.g18881.t1
Valid prediction for HiQ_model.g18888.t1
Valid prediction for snap_scaffold_11-snap.3375-T1
Valid prediction for snap_scaffold_11-snap.3393-T1
Valid prediction for Augustus_model.g18893.t1
Valid prediction for GlimmerHMM_glimmerT_28523-T1
Valid prediction for GlimmerHMM_glimmerT_28513-T1
Valid prediction for snap_scaffold_11-snap.3405-T1
Valid prediction for GlimmerHMM_glimmerT_28519-T1
Valid prediction for pasa_asmbl_7231.p1
Valid prediction for CodingQuarry_transcript_8347-T1
Valid prediction for HiQ_model.g18884.t1
Valid prediction for GlimmerHMM_glimmerT_28534-T1
Valid prediction for pasa_asmbl_7232.p1
Valid prediction for CodingQuarry_transcript_8344-T1
Valid prediction for snap_scaffold_11-snap.3370-T1
Valid prediction for GlimmerHMM_glimmerT_28511-T1
Valid prediction for Augustus_model.g18895.t1
Valid prediction for snap_scaffold_11-snap.3397-T1
Valid prediction for GlimmerHMM_glimmerT_28506-T1
Valid prediction for snap_scaffold_11-snap.3411-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 30798, rend_intergenic: 25443  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47671, rend_intergenic: 38147  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106124, rend_intergenic: 101242  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163090, rend_intergenic: 161654  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164728, rend_intergenic: 163659  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200479, rend_intergenic: 198942  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 236601
-exon list size: 411


building trellis

0.2    
0.5    
0.7    
1.0    
1.2    
1.5    
1.7    
1.9    
2.2    
2.4    
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2.9    
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3.4    
3.6    
3.9    
4.1    
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4.6    
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7.0    
7.3    
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9.0    
9.2    
9.4    
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10.4    
10.7    
10.9    
11.1    
11.4    
11.6    
11.9    
12.1    
12.3    
12.6    
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13.1    
13.3    
13.6    
13.8    
14.0    
14.3    
14.5    
14.8    
15.0    
15.3    
15.5    
15.7    
16.0    
16.2    
16.5    
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16.9    
17.2    
17.4    
17.7    
17.9    
18.2    
18.4    
18.6    
18.9    
19.1    
19.4    
19.6    
19.9    
20.1    
20.3    
20.6    
20.8    
21.1    
21.3    
21.5    
21.8    
22.0    
22.3    
22.5    
22.8    
23.0    
23.2    
23.5    
23.7    
24.0    
24.2    
24.5    
24.7    
24.9    
25.2    
25.4    
25.7    
25.9    
26.2    
26.4    
26.6    
26.9    
27.1    
27.4    
27.6    
27.8    
28.1    
28.3    
28.6    
28.8    
29.1    
29.3    
29.5    
29.8    
30.0    
30.3    
30.5    
30.8    
31.0    
31.2    
31.5    
31.7    
32.0    
32.2    
32.4    
32.7    
32.9    
33.2    
33.4    
33.7    
33.9    
34.1    
34.4    
34.6    
34.9    
35.1    
35.4    
35.6    
35.8    
36.1    
36.3    
36.6    
36.8    
37.0    
37.3    
37.5    
37.8    
38.0    
38.3    
38.5    
38.7    
39.0    
39.2    
39.5    
39.7    
40.0    
40.2    
40.4    
40.7    
40.9    
41.2    
41.4    
41.6    
41.9    
42.1    
42.4    
42.6    
42.9    
43.1    
43.3    
43.6    
43.8    
44.1    
44.3    
44.6    
44.8    
45.0    
45.3    
45.5    
45.8    
46.0    
46.2    
46.5    
46.7    
47.0    
47.2    
47.5    
47.7    
47.9    
48.2    
48.4    
48.7    
48.9    
49.2    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.8    
51.1    
51.3    
51.6    
51.8    
52.1    
52.3    
52.5    
52.8    
53.0    
53.3    
53.5    
53.8    
54.0    
54.2    
54.5    
54.7    
55.0    
55.2    
55.4    
55.7    
55.9    
56.2    
56.4    
56.7    
56.9    
57.1    
57.4    
57.6    
57.9    
58.1    
58.4    
58.6    
58.8    
59.1    
59.3    
59.6    
59.8    
60.0    
60.3    
60.5    
60.8    
61.0    
61.3    
61.5    
61.7    
62.0    
62.2    
62.5    
62.7    
63.0    
63.2    
63.4    
63.7    
63.9    
64.2    
64.4    
64.6    
64.9    
65.1    
65.4    
65.6    
65.9    
66.1    
66.3    
66.6    
66.8    
67.1    
67.3    
67.6    
67.8    
68.0    
68.3    
68.5    
68.8    
69.0    
69.2    
69.5    
69.7    
70.0    
70.2    
70.5    
70.7    
70.9    
71.2    
71.4    
71.7    
71.9    
72.2    
72.4    
72.6    
72.9    
73.1    
73.4    
73.6    
73.8    
74.1    
74.3    
74.6    
74.8    
75.1    
75.3    
75.5    
75.8    
76.0    
76.3    
76.5    
76.8    
77.0    
77.2    
77.5    
77.7    
78.0    
78.2    
78.5    
78.7    
78.9    
79.2    
79.4    
79.7    
79.9    
80.1    
80.4    
80.6    
80.9    
81.1    
81.4    
81.6    
81.8    
82.1    
82.3    
82.6    
82.8    
83.1    
83.3    
83.5    
83.8    
84.0    
84.3    
84.5    
84.7    
85.0    
85.2    
85.5    
85.7    
86.0    
86.2    
86.4    
86.7    
86.9    
87.2    
87.4    
87.7    
87.9    
88.1    
88.4    
88.6    
88.9    
89.1    
89.3    
89.6    
89.8    
90.1    
90.3    
90.6    
90.8    
91.0    
91.3    
91.5    
91.8    
92.0    
92.3    
92.5    
92.7    
93.0    
93.2    
93.5    
93.7    
93.9    
94.2    
94.4    
94.7    
94.9    
95.2    
95.4    
95.6    
95.9    
96.1    
96.4    
96.6    
96.9    
97.1    
97.3    
97.6    
97.8    
98.1    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 40 predictions from path traversal
Error with prediction: snap lend_intergenic: 30798, rend_intergenic: 25443  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47671, rend_intergenic: 38147  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106124, rend_intergenic: 101242  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163090, rend_intergenic: 161654  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164728, rend_intergenic: 163659  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200479, rend_intergenic: 198942  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 33 predictions persist after filtering for low support