-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_1470515-1673306

-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: +)Couldn't classify 131500, 131639
Couldn't classify 136644, 136757
Sorry, prediction pasa_asmbl_41113.p1 fails validation.
(AGG)	 AC	131500-131639	GT	AGG
(GGA)	 AG	132372-132475	GT	AGG
(GGG)	 AG	133459-133644	GT	GAG
(ACG)	 AG	134888-135057	GT	AGG
(GTC)	 AG	136313-136390	GT	CTG
(AAC)	 AG	136644-136757	GG	GTG
-recovered pasa_asmbl_41113.p1, internal, 132372, 132475
-recovered pasa_asmbl_41113.p1, internal, 133459, 133644
-recovered pasa_asmbl_41113.p1, internal, 134888, 135057
-recovered pasa_asmbl_41113.p1, internal, 136313, 136390
Valid prediction for GlimmerHMM_glimmerT_8795-T1
Valid prediction for snap_scaffold_4-snap.349-T1
Valid prediction for Augustus_model.g5681.t1
Couldn't classify 106351, 106419
Sorry, prediction pasa_asmbl_41111.p1 fails validation.
(ATG)	 TA	103881-103917	GT	CAG
(GTC)	 AG	105575-105834	GT	AGG
(AGT)	 AG	106351-106419	CA	GTC
-recovered pasa_asmbl_41111.p1, initial, 103881, 103917
-recovered pasa_asmbl_41111.p1, internal, 105575, 105834
Valid prediction for Augustus_model.g5686.t1
Valid prediction for GlimmerHMM_glimmerT_8812-T1
Valid prediction for CodingQuarry_transcript_48883-T1
Valid prediction for Augustus_model.g5682.t1
Valid prediction for GlimmerHMM_glimmerT_8800-T1
Valid prediction for GlimmerHMM_glimmerT_8809-T1
Valid prediction for snap_scaffold_4-snap.370-T1
Valid prediction for Augustus_model.g5683.t1
Valid prediction for CodingQuarry_transcript_48885-T1
Valid prediction for GlimmerHMM_glimmerT_8814-T1
Valid prediction for snap_scaffold_4-snap.391-T1
Valid prediction for GlimmerHMM_glimmerT_8796-T1
Valid prediction for Augustus_model.g5684.t1
Valid prediction for GlimmerHMM_glimmerT_8810-T1
Valid prediction for GlimmerHMM_glimmerT_8811-T1
Couldn't classify 170472, 170512
Sorry, prediction pasa_asmbl_41123.p1 fails validation.
(TCC)	 AG	170472-170512	GT	CTG
(GCA)	 AG	171063-171160	GT	AGG
(TGA)	 AG	171305-171379	GT	TGG
(GCA)	 AG	171550-171677	GT	AGG
(ATG)	 AG	172334-172483	GT	GGG
(GCT)	 AG	172849-172908	GT	AGG
(CTG)	 AG	173798-174010	CT	GAC
-recovered pasa_asmbl_41123.p1, initial, 172334, 172483
-recovered pasa_asmbl_41123.p1, terminal, 173798, 174010
-recovered pasa_asmbl_41123.p1, internal, 170472, 170512
-recovered pasa_asmbl_41123.p1, internal, 171063, 171160
-recovered pasa_asmbl_41123.p1, internal, 171305, 171379
-recovered pasa_asmbl_41123.p1, internal, 171550, 171677
-recovered pasa_asmbl_41123.p1, internal, 172334, 172483
-recovered pasa_asmbl_41123.p1, internal, 172849, 172908
Valid prediction for snap_scaffold_4-snap.353-T1
Valid prediction for GlimmerHMM_glimmerT_8802-T1
Valid prediction for GlimmerHMM_glimmerT_8816-T1
Valid prediction for Augustus_model.g5673.t1
Valid prediction for GlimmerHMM_glimmerT_8793-T1
Valid prediction for snap_scaffold_4-snap.361-T1
Valid prediction for snap_scaffold_4-snap.378-T1
Valid prediction for snap_scaffold_4-snap.362-T1
Couldn't classify 118678, 118746
Couldn't classify 123156, 123440
Sorry, prediction pasa_asmbl_41112.p1 fails validation.
(GGG)	 AT	118678-118746	GT	AGG
(GTG)	 AG	120927-121086	GC	AGG
(ACT)	 AG	122182-122286	GT	AGG
(GTA)	 AG	122913-123028	GT	AGG
(TTC)	 AG	123156-123440	TG	GGT
add_exon() Sorry, pasa_asmbl_41112.p1 122182-122286-terminal-1 is invalid.
-recovered pasa_asmbl_41112.p1, terminal, 122182, 122286
-recovered pasa_asmbl_41112.p1, internal, 120927, 121086
-recovered pasa_asmbl_41112.p1, internal, 122182, 122286
-recovered pasa_asmbl_41112.p1, internal, 122913, 123028
Valid prediction for snap_scaffold_4-snap.385-T1
Valid prediction for snap_scaffold_4-snap.357-T1
Valid prediction for CodingQuarry_transcript_48884-T1
Valid prediction for Augustus_model.g5672.t1
Valid prediction for Augustus_model.g5685.t1
Valid prediction for snap_scaffold_4-snap.375-T1
Valid prediction for HiQ_model.g5687.t1
Valid prediction for snap_scaffold_4-snap.371-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for Augustus_model.g5680.t1
Valid prediction for snap_scaffold_4-snap.360-T1
Valid prediction for GlimmerHMM_glimmerT_8815-T1
Valid prediction for HiQ_model.g5675.t1
Valid prediction for snap_scaffold_4-snap.390-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_8806-T1
Valid prediction for snap_scaffold_4-snap.352-T1
Valid prediction for pasa_asmbl_41117.p1
Valid prediction for GlimmerHMM_glimmerT_8794-T1
Couldn't classify 114214, 114357
Sorry, prediction pasa_asmbl_42284.p2 fails validation.
(ATG)	 CG	112909-112988	GT	AGG
(TAA)	 AG	113310-113370	GT	GGG
(GAA)	 AG	114046-114135	GT	AGG
(GCA)	 AG	114214-114357	GT	AGG
-recovered pasa_asmbl_42284.p2, initial, 112909, 112988
-recovered pasa_asmbl_42284.p2, internal, 113310, 113370
-recovered pasa_asmbl_42284.p2, internal, 114046, 114135
-recovered pasa_asmbl_42284.p2, internal, 114214, 114357
Couldn't classify 71129, 71270
Couldn't classify 72298, 72509
Sorry, prediction pasa_asmbl_42174.p1 fails validation.
(TGT)	 AA	71129-71270	GT	AGG
(AAT)	 AG	72298-72509	AA	GTA
Valid prediction for GlimmerHMM_glimmerT_8803-T1
Valid prediction for snap_scaffold_4-snap.383-T1
Couldn't classify 161159, 161224
Sorry, prediction pasa_asmbl_41120.p1 fails validation.
(CGA)	 GC	161159-161224	GT	TGG
(TAC)	 AG	161913-161975	GT	TGG
(ATC)	 AG	162322-162452	GT	CGG
(GGT)	 AG	163946-163997	GT	AGG
(GGT)	 AG	166839-166907	GT	AGG
(GAC)	 AG	168099-168242	GC	AGG
-recovered pasa_asmbl_41120.p1, terminal, 168099, 168242
-recovered pasa_asmbl_41120.p1, internal, 161913, 161975
-recovered pasa_asmbl_41120.p1, internal, 162322, 162452
-recovered pasa_asmbl_41120.p1, internal, 163946, 163997
-recovered pasa_asmbl_41120.p1, internal, 166839, 166907
-recovered pasa_asmbl_41120.p1, internal, 168099, 168242
Couldn't classify 176169, 176237
Sorry, prediction pasa_asmbl_41126.p1 fails validation.
(CTG)	 AG	176169-176237	GT	TGG
(ATA)	 AG	176487-176566	GT	AAG
(GTA)	 AG	176693-176791	GT	GGG
(GTA)	 AG	176908-177046	GT	AGG
(AGG)	 AG	178251-178320	GT	TGG
(CGT)	 AG	178740-178812	GT	AGG
(GAC)	 AG	179066-179159	GT	AGG
(GAC)	 AG	179505-179597	GT	CGG
(TTG)	 AG	180110-180167	GT	TGG
(GTG)	 AG	181300-181436	AT	GAA
-recovered pasa_asmbl_41126.p1, terminal, 181300, 181436
-recovered pasa_asmbl_41126.p1, internal, 176169, 176237
-recovered pasa_asmbl_41126.p1, internal, 176487, 176566
-recovered pasa_asmbl_41126.p1, internal, 176693, 176791
-recovered pasa_asmbl_41126.p1, internal, 176908, 177046
-recovered pasa_asmbl_41126.p1, internal, 178251, 178320
-recovered pasa_asmbl_41126.p1, internal, 178740, 178812
-recovered pasa_asmbl_41126.p1, internal, 179066, 179159
-recovered pasa_asmbl_41126.p1, internal, 179505, 179597
-recovered pasa_asmbl_41126.p1, internal, 180110, 180167
Valid prediction for snap_scaffold_4-snap.386-T1
Valid prediction for HiQ_model.g5676.t1
Valid prediction for snap_scaffold_4-snap.359-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.355-T1
Valid prediction for GlimmerHMM_glimmerT_8792-T1
Valid prediction for Augustus_model.g5674.t1
Valid prediction for snap_scaffold_4-snap.350-T1
Valid prediction for snap_scaffold_4-snap.379-T1
Valid prediction for Augustus_model.g5677.t1
Valid prediction for snap_scaffold_4-snap.388-T1
Valid prediction for snap_scaffold_4-snap.348-T1
Valid prediction for snap_scaffold_4-snap.374-T1
Valid prediction for GlimmerHMM_glimmerT_8807-T1
Valid prediction for snap_scaffold_4-snap.356-T1
Valid prediction for snap_scaffold_4-snap.382-T1
Valid prediction for GlimmerHMM_glimmerT_8798-T1
Valid prediction for GlimmerHMM_glimmerT_8799-T1
Valid prediction for snap_scaffold_4-snap.365-T1
Valid prediction for snap_scaffold_4-snap.354-T1
Valid prediction for snap_scaffold_4-snap.364-T1
Valid prediction for snap_scaffold_4-snap.363-T1
Valid prediction for snap_scaffold_4-snap.380-T1
Valid prediction for snap_scaffold_4-snap.366-T1
Valid prediction for snap_scaffold_4-snap.351-T1
Valid prediction for GlimmerHMM_glimmerT_8805-T1
Valid prediction for GlimmerHMM_glimmerT_8817-T1
Valid prediction for snap_scaffold_4-snap.389-T1
Valid prediction for snap_scaffold_4-snap.377-T1
Valid prediction for GlimmerHMM_glimmerT_8808-T1
Valid prediction for snap_scaffold_4-snap.376-T1
Valid prediction for snap_scaffold_4-snap.373-T1
Valid prediction for snap_scaffold_4-snap.372-T1
Valid prediction for snap_scaffold_4-snap.358-T1
Valid prediction for snap_scaffold_4-snap.347-T1
Valid prediction for snap_scaffold_4-snap.367-T1
Valid prediction for GlimmerHMM_glimmerT_8804-T1
Valid prediction for GlimmerHMM_glimmerT_8797-T1
Valid prediction for Augustus_model.g5678.t1
Valid prediction for GlimmerHMM_glimmerT_8813-T1
Valid prediction for snap_scaffold_4-snap.369-T1
Valid prediction for snap_scaffold_4-snap.368-T1
Valid prediction for snap_scaffold_4-snap.392-T1
Valid prediction for snap_scaffold_4-snap.387-T1
Valid prediction for snap_scaffold_4-snap.381-T1
Valid prediction for GlimmerHMM_glimmerT_8801-T1
Valid prediction for Augustus_model.g5688.t1
Valid prediction for snap_scaffold_4-snap.384-T1
Valid prediction for Augustus_model.g5679.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 20940, rend_intergenic: 11236  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25077, rend_intergenic: 23011  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30705, rend_intergenic: 26448  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37454, rend_intergenic: 30973  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40255, rend_intergenic: 37764  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48120, rend_intergenic: 46066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71353, rend_intergenic: 59294  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80739, rend_intergenic: 77756  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88234, rend_intergenic: 81041  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100022, rend_intergenic: 99524  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105550, rend_intergenic: 104134  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142052, rend_intergenic: 105750  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156165, rend_intergenic: 147502  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168266, rend_intergenic: 156459  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181436, rend_intergenic: 177442  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193413, rend_intergenic: 187002  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 202792
-exon list size: 390


building trellis

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10.7    
11.0    
11.2    
11.5    
11.7    
12.0    
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14.5    
14.8    
15.1    
15.3    
15.6    
15.8    
16.1    
16.3    
16.6    
16.8    
17.1    
17.3    
17.6    
17.9    
18.1    
18.4    
18.6    
18.9    
19.1    
19.4    
19.6    
19.9    
20.2    
20.4    
20.7    
20.9    
21.2    
21.4    
21.7    
21.9    
22.2    
22.4    
22.7    
23.0    
23.2    
23.5    
23.7    
24.0    
24.2    
24.5    
24.7    
25.0    
25.3    
25.5    
25.8    
26.0    
26.3    
26.5    
26.8    
27.0    
27.3    
27.6    
27.8    
28.1    
28.3    
28.6    
28.8    
29.1    
29.3    
29.6    
29.8    
30.1    
30.4    
30.6    
30.9    
31.1    
31.4    
31.6    
31.9    
32.1    
32.4    
32.7    
32.9    
33.2    
33.4    
33.7    
33.9    
34.2    
34.4    
34.7    
34.9    
35.2    
35.5    
35.7    
36.0    
36.2    
36.5    
36.7    
37.0    
37.2    
37.5    
37.8    
38.0    
38.3    
38.5    
38.8    
39.0    
39.3    
39.5    
39.8    
40.1    
40.3    
40.6    
40.8    
41.1    
41.3    
41.6    
41.8    
42.1    
42.3    
42.6    
42.9    
43.1    
43.4    
43.6    
43.9    
44.1    
44.4    
44.6    
44.9    
45.2    
45.4    
45.7    
45.9    
46.2    
46.4    
46.7    
46.9    
47.2    
47.4    
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    
52.6    
52.8    
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53.3    
53.6    
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54.1    
54.3    
54.6    
54.8    
55.1    
55.4    
55.6    
55.9    
56.1    
56.4    
56.6    
56.9    
57.1    
57.4    
57.7    
57.9    
58.2    
58.4    
58.7    
58.9    
59.2    
59.4    
59.7    
59.9    
60.2    
60.5    
60.7    
61.0    
61.2    
61.5    
61.7    
62.0    
62.2    
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62.8    
63.0    
63.3    
63.5    
63.8    
64.0    
64.3    
64.5    
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65.3    
65.6    
65.8    
66.1    
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66.8    
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68.1    
68.4    
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70.7    
70.9    
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71.9    
72.2    
72.4    
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73.0    
73.2    
73.5    
73.7    
74.0    
74.2    
74.5    
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75.0    
75.3    
75.5    
75.8    
76.0    
76.3    
76.5    
76.8    
77.0    
77.3    
77.6    
77.8    
78.1    
78.3    
78.6    
78.8    
79.1    
79.3    
79.6    
79.8    
80.1    
80.4    
80.6    
80.9    
81.1    
81.4    
81.6    
81.9    
82.1    
82.4    
82.7    
82.9    
83.2    
83.4    
83.7    
83.9    
84.2    
84.4    
84.7    
84.9    
85.2    
85.5    
85.7    
86.0    
86.2    
86.5    
86.7    
87.0    
87.2    
87.5    
87.8    
88.0    
88.3    
88.5    
88.8    
89.0    
89.3    
89.5    
89.8    
90.1    
90.3    
90.6    
90.8    
91.1    
91.3    
91.6    
91.8    
92.1    
92.3    
92.6    
92.9    
93.1    
93.4    
93.6    
93.9    
94.1    
94.4    
94.6    
94.9    
95.2    
95.4    
95.7    
95.9    
96.2    
96.4    
96.7    
96.9    
97.2    
97.4    
97.7    
98.0    
98.2    
98.5    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 20940, rend_intergenic: 11236  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25077, rend_intergenic: 23011  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30705, rend_intergenic: 26448  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37454, rend_intergenic: 30973  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40255, rend_intergenic: 37764  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48120, rend_intergenic: 46066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71353, rend_intergenic: 59294  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80739, rend_intergenic: 77756  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88234, rend_intergenic: 81041  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100022, rend_intergenic: 99524  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105550, rend_intergenic: 104134  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142052, rend_intergenic: 105750  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156165, rend_intergenic: 147502  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168266, rend_intergenic: 156459  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181436, rend_intergenic: 177442  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193413, rend_intergenic: 187002  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support