-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_5/scaffold_5_14628255-14783028

-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_13406-T1
Valid prediction for snap_scaffold_5-snap.2719-T1
Valid prediction for snap_scaffold_5-snap.2724-T1
Valid prediction for snap_scaffold_5-snap.2713-T1
Valid prediction for Augustus_model.g8974.t1
Valid prediction for CodingQuarry_transcript_52228-T1
Valid prediction for HiQ_model.g8967.t1
Couldn't classify 68269, 68307
Sorry, prediction pasa_asmbl_44625.p1 fails validation.
(AGA)	 AA	68269-68307	GT	AGG
(CTT)	 AG	69171-69273	GT	AGG
(ATG)	 AG	69529-69578	GT	AGG
(GAC)	 AG	69662-69729	GT	GAG
(GGC)	 AG	69911-69962	GT	AGG
(AAA)	 AG	70192-70265	GT	AGG
(GTT)	 AG	70351-70388	GT	AGG
(GTG)	 AG	70496-70518	GT	CAG
(CCT)	 AG	70613-70690	GT	AGG
(GTT)	 AG	70811-70894	GT	AGG
(GCA)	 AG	70980-71021	AC	AAA
add_exon() Sorry, pasa_asmbl_44625.p1 69529-69578-initial-1 is invalid.
-recovered pasa_asmbl_44625.p1, initial, 69529, 69578
-recovered pasa_asmbl_44625.p1, terminal, 70980, 71021
-recovered pasa_asmbl_44625.p1, internal, 69171, 69273
-recovered pasa_asmbl_44625.p1, internal, 69529, 69578
-recovered pasa_asmbl_44625.p1, internal, 69662, 69729
-recovered pasa_asmbl_44625.p1, internal, 69911, 69962
-recovered pasa_asmbl_44625.p1, internal, 70192, 70265
-recovered pasa_asmbl_44625.p1, internal, 70351, 70388
-recovered pasa_asmbl_44625.p1, internal, 70496, 70518
-recovered pasa_asmbl_44625.p1, internal, 70613, 70690
-recovered pasa_asmbl_44625.p1, internal, 70811, 70894
Valid prediction for HiQ_model.g8972.t1
Valid prediction for GlimmerHMM_glimmerT_13418-T1
Valid prediction for snap_scaffold_5-snap.2714-T1
Valid prediction for GeneMark_model.22517_t
Valid prediction for GeneMark_model.22490_t
Valid prediction for GeneMark_model.22502_t
Valid prediction for snap_scaffold_5-snap.2727-T1
Couldn't classify 11756, 11955
Sorry, prediction pasa_asmbl_44617.p1 fails validation.
(TTG)	 TG	11756-11955	GT	TTG
(ATA)	 AG	12505-13075	AT	AAA
-recovered pasa_asmbl_44617.p1, terminal, 12505, 13075
Valid prediction for snap_scaffold_5-snap.2722-T1
Valid prediction for GlimmerHMM_glimmerT_13408-T1
Valid prediction for HiQ_model.g8962.t1
Valid prediction for CodingQuarry_transcript_52227-T1
Valid prediction for GlimmerHMM_glimmerT_13393-T1
Valid prediction for Augustus_model.g8980.t1
Valid prediction for GlimmerHMM_glimmerT_13417-T1
Valid prediction for snap_scaffold_5-snap.2726-T1
Valid prediction for GlimmerHMM_glimmerT_13404-T1
Valid prediction for GeneMark_model.22505_t
Valid prediction for snap_scaffold_5-snap.2723-T1
Valid prediction for pasa_asmbl_44628.p1
Couldn't classify 26718, 27517
Sorry, prediction pasa_asmbl_44618.p1 fails validation.
(ATG)	 GT	25019-25397	GT	AGG
(GCA)	 AG	26718-27517	GA	CGG
-recovered pasa_asmbl_44618.p1, initial, 25019, 25397
Couldn't classify 32982, 33102
Sorry, prediction pasa_asmbl_44619.p1 fails validation.
(AGG)	 CC	32982-33102	GT	AGG
(GGC)	 AG	34212-35113	GT	AGG
(GGG)	 AG	35261-35341	GA	GAG
-recovered pasa_asmbl_44619.p1, terminal, 35261, 35341
-recovered pasa_asmbl_44619.p1, internal, 34212, 35113
Valid prediction for GeneMark_model.22488_t
Valid prediction for GlimmerHMM_glimmerT_13395-T1
Valid prediction for GlimmerHMM_glimmerT_13399-T1
Valid prediction for GeneMark_model.22503_t
Valid prediction for snap_scaffold_5-snap.2712-T1
Valid prediction for GeneMark_model.22516_t
Valid prediction for GlimmerHMM_glimmerT_13403-T1
Valid prediction for GeneMark_model.22513_t
Valid prediction for HiQ_model.g8970.t1
Couldn't classify 74385, 74604
Sorry, prediction pasa_asmbl_45097.p1 fails validation.
(CTT)	 TC	74385-74604	GT	TGG
(AGC)	 AG	74817-74887	GT	AGG
(GCG)	 AG	74987-76273	AC	GAA
-recovered pasa_asmbl_45097.p1, terminal, 74987, 76273
-recovered pasa_asmbl_45097.p1, internal, 74817, 74887
Valid prediction for snap_scaffold_5-snap.2739-T1
Valid prediction for GeneMark_model.22519_t
Valid prediction for GlimmerHMM_glimmerT_13416-T1
Valid prediction for GeneMark_model.22504_t
Valid prediction for GeneMark_model.22515_t
Valid prediction for GeneMark_model.22494_t
Valid prediction for snap_scaffold_5-snap.2710-T1
Valid prediction for GeneMark_model.22508_t
Valid prediction for snap_scaffold_5-snap.2715-T1
Valid prediction for pasa_asmbl_44623.p1
Valid prediction for GeneMark_model.22499_t
Valid prediction for GeneMark_model.22493_t
Valid prediction for GlimmerHMM_glimmerT_13402-T1
Valid prediction for Augustus_model.g8971.t1
Valid prediction for snap_scaffold_5-snap.2737-T1
Valid prediction for Augustus_model.g8963.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 pasa_asmbl_45998.p1
Valid prediction for snap_scaffold_5-snap.2718-T1
Valid prediction for CodingQuarry_transcript_52232-T1
Valid prediction for Augustus_model.g8973.t1
Valid prediction for snap_scaffold_5-snap.2736-T1
Valid prediction for GeneMark_model.22514_t
Valid prediction for CodingQuarry_transcript_52229-T1
Valid prediction for GeneMark_model.22507_t
Valid prediction for snap_scaffold_5-snap.2709-T1
Valid prediction for GlimmerHMM_glimmerT_13410-T1
Valid prediction for pasa_asmbl_46002.p1
Valid prediction for snap_scaffold_5-snap.2730-T1
Valid prediction for snap_scaffold_5-snap.2738-T1
Valid prediction for snap_scaffold_5-snap.2720-T1
Valid prediction for snap_scaffold_5-snap.2721-T1
Valid prediction for GlimmerHMM_glimmerT_13401-T1
Valid prediction for GlimmerHMM_glimmerT_13412-T1
Valid prediction for HiQ_model.g8966.t1
Valid prediction for Augustus_model.g8968.t1
Valid prediction for snap_scaffold_5-snap.2732-T1
Valid prediction for Augustus_model.g8978.t1
Valid prediction for GlimmerHMM_glimmerT_13411-T1
Valid prediction for GeneMark_model.22489_t
Valid prediction for GeneMark_model.22498_t
Valid prediction for GeneMark_model.22495_t
Valid prediction for snap_scaffold_5-snap.2740-T1
Valid prediction for GeneMark_model.22518_t
Valid prediction for Augustus_model.g8965.t1
Valid prediction for pasa_asmbl_45994.p1
Valid prediction for Augustus_model.g8977.t1
Valid prediction for Augustus_model.g8964.t1
Valid prediction for snap_scaffold_5-snap.2733-T1
Couldn't classify 114733, 114856
Sorry, prediction pasa_asmbl_45991.p1 fails validation.
(CAG)	 GA	114733-114856	GT	TGG
(ATG)	 AG	114967-115115	GT	TGG
(GCT)	 AG	115211-116182	TA	AGT
-recovered pasa_asmbl_45991.p1, initial, 114967, 115115
-recovered pasa_asmbl_45991.p1, terminal, 115211, 116182
-recovered pasa_asmbl_45991.p1, internal, 114967, 115115
Valid prediction for Augustus_model.g8961.t1
Valid prediction for GlimmerHMM_glimmerT_13405-T1
Valid prediction for CodingQuarry_transcript_52230-T1
Valid prediction for snap_scaffold_5-snap.2734-T1
Valid prediction for HiQ_model.g8976.t1
Valid prediction for GeneMark_model.22496_t
Valid prediction for GeneMark_model.22511_t
Valid prediction for GlimmerHMM_glimmerT_13400-T1
Valid prediction for GeneMark_model.22497_t
Valid prediction for GlimmerHMM_glimmerT_13394-T1
Valid prediction for HiQ_model.g8979.t1
Valid prediction for GeneMark_model.22509_t
Valid prediction for snap_scaffold_5-snap.2728-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_13396-T1
Valid prediction for GeneMark_model.22512_t
Valid prediction for snap_scaffold_5-snap.2711-T1
Valid prediction for snap_scaffold_5-snap.2716-T1
Valid prediction for snap_scaffold_5-snap.2729-T1
Valid prediction for GeneMark_model.22500_t
Couldn't classify 108279, 108710
Sorry, prediction pasa_asmbl_45993.p1 fails validation.
(ATG)	 AA	106992-106994	GT	TGG
(CGT)	 AG	107702-107924	GT	TGG
(ATG)	 AG	108035-108183	GT	TGG
(GCT)	 AG	108279-108710	GC	TGG
-recovered pasa_asmbl_45993.p1, initial, 106992, 106994
-recovered pasa_asmbl_45993.p1, initial, 108035, 108183
-recovered pasa_asmbl_45993.p1, internal, 107702, 107924
-recovered pasa_asmbl_45993.p1, internal, 108035, 108183
-recovered pasa_asmbl_45993.p1, internal, 108279, 108710
Valid prediction for GlimmerHMM_glimmerT_13397-T1
Valid prediction for GlimmerHMM_glimmerT_13398-T1
Valid prediction for CodingQuarry_transcript_52231-T1
Valid prediction for snap_scaffold_5-snap.2717-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for HiQ_model.g8975.t1
Valid prediction for GlimmerHMM_glimmerT_13413-T1
Valid prediction for snap_scaffold_5-snap.2725-T1
Valid prediction for GlimmerHMM_glimmerT_13409-T1
Valid prediction for snap_scaffold_5-snap.2735-T1
Valid prediction for GeneMark_model.22501_t
Valid prediction for Augustus_model.g8960.t1
Valid prediction for GeneMark_model.22510_t
Valid prediction for GeneMark_model.22506_t
Valid prediction for GeneMark_model.22492_t
Couldn't classify 112588, 112893
Sorry, prediction pasa_asmbl_45992.p1 fails validation.
(ATC)	 CA	112588-112893	GA	GTG
Valid prediction for GlimmerHMM_glimmerT_13414-T1
Valid prediction for GlimmerHMM_glimmerT_13407-T1
Valid prediction for GlimmerHMM_glimmerT_13415-T1
Valid prediction for Augustus_model.g8969.t1
Valid prediction for snap_scaffold_5-snap.2731-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 100840, rend_intergenic: 96919  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138731, rend_intergenic: 138579  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142126, rend_intergenic: 139374  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145714, rend_intergenic: 142682  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152596, rend_intergenic: 147933  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 154774
-exon list size: 408


building trellis

0.2    
0.5    
0.7    
1.0    
1.2    
1.5    
1.7    
2.0    
2.2    
2.4    
2.7    
2.9    
3.2    
3.4    
3.7    
3.9    
4.1    
4.4    
4.6    
4.9    
5.1    
5.4    
5.6    
5.9    
6.1    
6.3    
6.6    
6.8    
7.1    
7.3    
7.6    
7.8    
8.0    
8.3    
8.5    
8.8    
9.0    
9.3    
9.5    
9.8    
10.0    
10.2    
10.5    
10.7    
11.0    
11.2    
11.5    
11.7    
12.0    
12.2    
12.4    
12.7    
12.9    
13.2    
13.4    
13.7    
13.9    
14.1    
14.4    
14.6    
14.9    
15.1    
15.4    
15.6    
15.9    
16.1    
16.3    
16.6    
16.8    
17.1    
17.3    
17.6    
17.8    
18.0    
18.3    
18.5    
18.8    
19.0    
19.3    
19.5    
19.8    
20.0    
20.2    
20.5    
20.7    
21.0    
21.2    
21.5    
21.7    
22.0    
22.2    
22.4    
22.7    
22.9    
23.2    
23.4    
23.7    
23.9    
24.1    
24.4    
24.6    
24.9    
25.1    
25.4    
25.6    
25.9    
26.1    
26.3    
26.6    
26.8    
27.1    
27.3    
27.6    
27.8    
28.0    
28.3    
28.5    
28.8    
29.0    
29.3    
29.5    
29.8    
30.0    
30.2    
30.5    
30.7    
31.0    
31.2    
31.5    
31.7    
32.0    
32.2    
32.4    
32.7    
32.9    
33.2    
33.4    
33.7    
33.9    
34.1    
34.4    
34.6    
34.9    
35.1    
35.4    
35.6    
35.9    
36.1    
36.3    
36.6    
36.8    
37.1    
37.3    
37.6    
37.8    
38.0    
38.3    
38.5    
38.8    
39.0    
39.3    
39.5    
39.8    
40.0    
40.2    
40.5    
40.7    
41.0    
41.2    
41.5    
41.7    
42.0    
42.2    
42.4    
42.7    
42.9    
43.2    
43.4    
43.7    
43.9    
44.1    
44.4    
44.6    
44.9    
45.1    
45.4    
45.6    
45.9    
46.1    
46.3    
46.6    
46.8    
47.1    
47.3    
47.6    
47.8    
48.0    
48.3    
48.5    
48.8    
49.0    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
50.7    
51.0    
51.2    
51.5    
51.7    
52.0    
52.2    
52.4    
52.7    
52.9    
53.2    
53.4    
53.7    
53.9    
54.1    
54.4    
54.6    
54.9    
55.1    
55.4    
55.6    
55.9    
56.1    
56.3    
56.6    
56.8    
57.1    
57.3    
57.6    
57.8    
58.0    
58.3    
58.5    
58.8    
59.0    
59.3    
59.5    
59.8    
60.0    
60.2    
60.5    
60.7    
61.0    
61.2    
61.5    
61.7    
62.0    
62.2    
62.4    
62.7    
62.9    
63.2    
63.4    
63.7    
63.9    
64.1    
64.4    
64.6    
64.9    
65.1    
65.4    
65.6    
65.9    
66.1    
66.3    
66.6    
66.8    
67.1    
67.3    
67.6    
67.8    
68.0    
68.3    
68.5    
68.8    
69.0    
69.3    
69.5    
69.8    
70.0    
70.2    
70.5    
70.7    
71.0    
71.2    
71.5    
71.7    
72.0    
72.2    
72.4    
72.7    
72.9    
73.2    
73.4    
73.7    
73.9    
74.1    
74.4    
74.6    
74.9    
75.1    
75.4    
75.6    
75.9    
76.1    
76.3    
76.6    
76.8    
77.1    
77.3    
77.6    
77.8    
78.0    
78.3    
78.5    
78.8    
79.0    
79.3    
79.5    
79.8    
80.0    
80.2    
80.5    
80.7    
81.0    
81.2    
81.5    
81.7    
82.0    
82.2    
82.4    
82.7    
82.9    
83.2    
83.4    
83.7    
83.9    
84.1    
84.4    
84.6    
84.9    
85.1    
85.4    
85.6    
85.9    
86.1    
86.3    
86.6    
86.8    
87.1    
87.3    
87.6    
87.8    
88.0    
88.3    
88.5    
88.8    
89.0    
89.3    
89.5    
89.8    
90.0    
90.2    
90.5    
90.7    
91.0    
91.2    
91.5    
91.7    
92.0    
92.2    
92.4    
92.7    
92.9    
93.2    
93.4    
93.7    
93.9    
94.1    
94.4    
94.6    
94.9    
95.1    
95.4    
95.6    
95.9    
96.1    
96.3    
96.6    
96.8    
97.1    
97.3    
97.6    
97.8    
98.0    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 100840, rend_intergenic: 96919  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138731, rend_intergenic: 138579  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142126, rend_intergenic: 139374  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145714, rend_intergenic: 142682  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152596, rend_intergenic: 147933  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 12504
-exon list size: 7


building trellis

11.1    
22.2    
33.3    
44.4    
55.6    
66.7    
77.8    
88.9    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support