-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_4/scaffold_4_16822648-16968669

-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 CodingQuarry_transcript_49302-T1
Valid prediction for pasa_asmbl_42225.p1
Valid prediction for snap_scaffold_4-snap.3462-T1
Valid prediction for snap_scaffold_4-snap.3460-T1
Valid prediction for snap_scaffold_4-snap.3435-T1
Valid prediction for GlimmerHMM_glimmerT_10932-T1
Valid prediction for snap_scaffold_4-snap.3464-T1
Valid prediction for snap_scaffold_4-snap.3444-T1
Valid prediction for GlimmerHMM_glimmerT_10924-T1
Valid prediction for snap_scaffold_4-snap.3458-T1
Valid prediction for GlimmerHMM_glimmerT_10928-T1
Valid prediction for HiQ_model.g7173.t1
Valid prediction for snap_scaffold_4-snap.3452-T1
Valid prediction for GlimmerHMM_glimmerT_10933-T1
Valid prediction for Augustus_model.g7171.t1
Couldn't classify 114784, 116319
Sorry, prediction pasa_asmbl_42012.p1 fails validation.
(ATG)	 AG	114784-116319	AG	AGA
Valid prediction for snap_scaffold_4-snap.3456-T1
Valid prediction for pasa_asmbl_42009.p1
Valid prediction for GlimmerHMM_glimmerT_10927-T1
Valid prediction for GlimmerHMM_glimmerT_10920-T1
Valid prediction for GlimmerHMM_glimmerT_10922-T1
Couldn't classify 121252, 121275
Couldn't classify 123633, 123665
Sorry, prediction pasa_asmbl_42015.p1 fails validation.
(GAC)	 CG	121252-121275	GT	AGG
(GTG)	 AG	121724-121884	GT	AGG
(GTT)	 AG	122529-122681	GT	ATG
(GGA)	 AG	122783-122912	GT	AGG
(AAC)	 AG	123202-123276	GT	AGG
(CTG)	 AG	123633-123665	AT	AGA
-recovered pasa_asmbl_42015.p1, internal, 121724, 121884
-recovered pasa_asmbl_42015.p1, internal, 122529, 122681
-recovered pasa_asmbl_42015.p1, internal, 122783, 122912
-recovered pasa_asmbl_42015.p1, internal, 123202, 123276
Valid prediction for snap_scaffold_4-snap.3439-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g7168.t1
Valid prediction for snap_scaffold_4-snap.3446-T1
Valid prediction for snap_scaffold_4-snap.3443-T1
Couldn't classify 86294, 86364
Couldn't classify 86679, 86852
Sorry, prediction pasa_asmbl_42006.p2 fails validation.
(GAG)	 AC	86294-86364	GT	GGG
(ATT)	 AG	86451-86580	GT	AGG
(CTG)	 AG	86679-86852	AG	TGA
-recovered pasa_asmbl_42006.p2, internal, 86451, 86580
Valid prediction for GlimmerHMM_glimmerT_10931-T1
Valid prediction for snap_scaffold_4-snap.3451-T1
Valid prediction for snap_scaffold_4-snap.3426-T1
Valid prediction for snap_scaffold_4-snap.3447-T1
Valid prediction for snap_scaffold_4-snap.3432-T1
Valid prediction for HiQ_model.g7167.t1
Valid prediction for snap_scaffold_4-snap.3425-T1
Valid prediction for CodingQuarry_transcript_49297-T1
Valid prediction for snap_scaffold_4-snap.3442-T1
Couldn't classify 116902, 117483
Sorry, prediction pasa_asmbl_42014.p1 fails validation.
(GAA)	 GT	116902-117483	CG	AGC
Valid prediction for Augustus_model.g7161.t1
Valid prediction for snap_scaffold_4-snap.3440-T1
Valid prediction for snap_scaffold_4-snap.3437-T1
Valid prediction for GlimmerHMM_glimmerT_10921-T1
Valid prediction for snap_scaffold_4-snap.3449-T1
Valid prediction for Augustus_model.g7166.t1
Valid prediction for snap_scaffold_4-snap.3430-T1
Valid prediction for snap_scaffold_4-snap.3434-T1
Valid prediction for snap_scaffold_4-snap.3428-T1
Couldn't classify 129538, 129656
Sorry, prediction CodingQuarry_transcript_49301-T1 fails validation.
(ATG)	 AG	128658-128747	GT	CCG
(ATC)	 AG	128952-129030	GT	AGG
(GTG)	 CA	129538-129656	GT	AGG
(GAA)	 AG	129958-130023	GA	GAG
-recovered CodingQuarry_transcript_49301-T1, initial, 128658, 128747
-recovered CodingQuarry_transcript_49301-T1, terminal, 129958, 130023
-recovered CodingQuarry_transcript_49301-T1, internal, 128658, 128747
-recovered CodingQuarry_transcript_49301-T1, internal, 128952, 129030
Valid prediction for Augustus_model.g7172.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_4-snap.3463-T1
Valid prediction for CodingQuarry_transcript_49299-T1
Couldn't classify 94115, 94241
Couldn't classify 101628, 101783
Sorry, prediction pasa_asmbl_43228.p1 fails validation.
(GGG)	 CA	94115-94241	GT	TGG
(TCA)	 AG	94701-94785	GT	GGG
(GAT)	 AG	96101-96202	GT	CAG
(CCG)	 AG	96775-96859	GT	AGG
(CTC)	 AG	97577-97732	GT	AGG
(TTC)	 AG	97878-97947	GT	AGG
(GGG)	 AG	98064-98174	GT	AGG
(GCG)	 AG	98364-98577	GT	AGG
(CAA)	 AG	98693-98826	GT	GGG
(AAT)	 AG	98902-99065	GT	AGG
(AAC)	 AG	99173-99254	GT	AGG
(ACA)	 AG	99339-99424	GT	AGG
(GAG)	 AG	100194-100235	GT	AGG
(ATC)	 AG	100372-100476	GT	AGG
(ACC)	 AG	100801-100887	GT	AGG
(CTG)	 AG	101628-101783	AG	CCA
-recovered pasa_asmbl_43228.p1, terminal, 97878, 97947
add_exon() Sorry, pasa_asmbl_43228.p1 98064-98174-terminal-1 is invalid.
-recovered pasa_asmbl_43228.p1, terminal, 98064, 98174
-recovered pasa_asmbl_43228.p1, internal, 94701, 94785
-recovered pasa_asmbl_43228.p1, internal, 96101, 96202
-recovered pasa_asmbl_43228.p1, internal, 96775, 96859
-recovered pasa_asmbl_43228.p1, internal, 97577, 97732
-recovered pasa_asmbl_43228.p1, internal, 97878, 97947
-recovered pasa_asmbl_43228.p1, internal, 98064, 98174
-recovered pasa_asmbl_43228.p1, internal, 98364, 98577
-recovered pasa_asmbl_43228.p1, internal, 98693, 98826
-recovered pasa_asmbl_43228.p1, internal, 98902, 99065
-recovered pasa_asmbl_43228.p1, internal, 99173, 99254
-recovered pasa_asmbl_43228.p1, internal, 99339, 99424
-recovered pasa_asmbl_43228.p1, internal, 100194, 100235
-recovered pasa_asmbl_43228.p1, internal, 100372, 100476
-recovered pasa_asmbl_43228.p1, internal, 100801, 100887
Couldn't classify 86834, 86967
Sorry, prediction pasa_asmbl_43232.p1 fails validation.
(ATG)	 TG	83993-84149	GT	AGG
(ACT)	 AG	84451-84582	GT	AGG
(CAT)	 AG	84996-85124	GT	CGG
(GCT)	 AG	86834-86967	GT	AGG
-recovered pasa_asmbl_43232.p1, initial, 83993, 84149
-recovered pasa_asmbl_43232.p1, internal, 84451, 84582
-recovered pasa_asmbl_43232.p1, internal, 84996, 85124
-recovered pasa_asmbl_43232.p1, internal, 86834, 86967
Couldn't classify 138676, 138913
Couldn't classify 139474, 139550
Sorry, prediction pasa_asmbl_43655.p1 fails validation.
(CAG)	 GA	138676-138913	GT	AGG
(ACT)	 AG	139474-139550	AG	CCA
Valid prediction for GlimmerHMM_glimmerT_10925-T1
Valid prediction for snap_scaffold_4-snap.3431-T1
Valid prediction for pasa_asmbl_43238.p1
Valid prediction for Augustus_model.g7159.t1
Valid prediction for GlimmerHMM_glimmerT_10929-T1
Valid prediction for Augustus_model.g7160.t1
Valid prediction for CodingQuarry_transcript_49296-T1
Valid prediction for snap_scaffold_4-snap.3436-T1
Valid prediction for snap_scaffold_4-snap.3438-T1
Valid prediction for Augustus_model.g7162.t1
Valid prediction for Augustus_model.g7174.t1
Valid prediction for snap_scaffold_4-snap.3448-T1
Valid prediction for snap_scaffold_4-snap.3454-T1
Valid prediction for snap_scaffold_4-snap.3453-T1
Valid prediction for GlimmerHMM_glimmerT_10919-T1
Valid prediction for snap_scaffold_4-snap.3455-T1
Valid prediction for snap_scaffold_4-snap.3450-T1
Valid prediction for snap_scaffold_4-snap.3427-T1
Valid prediction for GlimmerHMM_glimmerT_10926-T1
Valid prediction for snap_scaffold_4-snap.3445-T1
Valid prediction for Augustus_model.g7170.t1
Valid prediction for CodingQuarry_transcript_49298-T1
Valid prediction for snap_scaffold_4-snap.3459-T1
Valid prediction for Augustus_model.g7165.t1
Valid prediction for Augustus_model.g7169.t1
Valid prediction for GlimmerHMM_glimmerT_10923-T1
Valid prediction for snap_scaffold_4-snap.3461-T1
Valid prediction for GlimmerHMM_glimmerT_10918-T1
Valid prediction for snap_scaffold_4-snap.3429-T1
Valid prediction for Augustus_model.g7163.t1
Couldn't classify 142454, 142492
Sorry, prediction pasa_asmbl_43223.p1 fails validation.
(GAC)	 AC	142454-142492	GT	TGG
(AGC)	 AG	142849-143027	GT	AGG
(GCG)	 AG	143267-143387	GT	AGG
(GAT)	 AG	143758-143871	TT	GAT
-recovered pasa_asmbl_43223.p1, terminal, 143758, 143871
-recovered pasa_asmbl_43223.p1, internal, 142849, 143027
-recovered pasa_asmbl_43223.p1, internal, 143267, 143387
Valid prediction for snap_scaffold_4-snap.3457-T1
Valid prediction for GlimmerHMM_glimmerT_10930-T1
Valid prediction for snap_scaffold_4-snap.3441-T1
Valid prediction for Augustus_model.g7164.t1
Valid prediction for snap_scaffold_4-snap.3433-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8293, rend_intergenic: 7642  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10626, rend_intergenic: 8792  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11681, rend_intergenic: 11218  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15978, rend_intergenic: 12891  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23554, rend_intergenic: 16654  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26831, rend_intergenic: 24372  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28318, rend_intergenic: 27170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32302, rend_intergenic: 28956  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45684, rend_intergenic: 43508  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53416, rend_intergenic: 48869  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72728, rend_intergenic: 56230  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81618, rend_intergenic: 75168  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89160, rend_intergenic: 85358  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95121, rend_intergenic: 91989  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102703, rend_intergenic: 101681  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117810, rend_intergenic: 114784  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125677, rend_intergenic: 120879  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135135, rend_intergenic: 134133  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139909, rend_intergenic: 137755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143507, rend_intergenic: 140881  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 146022
-exon list size: 364


building trellis

0.3    
0.5    
0.8    
1.1    
1.4    
1.6    
1.9    
2.2    
2.5    
2.7    
3.0    
3.3    
3.6    
3.8    
4.1    
4.4    
4.6    
4.9    
5.2    
5.5    
5.7    
6.0    
6.3    
6.6    
6.8    
7.1    
7.4    
7.7    
7.9    
8.2    
8.5    
8.7    
9.0    
9.3    
9.6    
9.8    
10.1    
10.4    
10.7    
10.9    
11.2    
11.5    
11.7    
12.0    
12.3    
12.6    
12.8    
13.1    
13.4    
13.7    
13.9    
14.2    
14.5    
14.8    
15.0    
15.3    
15.6    
15.8    
16.1    
16.4    
16.7    
16.9    
17.2    
17.5    
17.8    
18.0    
18.3    
18.6    
18.9    
19.1    
19.4    
19.7    
19.9    
20.2    
20.5    
20.8    
21.0    
21.3    
21.6    
21.9    
22.1    
22.4    
22.7    
23.0    
23.2    
23.5    
23.8    
24.0    
24.3    
24.6    
24.9    
25.1    
25.4    
25.7    
26.0    
26.2    
26.5    
26.8    
27.0    
27.3    
27.6    
27.9    
28.1    
28.4    
28.7    
29.0    
29.2    
29.5    
29.8    
30.1    
30.3    
30.6    
30.9    
31.1    
31.4    
31.7    
32.0    
32.2    
32.5    
32.8    
33.1    
33.3    
33.6    
33.9    
34.2    
34.4    
34.7    
35.0    
35.2    
35.5    
35.8    
36.1    
36.3    
36.6    
36.9    
37.2    
37.4    
37.7    
38.0    
38.3    
38.5    
38.8    
39.1    
39.3    
39.6    
39.9    
40.2    
40.4    
40.7    
41.0    
41.3    
41.5    
41.8    
42.1    
42.3    
42.6    
42.9    
43.2    
43.4    
43.7    
44.0    
44.3    
44.5    
44.8    
45.1    
45.4    
45.6    
45.9    
46.2    
46.4    
46.7    
47.0    
47.3    
47.5    
47.8    
48.1    
48.4    
48.6    
48.9    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.1    
51.4    
51.6    
51.9    
52.2    
52.5    
52.7    
53.0    
53.3    
53.6    
53.8    
54.1    
54.4    
54.6    
54.9    
55.2    
55.5    
55.7    
56.0    
56.3    
56.6    
56.8    
57.1    
57.4    
57.7    
57.9    
58.2    
58.5    
58.7    
59.0    
59.3    
59.6    
59.8    
60.1    
60.4    
60.7    
60.9    
61.2    
61.5    
61.7    
62.0    
62.3    
62.6    
62.8    
63.1    
63.4    
63.7    
63.9    
64.2    
64.5    
64.8    
65.0    
65.3    
65.6    
65.8    
66.1    
66.4    
66.7    
66.9    
67.2    
67.5    
67.8    
68.0    
68.3    
68.6    
68.9    
69.1    
69.4    
69.7    
69.9    
70.2    
70.5    
70.8    
71.0    
71.3    
71.6    
71.9    
72.1    
72.4    
72.7    
73.0    
73.2    
73.5    
73.8    
74.0    
74.3    
74.6    
74.9    
75.1    
75.4    
75.7    
76.0    
76.2    
76.5    
76.8    
77.0    
77.3    
77.6    
77.9    
78.1    
78.4    
78.7    
79.0    
79.2    
79.5    
79.8    
80.1    
80.3    
80.6    
80.9    
81.1    
81.4    
81.7    
82.0    
82.2    
82.5    
82.8    
83.1    
83.3    
83.6    
83.9    
84.2    
84.4    
84.7    
85.0    
85.2    
85.5    
85.8    
86.1    
86.3    
86.6    
86.9    
87.2    
87.4    
87.7    
88.0    
88.3    
88.5    
88.8    
89.1    
89.3    
89.6    
89.9    
90.2    
90.4    
90.7    
91.0    
91.3    
91.5    
91.8    
92.1    
92.3    
92.6    
92.9    
93.2    
93.4    
93.7    
94.0    
94.3    
94.5    
94.8    
95.1    
95.4    
95.6    
95.9    
96.2    
96.4    
96.7    
97.0    
97.3    
97.5    
97.8    
98.1    
98.4    
98.6    
98.9    
99.2    
99.5    
99.7    
-found 22 predictions from path traversal
Error with prediction: snap lend_intergenic: 8293, rend_intergenic: 7642  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10626, rend_intergenic: 8792  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11681, rend_intergenic: 11218  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15978, rend_intergenic: 12891  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23554, rend_intergenic: 16654  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26831, rend_intergenic: 24372  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28318, rend_intergenic: 27170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32302, rend_intergenic: 28956  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45684, rend_intergenic: 43508  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53416, rend_intergenic: 48869  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72728, rend_intergenic: 56230  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81618, rend_intergenic: 75168  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89160, rend_intergenic: 85358  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95121, rend_intergenic: 91989  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102703, rend_intergenic: 101681  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117810, rend_intergenic: 114784  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125677, rend_intergenic: 120879  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135135, rend_intergenic: 134133  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139909, rend_intergenic: 137755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143507, rend_intergenic: 140881  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