-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_19/scaffold_19_6668943-6785500

-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 snap_scaffold_19-snap.1369-T1
Valid prediction for snap_scaffold_19-snap.1372-T1
Valid prediction for Augustus_model.g29371.t1
Valid prediction for GlimmerHMM_glimmerT_44289-T1
Couldn't classify 74828, 75138
Sorry, prediction pasa_asmbl_21439.p1 fails validation.
(ATG)	 GC	73708-73765	GT	AGG
(GTG)	 AG	73904-74001	GT	AGG
(GGC)	 AG	74207-74291	GT	AGG
(TAA)	 AG	74828-75138	CC	AGC
-recovered pasa_asmbl_21439.p1, initial, 73708, 73765
-recovered pasa_asmbl_21439.p1, internal, 73904, 74001
-recovered pasa_asmbl_21439.p1, internal, 74207, 74291
Valid prediction for GlimmerHMM_glimmerT_44277-T1
Couldn't classify 63257, 63392
Couldn't classify 65145, 65196
Sorry, prediction pasa_asmbl_21436.p1 fails validation.
(CAG)	 TA	63257-63392	GT	AGG
(ATT)	 AG	63793-63871	GT	AGG
(AGA)	 AG	63977-64036	GT	GAG
(AAC)	 AG	64144-64284	GT	ATG
(ACC)	 AG	64457-64565	GT	TGG
(ATA)	 AG	64666-64761	GT	ATG
(GGT)	 AG	64973-64998	GT	AGG
(GAT)	 AG	65145-65196	AG	TCA
-recovered pasa_asmbl_21436.p1, internal, 63793, 63871
-recovered pasa_asmbl_21436.p1, internal, 63977, 64036
-recovered pasa_asmbl_21436.p1, internal, 64144, 64284
-recovered pasa_asmbl_21436.p1, internal, 64457, 64565
-recovered pasa_asmbl_21436.p1, internal, 64666, 64761
-recovered pasa_asmbl_21436.p1, internal, 64973, 64998
Valid prediction for snap_scaffold_19-snap.1366-T1
Couldn't classify 77419, 77499
Sorry, prediction pasa_asmbl_21894.p1 fails validation.
(ATG)	 CC	76981-77170	GC	AGG
(ATG)	 AG	77252-77343	GT	ATG
(GTG)	 AG	77419-77499	CA	CAC
-recovered pasa_asmbl_21894.p1, initial, 76981, 77170
add_exon() Sorry, pasa_asmbl_21894.p1 77252-77343-initial-1 is invalid.
-recovered pasa_asmbl_21894.p1, initial, 77252, 77343
-recovered pasa_asmbl_21894.p1, internal, 77252, 77343
Valid prediction for Augustus_model.g29368.t1
Valid prediction for GlimmerHMM_glimmerT_44290-T1
Valid prediction for snap_scaffold_19-snap.1373-T1
Valid prediction for pasa_asmbl_21431.p1
Valid prediction for Augustus_model.g29365.t1
Valid prediction for GlimmerHMM_glimmerT_44285-T1
Valid prediction for snap_scaffold_19-snap.1368-T1
Valid prediction for snap_scaffold_19-snap.1376-T1
Valid prediction for GlimmerHMM_glimmerT_44287-T1
Valid prediction for Augustus_model.g29364.t1
Couldn't classify 92867, 92980
Couldn't classify 93982, 94035
Sorry, prediction pasa_asmbl_21932.p1 fails validation.
(TCA)	 TT	92867-92980	GT	AGG
(TGG)	 AG	93690-93824	GT	AGG
(GGT)	 AG	93982-94035	CA	AAC
-recovered pasa_asmbl_21932.p1, internal, 93690, 93824
Valid prediction for HiQ_model.g29360.t1
Couldn't classify 77803, 78138
Sorry, prediction pasa_asmbl_21443.p1 fails validation.
(TTT)	 AG	77803-78138	AA	GGA
Valid prediction for snap_scaffold_19-snap.1375-T1
Valid prediction for GlimmerHMM_glimmerT_44278-T1
Valid prediction for CodingQuarry_transcript_25692-T1
Valid prediction for snap_scaffold_19-snap.1380-T1
Valid prediction for GlimmerHMM_glimmerT_44288-T1
Valid prediction for GlimmerHMM_glimmerT_44286-T1
Valid prediction for snap_scaffold_19-snap.1379-T1
Valid prediction for Augustus_model.g29359.t1
Valid prediction for snap_scaffold_19-snap.1367-T1
Valid prediction for Augustus_model.g29363.t1
Valid prediction for snap_scaffold_19-snap.1363-T1
Valid prediction for CodingQuarry_transcript_25693-T1
Valid prediction for snap_scaffold_19-snap.1370-T1
Couldn't classify 68684, 68719
Couldn't classify 73330, 73415
Sorry, prediction pasa_asmbl_21438.p1 fails validation.
(TAC)	 AG	68684-68719	GT	TGG
(CAA)	 AG	69374-69613	GT	AGG
(ATG)	 AG	69749-69872	GT	AGG
(GAT)	 AG	71500-71660	GT	AGG
(GTA)	 AG	71833-72023	GT	AGG
(TTC)	 AG	72596-72702	GT	AGG
(GTA)	 AG	73330-73415	CC	CCC
-recovered pasa_asmbl_21438.p1, initial, 69749, 69872
-recovered pasa_asmbl_21438.p1, internal, 68684, 68719
-recovered pasa_asmbl_21438.p1, internal, 69374, 69613
-recovered pasa_asmbl_21438.p1, internal, 69749, 69872
-recovered pasa_asmbl_21438.p1, internal, 71500, 71660
-recovered pasa_asmbl_21438.p1, internal, 71833, 72023
-recovered pasa_asmbl_21438.p1, internal, 72596, 72702
Valid prediction for snap_scaffold_19-snap.1362-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_22220.p1
Valid prediction for snap_scaffold_19-snap.1381-T1
Valid prediction for snap_scaffold_19-snap.1361-T1
Valid prediction for snap_scaffold_19-snap.1360-T1
Valid prediction for snap_scaffold_19-snap.1365-T1
Valid prediction for GlimmerHMM_glimmerT_44283-T1
Valid prediction for GlimmerHMM_glimmerT_44276-T1
Valid prediction for GlimmerHMM_glimmerT_44284-T1
Valid prediction for snap_scaffold_19-snap.1378-T1
Valid prediction for HiQ_model.g29358.t1
Valid prediction for Augustus_model.g29366.t1
Valid prediction for GlimmerHMM_glimmerT_44281-T1
Valid prediction for GlimmerHMM_glimmerT_44275-T1
Valid prediction for GlimmerHMM_glimmerT_44279-T1
Valid prediction for Augustus_model.g29370.t1
Valid prediction for snap_scaffold_19-snap.1382-T1
Valid prediction for CodingQuarry_transcript_25691-T1
Valid prediction for GlimmerHMM_glimmerT_44291-T1
Couldn't classify 105002, 105042
Sorry, prediction pasa_asmbl_22223.p1 fails validation.
(ATG)	 CC	104250-104375	GT	AGG
(GTG)	 AG	104567-104717	GT	AGG
(ACG)	 AG	105002-105042	CT	AGC
-recovered pasa_asmbl_22223.p1, initial, 104250, 104375
-recovered pasa_asmbl_22223.p1, internal, 104567, 104717
Valid prediction for Augustus_model.g29357.t1
Valid prediction for snap_scaffold_19-snap.1377-T1
Valid prediction for Augustus_model.g29367.t1
Valid prediction for snap_scaffold_19-snap.1374-T1
Valid prediction for GlimmerHMM_glimmerT_44280-T1
Valid prediction for Augustus_model.g29361.t1
Valid prediction for GlimmerHMM_glimmerT_44292-T1
Valid prediction for Augustus_model.g29369.t1
Valid prediction for Augustus_model.g29362.t1
Valid prediction for GlimmerHMM_glimmerT_44282-T1
Valid prediction for GlimmerHMM_glimmerT_44274-T1
Valid prediction for snap_scaffold_19-snap.1364-T1
Valid prediction for snap_scaffold_19-snap.1371-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 48769, rend_intergenic: 27988  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56848, rend_intergenic: 55497  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62533, rend_intergenic: 58839  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94230, rend_intergenic: 87876  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 116558
-exon list size: 282


building trellis

0.4    
0.7    
1.1    
1.4    
1.8    
2.1    
2.5    
2.8    
3.2    
3.5    
3.9    
4.2    
4.6    
4.9    
5.3    
5.6    
6.0    
6.3    
6.7    
7.0    
7.4    
7.7    
8.1    
8.5    
8.8    
9.2    
9.5    
9.9    
10.2    
10.6    
10.9    
11.3    
11.6    
12.0    
12.3    
12.7    
13.0    
13.4    
13.7    
14.1    
14.4    
14.8    
15.1    
15.5    
15.8    
16.2    
16.5    
16.9    
17.3    
17.6    
18.0    
18.3    
18.7    
19.0    
19.4    
19.7    
20.1    
20.4    
20.8    
21.1    
21.5    
21.8    
22.2    
22.5    
22.9    
23.2    
23.6    
23.9    
24.3    
24.6    
25.0    
25.4    
25.7    
26.1    
26.4    
26.8    
27.1    
27.5    
27.8    
28.2    
28.5    
28.9    
29.2    
29.6    
29.9    
30.3    
30.6    
31.0    
31.3    
31.7    
32.0    
32.4    
32.7    
33.1    
33.5    
33.8    
34.2    
34.5    
34.9    
35.2    
35.6    
35.9    
36.3    
36.6    
37.0    
37.3    
37.7    
38.0    
38.4    
38.7    
39.1    
39.4    
39.8    
40.1    
40.5    
40.8    
41.2    
41.5    
41.9    
42.3    
42.6    
43.0    
43.3    
43.7    
44.0    
44.4    
44.7    
45.1    
45.4    
45.8    
46.1    
46.5    
46.8    
47.2    
47.5    
47.9    
48.2    
48.6    
48.9    
49.3    
49.6    
50.0    
50.4    
50.7    
51.1    
51.4    
51.8    
52.1    
52.5    
52.8    
53.2    
53.5    
53.9    
54.2    
54.6    
54.9    
55.3    
55.6    
56.0    
56.3    
56.7    
57.0    
57.4    
57.7    
58.1    
58.5    
58.8    
59.2    
59.5    
59.9    
60.2    
60.6    
60.9    
61.3    
61.6    
62.0    
62.3    
62.7    
63.0    
63.4    
63.7    
64.1    
64.4    
64.8    
65.1    
65.5    
65.8    
66.2    
66.5    
66.9    
67.3    
67.6    
68.0    
68.3    
68.7    
69.0    
69.4    
69.7    
70.1    
70.4    
70.8    
71.1    
71.5    
71.8    
72.2    
72.5    
72.9    
73.2    
73.6    
73.9    
74.3    
74.6    
75.0    
75.4    
75.7    
76.1    
76.4    
76.8    
77.1    
77.5    
77.8    
78.2    
78.5    
78.9    
79.2    
79.6    
79.9    
80.3    
80.6    
81.0    
81.3    
81.7    
82.0    
82.4    
82.7    
83.1    
83.5    
83.8    
84.2    
84.5    
84.9    
85.2    
85.6    
85.9    
86.3    
86.6    
87.0    
87.3    
87.7    
88.0    
88.4    
88.7    
89.1    
89.4    
89.8    
90.1    
90.5    
90.8    
91.2    
91.5    
91.9    
92.3    
92.6    
93.0    
93.3    
93.7    
94.0    
94.4    
94.7    
95.1    
95.4    
95.8    
96.1    
96.5    
96.8    
97.2    
97.5    
97.9    
98.2    
98.6    
98.9    
99.3    
99.6    
-found 19 predictions from path traversal
Error with prediction: snap lend_intergenic: 48769, rend_intergenic: 27988  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56848, rend_intergenic: 55497  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62533, rend_intergenic: 58839  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94230, rend_intergenic: 87876  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 105134 - 116558
-exon list size: 5


building trellis

14.3    
28.6    
42.9    
57.1    
71.4    
85.7    
-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