-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_18/scaffold_18_3724850-3897197

-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 pasa_asmbl_20503.p1
Valid prediction for GeneMark_model.74396_t
Valid prediction for snap_scaffold_18-snap.786-T1
Valid prediction for pasa_asmbl_20505.p1
Valid prediction for GlimmerHMM_glimmerT_43069-T1
Valid prediction for GlimmerHMM_glimmerT_43061-T1
Valid prediction for GeneMark_model.74404_t
Valid prediction for GlimmerHMM_glimmerT_43076-T1
Valid prediction for snap_scaffold_18-snap.779-T1
Valid prediction for GlimmerHMM_glimmerT_43071-T1
Valid prediction for GeneMark_model.74391_t
Valid prediction for GlimmerHMM_glimmerT_43081-T1
Valid prediction for Augustus_model.g28809.t1
Valid prediction for GeneMark_model.74372_t
Valid prediction for snap_scaffold_18-snap.770-T1
Valid prediction for GlimmerHMM_glimmerT_43064-T1
Valid prediction for snap_scaffold_18-snap.758-T1
Valid prediction for Augustus_model.g28818.t1
Valid prediction for snap_scaffold_18-snap.785-T1
Valid prediction for GeneMark_model.74383_t
Valid prediction for pasa_asmbl_20509.p1
Valid prediction for snap_scaffold_18-snap.768-T1
Valid prediction for GeneMark_model.74403_t
Valid prediction for snap_scaffold_18-snap.780-T1
Valid prediction for GlimmerHMM_glimmerT_43063-T1
Valid prediction for GeneMark_model.74370_t
Valid prediction for GeneMark_model.74378_t
Couldn't classify 77490, 77529
Sorry, prediction pasa_asmbl_20508.p1 fails validation.
(GTG)	 TG	77490-77529	GT	AGG
(AGG)	 AG	77988-78115	GT	CGG
(TTC)	 AG	78420-78494	GT	AGG
(GCT)	 AG	78748-78843	GT	AGG
(TTC)	 AG	78969-79097	GT	AGG
(GCG)	 AG	79217-79378	GT	AGG
(CTG)	 AG	79500-79601	TC	GAT
-recovered pasa_asmbl_20508.p1, terminal, 79500, 79601
-recovered pasa_asmbl_20508.p1, internal, 77988, 78115
-recovered pasa_asmbl_20508.p1, internal, 78420, 78494
-recovered pasa_asmbl_20508.p1, internal, 78748, 78843
-recovered pasa_asmbl_20508.p1, internal, 78969, 79097
-recovered pasa_asmbl_20508.p1, internal, 79217, 79378
Valid prediction for GeneMark_model.74395_t
Valid prediction for snap_scaffold_18-snap.759-T1
Valid prediction for GlimmerHMM_glimmerT_43073-T1
Valid prediction for snap_scaffold_18-snap.787-T1
Valid prediction for snap_scaffold_18-snap.789-T1
Valid prediction for Augustus_model.g28813.t1
Valid prediction for GeneMark_model.74367_t
Valid prediction for GeneMark_model.74397_t
Valid prediction for snap_scaffold_18-snap.760-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for HiQ_model.g28808.t1
Valid prediction for snap_scaffold_18-snap.774-T1
Valid prediction for CodingQuarry_transcript_23670-T1
Valid prediction for GeneMark_model.74393_t
Valid prediction for GlimmerHMM_glimmerT_43072-T1
Valid prediction for GlimmerHMM_glimmerT_43083-T1
Valid prediction for HiQ_model.g28804.t1
Valid prediction for GeneMark_model.74380_t
Valid prediction for HiQ_model.g28806.t1
Valid prediction for GeneMark_model.74376_t
Valid prediction for GeneMark_model.74401_t
Valid prediction for GlimmerHMM_glimmerT_43078-T1
Valid prediction for GlimmerHMM_glimmerT_43067-T1
Valid prediction for Augustus_model.g28816.t1
Couldn't classify 147828, 147911
Sorry, prediction pasa_asmbl_20512.p1 fails validation.
(GTG)	 CA	147828-147911	GT	AGG
(ATG)	 AG	149221-149332	GT	AGG
(GGC)	 AG	150415-150536	GT	GGG
(ATA)	 AG	152833-153030	GC	GAG
-recovered pasa_asmbl_20512.p1, initial, 149221, 149332
-recovered pasa_asmbl_20512.p1, terminal, 152833, 153030
-recovered pasa_asmbl_20512.p1, internal, 149221, 149332
-recovered pasa_asmbl_20512.p1, internal, 150415, 150536
-recovered pasa_asmbl_20512.p1, internal, 152833, 153030
Valid prediction for GeneMark_model.74374_t
Valid prediction for GlimmerHMM_glimmerT_43085-T1
Valid prediction for snap_scaffold_18-snap.765-T1
Valid prediction for snap_scaffold_18-snap.766-T1
Valid prediction for snap_scaffold_18-snap.790-T1
Valid prediction for snap_scaffold_18-snap.775-T1
Valid prediction for GeneMark_model.74388_t
Valid prediction for Augustus_model.g28810.t1
Valid prediction for snap_scaffold_18-snap.771-T1
Valid prediction for GeneMark_model.74384_t
Valid prediction for GlimmerHMM_glimmerT_43068-T1
Valid prediction for GeneMark_model.74365_t
Valid prediction for HiQ_model.g28811.t1
Valid prediction for snap_scaffold_18-snap.777-T1
Valid prediction for Augustus_model.g28814.t1
Valid prediction for GlimmerHMM_glimmerT_43082-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_18-snap.781-T1
Valid prediction for CodingQuarry_transcript_23669-T1
Valid prediction for Augustus_model.g28802.t1
Valid prediction for GlimmerHMM_glimmerT_43070-T1
Valid prediction for GlimmerHMM_glimmerT_43080-T1
Valid prediction for GlimmerHMM_glimmerT_43079-T1
Valid prediction for GeneMark_model.74390_t
Valid prediction for snap_scaffold_18-snap.763-T1
Valid prediction for snap_scaffold_18-snap.773-T1
Valid prediction for GeneMark_model.74402_t
Valid prediction for GeneMark_model.74371_t
Valid prediction for Augustus_model.g28801.t1
Valid prediction for Augustus_model.g28803.t1
Valid prediction for pasa_asmbl_19815.p1
Valid prediction for snap_scaffold_18-snap.756-T1
Valid prediction for GeneMark_model.74385_t
Valid prediction for HiQ_model.g28805.t1
Valid prediction for GlimmerHMM_glimmerT_43059-T1
Valid prediction for GeneMark_model.74400_t
Valid prediction for GlimmerHMM_glimmerT_43077-T1
Valid prediction for GlimmerHMM_glimmerT_43066-T1
Valid prediction for snap_scaffold_18-snap.762-T1
Valid prediction for GeneMark_model.74394_t
Valid prediction for pasa_asmbl_19807.p1
Valid prediction for snap_scaffold_18-snap.782-T1
Valid prediction for HiQ_model.g28807.t1
Valid prediction for snap_scaffold_18-snap.769-T1
Couldn't classify 156767, 157721
Couldn't classify 159325, 159506
Sorry, prediction pasa_asmbl_19805.p1 fails validation.
(TTC)	 TC	156767-157721	GT	AGG
(TCC)	 AG	159325-159506	CA	CGC
Valid prediction for CodingQuarry_transcript_23668-T1
Valid prediction for GlimmerHMM_glimmerT_43062-T1
Valid prediction for snap_scaffold_18-snap.783-T1
Valid prediction for GlimmerHMM_glimmerT_43086-T1
Valid prediction for GlimmerHMM_glimmerT_43074-T1
Valid prediction for Augustus_model.g28812.t1
Valid prediction for GlimmerHMM_glimmerT_43075-T1
Valid prediction for Augustus_model.g28817.t1
Valid prediction for GeneMark_model.74373_t
Valid prediction for GeneMark_model.74375_t
Valid prediction for GeneMark_model.74389_t
Valid prediction for CodingQuarry_transcript_23671-T1
Valid prediction for snap_scaffold_18-snap.761-T1
Valid prediction for GlimmerHMM_glimmerT_43060-T1
Valid prediction for GeneMark_model.74366_t
Valid prediction for snap_scaffold_18-snap.772-T1
Valid prediction for GeneMark_model.74386_t
Valid prediction for snap_scaffold_18-snap.784-T1
Valid prediction for GlimmerHMM_glimmerT_43084-T1
Valid prediction for GeneMark_model.74382_t
Valid prediction for GeneMark_model.74398_t
Valid prediction for GeneMark_model.74387_t
Valid prediction for GlimmerHMM_glimmerT_43065-T1
Valid prediction for GlimmerHMM_glimmerT_43058-T1
Valid prediction for snap_scaffold_18-snap.776-T1
Valid prediction for GeneMark_model.74381_t
Valid prediction for snap_scaffold_18-snap.764-T1
Valid prediction for Augustus_model.g28815.t1
Valid prediction for GeneMark_model.74379_t
Valid prediction for GeneMark_model.74368_t
Valid prediction for GeneMark_model.74399_t
Couldn't classify 104046, 104237
Sorry, prediction pasa_asmbl_19813.p1 fails validation.
(TTC)	 GC	104046-104237	GT	AGG
(GAG)	 AG	104463-104576	GT	AGG
(ATT)	 AG	104806-104883	GT	AGG
(ACG)	 AG	105020-105115	GT	TGG
(GCT)	 AG	105234-105340	GT	AGG
(CCC)	 AG	105443-105512	GT	AGG
(GCA)	 AG	105731-105823	GT	AGG
(ACA)	 AG	106051-106179	GT	TGG
(GAC)	 AG	106557-106775	GT	CGG
(CTG)	 AG	107018-107072	GT	CCG
(GAA)	 AG	107269-107408	CA	GAC
-recovered pasa_asmbl_19813.p1, terminal, 107269, 107408
-recovered pasa_asmbl_19813.p1, internal, 104463, 104576
-recovered pasa_asmbl_19813.p1, internal, 104806, 104883
-recovered pasa_asmbl_19813.p1, internal, 105020, 105115
-recovered pasa_asmbl_19813.p1, internal, 105234, 105340
-recovered pasa_asmbl_19813.p1, internal, 105443, 105512
-recovered pasa_asmbl_19813.p1, internal, 105731, 105823
-recovered pasa_asmbl_19813.p1, internal, 106051, 106179
-recovered pasa_asmbl_19813.p1, internal, 106557, 106775
-recovered pasa_asmbl_19813.p1, internal, 107018, 107072
Valid prediction for snap_scaffold_18-snap.788-T1
Valid prediction for snap_scaffold_18-snap.757-T1
Valid prediction for GeneMark_model.74369_t
Valid prediction for snap_scaffold_18-snap.778-T1
Valid prediction for GeneMark_model.74392_t
Valid prediction for GeneMark_model.74377_t
Valid prediction for snap_scaffold_18-snap.767-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 20488, rend_intergenic: 12834  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47263, rend_intergenic: 41554  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57696, rend_intergenic: 55928  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72249, rend_intergenic: 64986  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88074, rend_intergenic: 86047  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119759, rend_intergenic: 116707  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134748, rend_intergenic: 131417  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170059, rend_intergenic: 159569  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 172348
-exon list size: 527


building trellis

0.2    
0.4    
0.6    
0.8    
0.9    
1.1    
1.3    
1.5    
1.7    
1.9    
2.1    
2.3    
2.5    
2.6    
2.8    
3.0    
3.2    
3.4    
3.6    
3.8    
4.0    
4.2    
4.3    
4.5    
4.7    
4.9    
5.1    
5.3    
5.5    
5.7    
5.9    
6.0    
6.2    
6.4    
6.6    
6.8    
7.0    
7.2    
7.4    
7.6    
7.8    
7.9    
8.1    
8.3    
8.5    
8.7    
8.9    
9.1    
9.3    
9.5    
9.6    
9.8    
10.0    
10.2    
10.4    
10.6    
10.8    
11.0    
11.2    
11.3    
11.5    
11.7    
11.9    
12.1    
12.3    
12.5    
12.7    
12.9    
13.0    
13.2    
13.4    
13.6    
13.8    
14.0    
14.2    
14.4    
14.6    
14.7    
14.9    
15.1    
15.3    
15.5    
15.7    
15.9    
16.1    
16.3    
16.4    
16.6    
16.8    
17.0    
17.2    
17.4    
17.6    
17.8    
18.0    
18.1    
18.3    
18.5    
18.7    
18.9    
19.1    
19.3    
19.5    
19.7    
19.8    
20.0    
20.2    
20.4    
20.6    
20.8    
21.0    
21.2    
21.4    
21.6    
21.7    
21.9    
22.1    
22.3    
22.5    
22.7    
22.9    
23.1    
23.3    
23.4    
23.6    
23.8    
24.0    
24.2    
24.4    
24.6    
24.8    
25.0    
25.1    
25.3    
25.5    
25.7    
25.9    
26.1    
26.3    
26.5    
26.7    
26.8    
27.0    
27.2    
27.4    
27.6    
27.8    
28.0    
28.2    
28.4    
28.5    
28.7    
28.9    
29.1    
29.3    
29.5    
29.7    
29.9    
30.1    
30.2    
30.4    
30.6    
30.8    
31.0    
31.2    
31.4    
31.6    
31.8    
31.9    
32.1    
32.3    
32.5    
32.7    
32.9    
33.1    
33.3    
33.5    
33.6    
33.8    
34.0    
34.2    
34.4    
34.6    
34.8    
35.0    
35.2    
35.3    
35.5    
35.7    
35.9    
36.1    
36.3    
36.5    
36.7    
36.9    
37.1    
37.2    
37.4    
37.6    
37.8    
38.0    
38.2    
38.4    
38.6    
38.8    
38.9    
39.1    
39.3    
39.5    
39.7    
39.9    
40.1    
40.3    
40.5    
40.6    
40.8    
41.0    
41.2    
41.4    
41.6    
41.8    
42.0    
42.2    
42.3    
42.5    
42.7    
42.9    
43.1    
43.3    
43.5    
43.7    
43.9    
44.0    
44.2    
44.4    
44.6    
44.8    
45.0    
45.2    
45.4    
45.6    
45.7    
45.9    
46.1    
46.3    
46.5    
46.7    
46.9    
47.1    
47.3    
47.4    
47.6    
47.8    
48.0    
48.2    
48.4    
48.6    
48.8    
49.0    
49.1    
49.3    
49.5    
49.7    
49.9    
50.1    
50.3    
50.5    
50.7    
50.9    
51.0    
51.2    
51.4    
51.6    
51.8    
52.0    
52.2    
52.4    
52.6    
52.7    
52.9    
53.1    
53.3    
53.5    
53.7    
53.9    
54.1    
54.3    
54.4    
54.6    
54.8    
55.0    
55.2    
55.4    
55.6    
55.8    
56.0    
56.1    
56.3    
56.5    
56.7    
56.9    
57.1    
57.3    
57.5    
57.7    
57.8    
58.0    
58.2    
58.4    
58.6    
58.8    
59.0    
59.2    
59.4    
59.5    
59.7    
59.9    
60.1    
60.3    
60.5    
60.7    
60.9    
61.1    
61.2    
61.4    
61.6    
61.8    
62.0    
62.2    
62.4    
62.6    
62.8    
62.9    
63.1    
63.3    
63.5    
63.7    
63.9    
64.1    
64.3    
64.5    
64.7    
64.8    
65.0    
65.2    
65.4    
65.6    
65.8    
66.0    
66.2    
66.4    
66.5    
66.7    
66.9    
67.1    
67.3    
67.5    
67.7    
67.9    
68.1    
68.2    
68.4    
68.6    
68.8    
69.0    
69.2    
69.4    
69.6    
69.8    
69.9    
70.1    
70.3    
70.5    
70.7    
70.9    
71.1    
71.3    
71.5    
71.6    
71.8    
72.0    
72.2    
72.4    
72.6    
72.8    
73.0    
73.2    
73.3    
73.5    
73.7    
73.9    
74.1    
74.3    
74.5    
74.7    
74.9    
75.0    
75.2    
75.4    
75.6    
75.8    
76.0    
76.2    
76.4    
76.6    
76.7    
76.9    
77.1    
77.3    
77.5    
77.7    
77.9    
78.1    
78.3    
78.4    
78.6    
78.8    
79.0    
79.2    
79.4    
79.6    
79.8    
80.0    
80.2    
80.3    
80.5    
80.7    
80.9    
81.1    
81.3    
81.5    
81.7    
81.9    
82.0    
82.2    
82.4    
82.6    
82.8    
83.0    
83.2    
83.4    
83.6    
83.7    
83.9    
84.1    
84.3    
84.5    
84.7    
84.9    
85.1    
85.3    
85.4    
85.6    
85.8    
86.0    
86.2    
86.4    
86.6    
86.8    
87.0    
87.1    
87.3    
87.5    
87.7    
87.9    
88.1    
88.3    
88.5    
88.7    
88.8    
89.0    
89.2    
89.4    
89.6    
89.8    
90.0    
90.2    
90.4    
90.5    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
91.9    
92.1    
92.2    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
94.0    
94.1    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.2    
99.4    
99.6    
99.8    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 20488, rend_intergenic: 12834  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47263, rend_intergenic: 41554  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57696, rend_intergenic: 55928  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72249, rend_intergenic: 64986  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88074, rend_intergenic: 86047  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119759, rend_intergenic: 116707  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134748, rend_intergenic: 131417  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170059, rend_intergenic: 159569  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 10326
-exon list size: 1


building trellis

33.3    
66.7    
-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