-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_2/scaffold_2_2925284-3074484

-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 70010, 70164
Couldn't classify 70228, 70381
Sorry, prediction CodingQuarry_transcript_28488-T1 fails validation.
(ATG)	 CG	70010-70164	CT	GCC
(CTC)	 GC	70228-70381	GG	AAG
Valid prediction for snap_scaffold_2-snap.689-T1
Valid prediction for snap_scaffold_2-snap.679-T1
Valid prediction for GlimmerHMM_glimmerT_3453-T1
Valid prediction for GlimmerHMM_glimmerT_3451-T1
Valid prediction for GlimmerHMM_glimmerT_3457-T1
Valid prediction for snap_scaffold_2-snap.712-T1
Valid prediction for GlimmerHMM_glimmerT_3439-T1
Couldn't classify 70010, 70185
Couldn't classify 70228, 70381
Sorry, prediction CodingQuarry_transcript_28487-T1 fails validation.
(ATG)	 CG	70010-70185	CT	GCC
(CTC)	 GC	70228-70381	GG	AAG
Valid prediction for snap_scaffold_2-snap.692-T1
Valid prediction for snap_scaffold_2-snap.691-T1
Couldn't classify 136534, 136662
Couldn't classify 138573, 138751
Sorry, prediction pasa_asmbl_25443.p1 fails validation.
(GAG)	 CA	136534-136662	GT	TGG
(GAA)	 AG	138007-138172	GT	CGG
(GTT)	 AG	138573-138751	GT	ACG
-recovered pasa_asmbl_25443.p1, internal, 138007, 138172
-recovered pasa_asmbl_25443.p1, internal, 138573, 138751
Couldn't classify 31572, 31818
Sorry, prediction pasa_asmbl_24257.p1 fails validation.
(GAG)	 AG	31572-31818	GT	AGG
(ATA)	 AG	32128-32268	GT	AGG
(CGC)	 AG	32775-32821	AC	AGA
-recovered pasa_asmbl_24257.p1, terminal, 32775, 32821
-recovered pasa_asmbl_24257.p1, internal, 31572, 31818
-recovered pasa_asmbl_24257.p1, internal, 32128, 32268
Valid prediction for GlimmerHMM_glimmerT_3448-T1
Valid prediction for HiQ_model.g2310.t1
Valid prediction for GlimmerHMM_glimmerT_3455-T1
Couldn't classify 70010, 70059
Couldn't classify 70081, 70185
Couldn't classify 70207, 70381
Sorry, prediction CodingQuarry_transcript_28489-T1 fails validation.
(ATG)	 CG	70010-70059	CT	GCC
(CTC)	 GC	70081-70185	CT	GCC
(CTC)	 GC	70207-70381	GG	AAG
Valid prediction for snap_scaffold_2-snap.700-T1
Valid prediction for snap_scaffold_2-snap.694-T1
Valid prediction for GlimmerHMM_glimmerT_3452-T1
Couldn't classify 56769, 56870
Couldn't classify 62970, 63086
Sorry, prediction pasa_asmbl_24264.p1 fails validation.
(GTG)	 AG	56769-56870	GT	AGG
(ACG)	 AG	57445-57561	GT	AGG
(ACC)	 AG	59239-59577	GT	AGG
(CTC)	 AG	60152-60301	GT	TGG
(CTG)	 AG	60548-60667	GT	AGG
(AAT)	 AG	60810-61013	GC	AGG
(GTG)	 AG	61229-61429	GT	AGG
(CTG)	 AG	62423-62536	GT	AGG
(GAG)	 AG	62650-62805	GT	AGG
(AAC)	 AG	62970-63086	CT	GCC
-recovered pasa_asmbl_24264.p1, internal, 56769, 56870
-recovered pasa_asmbl_24264.p1, internal, 57445, 57561
-recovered pasa_asmbl_24264.p1, internal, 59239, 59577
-recovered pasa_asmbl_24264.p1, internal, 60152, 60301
-recovered pasa_asmbl_24264.p1, internal, 60548, 60667
-recovered pasa_asmbl_24264.p1, internal, 60810, 61013
-recovered pasa_asmbl_24264.p1, internal, 61229, 61429
-recovered pasa_asmbl_24264.p1, internal, 62423, 62536
-recovered pasa_asmbl_24264.p1, internal, 62650, 62805
Valid prediction for snap_scaffold_2-snap.703-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_3444-T1
Valid prediction for Augustus_model.g2311.t1
Valid prediction for GlimmerHMM_glimmerT_3445-T1
Valid prediction for Augustus_model.g2316.t1
Valid prediction for snap_scaffold_2-snap.683-T1
Valid prediction for GlimmerHMM_glimmerT_3443-T1
Couldn't classify 130232, 130330
Couldn't classify 131441, 131596
Sorry, prediction pasa_asmbl_25450.p1 fails validation.
(TAC)	 CT	130232-130330	GT	AGG
(CTT)	 AG	131083-131199	GT	AGG
(ATC)	 AG	131441-131596	CT	ACC
-recovered pasa_asmbl_25450.p1, internal, 131083, 131199
Couldn't classify 64115, 64429
Sorry, prediction pasa_asmbl_24266.p1 fails validation.
(GAG)	 AG	64115-64429	GT	AGG
(GTC)	 AG	64715-64816	GT	AGG
(GCA)	 AG	64972-65166	GC	AGG
(ACC)	 AG	65291-65473	GT	AGG
(ACG)	 AG	65737-65922	GT	AGG
(GGC)	 AG	66283-66414	GT	AGG
(GAG)	 AG	66574-66759	GT	TGG
(GTC)	 AG	66980-67218	GT	CGG
(GTG)	 AG	67680-67800	GT	AGG
(ATA)	 AG	67890-67988	GT	AGG
(CAC)	 AG	68457-68579	TC	GAT
-recovered pasa_asmbl_24266.p1, terminal, 68457, 68579
-recovered pasa_asmbl_24266.p1, internal, 64115, 64429
-recovered pasa_asmbl_24266.p1, internal, 64715, 64816
-recovered pasa_asmbl_24266.p1, internal, 64972, 65166
-recovered pasa_asmbl_24266.p1, internal, 65291, 65473
-recovered pasa_asmbl_24266.p1, internal, 65737, 65922
-recovered pasa_asmbl_24266.p1, internal, 66283, 66414
-recovered pasa_asmbl_24266.p1, internal, 66574, 66759
-recovered pasa_asmbl_24266.p1, internal, 66980, 67218
-recovered pasa_asmbl_24266.p1, internal, 67680, 67800
-recovered pasa_asmbl_24266.p1, internal, 67890, 67988
Valid prediction for GlimmerHMM_glimmerT_3446-T1
Valid prediction for GlimmerHMM_glimmerT_3440-T1
Valid prediction for snap_scaffold_2-snap.684-T1
Valid prediction for GlimmerHMM_glimmerT_3454-T1
Valid prediction for snap_scaffold_2-snap.710-T1
Valid prediction for snap_scaffold_2-snap.686-T1
Valid prediction for snap_scaffold_2-snap.711-T1
Valid prediction for Augustus_model.g2319.t1
Valid prediction for Augustus_model.g2307.t1
Valid prediction for GlimmerHMM_glimmerT_3438-T1
Valid prediction for Augustus_model.g2309.t1
Valid prediction for GlimmerHMM_glimmerT_3456-T1
Valid prediction for GlimmerHMM_glimmerT_3441-T1
Valid prediction for Augustus_model.g2317.t1
Couldn't classify 40075, 40236
Sorry, prediction pasa_asmbl_24261.p1 fails validation.
(TTT)	 AG	40075-40236	GT	CTG
(GTC)	 AG	40435-40545	GT	AGG
(GCT)	 AG	42702-42746	GT	AGG
(CAC)	 AG	43160-43247	GT	CGG
(GTC)	 AG	45775-45986	GA	AGG
-recovered pasa_asmbl_24261.p1, terminal, 45775, 45986
-recovered pasa_asmbl_24261.p1, internal, 40075, 40236
-recovered pasa_asmbl_24261.p1, internal, 40435, 40545
-recovered pasa_asmbl_24261.p1, internal, 42702, 42746
-recovered pasa_asmbl_24261.p1, internal, 43160, 43247
Valid prediction for GlimmerHMM_glimmerT_3437-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_2-snap.680-T1
Valid prediction for snap_scaffold_2-snap.696-T1
Couldn't classify 13107, 13676
Sorry, prediction pasa_asmbl_22957.p1 fails validation.
(CCA)	 CC	13107-13676	GA	AGG
Valid prediction for Augustus_model.g2314.t1
Valid prediction for Augustus_model.g2308.t1
Valid prediction for snap_scaffold_2-snap.682-T1
Valid prediction for snap_scaffold_2-snap.693-T1
Valid prediction for snap_scaffold_2-snap.714-T1
Valid prediction for snap_scaffold_2-snap.695-T1
Valid prediction for GlimmerHMM_glimmerT_3450-T1
Valid prediction for snap_scaffold_2-snap.704-T1
Valid prediction for snap_scaffold_2-snap.698-T1
Valid prediction for snap_scaffold_2-snap.707-T1
Valid prediction for snap_scaffold_2-snap.713-T1
Valid prediction for snap_scaffold_2-snap.685-T1
Valid prediction for snap_scaffold_2-snap.702-T1
Valid prediction for snap_scaffold_2-snap.690-T1
Valid prediction for snap_scaffold_2-snap.708-T1
Valid prediction for Augustus_model.g2313.t1
Valid prediction for snap_scaffold_2-snap.681-T1
Valid prediction for snap_scaffold_2-snap.701-T1
Valid prediction for GlimmerHMM_glimmerT_3449-T1
Valid prediction for snap_scaffold_2-snap.706-T1
Valid prediction for GlimmerHMM_glimmerT_3447-T1
Valid prediction for GlimmerHMM_glimmerT_3442-T1
Valid prediction for Augustus_model.g2312.t1
Valid prediction for GlimmerHMM_glimmerT_3458-T1
Valid prediction for snap_scaffold_2-snap.688-T1
Valid prediction for Augustus_model.g2315.t1
Valid prediction for snap_scaffold_2-snap.697-T1
Couldn't classify 76633, 76786
Sorry, prediction pasa_asmbl_22954.p2 fails validation.
(AAG)	 AG	76633-76786	GT	TGG
(CGA)	 AG	77237-77334	GT	AGG
(AGG)	 AG	77902-78000	TT	GAT
-recovered pasa_asmbl_22954.p2, terminal, 77902, 78000
-recovered pasa_asmbl_22954.p2, internal, 76633, 76786
-recovered pasa_asmbl_22954.p2, internal, 77237, 77334
Valid prediction for snap_scaffold_2-snap.687-T1
Valid prediction for Augustus_model.g2318.t1
Valid prediction for snap_scaffold_2-snap.709-T1
Valid prediction for snap_scaffold_2-snap.699-T1
Valid prediction for snap_scaffold_2-snap.705-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 20614, rend_intergenic: 5987  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32821, rend_intergenic: 30420  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43762, rend_intergenic: 40392  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50859, rend_intergenic: 49146  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73418, rend_intergenic: 52205  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83701, rend_intergenic: 74721  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124190, rend_intergenic: 93322  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136709, rend_intergenic: 126273  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146857, rend_intergenic: 137818  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 149201
-exon list size: 409


building trellis

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3.9    
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10.9    
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11.9    
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13.6    
13.9    
14.1    
14.4    
14.6    
14.8    
15.1    
15.3    
15.6    
15.8    
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16.3    
16.5    
16.8    
17.0    
17.3    
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17.8    
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18.2    
18.5    
18.7    
19.0    
19.2    
19.5    
19.7    
20.0    
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20.4    
20.7    
20.9    
21.2    
21.4    
21.7    
21.9    
22.1    
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22.6    
22.9    
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23.4    
23.6    
23.8    
24.1    
24.3    
24.6    
24.8    
25.1    
25.3    
25.5    
25.8    
26.0    
26.3    
26.5    
26.8    
27.0    
27.3    
27.5    
27.7    
28.0    
28.2    
28.5    
28.7    
29.0    
29.2    
29.4    
29.7    
29.9    
30.2    
30.4    
30.7    
30.9    
31.1    
31.4    
31.6    
31.9    
32.1    
32.4    
32.6    
32.8    
33.1    
33.3    
33.6    
33.8    
34.1    
34.3    
34.5    
34.8    
35.0    
35.3    
35.5    
35.8    
36.0    
36.3    
36.5    
36.7    
37.0    
37.2    
37.5    
37.7    
38.0    
38.2    
38.4    
38.7    
38.9    
39.2    
39.4    
39.7    
39.9    
40.1    
40.4    
40.6    
40.9    
41.1    
41.4    
41.6    
41.8    
42.1    
42.3    
42.6    
42.8    
43.1    
43.3    
43.6    
43.8    
44.0    
44.3    
44.5    
44.8    
45.0    
45.3    
45.5    
45.7    
46.0    
46.2    
46.5    
46.7    
47.0    
47.2    
47.4    
47.7    
47.9    
48.2    
48.4    
48.7    
48.9    
49.1    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.9    
51.1    
51.3    
51.6    
51.8    
52.1    
52.3    
52.6    
52.8    
53.0    
53.3    
53.5    
53.8    
54.0    
54.3    
54.5    
54.7    
55.0    
55.2    
55.5    
55.7    
56.0    
56.2    
56.4    
56.7    
56.9    
57.2    
57.4    
57.7    
57.9    
58.2    
58.4    
58.6    
58.9    
59.1    
59.4    
59.6    
59.9    
60.1    
60.3    
60.6    
60.8    
61.1    
61.3    
61.6    
61.8    
62.0    
62.3    
62.5    
62.8    
63.0    
63.3    
63.5    
63.7    
64.0    
64.2    
64.5    
64.7    
65.0    
65.2    
65.5    
65.7    
65.9    
66.2    
66.4    
66.7    
66.9    
67.2    
67.4    
67.6    
67.9    
68.1    
68.4    
68.6    
68.9    
69.1    
69.3    
69.6    
69.8    
70.1    
70.3    
70.6    
70.8    
71.0    
71.3    
71.5    
71.8    
72.0    
72.3    
72.5    
72.7    
73.0    
73.2    
73.5    
73.7    
74.0    
74.2    
74.5    
74.7    
74.9    
75.2    
75.4    
75.7    
75.9    
76.2    
76.4    
76.6    
76.9    
77.1    
77.4    
77.6    
77.9    
78.1    
78.3    
78.6    
78.8    
79.1    
79.3    
79.6    
79.8    
80.0    
80.3    
80.5    
80.8    
81.0    
81.3    
81.5    
81.8    
82.0    
82.2    
82.5    
82.7    
83.0    
83.2    
83.5    
83.7    
83.9    
84.2    
84.4    
84.7    
84.9    
85.2    
85.4    
85.6    
85.9    
86.1    
86.4    
86.6    
86.9    
87.1    
87.3    
87.6    
87.8    
88.1    
88.3    
88.6    
88.8    
89.1    
89.3    
89.5    
89.8    
90.0    
90.3    
90.5    
90.8    
91.0    
91.2    
91.5    
91.7    
92.0    
92.2    
92.5    
92.7    
92.9    
93.2    
93.4    
93.7    
93.9    
94.2    
94.4    
94.6    
94.9    
95.1    
95.4    
95.6    
95.9    
96.1    
96.4    
96.6    
96.8    
97.1    
97.3    
97.6    
97.8    
98.1    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 20 predictions from path traversal
Error with prediction: snap lend_intergenic: 20614, rend_intergenic: 5987  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32821, rend_intergenic: 30420  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43762, rend_intergenic: 40392  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50859, rend_intergenic: 49146  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73418, rend_intergenic: 52205  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83701, rend_intergenic: 74721  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124190, rend_intergenic: 93322  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136709, rend_intergenic: 126273  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146857, rend_intergenic: 137818  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