-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_27/scaffold_27_6709733-6856102

-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_27-snap.1599-T1
Valid prediction for Augustus_model.g38107.t1
Valid prediction for snap_scaffold_27-snap.1598-T1
Valid prediction for snap_scaffold_27-snap.1592-T1
Valid prediction for snap_scaffold_27-snap.1600-T1
Valid prediction for snap_scaffold_27-snap.1587-T1
Valid prediction for Augustus_model.g38109.t1
Valid prediction for GlimmerHMM_glimmerT_57523-T1
Valid prediction for snap_scaffold_27-snap.1593-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_57510-T1
Couldn't classify 2528, 2686
Sorry, prediction pasa_asmbl_36578.p1 fails validation.
(ATG)	 CA	2267-2428	GT	AGG
(GTG)	 AG	2528-2686	AG	ACA
-recovered pasa_asmbl_36578.p1, initial, 2267, 2428
Valid prediction for Augustus_model.g38125.t1
Valid prediction for snap_scaffold_27-snap.1572-T1
Valid prediction for snap_scaffold_27-snap.1606-T1
Valid prediction for snap_scaffold_27-snap.1603-T1
Couldn't classify 29848, 29956
Sorry, prediction pasa_asmbl_36411.p3 fails validation.
(ATC)	 AG	29848-29956	GT	GGG
(ACT)	 AG	30338-30424	GT	AGG
(CCC)	 AG	31926-32003	GT	AGG
(GCC)	 AG	32420-32472	AT	AGA
-recovered pasa_asmbl_36411.p3, terminal, 32420, 32472
-recovered pasa_asmbl_36411.p3, internal, 29848, 29956
-recovered pasa_asmbl_36411.p3, internal, 30338, 30424
-recovered pasa_asmbl_36411.p3, internal, 31926, 32003
Valid prediction for snap_scaffold_27-snap.1567-T1
Valid prediction for GlimmerHMM_glimmerT_57526-T1
Valid prediction for GlimmerHMM_glimmerT_57527-T1
Valid prediction for snap_scaffold_27-snap.1574-T1
Valid prediction for CodingQuarry_transcript_41925-T1
Valid prediction for Augustus_model.g38123.t1
Valid prediction for Augustus_model.g38117.t1
Couldn't classify 7097, 7113
Sorry, prediction pasa_asmbl_36406.p1 fails validation.
(ATG)	 AG	3706-3794	GT	TGG
(GGA)	 AG	3936-4041	GT	AGG
(GGG)	 AG	5812-5970	GT	TGG
(GCT)	 AG	6553-6679	GT	TGG
(GTG)	 AG	6793-6927	GT	AGG
(CCG)	 AG	7097-7113	CT	AGC
-recovered pasa_asmbl_36406.p1, initial, 3706, 3794
-recovered pasa_asmbl_36406.p1, internal, 3706, 3794
-recovered pasa_asmbl_36406.p1, internal, 3936, 4041
-recovered pasa_asmbl_36406.p1, internal, 5812, 5970
-recovered pasa_asmbl_36406.p1, internal, 6553, 6679
-recovered pasa_asmbl_36406.p1, internal, 6793, 6927
Valid prediction for snap_scaffold_27-snap.1607-T1
Valid prediction for snap_scaffold_27-snap.1595-T1
Valid prediction for snap_scaffold_27-snap.1591-T1
Valid prediction for GlimmerHMM_glimmerT_57512-T1
Valid prediction for GlimmerHMM_glimmerT_57522-T1
Valid prediction for snap_scaffold_27-snap.1589-T1
Couldn't classify 110093, 110235
Sorry, prediction pasa_asmbl_36414.p1 fails validation.
(ATG)	 GC	105892-105924	GC	AGG
(GCT)	 AG	106252-106299	GT	TGG
(AAC)	 AG	106531-106603	GT	CTG
(CCT)	 AG	106792-106900	GT	AGG
(GCA)	 AG	107089-107177	GT	CGG
(ACC)	 AG	107385-107570	GT	TGG
(CCT)	 AG	110093-110235	TC	AGT
-recovered pasa_asmbl_36414.p1, initial, 105892, 105924
-recovered pasa_asmbl_36414.p1, internal, 106252, 106299
-recovered pasa_asmbl_36414.p1, internal, 106531, 106603
-recovered pasa_asmbl_36414.p1, internal, 106792, 106900
-recovered pasa_asmbl_36414.p1, internal, 107089, 107177
-recovered pasa_asmbl_36414.p1, internal, 107385, 107570
Valid prediction for GlimmerHMM_glimmerT_57511-T1
Valid prediction for snap_scaffold_27-snap.1582-T1
Valid prediction for Augustus_model.g38124.t1
Valid prediction for GlimmerHMM_glimmerT_57529-T1
Valid prediction for GlimmerHMM_glimmerT_57521-T1
Valid prediction for GlimmerHMM_glimmerT_57530-T1
Valid prediction for Augustus_model.g38116.t1
Valid prediction for GlimmerHMM_glimmerT_57514-T1
Valid prediction for CodingQuarry_transcript_41923-T1
Valid prediction for snap_scaffold_27-snap.1583-T1
Valid prediction for Augustus_model.g38120.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_27-snap.1577-T1
Valid prediction for snap_scaffold_27-snap.1588-T1
Valid prediction for Augustus_model.g38111.t1
Valid prediction for Augustus_model.g38118.t1
Valid prediction for snap_scaffold_27-snap.1596-T1
Valid prediction for snap_scaffold_27-snap.1601-T1
Valid prediction for snap_scaffold_27-snap.1581-T1
Valid prediction for GlimmerHMM_glimmerT_57524-T1
Valid prediction for snap_scaffold_27-snap.1585-T1
Valid prediction for GlimmerHMM_glimmerT_57525-T1
Valid prediction for snap_scaffold_27-snap.1570-T1
Valid prediction for Augustus_model.g38110.t1
Valid prediction for snap_scaffold_27-snap.1576-T1
Valid prediction for snap_scaffold_27-snap.1580-T1
Valid prediction for GlimmerHMM_glimmerT_57516-T1
Valid prediction for snap_scaffold_27-snap.1608-T1
Valid prediction for snap_scaffold_27-snap.1573-T1
Valid prediction for snap_scaffold_27-snap.1584-T1
Valid prediction for snap_scaffold_27-snap.1575-T1
Valid prediction for snap_scaffold_27-snap.1568-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_57520-T1
Valid prediction for Augustus_model.g38122.t1
Valid prediction for snap_scaffold_27-snap.1586-T1
Valid prediction for snap_scaffold_27-snap.1578-T1
Valid prediction for snap_scaffold_27-snap.1605-T1
Valid prediction for GlimmerHMM_glimmerT_57517-T1
Valid prediction for GlimmerHMM_glimmerT_57528-T1
Valid prediction for snap_scaffold_27-snap.1597-T1
Valid prediction for GlimmerHMM_glimmerT_57519-T1
Valid prediction for GlimmerHMM_glimmerT_57531-T1
Valid prediction for Augustus_model.g38121.t1
Couldn't classify 137970, 138383
Sorry, prediction pasa_asmbl_36407.p1 fails validation.
(ATG)	 TC	137970-138383	TC	TCT
Valid prediction for snap_scaffold_27-snap.1604-T1
Valid prediction for snap_scaffold_27-snap.1569-T1
Valid prediction for GlimmerHMM_glimmerT_57518-T1
Couldn't classify 42321, 42621
Sorry, prediction pasa_asmbl_37085.p1 fails validation.
(CAT)	 AC	42321-42621	GT	GGG
(GTG)	 AG	42760-43005	GT	TGG
(GGC)	 AG	43436-43608	GT	AGG
(ACG)	 AG	43696-43834	GT	AGG
(ACG)	 AG	43979-44095	GT	GGG
(GTG)	 AG	44322-44445	GT	GCG
(GGG)	 AG	44899-45028	CA	GAC
-recovered pasa_asmbl_37085.p1, terminal, 44899, 45028
-recovered pasa_asmbl_37085.p1, internal, 42760, 43005
-recovered pasa_asmbl_37085.p1, internal, 43436, 43608
-recovered pasa_asmbl_37085.p1, internal, 43696, 43834
-recovered pasa_asmbl_37085.p1, internal, 43979, 44095
-recovered pasa_asmbl_37085.p1, internal, 44322, 44445
Valid prediction for Augustus_model.g38119.t1
Valid prediction for GlimmerHMM_glimmerT_57515-T1
Valid prediction for snap_scaffold_27-snap.1594-T1
Valid prediction for Augustus_model.g38113.t1
Valid prediction for GlimmerHMM_glimmerT_57513-T1
Valid prediction for snap_scaffold_27-snap.1609-T1
Valid prediction for snap_scaffold_27-snap.1602-T1
Valid prediction for Augustus_model.g38108.t1
Valid prediction for Augustus_model.g38114.t1
Valid prediction for Augustus_model.g38115.t1
Valid prediction for snap_scaffold_27-snap.1579-T1
Valid prediction for snap_scaffold_27-snap.1571-T1
Valid prediction for Augustus_model.g38112.t1
Valid prediction for snap_scaffold_27-snap.1590-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10805, rend_intergenic: 2318  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24928, rend_intergenic: 16930  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29107, rend_intergenic: 25288  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29924, rend_intergenic: 29132  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83805, rend_intergenic: 80405  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94259, rend_intergenic: 88783  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97921, rend_intergenic: 96371  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102396, rend_intergenic: 101033  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118138, rend_intergenic: 110503  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123742, rend_intergenic: 118163  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124631, rend_intergenic: 123948  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129094, rend_intergenic: 125834  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136855, rend_intergenic: 130260  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145556, rend_intergenic: 137141  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 146370
-exon list size: 324


building trellis

0.3    
0.6    
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1.2    
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3.7    
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7.1    
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8.0    
8.3    
8.6    
8.9    
9.2    
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9.8    
10.1    
10.4    
10.7    
11.0    
11.3    
11.7    
12.0    
12.3    
12.6    
12.9    
13.2    
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13.8    
14.1    
14.4    
14.7    
15.0    
15.3    
15.6    
16.0    
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17.2    
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18.1    
18.4    
18.7    
19.0    
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20.9    
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21.5    
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22.1    
22.4    
22.7    
23.0    
23.3    
23.6    
23.9    
24.2    
24.5    
24.8    
25.2    
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26.7    
27.0    
27.3    
27.6    
27.9    
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28.8    
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29.4    
29.8    
30.1    
30.4    
30.7    
31.0    
31.3    
31.6    
31.9    
32.2    
32.5    
32.8    
33.1    
33.4    
33.7    
34.0    
34.4    
34.7    
35.0    
35.3    
35.6    
35.9    
36.2    
36.5    
36.8    
37.1    
37.4    
37.7    
38.0    
38.3    
38.7    
39.0    
39.3    
39.6    
39.9    
40.2    
40.5    
40.8    
41.1    
41.4    
41.7    
42.0    
42.3    
42.6    
42.9    
43.3    
43.6    
43.9    
44.2    
44.5    
44.8    
45.1    
45.4    
45.7    
46.0    
46.3    
46.6    
46.9    
47.2    
47.5    
47.9    
48.2    
48.5    
48.8    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.2    
51.5    
51.8    
52.1    
52.5    
52.8    
53.1    
53.4    
53.7    
54.0    
54.3    
54.6    
54.9    
55.2    
55.5    
55.8    
56.1    
56.4    
56.7    
57.1    
57.4    
57.7    
58.0    
58.3    
58.6    
58.9    
59.2    
59.5    
59.8    
60.1    
60.4    
60.7    
61.0    
61.3    
61.7    
62.0    
62.3    
62.6    
62.9    
63.2    
63.5    
63.8    
64.1    
64.4    
64.7    
65.0    
65.3    
65.6    
66.0    
66.3    
66.6    
66.9    
67.2    
67.5    
67.8    
68.1    
68.4    
68.7    
69.0    
69.3    
69.6    
69.9    
70.2    
70.6    
70.9    
71.2    
71.5    
71.8    
72.1    
72.4    
72.7    
73.0    
73.3    
73.6    
73.9    
74.2    
74.5    
74.8    
75.2    
75.5    
75.8    
76.1    
76.4    
76.7    
77.0    
77.3    
77.6    
77.9    
78.2    
78.5    
78.8    
79.1    
79.4    
79.8    
80.1    
80.4    
80.7    
81.0    
81.3    
81.6    
81.9    
82.2    
82.5    
82.8    
83.1    
83.4    
83.7    
84.0    
84.4    
84.7    
85.0    
85.3    
85.6    
85.9    
86.2    
86.5    
86.8    
87.1    
87.4    
87.7    
88.0    
88.3    
88.7    
89.0    
89.3    
89.6    
89.9    
90.2    
90.5    
90.8    
91.1    
91.4    
91.7    
92.0    
92.3    
92.6    
92.9    
93.3    
93.6    
93.9    
94.2    
94.5    
94.8    
95.1    
95.4    
95.7    
96.0    
96.3    
96.6    
96.9    
97.2    
97.5    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 10805, rend_intergenic: 2318  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24928, rend_intergenic: 16930  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29107, rend_intergenic: 25288  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29924, rend_intergenic: 29132  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83805, rend_intergenic: 80405  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94259, rend_intergenic: 88783  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97921, rend_intergenic: 96371  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102396, rend_intergenic: 101033  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118138, rend_intergenic: 110503  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123742, rend_intergenic: 118163  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124631, rend_intergenic: 123948  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129094, rend_intergenic: 125834  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136855, rend_intergenic: 130260  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145556, rend_intergenic: 137141  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 133881 - 146370
-exon list size: 16


building trellis

5.6    
11.1    
16.7    
22.2    
27.8    
33.3    
38.9    
44.4    
50.0    
55.6    
61.1    
66.7    
72.2    
77.8    
83.3    
88.9    
94.4    
-found 1 predictions from path traversal

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