-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_26/scaffold_26_7864325-7971113

-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.100268_t
Valid prediction for CodingQuarry_transcript_40312-T1
Valid prediction for Augustus_model.g38311.t1
Valid prediction for snap_scaffold_26-snap.1855-T1
Valid prediction for Augustus_model.g38315.t1
Valid prediction for GeneMark_model.100281_t
Valid prediction for GeneMark_model.100257_t
Valid prediction for GeneMark_model.100266_t
Valid prediction for Augustus_model.g38314.t1
Valid prediction for GlimmerHMM_glimmerT_57505-T1
Valid prediction for snap_scaffold_26-snap.1857-T1
Valid prediction for snap_scaffold_26-snap.1878-T1
Valid prediction for Augustus_model.g38318.t1
Valid prediction for GlimmerHMM_glimmerT_57500-T1
Valid prediction for GlimmerHMM_glimmerT_57513-T1
Valid prediction for snap_scaffold_26-snap.1865-T1
Valid prediction for GeneMark_model.100262_t
Valid prediction for snap_scaffold_26-snap.1867-T1
Valid prediction for GeneMark_model.100260_t
Valid prediction for snap_scaffold_26-snap.1875-T1
Valid prediction for GlimmerHMM_glimmerT_57508-T1
Valid prediction for GeneMark_model.100276_t
Valid prediction for GlimmerHMM_glimmerT_57499-T1
Valid prediction for snap_scaffold_26-snap.1870-T1
Valid prediction for snap_scaffold_26-snap.1882-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_57502-T1
Valid prediction for snap_scaffold_26-snap.1866-T1
Valid prediction for Augustus_model.g38324.t1
Valid prediction for GeneMark_model.100275_t
Valid prediction for snap_scaffold_26-snap.1858-T1
Valid prediction for GlimmerHMM_glimmerT_57504-T1
Valid prediction for GlimmerHMM_glimmerT_57497-T1
Valid prediction for snap_scaffold_26-snap.1862-T1
Valid prediction for GeneMark_model.100271_t
Valid prediction for GeneMark_model.100270_t
Valid prediction for snap_scaffold_26-snap.1872-T1
Valid prediction for snap_scaffold_26-snap.1883-T1
Valid prediction for snap_scaffold_26-snap.1880-T1
Valid prediction for snap_scaffold_26-snap.1860-T1
Valid prediction for GlimmerHMM_glimmerT_57495-T1
Valid prediction for GeneMark_model.100278_t
Couldn't classify 38050, 38119
Sorry, prediction pasa_asmbl_35679.p1 fails validation.
(ATG)	 TC	36114-36230	GT	AGG
(CCG)	 AG	36323-36445	GT	TGG
(GGC)	 AG	36546-36619	GT	ATG
(GCT)	 AG	36705-36918	GT	AGG
(ACG)	 AG	37100-37263	GT	AGG
(CTA)	 AG	38050-38119	CG	GAC
-recovered pasa_asmbl_35679.p1, initial, 36114, 36230
-recovered pasa_asmbl_35679.p1, internal, 36323, 36445
-recovered pasa_asmbl_35679.p1, internal, 36546, 36619
-recovered pasa_asmbl_35679.p1, internal, 36705, 36918
-recovered pasa_asmbl_35679.p1, internal, 37100, 37263
Valid prediction for GlimmerHMM_glimmerT_57501-T1
Valid prediction for Augustus_model.g38321.t1
Valid prediction for Augustus_model.g38317.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 GeneMark_model.100273_t
Valid prediction for GeneMark_model.100272_t
Valid prediction for snap_scaffold_26-snap.1873-T1
Valid prediction for Augustus_model.g38310.t1
Valid prediction for GlimmerHMM_glimmerT_57512-T1
Valid prediction for GeneMark_model.100267_t
Valid prediction for GeneMark_model.100282_t
Valid prediction for snap_scaffold_26-snap.1874-T1
Valid prediction for snap_scaffold_26-snap.1856-T1
Valid prediction for GlimmerHMM_glimmerT_57514-T1
Couldn't classify 64149, 64234
Sorry, prediction pasa_asmbl_34994.p1 fails validation.
(ACT)	 GG	64149-64234	GT	AGG
(CGG)	 AG	64325-64392	GT	CGG
(ACC)	 AG	64490-64578	GT	AGG
(GAG)	 AG	64676-64753	GT	GGG
(AAC)	 AG	64850-64984	GT	AGG
(CAC)	 AG	65413-65496	TA	AGT
-recovered pasa_asmbl_34994.p1, terminal, 65413, 65496
-recovered pasa_asmbl_34994.p1, internal, 64325, 64392
-recovered pasa_asmbl_34994.p1, internal, 64490, 64578
-recovered pasa_asmbl_34994.p1, internal, 64676, 64753
-recovered pasa_asmbl_34994.p1, internal, 64850, 64984
Valid prediction for GeneMark_model.100259_t
Valid prediction for GeneMark_model.100283_t
Valid prediction for GeneMark_model.100265_t
Valid prediction for snap_scaffold_26-snap.1877-T1
Valid prediction for GlimmerHMM_glimmerT_57511-T1
Valid prediction for GlimmerHMM_glimmerT_57498-T1
Valid prediction for snap_scaffold_26-snap.1871-T1
Valid prediction for snap_scaffold_26-snap.1876-T1
Valid prediction for snap_scaffold_26-snap.1863-T1
Valid prediction for snap_scaffold_26-snap.1881-T1
Valid prediction for GeneMark_model.100277_t
Valid prediction for snap_scaffold_26-snap.1868-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_57510-T1
Valid prediction for GeneMark_model.100263_t
Couldn't classify 63925, 64032
Sorry, prediction pasa_asmbl_35100.p1 fails validation.
(ATG)	 CC	59197-59322	GT	AGG
(CCC)	 AG	59684-59754	GT	AGG
(CTT)	 AG	60291-60408	GT	TGG
(GGC)	 AG	60789-60820	GT	ATG
(CTG)	 AG	61004-61056	GT	AGG
(TCG)	 AG	61201-61351	GT	CGG
(CGT)	 AG	61472-61550	GT	AGG
(CAC)	 AG	61644-61767	GT	AGG
(GCA)	 AG	61900-62056	GT	AGG
(GCC)	 AG	62149-62236	GT	AGG
(GAC)	 AG	62425-62505	GT	AGG
(GTG)	 AG	62598-62755	GT	GAG
(CGA)	 AG	62843-62919	GT	CCG
(TGT)	 AG	63070-63242	GT	AGG
(CTG)	 AG	63345-63504	GT	GGG
(ACG)	 AG	63620-63762	GC	AGG
(CTG)	 AG	63925-64032	AC	TCA
-recovered pasa_asmbl_35100.p1, initial, 59197, 59322
add_exon() Sorry, pasa_asmbl_35100.p1 62598-62755-terminal-2 is invalid.
-recovered pasa_asmbl_35100.p1, terminal, 62598, 62755
-recovered pasa_asmbl_35100.p1, internal, 59684, 59754
-recovered pasa_asmbl_35100.p1, internal, 60291, 60408
-recovered pasa_asmbl_35100.p1, internal, 60789, 60820
-recovered pasa_asmbl_35100.p1, internal, 61004, 61056
-recovered pasa_asmbl_35100.p1, internal, 61201, 61351
-recovered pasa_asmbl_35100.p1, internal, 61472, 61550
-recovered pasa_asmbl_35100.p1, internal, 61644, 61767
-recovered pasa_asmbl_35100.p1, internal, 61900, 62056
-recovered pasa_asmbl_35100.p1, internal, 62149, 62236
-recovered pasa_asmbl_35100.p1, internal, 62425, 62505
-recovered pasa_asmbl_35100.p1, internal, 62598, 62755
-recovered pasa_asmbl_35100.p1, internal, 62843, 62919
-recovered pasa_asmbl_35100.p1, internal, 63070, 63242
-recovered pasa_asmbl_35100.p1, internal, 63345, 63504
-recovered pasa_asmbl_35100.p1, internal, 63620, 63762
Valid prediction for GeneMark_model.100279_t
Valid prediction for CodingQuarry_transcript_40313-T1
Valid prediction for snap_scaffold_26-snap.1861-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_26-snap.1859-T1
Valid prediction for snap_scaffold_26-snap.1879-T1
Valid prediction for GlimmerHMM_glimmerT_57507-T1
Valid prediction for GeneMark_model.100280_t
Couldn't classify 44904, 45434
Sorry, prediction pasa_asmbl_34997.p1 fails validation.
(ATG)	 AA	44904-45434	TA	AGT
Valid prediction for snap_scaffold_26-snap.1864-T1
Valid prediction for Augustus_model.g38316.t1
Valid prediction for snap_scaffold_26-snap.1869-T1
Valid prediction for GeneMark_model.100256_t
Valid prediction for Augustus_model.g38322.t1
Valid prediction for GlimmerHMM_glimmerT_57503-T1
Valid prediction for GlimmerHMM_glimmerT_57496-T1
Valid prediction for Augustus_model.g38313.t1
Valid prediction for GeneMark_model.100258_t
Valid prediction for HiQ_model.g38320.t1
Valid prediction for Augustus_model.g38323.t1
Valid prediction for GlimmerHMM_glimmerT_57506-T1
Valid prediction for GlimmerHMM_glimmerT_57494-T1
Valid prediction for Augustus_model.g38319.t1
Valid prediction for GlimmerHMM_glimmerT_57509-T1
Valid prediction for GeneMark_model.100269_t
Valid prediction for GeneMark_model.100264_t
Valid prediction for Augustus_model.g38312.t1
Valid prediction for GeneMark_model.100261_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15908, rend_intergenic: 6744  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49791, rend_intergenic: 48827  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53137, rend_intergenic: 50086  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54001, rend_intergenic: 53807  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56710, rend_intergenic: 54215  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 106789
-exon list size: 432


building trellis

0.2    
0.5    
0.7    
0.9    
1.2    
1.4    
1.6    
1.8    
2.1    
2.3    
2.5    
2.8    
3.0    
3.2    
3.5    
3.7    
3.9    
4.1    
4.4    
4.6    
4.8    
5.1    
5.3    
5.5    
5.8    
6.0    
6.2    
6.5    
6.7    
6.9    
7.1    
7.4    
7.6    
7.8    
8.1    
8.3    
8.5    
8.8    
9.0    
9.2    
9.4    
9.7    
9.9    
10.1    
10.4    
10.6    
10.8    
11.1    
11.3    
11.5    
11.8    
12.0    
12.2    
12.4    
12.7    
12.9    
13.1    
13.4    
13.6    
13.8    
14.1    
14.3    
14.5    
14.7    
15.0    
15.2    
15.4    
15.7    
15.9    
16.1    
16.4    
16.6    
16.8    
17.1    
17.3    
17.5    
17.7    
18.0    
18.2    
18.4    
18.7    
18.9    
19.1    
19.4    
19.6    
19.8    
20.0    
20.3    
20.5    
20.7    
21.0    
21.2    
21.4    
21.7    
21.9    
22.1    
22.4    
22.6    
22.8    
23.0    
23.3    
23.5    
23.7    
24.0    
24.2    
24.4    
24.7    
24.9    
25.1    
25.3    
25.6    
25.8    
26.0    
26.3    
26.5    
26.7    
27.0    
27.2    
27.4    
27.6    
27.9    
28.1    
28.3    
28.6    
28.8    
29.0    
29.3    
29.5    
29.7    
30.0    
30.2    
30.4    
30.6    
30.9    
31.1    
31.3    
31.6    
31.8    
32.0    
32.3    
32.5    
32.7    
32.9    
33.2    
33.4    
33.6    
33.9    
34.1    
34.3    
34.6    
34.8    
35.0    
35.3    
35.5    
35.7    
35.9    
36.2    
36.4    
36.6    
36.9    
37.1    
37.3    
37.6    
37.8    
38.0    
38.2    
38.5    
38.7    
38.9    
39.2    
39.4    
39.6    
39.9    
40.1    
40.3    
40.6    
40.8    
41.0    
41.2    
41.5    
41.7    
41.9    
42.2    
42.4    
42.6    
42.9    
43.1    
43.3    
43.5    
43.8    
44.0    
44.2    
44.5    
44.7    
44.9    
45.2    
45.4    
45.6    
45.9    
46.1    
46.3    
46.5    
46.8    
47.0    
47.2    
47.5    
47.7    
47.9    
48.2    
48.4    
48.6    
48.8    
49.1    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
50.7    
50.9    
51.2    
51.4    
51.6    
51.8    
52.1    
52.3    
52.5    
52.8    
53.0    
53.2    
53.5    
53.7    
53.9    
54.1    
54.4    
54.6    
54.8    
55.1    
55.3    
55.5    
55.8    
56.0    
56.2    
56.5    
56.7    
56.9    
57.1    
57.4    
57.6    
57.8    
58.1    
58.3    
58.5    
58.8    
59.0    
59.2    
59.4    
59.7    
59.9    
60.1    
60.4    
60.6    
60.8    
61.1    
61.3    
61.5    
61.8    
62.0    
62.2    
62.4    
62.7    
62.9    
63.1    
63.4    
63.6    
63.8    
64.1    
64.3    
64.5    
64.7    
65.0    
65.2    
65.4    
65.7    
65.9    
66.1    
66.4    
66.6    
66.8    
67.1    
67.3    
67.5    
67.7    
68.0    
68.2    
68.4    
68.7    
68.9    
69.1    
69.4    
69.6    
69.8    
70.0    
70.3    
70.5    
70.7    
71.0    
71.2    
71.4    
71.7    
71.9    
72.1    
72.4    
72.6    
72.8    
73.0    
73.3    
73.5    
73.7    
74.0    
74.2    
74.4    
74.7    
74.9    
75.1    
75.3    
75.6    
75.8    
76.0    
76.3    
76.5    
76.7    
77.0    
77.2    
77.4    
77.6    
77.9    
78.1    
78.3    
78.6    
78.8    
79.0    
79.3    
79.5    
79.7    
80.0    
80.2    
80.4    
80.6    
80.9    
81.1    
81.3    
81.6    
81.8    
82.0    
82.3    
82.5    
82.7    
82.9    
83.2    
83.4    
83.6    
83.9    
84.1    
84.3    
84.6    
84.8    
85.0    
85.3    
85.5    
85.7    
85.9    
86.2    
86.4    
86.6    
86.9    
87.1    
87.3    
87.6    
87.8    
88.0    
88.2    
88.5    
88.7    
88.9    
89.2    
89.4    
89.6    
89.9    
90.1    
90.3    
90.6    
90.8    
91.0    
91.2    
91.5    
91.7    
91.9    
92.2    
92.4    
92.6    
92.9    
93.1    
93.3    
93.5    
93.8    
94.0    
94.2    
94.5    
94.7    
94.9    
95.2    
95.4    
95.6    
95.9    
96.1    
96.3    
96.5    
96.8    
97.0    
97.2    
97.5    
97.7    
97.9    
98.2    
98.4    
98.6    
98.8    
99.1    
99.3    
99.5    
99.8    
-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 15908, rend_intergenic: 6744  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49791, rend_intergenic: 48827  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53137, rend_intergenic: 50086  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54001, rend_intergenic: 53807  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56710, rend_intergenic: 54215  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support