-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_24/scaffold_24_988599-1077572

-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 Augustus_model.g34637.t1
Couldn't classify 43899, 44025
Sorry, prediction pasa_asmbl_32060.p1 fails validation.
(AAG)	 TC	43899-44025	GT	AGG
(GTC)	 AG	46580-46735	GT	GGG
(ATG)	 AG	46997-47181	GT	GGG
(CCT)	 AG	47323-47406	GT	AGG
(AGG)	 AG	47582-47839	CC	GAC
add_exon() Sorry, pasa_asmbl_32060.p1 46997-47181-initial-1 is invalid.
-recovered pasa_asmbl_32060.p1, initial, 46997, 47181
-recovered pasa_asmbl_32060.p1, terminal, 47582, 47839
-recovered pasa_asmbl_32060.p1, internal, 46580, 46735
-recovered pasa_asmbl_32060.p1, internal, 46997, 47181
-recovered pasa_asmbl_32060.p1, internal, 47323, 47406
Valid prediction for GlimmerHMM_glimmerT_51974-T1
Valid prediction for Augustus_model.g34633.t1
Valid prediction for snap_scaffold_24-snap.264-T1
Valid prediction for snap_scaffold_24-snap.261-T1
Valid prediction for snap_scaffold_24-snap.255-T1
Valid prediction for snap_scaffold_24-snap.266-T1
Valid prediction for snap_scaffold_24-snap.256-T1
Couldn't classify 29373, 29717
Sorry, prediction pasa_asmbl_32713.p1 fails validation.
(CCA)	 TA	29373-29717	TG	GCT
Valid prediction for GlimmerHMM_glimmerT_51964-T1
Valid prediction for snap_scaffold_24-snap.246-T1
Valid prediction for GlimmerHMM_glimmerT_51962-T1
Valid prediction for GlimmerHMM_glimmerT_51972-T1
Valid prediction for Augustus_model.g34635.t1
Valid prediction for snap_scaffold_24-snap.247-T1
Valid prediction for Augustus_model.g34639.t1
Valid prediction for snap_scaffold_24-snap.253-T1
Valid prediction for snap_scaffold_24-snap.260-T1
Valid prediction for GlimmerHMM_glimmerT_51970-T1
Valid prediction for snap_scaffold_24-snap.265-T1
Valid prediction for snap_scaffold_24-snap.258-T1
Valid prediction for snap_scaffold_24-snap.250-T1
Valid prediction for snap_scaffold_24-snap.268-T1
Valid prediction for CodingQuarry_transcript_37229-T1
Valid prediction for GlimmerHMM_glimmerT_51968-T1
Valid prediction for snap_scaffold_24-snap.245-T1
Valid prediction for HiQ_model.g34642.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_24-snap.252-T1
Valid prediction for Augustus_model.g34636.t1
Valid prediction for snap_scaffold_24-snap.243-T1
Valid prediction for snap_scaffold_24-snap.262-T1
Valid prediction for GlimmerHMM_glimmerT_51971-T1
Valid prediction for Augustus_model.g34643.t1
Valid prediction for GlimmerHMM_glimmerT_51969-T1
Valid prediction for Augustus_model.g34641.t1
Valid prediction for snap_scaffold_24-snap.259-T1
Couldn't classify 63308, 63432
Sorry, prediction pasa_asmbl_32712.p1 fails validation.
(TCT)	 GG	63308-63432	GT	TGG
(GAA)	 AG	63593-63700	GT	AGG
(AGA)	 AG	63839-63905	AC	GAA
-recovered pasa_asmbl_32712.p1, terminal, 63839, 63905
-recovered pasa_asmbl_32712.p1, internal, 63593, 63700
Valid prediction for GlimmerHMM_glimmerT_51966-T1
Valid prediction for HiQ_model.g34634.t1
Valid prediction for CodingQuarry_transcript_37228-T1
Valid prediction for pasa_asmbl_32710.p1
Valid prediction for snap_scaffold_24-snap.244-T1
Valid prediction for Augustus_model.g34638.t1
Couldn't classify 79695, 79911
Sorry, prediction pasa_asmbl_32711.p1 fails validation.
(GTG)	 GT	79695-79911	GT	GGG
(GTG)	 AG	80085-80623	TC	GAT
-recovered pasa_asmbl_32711.p1, terminal, 80085, 80623
Valid prediction for Augustus_model.g34640.t1
Valid prediction for snap_scaffold_24-snap.251-T1
Valid prediction for GlimmerHMM_glimmerT_51967-T1
Valid prediction for CodingQuarry_transcript_37227-T1
Valid prediction for snap_scaffold_24-snap.257-T1
Valid prediction for GlimmerHMM_glimmerT_51965-T1
Valid prediction for snap_scaffold_24-snap.267-T1
Valid prediction for GlimmerHMM_glimmerT_51963-T1
Valid prediction for GlimmerHMM_glimmerT_51975-T1
Valid prediction for GlimmerHMM_glimmerT_51973-T1
Valid prediction for snap_scaffold_24-snap.263-T1
Valid prediction for snap_scaffold_24-snap.254-T1
Couldn't classify 17354, 17455
Couldn't classify 22841, 22951
Sorry, prediction pasa_asmbl_32714.p1 fails validation.
(GAG)	 AG	17354-17455	GT	TGG
(TTC)	 AG	18349-18515	GT	AGG
(AAC)	 AG	19614-19724	GT	TGG
(GAG)	 AG	21519-21569	GT	AAG
(TAA)	 AG	21910-22117	GT	GGG
(GAG)	 AG	22841-22951	GA	AGG
-recovered pasa_asmbl_32714.p1, internal, 17354, 17455
-recovered pasa_asmbl_32714.p1, internal, 18349, 18515
-recovered pasa_asmbl_32714.p1, internal, 19614, 19724
-recovered pasa_asmbl_32714.p1, internal, 21519, 21569
-recovered pasa_asmbl_32714.p1, internal, 21910, 22117
Valid prediction for snap_scaffold_24-snap.248-T1
Valid prediction for snap_scaffold_24-snap.249-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 5097, rend_intergenic: 3548  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14240, rend_intergenic: 8352  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24104, rend_intergenic: 21417  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29648, rend_intergenic: 25238  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32256, rend_intergenic: 31094  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39192, rend_intergenic: 35426  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45466, rend_intergenic: 43863  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55559, rend_intergenic: 49148  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72610, rend_intergenic: 55896  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79928, rend_intergenic: 77131  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86113, rend_intergenic: 80305  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 88974
-exon list size: 204


building trellis

0.5    
1.0    
1.5    
1.9    
2.4    
2.9    
3.4    
3.9    
4.4    
4.9    
5.3    
5.8    
6.3    
6.8    
7.3    
7.8    
8.3    
8.7    
9.2    
9.7    
10.2    
10.7    
11.2    
11.7    
12.1    
12.6    
13.1    
13.6    
14.1    
14.6    
15.0    
15.5    
16.0    
16.5    
17.0    
17.5    
18.0    
18.4    
18.9    
19.4    
19.9    
20.4    
20.9    
21.4    
21.8    
22.3    
22.8    
23.3    
23.8    
24.3    
24.8    
25.2    
25.7    
26.2    
26.7    
27.2    
27.7    
28.2    
28.6    
29.1    
29.6    
30.1    
30.6    
31.1    
31.6    
32.0    
32.5    
33.0    
33.5    
34.0    
34.5    
35.0    
35.4    
35.9    
36.4    
36.9    
37.4    
37.9    
38.3    
38.8    
39.3    
39.8    
40.3    
40.8    
41.3    
41.7    
42.2    
42.7    
43.2    
43.7    
44.2    
44.7    
45.1    
45.6    
46.1    
46.6    
47.1    
47.6    
48.1    
48.5    
49.0    
49.5    
50.0    
50.5    
51.0    
51.5    
51.9    
52.4    
52.9    
53.4    
53.9    
54.4    
54.9    
55.3    
55.8    
56.3    
56.8    
57.3    
57.8    
58.3    
58.7    
59.2    
59.7    
60.2    
60.7    
61.2    
61.7    
62.1    
62.6    
63.1    
63.6    
64.1    
64.6    
65.0    
65.5    
66.0    
66.5    
67.0    
67.5    
68.0    
68.4    
68.9    
69.4    
69.9    
70.4    
70.9    
71.4    
71.8    
72.3    
72.8    
73.3    
73.8    
74.3    
74.8    
75.2    
75.7    
76.2    
76.7    
77.2    
77.7    
78.2    
78.6    
79.1    
79.6    
80.1    
80.6    
81.1    
81.6    
82.0    
82.5    
83.0    
83.5    
84.0    
84.5    
85.0    
85.4    
85.9    
86.4    
86.9    
87.4    
87.9    
88.3    
88.8    
89.3    
89.8    
90.3    
90.8    
91.3    
91.7    
92.2    
92.7    
93.2    
93.7    
94.2    
94.7    
95.1    
95.6    
96.1    
96.6    
97.1    
97.6    
98.1    
98.5    
99.0    
99.5    
-found 14 predictions from path traversal
Error with prediction: snap lend_intergenic: 5097, rend_intergenic: 3548  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14240, rend_intergenic: 8352  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24104, rend_intergenic: 21417  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29648, rend_intergenic: 25238  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32256, rend_intergenic: 31094  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39192, rend_intergenic: 35426  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45466, rend_intergenic: 43863  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55559, rend_intergenic: 49148  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72610, rend_intergenic: 55896  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79928, rend_intergenic: 77131  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86113, rend_intergenic: 80305  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 10 predictions persist after filtering for low support