-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_1/scaffold_1_14604936-14808750

-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_1903-T1
Valid prediction for snap_scaffold_1-snap.2519-T1
Valid prediction for CodingQuarry_transcript_2927-T1
Valid prediction for snap_scaffold_1-snap.2507-T1
Valid prediction for snap_scaffold_1-snap.2514-T1
Valid prediction for Augustus_model.g1454.t1
Valid prediction for snap_scaffold_1-snap.2523-T1
Valid prediction for snap_scaffold_1-snap.2520-T1
Couldn't classify 18371, 18418
Sorry, prediction pasa_asmbl_2409.p1 fails validation.
(ATC)	 AC	18371-18418	GT	CGG
(AGT)	 AG	19087-19179	GT	GGG
(GTG)	 AG	19375-19446	GT	TGG
(ATA)	 AG	20049-20135	GT	AGG
(GAG)	 AG	21178-21246	GT	AGG
(CTT)	 AG	21491-21552	GT	AAG
(GGA)	 AG	21822-21941	GT	CTG
(ATA)	 AG	22392-22494	GT	AGG
(GGC)	 AG	22782-22928	GT	AGG
-recovered pasa_asmbl_2409.p1, terminal, 22782, 22928
-recovered pasa_asmbl_2409.p1, internal, 19087, 19179
-recovered pasa_asmbl_2409.p1, internal, 19375, 19446
-recovered pasa_asmbl_2409.p1, internal, 20049, 20135
-recovered pasa_asmbl_2409.p1, internal, 21178, 21246
-recovered pasa_asmbl_2409.p1, internal, 21491, 21552
-recovered pasa_asmbl_2409.p1, internal, 21822, 21941
-recovered pasa_asmbl_2409.p1, internal, 22392, 22494
-recovered pasa_asmbl_2409.p1, internal, 22782, 22928
Valid prediction for snap_scaffold_1-snap.2505-T1
Valid prediction for snap_scaffold_1-snap.2512-T1
Valid prediction for snap_scaffold_1-snap.2538-T1
Valid prediction for GlimmerHMM_glimmerT_1917-T1
Valid prediction for pasa_asmbl_2405.p1
Valid prediction for Augustus_model.g1457.t1
Valid prediction for Augustus_model.g1459.t1
Valid prediction for CodingQuarry_transcript_2928-T1
Valid prediction for CodingQuarry_transcript_2930-T1
Valid prediction for GlimmerHMM_glimmerT_1904-T1
Couldn't classify 2379, 2395
Sorry, prediction pasa_asmbl_2401.p1 fails validation.
(GCG)	 TG	2379-2395	GT	CCG
(GAT)	 AG	3351-3471	GT	AGG
(ACT)	 AG	3594-3674	GT	TGG
(GCC)	 AG	3814-3896	GT	AGG
(ACC)	 AG	3991-4071	GT	CCG
(ACA)	 AG	4193-4236	GT	ACG
(AAT)	 AG	4323-4387	GT	TGG
(CTT)	 AG	4493-4648	GT	AGG
(ATC)	 AG	4769-4871	GT	AGG
(ATG)	 AG	4976-5089	GT	GGG
(GTG)	 AG	5363-5416	GT	TGG
(CGG)	 AG	5576-5612	GT	AGG
(TGC)	 AG	5722-5803	GT	AGG
(GAT)	 AG	5906-6006	GT	CTG
(ACA)	 AG	6148-6211	GT	AGG
(AGT)	 AG	6358-6412	GT	AGG
(AAC)	 AG	6979-7067	GA	AGG
add_exon() Sorry, pasa_asmbl_2401.p1 4976-5089-initial-1 is invalid.
-recovered pasa_asmbl_2401.p1, initial, 4976, 5089
-recovered pasa_asmbl_2401.p1, terminal, 6979, 7067
-recovered pasa_asmbl_2401.p1, internal, 3351, 3471
-recovered pasa_asmbl_2401.p1, internal, 3594, 3674
-recovered pasa_asmbl_2401.p1, internal, 3814, 3896
-recovered pasa_asmbl_2401.p1, internal, 3991, 4071
-recovered pasa_asmbl_2401.p1, internal, 4193, 4236
-recovered pasa_asmbl_2401.p1, internal, 4323, 4387
-recovered pasa_asmbl_2401.p1, internal, 4493, 4648
-recovered pasa_asmbl_2401.p1, internal, 4769, 4871
-recovered pasa_asmbl_2401.p1, internal, 4976, 5089
-recovered pasa_asmbl_2401.p1, internal, 5363, 5416
-recovered pasa_asmbl_2401.p1, internal, 5576, 5612
-recovered pasa_asmbl_2401.p1, internal, 5722, 5803
-recovered pasa_asmbl_2401.p1, internal, 5906, 6006
-recovered pasa_asmbl_2401.p1, internal, 6148, 6211
-recovered pasa_asmbl_2401.p1, internal, 6358, 6412
Valid prediction for GlimmerHMM_glimmerT_1905-T1
Valid prediction for Augustus_model.g1453.t1
Valid prediction for snap_scaffold_1-snap.2504-T1
Valid prediction for snap_scaffold_1-snap.2537-T1
Valid prediction for Augustus_model.g1455.t1
Valid prediction for Augustus_model.g1448.t1
Valid prediction for GlimmerHMM_glimmerT_1910-T1
Valid prediction for GlimmerHMM_glimmerT_1902-T1
Valid prediction for Augustus_model.g1445.t1
Valid prediction for Augustus_model.g1452.t1
Valid prediction for snap_scaffold_1-snap.2541-T1
Valid prediction for CodingQuarry_transcript_2931-T1
Valid prediction for GlimmerHMM_glimmerT_1925-T1
Valid prediction for GlimmerHMM_glimmerT_1914-T1
Couldn't classify 10354, 10498
Sorry, prediction CodingQuarry_transcript_2929-T1 fails validation.
(ATG)	 GA	8184-8319	GT	CGG
(ATG)	 AG	8426-9804	GT	AGG
(GTG)	 AG	10022-10125	GT	GAG
(GAC)	 GG	10354-10498	GT	AGG
(GAG)	 AG	10580-10685	GT	GGG
(GTG)	 AG	10766-10908	GT	AGG
(GTT)	 AG	11236-11402	GT	AAG
(GGA)	 AG	11552-11708	GT	AGG
(GTA)	 AG	11804-11896	GT	AGG
(AGA)	 AG	12060-12216	GT	AGG
(TGG)	 AG	12328-12520	GT	AGG
(AGA)	 AG	12683-12752	GT	AGG
(CTT)	 AG	12836-12928	GT	AGG
(GAG)	 AG	13046-13168	GT	TGG
(GAT)	 AG	13270-13422	GT	AGG
(CTG)	 AG	13551-13676	GT	AGG
(GAC)	 AG	13949-14089	GC	AGG
-recovered CodingQuarry_transcript_2929-T1, initial, 8184, 8319
add_exon() Sorry, CodingQuarry_transcript_2929-T1 8426-9804-initial-1 is invalid.
-recovered CodingQuarry_transcript_2929-T1, initial, 8426, 9804
add_exon() Sorry, CodingQuarry_transcript_2929-T1 12060-12216-terminal-3 is invalid.
-recovered CodingQuarry_transcript_2929-T1, terminal, 12060, 12216
-recovered CodingQuarry_transcript_2929-T1, terminal, 13949, 14089
-recovered CodingQuarry_transcript_2929-T1, internal, 8426, 9804
-recovered CodingQuarry_transcript_2929-T1, internal, 10022, 10125
-recovered CodingQuarry_transcript_2929-T1, internal, 10580, 10685
-recovered CodingQuarry_transcript_2929-T1, internal, 10766, 10908
-recovered CodingQuarry_transcript_2929-T1, internal, 11236, 11402
-recovered CodingQuarry_transcript_2929-T1, internal, 11552, 11708
-recovered CodingQuarry_transcript_2929-T1, internal, 11804, 11896
-recovered CodingQuarry_transcript_2929-T1, internal, 12060, 12216
-recovered CodingQuarry_transcript_2929-T1, internal, 12328, 12520
-recovered CodingQuarry_transcript_2929-T1, internal, 12683, 12752
-recovered CodingQuarry_transcript_2929-T1, internal, 12836, 12928
-recovered CodingQuarry_transcript_2929-T1, internal, 13046, 13168
-recovered CodingQuarry_transcript_2929-T1, internal, 13270, 13422
-recovered CodingQuarry_transcript_2929-T1, internal, 13551, 13676
-recovered CodingQuarry_transcript_2929-T1, internal, 13949, 14089
Valid prediction for Augustus_model.g1447.t1
Valid prediction for HiQ_model.g1443.t1
Valid prediction for snap_scaffold_1-snap.2515-T1
Valid prediction for snap_scaffold_1-snap.2536-T1
Couldn't classify 17281, 17370
Couldn't classify 18117, 18219
Sorry, prediction pasa_asmbl_2802.p1 fails validation.
(GCC)	 CA	17281-17370	GT	CTG
(GAG)	 AG	17642-17736	GT	AGG
(GTA)	 AG	17852-17956	GT	TGG
(GTA)	 AG	18117-18219	GC	ATG
-recovered pasa_asmbl_2802.p1, internal, 17642, 17736
-recovered pasa_asmbl_2802.p1, internal, 17852, 17956
-recovered pasa_asmbl_2802.p1, internal, 18117, 18219
Valid prediction for GlimmerHMM_glimmerT_1918-T1
Valid prediction for GlimmerHMM_glimmerT_1916-T1
Valid prediction for GlimmerHMM_glimmerT_1907-T1
Valid prediction for GlimmerHMM_glimmerT_1908-T1
Valid prediction for snap_scaffold_1-snap.2532-T1
Valid prediction for snap_scaffold_1-snap.2524-T1
Valid prediction for snap_scaffold_1-snap.2509-T1
Valid prediction for snap_scaffold_1-snap.2526-T1
Valid prediction for GlimmerHMM_glimmerT_1912-T1
Valid prediction for HiQ_model.g1444.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_1-snap.2534-T1
Valid prediction for Augustus_model.g1450.t1
Valid prediction for snap_scaffold_1-snap.2528-T1
Valid prediction for snap_scaffold_1-snap.2506-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_1921-T1
Valid prediction for GlimmerHMM_glimmerT_1924-T1
Valid prediction for snap_scaffold_1-snap.2525-T1
Valid prediction for GlimmerHMM_glimmerT_1919-T1
Valid prediction for snap_scaffold_1-snap.2535-T1
Valid prediction for Augustus_model.g1460.t1
Valid prediction for snap_scaffold_1-snap.2529-T1
Valid prediction for snap_scaffold_1-snap.2540-T1
Valid prediction for snap_scaffold_1-snap.2510-T1
Valid prediction for GlimmerHMM_glimmerT_1911-T1
Valid prediction for Augustus_model.g1446.t1
Valid prediction for snap_scaffold_1-snap.2522-T1
Valid prediction for snap_scaffold_1-snap.2517-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_1922-T1
Valid prediction for snap_scaffold_1-snap.2513-T1
Valid prediction for snap_scaffold_1-snap.2530-T1
Valid prediction for GlimmerHMM_glimmerT_1913-T1
Valid prediction for GlimmerHMM_glimmerT_1906-T1
Valid prediction for GlimmerHMM_glimmerT_1920-T1
Valid prediction for snap_scaffold_1-snap.2511-T1
Valid prediction for snap_scaffold_1-snap.2531-T1
Valid prediction for GlimmerHMM_glimmerT_1923-T1
Valid prediction for snap_scaffold_1-snap.2518-T1
Valid prediction for GlimmerHMM_glimmerT_1915-T1
Valid prediction for snap_scaffold_1-snap.2516-T1
Valid prediction for Augustus_model.g1449.t1
Valid prediction for snap_scaffold_1-snap.2533-T1
Valid prediction for Augustus_model.g1458.t1
Valid prediction for snap_scaffold_1-snap.2521-T1
Valid prediction for Augustus_model.g1456.t1
Valid prediction for snap_scaffold_1-snap.2539-T1
Valid prediction for snap_scaffold_1-snap.2527-T1
Valid prediction for snap_scaffold_1-snap.2508-T1
Valid prediction for Augustus_model.g1451.t1
Valid prediction for GlimmerHMM_glimmerT_1909-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14089, rend_intergenic: 8469  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32474, rend_intergenic: 29641  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38236, rend_intergenic: 32693  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40105, rend_intergenic: 38292  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46769, rend_intergenic: 43481  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54835, rend_intergenic: 54383  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62278, rend_intergenic: 60371  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93434, rend_intergenic: 90147  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117731, rend_intergenic: 115334  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149527, rend_intergenic: 143018  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198081, rend_intergenic: 195121  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 203815
-exon list size: 302


building trellis

0.3    
0.7    
1.0    
1.3    
1.6    
2.0    
2.3    
2.6    
3.0    
3.3    
3.6    
3.9    
4.3    
4.6    
4.9    
5.3    
5.6    
5.9    
6.2    
6.6    
6.9    
7.2    
7.6    
7.9    
8.2    
8.6    
8.9    
9.2    
9.5    
9.9    
10.2    
10.5    
10.9    
11.2    
11.5    
11.8    
12.2    
12.5    
12.8    
13.2    
13.5    
13.8    
14.1    
14.5    
14.8    
15.1    
15.5    
15.8    
16.1    
16.4    
16.8    
17.1    
17.4    
17.8    
18.1    
18.4    
18.8    
19.1    
19.4    
19.7    
20.1    
20.4    
20.7    
21.1    
21.4    
21.7    
22.0    
22.4    
22.7    
23.0    
23.4    
23.7    
24.0    
24.3    
24.7    
25.0    
25.3    
25.7    
26.0    
26.3    
26.6    
27.0    
27.3    
27.6    
28.0    
28.3    
28.6    
28.9    
29.3    
29.6    
29.9    
30.3    
30.6    
30.9    
31.2    
31.6    
31.9    
32.2    
32.6    
32.9    
33.2    
33.6    
33.9    
34.2    
34.5    
34.9    
35.2    
35.5    
35.9    
36.2    
36.5    
36.8    
37.2    
37.5    
37.8    
38.2    
38.5    
38.8    
39.1    
39.5    
39.8    
40.1    
40.5    
40.8    
41.1    
41.4    
41.8    
42.1    
42.4    
42.8    
43.1    
43.4    
43.8    
44.1    
44.4    
44.7    
45.1    
45.4    
45.7    
46.1    
46.4    
46.7    
47.0    
47.4    
47.7    
48.0    
48.4    
48.7    
49.0    
49.3    
49.7    
50.0    
50.3    
50.7    
51.0    
51.3    
51.6    
52.0    
52.3    
52.6    
53.0    
53.3    
53.6    
53.9    
54.3    
54.6    
54.9    
55.3    
55.6    
55.9    
56.2    
56.6    
56.9    
57.2    
57.6    
57.9    
58.2    
58.6    
58.9    
59.2    
59.5    
59.9    
60.2    
60.5    
60.9    
61.2    
61.5    
61.8    
62.2    
62.5    
62.8    
63.2    
63.5    
63.8    
64.1    
64.5    
64.8    
65.1    
65.5    
65.8    
66.1    
66.4    
66.8    
67.1    
67.4    
67.8    
68.1    
68.4    
68.8    
69.1    
69.4    
69.7    
70.1    
70.4    
70.7    
71.1    
71.4    
71.7    
72.0    
72.4    
72.7    
73.0    
73.4    
73.7    
74.0    
74.3    
74.7    
75.0    
75.3    
75.7    
76.0    
76.3    
76.6    
77.0    
77.3    
77.6    
78.0    
78.3    
78.6    
78.9    
79.3    
79.6    
79.9    
80.3    
80.6    
80.9    
81.2    
81.6    
81.9    
82.2    
82.6    
82.9    
83.2    
83.6    
83.9    
84.2    
84.5    
84.9    
85.2    
85.5    
85.9    
86.2    
86.5    
86.8    
87.2    
87.5    
87.8    
88.2    
88.5    
88.8    
89.1    
89.5    
89.8    
90.1    
90.5    
90.8    
91.1    
91.4    
91.8    
92.1    
92.4    
92.8    
93.1    
93.4    
93.8    
94.1    
94.4    
94.7    
95.1    
95.4    
95.7    
96.1    
96.4    
96.7    
97.0    
97.4    
97.7    
98.0    
98.4    
98.7    
99.0    
99.3    
99.7    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 14089, rend_intergenic: 8469  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32474, rend_intergenic: 29641  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38236, rend_intergenic: 32693  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40105, rend_intergenic: 38292  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46769, rend_intergenic: 43481  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54835, rend_intergenic: 54383  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62278, rend_intergenic: 60371  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93434, rend_intergenic: 90147  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117731, rend_intergenic: 115334  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149527, rend_intergenic: 143018  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198081, rend_intergenic: 195121  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support