-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_3/scaffold_3_4488756-4662266

-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_6434-T1
Valid prediction for snap_scaffold_3-snap.981-T1
Valid prediction for Augustus_model.g4156.t1
Valid prediction for GlimmerHMM_glimmerT_6422-T1
Valid prediction for Augustus_model.g4170.t1
Valid prediction for snap_scaffold_3-snap.990-T1
Valid prediction for HiQ_model.g4166.t1
Valid prediction for GlimmerHMM_glimmerT_6421-T1
Valid prediction for snap_scaffold_3-snap.973-T1
Valid prediction for GlimmerHMM_glimmerT_6420-T1
Valid prediction for GlimmerHMM_glimmerT_6435-T1
Valid prediction for snap_scaffold_3-snap.993-T1
Couldn't classify 48096, 48165
Sorry, prediction pasa_asmbl_40015.p1 fails validation.
(CAC)	 GT	48096-48165	GT	AGG
(CTC)	 AG	48600-48835	GT	AGG
(GAG)	 AG	49054-49172	GT	AGG
(ATG)	 AG	49291-49545	GT	AGG
(TGG)	 AG	49801-49915	GA	AGG
add_exon() Sorry, pasa_asmbl_40015.p1 49291-49545-initial-1 is invalid.
-recovered pasa_asmbl_40015.p1, initial, 49291, 49545
-recovered pasa_asmbl_40015.p1, terminal, 49801, 49915
-recovered pasa_asmbl_40015.p1, internal, 48600, 48835
-recovered pasa_asmbl_40015.p1, internal, 49054, 49172
-recovered pasa_asmbl_40015.p1, internal, 49291, 49545
Valid prediction for snap_scaffold_3-snap.962-T1
Valid prediction for GlimmerHMM_glimmerT_6426-T1
Valid prediction for HiQ_model.g4159.t1
Valid prediction for pasa_asmbl_40017.p1
Valid prediction for GlimmerHMM_glimmerT_6437-T1
Valid prediction for snap_scaffold_3-snap.964-T1
Couldn't classify 42739, 42859
Couldn't classify 44292, 44353
Sorry, prediction pasa_asmbl_40885.p1 fails validation.
(GCC)	 CA	42739-42859	GT	AGG
(GCG)	 AG	43223-43443	GT	AGG
(GTG)	 AG	43686-43858	GT	AGG
(GTC)	 AG	43974-44206	GT	AGG
(ACC)	 AG	44292-44353	CC	CCC
-recovered pasa_asmbl_40885.p1, internal, 43223, 43443
-recovered pasa_asmbl_40885.p1, internal, 43686, 43858
-recovered pasa_asmbl_40885.p1, internal, 43974, 44206
Valid prediction for snap_scaffold_3-snap.988-T1
Valid prediction for CodingQuarry_transcript_46136-T1
Valid prediction for Augustus_model.g4157.t1
Valid prediction for snap_scaffold_3-snap.970-T1
Valid prediction for CodingQuarry_transcript_46139-T1
Valid prediction for snap_scaffold_3-snap.974-T1
Valid prediction for CodingQuarry_transcript_46143-T1
Valid prediction for GlimmerHMM_glimmerT_6423-T1
Couldn't classify 144667, 144764
Couldn't classify 144837, 144896
Sorry, prediction CodingQuarry_transcript_46142-T1 fails validation.
(ATG)	 CC	142007-142144	GT	AAG
(CCA)	 AG	143441-143555	GT	CAG
(CCG)	 AG	144667-144764	AG	TCA
(AGT)	 TA	144837-144896	TC	GAT
-recovered CodingQuarry_transcript_46142-T1, initial, 142007, 142144
-recovered CodingQuarry_transcript_46142-T1, internal, 143441, 143555
Valid prediction for Augustus_model.g4158.t1
Valid prediction for pasa_asmbl_40026.p1
Valid prediction for snap_scaffold_3-snap.992-T1
Valid prediction for snap_scaffold_3-snap.966-T1
Valid prediction for GlimmerHMM_glimmerT_6432-T1
Valid prediction for CodingQuarry_transcript_46138-T1
Couldn't classify 86072, 86149
Couldn't classify 91626, 91700
Sorry, prediction pasa_asmbl_40019.p1 fails validation.
(GAG)	 CA	86072-86149	GT	AGG
(ACG)	 AG	86302-86348	GT	GAG
(GTT)	 AG	86539-86652	GT	AAG
(ATG)	 AG	88200-88275	GT	AGG
(CTG)	 AG	89551-89665	GT	AGG
(GTA)	 AG	90727-90857	GT	CGG
(AAA)	 AG	91255-91362	GT	CGG
(GAT)	 AG	91626-91700	GT	AGG
add_exon() Sorry, pasa_asmbl_40019.p1 88200-88275-initial-1 is invalid.
-recovered pasa_asmbl_40019.p1, initial, 88200, 88275
add_exon() Sorry, pasa_asmbl_40019.p1 89551-89665-terminal-3 is invalid.
-recovered pasa_asmbl_40019.p1, terminal, 89551, 89665
-recovered pasa_asmbl_40019.p1, internal, 86302, 86348
-recovered pasa_asmbl_40019.p1, internal, 86539, 86652
-recovered pasa_asmbl_40019.p1, internal, 88200, 88275
-recovered pasa_asmbl_40019.p1, internal, 89551, 89665
-recovered pasa_asmbl_40019.p1, internal, 90727, 90857
-recovered pasa_asmbl_40019.p1, internal, 91255, 91362
-recovered pasa_asmbl_40019.p1, internal, 91626, 91700
Valid prediction for snap_scaffold_3-snap.968-T1
Valid prediction for CodingQuarry_transcript_46141-T1
Valid prediction for GlimmerHMM_glimmerT_6436-T1
Valid prediction for HiQ_model.g4172.t1
Valid prediction for GlimmerHMM_glimmerT_6416-T1
Valid prediction for snap_scaffold_3-snap.989-T1
Valid prediction for Augustus_model.g4164.t1
Valid prediction for pasa_asmbl_40012.p1
Valid prediction for HiQ_model.g4163.t1
Valid prediction for snap_scaffold_3-snap.979-T1
Couldn't classify 27813, 28787
Sorry, prediction pasa_asmbl_40010.p1 fails validation.
(TCG)	 GC	27813-28787	TC	CCT
Valid prediction for Augustus_model.g4162.t1
Valid prediction for GlimmerHMM_glimmerT_6417-T1
Valid prediction for HiQ_model.g4161.t1
Valid prediction for CodingQuarry_transcript_46140-T1
Valid prediction for GlimmerHMM_glimmerT_6418-T1
Valid prediction for snap_scaffold_3-snap.984-T1
Couldn't classify 41353, 41449
Couldn't classify 41895, 41979
Sorry, prediction pasa_asmbl_40837.p1 fails validation.
(GTG)	 CA	41353-41449	GT	AGG
(GGA)	 AG	41668-41782	GT	AGG
(GCA)	 AG	41895-41979	GC	AGG
-recovered pasa_asmbl_40837.p1, internal, 41668, 41782
-recovered pasa_asmbl_40837.p1, internal, 41895, 41979
Valid prediction for GlimmerHMM_glimmerT_6431-T1
Valid prediction for GlimmerHMM_glimmerT_6415-T1
Valid prediction for GlimmerHMM_glimmerT_6424-T1
Valid prediction for snap_scaffold_3-snap.971-T1
Couldn't classify 44783, 44833
Sorry, prediction pasa_asmbl_40013.p1 fails validation.
(AAC)	 CC	44783-44833	GT	AGG
(GTT)	 AG	44959-45058	GT	GGG
(TGG)	 AG	45215-45414	GT	AAG
(ACA)	 AG	45551-45701	GT	AGG
(AAC)	 AG	45942-46044	GT	AGG
(GCT)	 AG	46531-46642	GA	AGG
-recovered pasa_asmbl_40013.p1, terminal, 46531, 46642
-recovered pasa_asmbl_40013.p1, internal, 44959, 45058
-recovered pasa_asmbl_40013.p1, internal, 45215, 45414
-recovered pasa_asmbl_40013.p1, internal, 45551, 45701
-recovered pasa_asmbl_40013.p1, internal, 45942, 46044
Valid prediction for snap_scaffold_3-snap.960-T1
Valid prediction for CodingQuarry_transcript_46135-T1
Valid prediction for snap_scaffold_3-snap.987-T1
Couldn't classify 66938, 67432
Sorry, prediction pasa_asmbl_40018.p1 fails validation.
(CAA)	 CT	66938-67432	GT	AGG
(ATT)	 AG	67511-67680	GT	AGG
(GAA)	 AG	67793-67906	GT	AGG
(ACA)	 AG	68278-68419	AG	GAA
add_exon() Sorry, pasa_asmbl_40018.p1 67793-67906-terminal-1 is invalid.
-recovered pasa_asmbl_40018.p1, terminal, 67793, 67906
-recovered pasa_asmbl_40018.p1, terminal, 68278, 68419
-recovered pasa_asmbl_40018.p1, internal, 67511, 67680
-recovered pasa_asmbl_40018.p1, internal, 67793, 67906

-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_3-snap.983-T1
Valid prediction for snap_scaffold_3-snap.986-T1
Valid prediction for GlimmerHMM_glimmerT_6429-T1
Valid prediction for HiQ_model.g4160.t1
Valid prediction for snap_scaffold_3-snap.977-T1
Valid prediction for GlimmerHMM_glimmerT_6419-T1
Valid prediction for GlimmerHMM_glimmerT_6430-T1
Valid prediction for HiQ_model.g4167.t1
Valid prediction for snap_scaffold_3-snap.991-T1
Valid prediction for Augustus_model.g4165.t1
Valid prediction for Augustus_model.g4169.t1
Valid prediction for snap_scaffold_3-snap.959-T1
Valid prediction for GlimmerHMM_glimmerT_6433-T1
Valid prediction for snap_scaffold_3-snap.961-T1
Valid prediction for snap_scaffold_3-snap.982-T1
Valid prediction for snap_scaffold_3-snap.963-T1
Valid prediction for GlimmerHMM_glimmerT_6427-T1
Valid prediction for snap_scaffold_3-snap.972-T1
Valid prediction for snap_scaffold_3-snap.985-T1
Valid prediction for snap_scaffold_3-snap.980-T1
Valid prediction for snap_scaffold_3-snap.965-T1
Valid prediction for snap_scaffold_3-snap.958-T1
Valid prediction for snap_scaffold_3-snap.969-T1
Valid prediction for HiQ_model.g4171.t1
Valid prediction for GlimmerHMM_glimmerT_6425-T1
Valid prediction for snap_scaffold_3-snap.957-T1
Valid prediction for GlimmerHMM_glimmerT_6414-T1
Valid prediction for CodingQuarry_transcript_46137-T1
Valid prediction for pasa_asmbl_38810.p1
Valid prediction for snap_scaffold_3-snap.967-T1
Valid prediction for snap_scaffold_3-snap.975-T1
Valid prediction for snap_scaffold_3-snap.976-T1
Valid prediction for GlimmerHMM_glimmerT_6428-T1
Couldn't classify 33880, 33975
Couldn't classify 38308, 38492
Sorry, prediction pasa_asmbl_38813.p1 fails validation.
(TGC)	 AT	33880-33975	GT	TGG
(GAC)	 AG	35434-35521	GT	AGG
(GCT)	 AG	35712-35755	GT	TCG
(GGC)	 AG	37259-37388	GT	GGG
(GTC)	 AG	37685-37894	GT	CGG
(GTC)	 AG	38308-38492	TG	CCT
add_exon() Sorry, pasa_asmbl_38813.p1 35434-35521-terminal-3 is invalid.
-recovered pasa_asmbl_38813.p1, terminal, 35434, 35521
-recovered pasa_asmbl_38813.p1, internal, 35434, 35521
-recovered pasa_asmbl_38813.p1, internal, 35712, 35755
-recovered pasa_asmbl_38813.p1, internal, 37259, 37388
-recovered pasa_asmbl_38813.p1, internal, 37685, 37894
Valid prediction for snap_scaffold_3-snap.978-T1
Valid prediction for pasa_asmbl_38809.p1
Valid prediction for Augustus_model.g4168.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11841, rend_intergenic: 8461  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27154, rend_intergenic: 13739  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33565, rend_intergenic: 29410  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46642, rend_intergenic: 40404  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59115, rend_intergenic: 58111  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65554, rend_intergenic: 61270  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96106, rend_intergenic: 73401  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114424, rend_intergenic: 105970  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119459, rend_intergenic: 116475  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132668, rend_intergenic: 126309  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136314, rend_intergenic: 134345  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143130, rend_intergenic: 139890  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167859, rend_intergenic: 161662  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 173511
-exon list size: 392


building trellis

0.3    
0.5    
0.8    
1.0    
1.3    
1.5    
1.8    
2.0    
2.3    
2.5    
2.8    
3.0    
3.3    
3.6    
3.8    
4.1    
4.3    
4.6    
4.8    
5.1    
5.3    
5.6    
5.8    
6.1    
6.3    
6.6    
6.9    
7.1    
7.4    
7.6    
7.9    
8.1    
8.4    
8.6    
8.9    
9.1    
9.4    
9.6    
9.9    
10.2    
10.4    
10.7    
10.9    
11.2    
11.4    
11.7    
11.9    
12.2    
12.4    
12.7    
12.9    
13.2    
13.5    
13.7    
14.0    
14.2    
14.5    
14.7    
15.0    
15.2    
15.5    
15.7    
16.0    
16.2    
16.5    
16.8    
17.0    
17.3    
17.5    
17.8    
18.0    
18.3    
18.5    
18.8    
19.0    
19.3    
19.5    
19.8    
20.1    
20.3    
20.6    
20.8    
21.1    
21.3    
21.6    
21.8    
22.1    
22.3    
22.6    
22.8    
23.1    
23.4    
23.6    
23.9    
24.1    
24.4    
24.6    
24.9    
25.1    
25.4    
25.6    
25.9    
26.1    
26.4    
26.6    
26.9    
27.2    
27.4    
27.7    
27.9    
28.2    
28.4    
28.7    
28.9    
29.2    
29.4    
29.7    
29.9    
30.2    
30.5    
30.7    
31.0    
31.2    
31.5    
31.7    
32.0    
32.2    
32.5    
32.7    
33.0    
33.2    
33.5    
33.8    
34.0    
34.3    
34.5    
34.8    
35.0    
35.3    
35.5    
35.8    
36.0    
36.3    
36.5    
36.8    
37.1    
37.3    
37.6    
37.8    
38.1    
38.3    
38.6    
38.8    
39.1    
39.3    
39.6    
39.8    
40.1    
40.4    
40.6    
40.9    
41.1    
41.4    
41.6    
41.9    
42.1    
42.4    
42.6    
42.9    
43.1    
43.4    
43.7    
43.9    
44.2    
44.4    
44.7    
44.9    
45.2    
45.4    
45.7    
45.9    
46.2    
46.4    
46.7    
47.0    
47.2    
47.5    
47.7    
48.0    
48.2    
48.5    
48.7    
49.0    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.0    
51.3    
51.5    
51.8    
52.0    
52.3    
52.5    
52.8    
53.0    
53.3    
53.6    
53.8    
54.1    
54.3    
54.6    
54.8    
55.1    
55.3    
55.6    
55.8    
56.1    
56.3    
56.6    
56.9    
57.1    
57.4    
57.6    
57.9    
58.1    
58.4    
58.6    
58.9    
59.1    
59.4    
59.6    
59.9    
60.2    
60.4    
60.7    
60.9    
61.2    
61.4    
61.7    
61.9    
62.2    
62.4    
62.7    
62.9    
63.2    
63.5    
63.7    
64.0    
64.2    
64.5    
64.7    
65.0    
65.2    
65.5    
65.7    
66.0    
66.2    
66.5    
66.8    
67.0    
67.3    
67.5    
67.8    
68.0    
68.3    
68.5    
68.8    
69.0    
69.3    
69.5    
69.8    
70.1    
70.3    
70.6    
70.8    
71.1    
71.3    
71.6    
71.8    
72.1    
72.3    
72.6    
72.8    
73.1    
73.4    
73.6    
73.9    
74.1    
74.4    
74.6    
74.9    
75.1    
75.4    
75.6    
75.9    
76.1    
76.4    
76.6    
76.9    
77.2    
77.4    
77.7    
77.9    
78.2    
78.4    
78.7    
78.9    
79.2    
79.4    
79.7    
79.9    
80.2    
80.5    
80.7    
81.0    
81.2    
81.5    
81.7    
82.0    
82.2    
82.5    
82.7    
83.0    
83.2    
83.5    
83.8    
84.0    
84.3    
84.5    
84.8    
85.0    
85.3    
85.5    
85.8    
86.0    
86.3    
86.5    
86.8    
87.1    
87.3    
87.6    
87.8    
88.1    
88.3    
88.6    
88.8    
89.1    
89.3    
89.6    
89.8    
90.1    
90.4    
90.6    
90.9    
91.1    
91.4    
91.6    
91.9    
92.1    
92.4    
92.6    
92.9    
93.1    
93.4    
93.7    
93.9    
94.2    
94.4    
94.7    
94.9    
95.2    
95.4    
95.7    
95.9    
96.2    
96.4    
96.7    
97.0    
97.2    
97.5    
97.7    
98.0    
98.2    
98.5    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 11841, rend_intergenic: 8461  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27154, rend_intergenic: 13739  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33565, rend_intergenic: 29410  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46642, rend_intergenic: 40404  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59115, rend_intergenic: 58111  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65554, rend_intergenic: 61270  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96106, rend_intergenic: 73401  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114424, rend_intergenic: 105970  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119459, rend_intergenic: 116475  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132668, rend_intergenic: 126309  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136314, rend_intergenic: 134345  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143130, rend_intergenic: 139890  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167859, rend_intergenic: 161662  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support