-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_4/scaffold_4_9160842-9383618

-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 GeneMark_model.16375_t
Valid prediction for snap_scaffold_4-snap.1972-T1
Valid prediction for GeneMark_model.16398_t
Valid prediction for snap_scaffold_4-snap.1942-T1
Valid prediction for snap_scaffold_4-snap.1921-T1
Valid prediction for snap_scaffold_4-snap.1941-T1
Valid prediction for GeneMark_model.16424_t
Valid prediction for GlimmerHMM_glimmerT_10104-T1
Valid prediction for GeneMark_model.16406_t
Valid prediction for Augustus_model.g6619.t1
Valid prediction for GeneMark_model.16391_t
Valid prediction for GeneMark_model.16432_t
Valid prediction for GlimmerHMM_glimmerT_10080-T1
Valid prediction for Augustus_model.g6617.t1
Valid prediction for snap_scaffold_4-snap.1952-T1
Valid prediction for GeneMark_model.16373_t
Valid prediction for snap_scaffold_4-snap.1961-T1
Valid prediction for snap_scaffold_4-snap.1934-T1
Valid prediction for Augustus_model.g6616.t1
Valid prediction for GeneMark_model.16385_t
Valid prediction for Augustus_model.g6622.t1
Valid prediction for Augustus_model.g6626.t1
Valid prediction for GeneMark_model.16420_t
Valid prediction for GlimmerHMM_glimmerT_10096-T1
Valid prediction for GeneMark_model.16395_t
Valid prediction for snap_scaffold_4-snap.1940-T1
Valid prediction for GeneMark_model.16401_t
Valid prediction for snap_scaffold_4-snap.1928-T1
Valid prediction for GeneMark_model.16384_t
Valid prediction for GeneMark_model.16382_t
Valid prediction for GlimmerHMM_glimmerT_10088-T1
Valid prediction for snap_scaffold_4-snap.1937-T1
Valid prediction for GeneMark_model.16411_t
Valid prediction for snap_scaffold_4-snap.1933-T1
Valid prediction for snap_scaffold_4-snap.1962-T1
Valid prediction for GeneMark_model.16422_t
Valid prediction for snap_scaffold_4-snap.1969-T1
Valid prediction for Augustus_model.g6614.t1
Valid prediction for snap_scaffold_4-snap.1957-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g6618.t1
Valid prediction for snap_scaffold_4-snap.1945-T1
Valid prediction for GeneMark_model.16399_t
Valid prediction for Augustus_model.g6620.t1
Valid prediction for snap_scaffold_4-snap.1950-T1
Valid prediction for GeneMark_model.16387_t
Valid prediction for GeneMark_model.16426_t
Valid prediction for GeneMark_model.16374_t
Valid prediction for snap_scaffold_4-snap.1936-T1
Valid prediction for snap_scaffold_4-snap.1930-T1
Valid prediction for GeneMark_model.16409_t
Valid prediction for GlimmerHMM_glimmerT_10097-T1
Valid prediction for GeneMark_model.16376_t
Valid prediction for GeneMark_model.16392_t
Valid prediction for GlimmerHMM_glimmerT_10082-T1
Valid prediction for snap_scaffold_4-snap.1926-T1
Valid prediction for GlimmerHMM_glimmerT_10106-T1
Valid prediction for snap_scaffold_4-snap.1924-T1
Valid prediction for GlimmerHMM_glimmerT_10089-T1
Valid prediction for GeneMark_model.16435_t
Valid prediction for GeneMark_model.16430_t
Valid prediction for snap_scaffold_4-snap.1947-T1
Valid prediction for GlimmerHMM_glimmerT_10084-T1
Valid prediction for Augustus_model.g6615.t1
Valid prediction for GeneMark_model.16417_t
Valid prediction for snap_scaffold_4-snap.1971-T1
Valid prediction for snap_scaffold_4-snap.1955-T1
Valid prediction for GeneMark_model.16415_t
Couldn't classify 89418, 90544
Sorry, prediction pasa_asmbl_42940.p1 fails validation.
(GAT)	 CA	89418-90544	GT	AGG
(CCC)	 AG	93303-93810	AG	AAA
-recovered pasa_asmbl_42940.p1, terminal, 93303, 93810
Valid prediction for GlimmerHMM_glimmerT_10092-T1
Valid prediction for GeneMark_model.16438_t
Valid prediction for snap_scaffold_4-snap.1954-T1
Valid prediction for GeneMark_model.16407_t
Valid prediction for snap_scaffold_4-snap.1931-T1
Valid prediction for GeneMark_model.16389_t
Valid prediction for GlimmerHMM_glimmerT_10094-T1
Valid prediction for GeneMark_model.16413_t
Valid prediction for Augustus_model.g6611.t1
Valid prediction for Augustus_model.g6621.t1
Valid prediction for GlimmerHMM_glimmerT_10090-T1
Valid prediction for GeneMark_model.16403_t
Valid prediction for GeneMark_model.16436_t
Valid prediction for GeneMark_model.16372_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_4-snap.1964-T1
Valid prediction for snap_scaffold_4-snap.1929-T1
Valid prediction for snap_scaffold_4-snap.1953-T1
Valid prediction for GeneMark_model.16418_t
Valid prediction for GlimmerHMM_glimmerT_10087-T1
Valid prediction for snap_scaffold_4-snap.1920-T1
Valid prediction for GlimmerHMM_glimmerT_10085-T1
Valid prediction for snap_scaffold_4-snap.1963-T1
Couldn't classify 72675, 73358
Sorry, prediction pasa_asmbl_41545.p1 fails validation.
(ATG)	 CC	72675-73358	GA	GGG
Valid prediction for GlimmerHMM_glimmerT_10105-T1
Valid prediction for GeneMark_model.16383_t
Valid prediction for GeneMark_model.16421_t
Valid prediction for Augustus_model.g6624.t1
Valid prediction for GeneMark_model.16416_t
Valid prediction for GeneMark_model.16377_t
Valid prediction for GeneMark_model.16408_t
Valid prediction for GeneMark_model.16414_t
Valid prediction for snap_scaffold_4-snap.1938-T1
Valid prediction for GeneMark_model.16427_t
Valid prediction for snap_scaffold_4-snap.1948-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GeneMark_model.16423_t
Valid prediction for GeneMark_model.16434_t
Valid prediction for GeneMark_model.16393_t
Valid prediction for snap_scaffold_4-snap.1970-T1
Valid prediction for snap_scaffold_4-snap.1960-T1
Valid prediction for GeneMark_model.16396_t
Valid prediction for snap_scaffold_4-snap.1939-T1
Valid prediction for GeneMark_model.16404_t
Valid prediction for GeneMark_model.16381_t
Valid prediction for GlimmerHMM_glimmerT_10095-T1
Valid prediction for snap_scaffold_4-snap.1965-T1
Valid prediction for GeneMark_model.16425_t
Valid prediction for GeneMark_model.16394_t
Valid prediction for snap_scaffold_4-snap.1959-T1
Valid prediction for GlimmerHMM_glimmerT_10099-T1
Valid prediction for snap_scaffold_4-snap.1943-T1
Valid prediction for GlimmerHMM_glimmerT_10093-T1
Valid prediction for GlimmerHMM_glimmerT_10108-T1
Valid prediction for snap_scaffold_4-snap.1968-T1
Couldn't classify 88807, 89127
Sorry, prediction pasa_asmbl_42945.p1 fails validation.
(CCT)	 TC	88807-89127	CC	TCC
Valid prediction for GlimmerHMM_glimmerT_10102-T1
Valid prediction for GlimmerHMM_glimmerT_10100-T1
Valid prediction for snap_scaffold_4-snap.1958-T1
Valid prediction for Augustus_model.g6623.t1
Valid prediction for pasa_asmbl_41549.p1
Valid prediction for snap_scaffold_4-snap.1935-T1
Valid prediction for snap_scaffold_4-snap.1946-T1
Valid prediction for snap_scaffold_4-snap.1922-T1
Valid prediction for Augustus_model.g6627.t1
Valid prediction for GlimmerHMM_glimmerT_10098-T1
Valid prediction for GlimmerHMM_glimmerT_10103-T1
Valid prediction for GeneMark_model.16386_t
Valid prediction for snap_scaffold_4-snap.1967-T1
Valid prediction for GlimmerHMM_glimmerT_10107-T1
Valid prediction for GeneMark_model.16410_t
Valid prediction for GlimmerHMM_glimmerT_10091-T1
Valid prediction for GlimmerHMM_glimmerT_10083-T1
Valid prediction for snap_scaffold_4-snap.1925-T1
Valid prediction for GeneMark_model.16405_t
Valid prediction for Augustus_model.g6612.t1
Valid prediction for snap_scaffold_4-snap.1932-T1
Valid prediction for snap_scaffold_4-snap.1923-T1
Valid prediction for snap_scaffold_4-snap.1944-T1
Valid prediction for GeneMark_model.16429_t
Valid prediction for GeneMark_model.16437_t
Valid prediction for GeneMark_model.16388_t
Valid prediction for GeneMark_model.16380_t
Valid prediction for GlimmerHMM_glimmerT_10101-T1
Valid prediction for Augustus_model.g6613.t1
Valid prediction for snap_scaffold_4-snap.1956-T1
Valid prediction for GeneMark_model.16371_t
Valid prediction for GeneMark_model.16412_t
Valid prediction for snap_scaffold_4-snap.1927-T1
Valid prediction for GeneMark_model.16397_t
Valid prediction for GeneMark_model.16390_t
Valid prediction for GeneMark_model.16431_t
Valid prediction for GeneMark_model.16419_t
Valid prediction for GlimmerHMM_glimmerT_10086-T1
Valid prediction for GlimmerHMM_glimmerT_10081-T1
Couldn't classify 2635, 2679
Couldn't classify 13839, 13921
Sorry, prediction pasa_asmbl_41550.p1 fails validation.
(CAG)	 TC	2635-2679	GT	AGG
(CAC)	 AG	5106-5120	GT	CGG
(GCC)	 AG	6523-6612	GT	TGG
(CCC)	 AG	8776-8853	GT	AGG
(GTC)	 AG	9138-9230	GT	AGG
(ATC)	 AG	10577-10743	GT	CGG
(GCC)	 AG	13463-13578	GT	AGG
(ATG)	 AG	13839-13921	GT	ATG
-recovered pasa_asmbl_41550.p1, initial, 13839, 13921
-recovered pasa_asmbl_41550.p1, internal, 5106, 5120
-recovered pasa_asmbl_41550.p1, internal, 6523, 6612
-recovered pasa_asmbl_41550.p1, internal, 8776, 8853
-recovered pasa_asmbl_41550.p1, internal, 9138, 9230
-recovered pasa_asmbl_41550.p1, internal, 10577, 10743
-recovered pasa_asmbl_41550.p1, internal, 13463, 13578
-recovered pasa_asmbl_41550.p1, internal, 13839, 13921
Valid prediction for snap_scaffold_4-snap.1951-T1
Valid prediction for GeneMark_model.16400_t
Valid prediction for HiQ_model.g6628.t1
Valid prediction for GeneMark_model.16378_t
Valid prediction for GeneMark_model.16402_t
Valid prediction for Augustus_model.g6625.t1
Valid prediction for snap_scaffold_4-snap.1966-T1
Valid prediction for snap_scaffold_4-snap.1949-T1
Valid prediction for GeneMark_model.16379_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 55389, rend_intergenic: 55292  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59662, rend_intergenic: 55926  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68605, rend_intergenic: 60061  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84136, rend_intergenic: 77482  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100942, rend_intergenic: 86777  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113663, rend_intergenic: 109836  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117998, rend_intergenic: 115864  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121883, rend_intergenic: 120188  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133775, rend_intergenic: 123328  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136620, rend_intergenic: 133852  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137960, rend_intergenic: 137724  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139892, rend_intergenic: 138520  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145515, rend_intergenic: 142799  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150103, rend_intergenic: 148419  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153214, rend_intergenic: 150117  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173494, rend_intergenic: 160635  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180133, rend_intergenic: 175202  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 210552, rend_intergenic: 210110  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 213152, rend_intergenic: 212031  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 220911, rend_intergenic: 214946  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 222777
-exon list size: 861


building trellis

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66.6    
66.7    
66.9    
67.0    
67.1    
67.2    
67.3    
67.4    
67.6    
67.7    
67.8    
67.9    
68.0    
68.1    
68.3    
68.4    
68.5    
68.6    
68.7    
68.8    
68.9    
69.1    
69.2    
69.3    
69.4    
69.5    
69.6    
69.8    
69.9    
70.0    
70.1    
70.2    
70.3    
70.5    
70.6    
70.7    
70.8    
70.9    
71.0    
71.1    
71.3    
71.4    
71.5    
71.6    
71.7    
71.8    
72.0    
72.1    
72.2    
72.3    
72.4    
72.5    
72.7    
72.8    
72.9    
73.0    
73.1    
73.2    
73.3    
73.5    
73.6    
73.7    
73.8    
73.9    
74.0    
74.2    
74.3    
74.4    
74.5    
74.6    
74.7    
74.9    
75.0    
75.1    
75.2    
75.3    
75.4    
75.6    
75.7    
75.8    
75.9    
76.0    
76.1    
76.2    
76.4    
76.5    
76.6    
76.7    
76.8    
76.9    
77.1    
77.2    
77.3    
77.4    
77.5    
77.6    
77.8    
77.9    
78.0    
78.1    
78.2    
78.3    
78.4    
78.6    
78.7    
78.8    
78.9    
79.0    
79.1    
79.3    
79.4    
79.5    
79.6    
79.7    
79.8    
80.0    
80.1    
80.2    
80.3    
80.4    
80.5    
80.6    
80.8    
80.9    
81.0    
81.1    
81.2    
81.3    
81.5    
81.6    
81.7    
81.8    
81.9    
82.0    
82.2    
82.3    
82.4    
82.5    
82.6    
82.7    
82.9    
83.0    
83.1    
83.2    
83.3    
83.4    
83.5    
83.7    
83.8    
83.9    
84.0    
84.1    
84.2    
84.4    
84.5    
84.6    
84.7    
84.8    
84.9    
85.1    
85.2    
85.3    
85.4    
85.5    
85.6    
85.7    
85.9    
86.0    
86.1    
86.2    
86.3    
86.4    
86.6    
86.7    
86.8    
86.9    
87.0    
87.1    
87.3    
87.4    
87.5    
87.6    
87.7    
87.8    
87.9    
88.1    
88.2    
88.3    
88.4    
88.5    
88.6    
88.8    
88.9    
89.0    
89.1    
89.2    
89.3    
89.5    
89.6    
89.7    
89.8    
89.9    
90.0    
90.2    
90.3    
90.4    
90.5    
90.6    
90.7    
90.8    
91.0    
91.1    
91.2    
91.3    
91.4    
91.5    
91.7    
91.8    
91.9    
92.0    
92.1    
92.2    
92.4    
92.5    
92.6    
92.7    
92.8    
92.9    
93.0    
93.2    
93.3    
93.4    
93.5    
93.6    
93.7    
93.9    
94.0    
94.1    
94.2    
94.3    
94.4    
94.6    
94.7    
94.8    
94.9    
95.0    
95.1    
95.2    
95.4    
95.5    
95.6    
95.7    
95.8    
95.9    
96.1    
96.2    
96.3    
96.4    
96.5    
96.6    
96.8    
96.9    
97.0    
97.1    
97.2    
97.3    
97.5    
97.6    
97.7    
97.8    
97.9    
98.0    
98.1    
98.3    
98.4    
98.5    
98.6    
98.7    
98.8    
99.0    
99.1    
99.2    
99.3    
99.4    
99.5    
99.7    
99.8    
99.9    
-found 39 predictions from path traversal
Error with prediction: snap lend_intergenic: 55389, rend_intergenic: 55292  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59662, rend_intergenic: 55926  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68605, rend_intergenic: 60061  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84136, rend_intergenic: 77482  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100942, rend_intergenic: 86777  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113663, rend_intergenic: 109836  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117998, rend_intergenic: 115864  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121883, rend_intergenic: 120188  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133775, rend_intergenic: 123328  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136620, rend_intergenic: 133852  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137960, rend_intergenic: 137724  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139892, rend_intergenic: 138520  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145515, rend_intergenic: 142799  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150103, rend_intergenic: 148419  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153214, rend_intergenic: 150117  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173494, rend_intergenic: 160635  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180133, rend_intergenic: 175202  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 210552, rend_intergenic: 210110  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 213152, rend_intergenic: 212031  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 220911, rend_intergenic: 214946  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

-building DP trellis

-building trellis in range 1 - 17368
-exon list size: 23


building trellis

4.0    
8.0    
12.0    
16.0    
20.0    
24.0    
28.0    
32.0    
36.0    
40.0    
44.0    
48.0    
52.0    
56.0    
60.0    
64.0    
68.0    
72.0    
76.0    
80.0    
84.0    
88.0    
92.0    
96.0    
-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 - 16923
-exon list size: 22


building trellis

4.2    
8.3    
12.5    
16.7    
20.8    
25.0    
29.2    
33.3    
37.5    
41.7    
45.8    
50.0    
54.2    
58.3    
62.5    
66.7    
70.8    
75.0    
79.2    
83.3    
87.5    
91.7    
95.8    
-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 - 16862
-exon list size: 21


building trellis

4.3    
8.7    
13.0    
17.4    
21.7    
26.1    
30.4    
34.8    
39.1    
43.5    
47.8    
52.2    
56.5    
60.9    
65.2    
69.6    
73.9    
78.3    
82.6    
87.0    
91.3    
95.7    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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

-building DP trellis

-building trellis in range 1 - 12447
-exon list size: 15


building trellis

5.9    
11.8    
17.6    
23.5    
29.4    
35.3    
41.2    
47.1    
52.9    
58.8    
64.7    
70.6    
76.5    
82.4    
88.2    
94.1    
-found 1 predictions from path traversal

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