-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_21/scaffold_21_7579637-7739672

-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: +)Couldn't classify 35096, 35188
Couldn't classify 36413, 36416
Sorry, prediction pasa_asmbl_28759.p1 fails validation.
(TAC)	 GG	35096-35188	GT	TGG
(GAG)	 AG	35402-35504	GT	TCG
(GGG)	 AG	35913-36020	GT	CAG
(AGA)	 AG	36162-36174	GT	AGG
(CAA)	 AG	36413-36416	CC	AAC
-recovered pasa_asmbl_28759.p1, internal, 35402, 35504
-recovered pasa_asmbl_28759.p1, internal, 35913, 36020
-recovered pasa_asmbl_28759.p1, internal, 36162, 36174
Valid prediction for Augustus_model.g32118.t1
Valid prediction for HiQ_model.g32109.t1
Valid prediction for snap_scaffold_21-snap.1586-T1
Valid prediction for Augustus_model.g32116.t1
Couldn't classify 144967, 145007
Couldn't classify 146450, 146556
Sorry, prediction pasa_asmbl_28767.p2 fails validation.
(AAA)	 CC	144967-145007	GT	CTG
(GCT)	 AG	146200-146360	GT	TGG
(GCA)	 AG	146450-146556	GG	CAG
-recovered pasa_asmbl_28767.p2, internal, 146200, 146360
Valid prediction for Augustus_model.g32105.t1
Valid prediction for snap_scaffold_21-snap.1600-T1
Couldn't classify 2836, 3216
Sorry, prediction pasa_asmbl_28752.p1 fails validation.
(ATG)	 AG	2836-3216	GG	TAG
Valid prediction for CodingQuarry_transcript_32636-T1
Valid prediction for GlimmerHMM_glimmerT_48080-T1
Valid prediction for snap_scaffold_21-snap.1598-T1
Valid prediction for snap_scaffold_21-snap.1624-T1
Valid prediction for GlimmerHMM_glimmerT_48093-T1
Valid prediction for GlimmerHMM_glimmerT_48089-T1
Valid prediction for snap_scaffold_21-snap.1616-T1
Couldn't classify 146742, 146921
Sorry, prediction pasa_asmbl_28766.p1 fails validation.
(GAG)	 CA	146742-146921	GT	AGG
(AGA)	 AG	148974-149066	GT	AGG
(GGT)	 AG	149316-149409	GT	CAG
(TCT)	 AG	151283-151420	GT	AAG
(CCC)	 AG	151640-151771	GT	AGG
(GGC)	 AG	152075-152187	GT	ATG
(GAT)	 AG	152392-152473	GT	AGG
(GGA)	 AG	152728-152810	TA	GAT
-recovered pasa_asmbl_28766.p1, terminal, 152728, 152810
-recovered pasa_asmbl_28766.p1, internal, 148974, 149066
-recovered pasa_asmbl_28766.p1, internal, 149316, 149409
-recovered pasa_asmbl_28766.p1, internal, 151283, 151420
-recovered pasa_asmbl_28766.p1, internal, 151640, 151771
-recovered pasa_asmbl_28766.p1, internal, 152075, 152187
-recovered pasa_asmbl_28766.p1, internal, 152392, 152473
Valid prediction for CodingQuarry_transcript_32637-T1
Couldn't classify 32270, 32516
Couldn't classify 34986, 35029
Sorry, prediction pasa_asmbl_28758.p1 fails validation.
(TTT)	 AG	32270-32516	GT	AGG
(ATG)	 AG	33943-33999	GT	GGG
(GTA)	 AG	34171-34284	GT	CAG
(CAC)	 AG	34698-34838	GT	AGG
(TTC)	 AG	34986-35029	AC	CCA
add_exon() Sorry, pasa_asmbl_28758.p1 33943-33999-initial-1 is invalid.
-recovered pasa_asmbl_28758.p1, initial, 33943, 33999
add_exon() Sorry, pasa_asmbl_28758.p1 34698-34838-terminal-1 is invalid.
-recovered pasa_asmbl_28758.p1, terminal, 34698, 34838
-recovered pasa_asmbl_28758.p1, internal, 32270, 32516
-recovered pasa_asmbl_28758.p1, internal, 33943, 33999
-recovered pasa_asmbl_28758.p1, internal, 34171, 34284
-recovered pasa_asmbl_28758.p1, internal, 34698, 34838
Valid prediction for GlimmerHMM_glimmerT_48099-T1
Valid prediction for GlimmerHMM_glimmerT_48076-T1
Valid prediction for Augustus_model.g32111.t1
Valid prediction for snap_scaffold_21-snap.1597-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_21-snap.1614-T1
Valid prediction for GlimmerHMM_glimmerT_48085-T1
Valid prediction for GlimmerHMM_glimmerT_48084-T1
Valid prediction for snap_scaffold_21-snap.1608-T1
Valid prediction for GlimmerHMM_glimmerT_48083-T1
Valid prediction for snap_scaffold_21-snap.1623-T1
Valid prediction for snap_scaffold_21-snap.1595-T1
Valid prediction for GlimmerHMM_glimmerT_48094-T1
Valid prediction for Augustus_model.g32106.t1
Valid prediction for snap_scaffold_21-snap.1602-T1
Valid prediction for GlimmerHMM_glimmerT_48090-T1
Valid prediction for snap_scaffold_21-snap.1588-T1
Valid prediction for snap_scaffold_21-snap.1592-T1
Couldn't classify 138523, 139122
Sorry, prediction pasa_asmbl_28763.p1 fails validation.
(ATG)	 AG	138523-139122	AA	ACA
Valid prediction for Augustus_model.g32107.t1
Valid prediction for GlimmerHMM_glimmerT_48103-T1
Valid prediction for Augustus_model.g32110.t1
Valid prediction for Augustus_model.g32112.t1
Valid prediction for GlimmerHMM_glimmerT_48078-T1
Valid prediction for GlimmerHMM_glimmerT_48077-T1
Valid prediction for snap_scaffold_21-snap.1610-T1
Valid prediction for snap_scaffold_21-snap.1617-T1
Valid prediction for GlimmerHMM_glimmerT_48092-T1
Valid prediction for snap_scaffold_21-snap.1613-T1
Valid prediction for pasa_asmbl_28756.p1
Valid prediction for GlimmerHMM_glimmerT_48081-T1
Valid prediction for GlimmerHMM_glimmerT_48095-T1
Valid prediction for snap_scaffold_21-snap.1594-T1
Valid prediction for CodingQuarry_transcript_32632-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 GlimmerHMM_glimmerT_48086-T1
Valid prediction for snap_scaffold_21-snap.1626-T1
Valid prediction for Augustus_model.g32108.t1
Valid prediction for snap_scaffold_21-snap.1593-T1
Valid prediction for GlimmerHMM_glimmerT_48088-T1
Valid prediction for Augustus_model.g32117.t1
Valid prediction for Augustus_model.g32115.t1
Valid prediction for snap_scaffold_21-snap.1604-T1
Valid prediction for GlimmerHMM_glimmerT_48098-T1
Valid prediction for CodingQuarry_transcript_32633-T1
Valid prediction for pasa_asmbl_27841.p1
Valid prediction for snap_scaffold_21-snap.1607-T1
Valid prediction for snap_scaffold_21-snap.1596-T1
Valid prediction for snap_scaffold_21-snap.1591-T1
Valid prediction for Augustus_model.g32113.t1
Valid prediction for Augustus_model.g32114.t1
Valid prediction for snap_scaffold_21-snap.1620-T1
Valid prediction for GlimmerHMM_glimmerT_48100-T1
Valid prediction for snap_scaffold_21-snap.1601-T1
Valid prediction for snap_scaffold_21-snap.1627-T1
Valid prediction for GlimmerHMM_glimmerT_48096-T1
Valid prediction for GlimmerHMM_glimmerT_48104-T1
Valid prediction for snap_scaffold_21-snap.1603-T1
Valid prediction for snap_scaffold_21-snap.1615-T1
Valid prediction for GlimmerHMM_glimmerT_48091-T1
Valid prediction for snap_scaffold_21-snap.1625-T1
Valid prediction for Augustus_model.g32119.t1
Valid prediction for snap_scaffold_21-snap.1621-T1
Couldn't classify 18365, 18377
Sorry, prediction pasa_asmbl_27845.p1 fails validation.
(CCG)	 CA	18365-18377	GT	AGG
(GAT)	 AG	18488-18566	GT	AGG
(CCA)	 AG	18664-18870	GT	AGG
(AGG)	 AG	18959-18992	GT	TGG
(CCC)	 AG	19103-19172	GT	AGG
(AGA)	 AG	19314-19408	AA	GAA
-recovered pasa_asmbl_27845.p1, terminal, 19314, 19408
-recovered pasa_asmbl_27845.p1, internal, 18488, 18566
-recovered pasa_asmbl_27845.p1, internal, 18664, 18870
-recovered pasa_asmbl_27845.p1, internal, 18959, 18992
-recovered pasa_asmbl_27845.p1, internal, 19103, 19172
Valid prediction for snap_scaffold_21-snap.1589-T1
Valid prediction for snap_scaffold_21-snap.1599-T1
Valid prediction for snap_scaffold_21-snap.1587-T1
Valid prediction for GlimmerHMM_glimmerT_48082-T1
Valid prediction for snap_scaffold_21-snap.1609-T1
Couldn't classify 16983, 17023
Couldn't classify 17433, 17559
Sorry, prediction pasa_asmbl_27846.p1 fails validation.
(AAA)	 CT	16983-17023	GT	AGG
(GAT)	 AG	17154-17306	GT	GAG
(GCT)	 AG	17433-17559	GA	AGG
add_exon() Sorry, pasa_asmbl_27846.p1 17154-17306-terminal-1 is invalid.
-recovered pasa_asmbl_27846.p1, terminal, 17154, 17306
-recovered pasa_asmbl_27846.p1, internal, 17154, 17306
Valid prediction for CodingQuarry_transcript_32635-T1
Valid prediction for GlimmerHMM_glimmerT_48097-T1
Valid prediction for snap_scaffold_21-snap.1619-T1
Valid prediction for GlimmerHMM_glimmerT_48102-T1
Valid prediction for snap_scaffold_21-snap.1605-T1
Valid prediction for snap_scaffold_21-snap.1622-T1
Valid prediction for snap_scaffold_21-snap.1606-T1
Valid prediction for GlimmerHMM_glimmerT_48101-T1
Valid prediction for GlimmerHMM_glimmerT_48079-T1
Valid prediction for snap_scaffold_21-snap.1618-T1
Valid prediction for GlimmerHMM_glimmerT_48087-T1
Valid prediction for snap_scaffold_21-snap.1611-T1
Valid prediction for snap_scaffold_21-snap.1590-T1
Valid prediction for snap_scaffold_21-snap.1612-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9973, rend_intergenic: 2935  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11670, rend_intergenic: 10568  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18129, rend_intergenic: 12275  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21709, rend_intergenic: 20265  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56378, rend_intergenic: 54886  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59245, rend_intergenic: 57037  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61041, rend_intergenic: 59362  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66091, rend_intergenic: 61081  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88482, rend_intergenic: 66994  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99969, rend_intergenic: 97843  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101649, rend_intergenic: 100283  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109244, rend_intergenic: 101990  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117009, rend_intergenic: 109718  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126315, rend_intergenic: 120041  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130871, rend_intergenic: 127844  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152810, rend_intergenic: 149815  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 160036
-exon list size: 371


building trellis

0.3    
0.5    
0.8    
1.1    
1.3    
1.6    
1.9    
2.1    
2.4    
2.7    
2.9    
3.2    
3.5    
3.8    
4.0    
4.3    
4.6    
4.8    
5.1    
5.4    
5.6    
5.9    
6.2    
6.4    
6.7    
7.0    
7.2    
7.5    
7.8    
8.0    
8.3    
8.6    
8.8    
9.1    
9.4    
9.7    
9.9    
10.2    
10.5    
10.7    
11.0    
11.3    
11.5    
11.8    
12.1    
12.3    
12.6    
12.9    
13.1    
13.4    
13.7    
13.9    
14.2    
14.5    
14.7    
15.0    
15.3    
15.5    
15.8    
16.1    
16.4    
16.6    
16.9    
17.2    
17.4    
17.7    
18.0    
18.2    
18.5    
18.8    
19.0    
19.3    
19.6    
19.8    
20.1    
20.4    
20.6    
20.9    
21.2    
21.4    
21.7    
22.0    
22.3    
22.5    
22.8    
23.1    
23.3    
23.6    
23.9    
24.1    
24.4    
24.7    
24.9    
25.2    
25.5    
25.7    
26.0    
26.3    
26.5    
26.8    
27.1    
27.3    
27.6    
27.9    
28.2    
28.4    
28.7    
29.0    
29.2    
29.5    
29.8    
30.0    
30.3    
30.6    
30.8    
31.1    
31.4    
31.6    
31.9    
32.2    
32.4    
32.7    
33.0    
33.2    
33.5    
33.8    
34.0    
34.3    
34.6    
34.9    
35.1    
35.4    
35.7    
35.9    
36.2    
36.5    
36.7    
37.0    
37.3    
37.5    
37.8    
38.1    
38.3    
38.6    
38.9    
39.1    
39.4    
39.7    
39.9    
40.2    
40.5    
40.8    
41.0    
41.3    
41.6    
41.8    
42.1    
42.4    
42.6    
42.9    
43.2    
43.4    
43.7    
44.0    
44.2    
44.5    
44.8    
45.0    
45.3    
45.6    
45.8    
46.1    
46.4    
46.6    
46.9    
47.2    
47.5    
47.7    
48.0    
48.3    
48.5    
48.8    
49.1    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
50.9    
51.2    
51.5    
51.7    
52.0    
52.3    
52.5    
52.8    
53.1    
53.4    
53.6    
53.9    
54.2    
54.4    
54.7    
55.0    
55.2    
55.5    
55.8    
56.0    
56.3    
56.6    
56.8    
57.1    
57.4    
57.6    
57.9    
58.2    
58.4    
58.7    
59.0    
59.2    
59.5    
59.8    
60.1    
60.3    
60.6    
60.9    
61.1    
61.4    
61.7    
61.9    
62.2    
62.5    
62.7    
63.0    
63.3    
63.5    
63.8    
64.1    
64.3    
64.6    
64.9    
65.1    
65.4    
65.7    
66.0    
66.2    
66.5    
66.8    
67.0    
67.3    
67.6    
67.8    
68.1    
68.4    
68.6    
68.9    
69.2    
69.4    
69.7    
70.0    
70.2    
70.5    
70.8    
71.0    
71.3    
71.6    
71.8    
72.1    
72.4    
72.7    
72.9    
73.2    
73.5    
73.7    
74.0    
74.3    
74.5    
74.8    
75.1    
75.3    
75.6    
75.9    
76.1    
76.4    
76.7    
76.9    
77.2    
77.5    
77.7    
78.0    
78.3    
78.6    
78.8    
79.1    
79.4    
79.6    
79.9    
80.2    
80.4    
80.7    
81.0    
81.2    
81.5    
81.8    
82.0    
82.3    
82.6    
82.8    
83.1    
83.4    
83.6    
83.9    
84.2    
84.5    
84.7    
85.0    
85.3    
85.5    
85.8    
86.1    
86.3    
86.6    
86.9    
87.1    
87.4    
87.7    
87.9    
88.2    
88.5    
88.7    
89.0    
89.3    
89.5    
89.8    
90.1    
90.3    
90.6    
90.9    
91.2    
91.4    
91.7    
92.0    
92.2    
92.5    
92.8    
93.0    
93.3    
93.6    
93.8    
94.1    
94.4    
94.6    
94.9    
95.2    
95.4    
95.7    
96.0    
96.2    
96.5    
96.8    
97.1    
97.3    
97.6    
97.9    
98.1    
98.4    
98.7    
98.9    
99.2    
99.5    
99.7    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 9973, rend_intergenic: 2935  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11670, rend_intergenic: 10568  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18129, rend_intergenic: 12275  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21709, rend_intergenic: 20265  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56378, rend_intergenic: 54886  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59245, rend_intergenic: 57037  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61041, rend_intergenic: 59362  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66091, rend_intergenic: 61081  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88482, rend_intergenic: 66994  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99969, rend_intergenic: 97843  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101649, rend_intergenic: 100283  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109244, rend_intergenic: 101990  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117009, rend_intergenic: 109718  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126315, rend_intergenic: 120041  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130871, rend_intergenic: 127844  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152810, rend_intergenic: 149815  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support