-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_21/scaffold_21_8260748-8420362

-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 Augustus_model.g32196.t1
Valid prediction for snap_scaffold_21-snap.1765-T1
Valid prediction for Augustus_model.g32200.t1
Couldn't classify 14618, 14752
Sorry, prediction pasa_asmbl_28802.p1 fails validation.
(ACA)	 AC	14618-14752	GT	GAG
(ACA)	 AG	15014-15164	GT	CGG
(AGG)	 AG	15383-15507	GT	GGG
(GCT)	 AG	15648-15794	CA	AAC
-recovered pasa_asmbl_28802.p1, terminal, 15648, 15794
-recovered pasa_asmbl_28802.p1, internal, 15014, 15164
-recovered pasa_asmbl_28802.p1, internal, 15383, 15507
Valid prediction for GlimmerHMM_glimmerT_48206-T1
Valid prediction for snap_scaffold_21-snap.1753-T1
Valid prediction for snap_scaffold_21-snap.1779-T1
Valid prediction for snap_scaffold_21-snap.1759-T1
Valid prediction for HiQ_model.g32198.t1
Valid prediction for snap_scaffold_21-snap.1746-T1
Valid prediction for Augustus_model.g32205.t1
Valid prediction for GlimmerHMM_glimmerT_48200-T1
Valid prediction for snap_scaffold_21-snap.1781-T1
Valid prediction for GlimmerHMM_glimmerT_48188-T1
Valid prediction for GlimmerHMM_glimmerT_48213-T1
Valid prediction for Augustus_model.g32210.t1
Valid prediction for snap_scaffold_21-snap.1757-T1
Valid prediction for CodingQuarry_transcript_32666-T1
Valid prediction for snap_scaffold_21-snap.1764-T1
Valid prediction for GlimmerHMM_glimmerT_48189-T1
Valid prediction for CodingQuarry_transcript_32668-T1
Valid prediction for Augustus_model.g32202.t1
Valid prediction for pasa_asmbl_28805.p1
Valid prediction for snap_scaffold_21-snap.1784-T1
Valid prediction for Augustus_model.g32194.t1
Valid prediction for GlimmerHMM_glimmerT_48198-T1
Valid prediction for GlimmerHMM_glimmerT_48187-T1
Valid prediction for GlimmerHMM_glimmerT_48212-T1
Couldn't classify 58723, 58842
Couldn't classify 59030, 59117
Sorry, prediction pasa_asmbl_28808.p1 fails validation.
(ATG)	 AA	58219-58323	GT	AGG
(GTG)	 AG	58723-58842	AT	AGA
(AGG)	 AC	59030-59117	GT	AGG
(ATG)	 AG	59227-59315	GT	AAG
(ACG)	 AG	59433-59488	GT	GAG
(TTA)	 AG	59594-59725	GT	AGG
(CTT)	 AG	59960-60003	GT	AGG
(TGT)	 AG	60270-60418	GG	GAG
-recovered pasa_asmbl_28808.p1, initial, 58219, 58323
add_exon() Sorry, pasa_asmbl_28808.p1 59227-59315-initial-1 is invalid.
-recovered pasa_asmbl_28808.p1, initial, 59227, 59315
-recovered pasa_asmbl_28808.p1, terminal, 59594, 59725
-recovered pasa_asmbl_28808.p1, terminal, 60270, 60418
-recovered pasa_asmbl_28808.p1, internal, 59227, 59315
-recovered pasa_asmbl_28808.p1, internal, 59433, 59488
-recovered pasa_asmbl_28808.p1, internal, 59594, 59725
-recovered pasa_asmbl_28808.p1, internal, 59960, 60003
Valid prediction for snap_scaffold_21-snap.1773-T1
Valid prediction for snap_scaffold_21-snap.1758-T1
Valid prediction for GlimmerHMM_glimmerT_48204-T1
Valid prediction for snap_scaffold_21-snap.1744-T1
Valid prediction for GlimmerHMM_glimmerT_48195-T1
Couldn't classify 58723, 58842
Couldn't classify 59030, 59117
Sorry, prediction CodingQuarry_transcript_32674-T1 fails validation.
(ATG)	 TT	58303-58323	GT	AGG
(GTG)	 AG	58723-58842	AT	AGA
(AGG)	 AC	59030-59117	GT	AGG
(ATG)	 AG	59227-59315	GT	AAG
(ACG)	 AG	59433-59488	GT	GAG
(TTA)	 AG	59594-59725	GT	AGG
(CTT)	 AG	59960-60003	GT	AGG
(TGT)	 AG	60270-60418	GG	GAG
-recovered CodingQuarry_transcript_32674-T1, initial, 58303, 58323
add_exon() Sorry, CodingQuarry_transcript_32674-T1 59227-59315-initial-1 is invalid.
-recovered CodingQuarry_transcript_32674-T1, initial, 59227, 59315
-recovered CodingQuarry_transcript_32674-T1, terminal, 59594, 59725
-recovered CodingQuarry_transcript_32674-T1, terminal, 60270, 60418
-recovered CodingQuarry_transcript_32674-T1, internal, 59227, 59315
-recovered CodingQuarry_transcript_32674-T1, internal, 59433, 59488
-recovered CodingQuarry_transcript_32674-T1, internal, 59594, 59725
-recovered CodingQuarry_transcript_32674-T1, internal, 59960, 60003
Valid prediction for snap_scaffold_21-snap.1754-T1
Valid prediction for Augustus_model.g32190.t1
Valid prediction for snap_scaffold_21-snap.1763-T1
Valid prediction for Augustus_model.g32189.t1
Valid prediction for CodingQuarry_transcript_32670-T1
Valid prediction for snap_scaffold_21-snap.1749-T1
Valid prediction for snap_scaffold_21-snap.1782-T1
Valid prediction for snap_scaffold_21-snap.1768-T1
Valid prediction for GlimmerHMM_glimmerT_48185-T1
Valid prediction for snap_scaffold_21-snap.1755-T1
Valid prediction for CodingQuarry_transcript_32667-T1
Valid prediction for Augustus_model.g32188.t1
Valid prediction for GlimmerHMM_glimmerT_48207-T1
Valid prediction for CodingQuarry_transcript_32669-T1
Valid prediction for GlimmerHMM_glimmerT_48201-T1
Valid prediction for snap_scaffold_21-snap.1745-T1
Valid prediction for GlimmerHMM_glimmerT_48203-T1
Valid prediction for snap_scaffold_21-snap.1766-T1
Valid prediction for snap_scaffold_21-snap.1775-T1
Valid prediction for snap_scaffold_21-snap.1767-T1
Valid prediction for GlimmerHMM_glimmerT_48194-T1
Valid prediction for GlimmerHMM_glimmerT_48209-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: -)Couldn't classify 116966, 116993
Sorry, prediction pasa_asmbl_27921.p1 fails validation.
(TTC)	 CA	116966-116993	GT	TGG
(GTC)	 AG	117092-117168	GT	AGG
(GTG)	 AG	117599-117673	GT	CAG
(ATC)	 AG	118063-118176	GT	AAG
(GGC)	 AG	118603-118715	GT	AGG
(CCC)	 AG	118850-118950	GT	AGG
(ATG)	 AG	119304-119413	CA	AAC
-recovered pasa_asmbl_27921.p1, terminal, 119304, 119413
-recovered pasa_asmbl_27921.p1, internal, 117092, 117168
-recovered pasa_asmbl_27921.p1, internal, 117599, 117673
-recovered pasa_asmbl_27921.p1, internal, 118063, 118176
-recovered pasa_asmbl_27921.p1, internal, 118603, 118715
-recovered pasa_asmbl_27921.p1, internal, 118850, 118950
Valid prediction for snap_scaffold_21-snap.1751-T1
Valid prediction for snap_scaffold_21-snap.1747-T1
Valid prediction for snap_scaffold_21-snap.1748-T1
Valid prediction for Augustus_model.g32195.t1
Valid prediction for GlimmerHMM_glimmerT_48192-T1
Valid prediction for GlimmerHMM_glimmerT_48214-T1
Valid prediction for snap_scaffold_21-snap.1774-T1
Valid prediction for snap_scaffold_21-snap.1761-T1
Valid prediction for GlimmerHMM_glimmerT_48191-T1
Couldn't classify 103364, 103542
Sorry, prediction pasa_asmbl_27923.p2 fails validation.
(TAT)	 TG	103364-103542	GT	AAG
(GAA)	 AG	103830-104016	AC	GAA
-recovered pasa_asmbl_27923.p2, terminal, 103830, 104016
Valid prediction for Augustus_model.g32201.t1
Valid prediction for GlimmerHMM_glimmerT_48197-T1
Valid prediction for snap_scaffold_21-snap.1770-T1
Valid prediction for HiQ_model.g32193.t1
Valid prediction for snap_scaffold_21-snap.1750-T1
Valid prediction for Augustus_model.g32197.t1
Valid prediction for Augustus_model.g32208.t1
Valid prediction for Augustus_model.g32204.t1
Valid prediction for GlimmerHMM_glimmerT_48193-T1
Valid prediction for Augustus_model.g32203.t1
Valid prediction for snap_scaffold_21-snap.1762-T1
Valid prediction for CodingQuarry_transcript_32672-T1
Valid prediction for Augustus_model.g32199.t1
Valid prediction for snap_scaffold_21-snap.1780-T1
Valid prediction for pasa_asmbl_27916.p1
Valid prediction for snap_scaffold_21-snap.1756-T1
Couldn't classify 137680, 137721
Sorry, prediction pasa_asmbl_27913.p1 fails validation.
(ATG)	 AA	137038-137095	GT	AGG
(GTG)	 AG	137250-137446	GT	AGG
(GTT)	 AG	137680-137721	TA	AGT
-recovered pasa_asmbl_27913.p1, initial, 137038, 137095
-recovered pasa_asmbl_27913.p1, internal, 137250, 137446
Valid prediction for Augustus_model.g32191.t1
Valid prediction for GlimmerHMM_glimmerT_48184-T1
Valid prediction for snap_scaffold_21-snap.1778-T1
Valid prediction for GlimmerHMM_glimmerT_48210-T1
Valid prediction for snap_scaffold_21-snap.1769-T1
Valid prediction for pasa_asmbl_27918.p1
Valid prediction for HiQ_model.g32192.t1
Valid prediction for snap_scaffold_21-snap.1777-T1
Valid prediction for snap_scaffold_21-snap.1760-T1
Valid prediction for snap_scaffold_21-snap.1743-T1
Valid prediction for Augustus_model.g32206.t1
Valid prediction for GlimmerHMM_glimmerT_48202-T1
Valid prediction for GlimmerHMM_glimmerT_48208-T1
Valid prediction for GlimmerHMM_glimmerT_48205-T1
Valid prediction for GlimmerHMM_glimmerT_48211-T1
Valid prediction for CodingQuarry_transcript_32673-T1
Valid prediction for snap_scaffold_21-snap.1771-T1
Valid prediction for Augustus_model.g32209.t1
Valid prediction for CodingQuarry_transcript_32671-T1
Valid prediction for GlimmerHMM_glimmerT_48196-T1
Valid prediction for GlimmerHMM_glimmerT_48199-T1
Valid prediction for snap_scaffold_21-snap.1772-T1
Valid prediction for GlimmerHMM_glimmerT_48190-T1
Valid prediction for snap_scaffold_21-snap.1776-T1
Valid prediction for snap_scaffold_21-snap.1752-T1
Valid prediction for Augustus_model.g32207.t1
Couldn't classify 138390, 138420
Sorry, prediction pasa_asmbl_27912.p1 fails validation.
(GCT)	 CA	138390-138420	GT	AGG
(GGA)	 AG	138617-138720	GT	GGG
(GTC)	 AG	138892-139011	GT	AGG
(GAG)	 AG	139180-139348	GT	CGG
(GAC)	 AG	139537-139617	GT	AAG
(AGC)	 AG	139974-140096	GT	TGG
(GTT)	 AG	140233-140393	AC	GAA
-recovered pasa_asmbl_27912.p1, terminal, 140233, 140393
-recovered pasa_asmbl_27912.p1, internal, 138617, 138720
-recovered pasa_asmbl_27912.p1, internal, 138892, 139011
-recovered pasa_asmbl_27912.p1, internal, 139180, 139348
-recovered pasa_asmbl_27912.p1, internal, 139537, 139617
-recovered pasa_asmbl_27912.p1, internal, 139974, 140096
Valid prediction for GlimmerHMM_glimmerT_48186-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7249, rend_intergenic: 3260  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18810, rend_intergenic: 16838  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32991, rend_intergenic: 30173  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50793, rend_intergenic: 43773  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66557, rend_intergenic: 64706  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114881, rend_intergenic: 113712  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116988, rend_intergenic: 115321  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138075, rend_intergenic: 136377  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142098, rend_intergenic: 140687  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144605, rend_intergenic: 143406  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 159615
-exon list size: 372


building trellis

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1.6    
1.9    
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3.7    
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4.5    
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5.3    
5.6    
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7.0    
7.2    
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8.0    
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10.2    
10.4    
10.7    
11.0    
11.2    
11.5    
11.8    
12.0    
12.3    
12.6    
12.8    
13.1    
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15.0    
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16.6    
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17.4    
17.6    
17.9    
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18.4    
18.7    
19.0    
19.3    
19.5    
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20.9    
21.1    
21.4    
21.7    
21.9    
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22.5    
22.7    
23.0    
23.3    
23.5    
23.8    
24.1    
24.3    
24.6    
24.9    
25.1    
25.4    
25.7    
25.9    
26.2    
26.5    
26.7    
27.0    
27.3    
27.5    
27.8    
28.1    
28.3    
28.6    
28.9    
29.1    
29.4    
29.7    
29.9    
30.2    
30.5    
30.7    
31.0    
31.3    
31.6    
31.8    
32.1    
32.4    
32.6    
32.9    
33.2    
33.4    
33.7    
34.0    
34.2    
34.5    
34.8    
35.0    
35.3    
35.6    
35.8    
36.1    
36.4    
36.6    
36.9    
37.2    
37.4    
37.7    
38.0    
38.2    
38.5    
38.8    
39.0    
39.3    
39.6    
39.8    
40.1    
40.4    
40.6    
40.9    
41.2    
41.4    
41.7    
42.0    
42.2    
42.5    
42.8    
43.0    
43.3    
43.6    
43.9    
44.1    
44.4    
44.7    
44.9    
45.2    
45.5    
45.7    
46.0    
46.3    
46.5    
46.8    
47.1    
47.3    
47.6    
47.9    
48.1    
48.4    
48.7    
48.9    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.1    
51.3    
51.6    
51.9    
52.1    
52.4    
52.7    
52.9    
53.2    
53.5    
53.7    
54.0    
54.3    
54.5    
54.8    
55.1    
55.3    
55.6    
55.9    
56.1    
56.4    
56.7    
57.0    
57.2    
57.5    
57.8    
58.0    
58.3    
58.6    
58.8    
59.1    
59.4    
59.6    
59.9    
60.2    
60.4    
60.7    
61.0    
61.2    
61.5    
61.8    
62.0    
62.3    
62.6    
62.8    
63.1    
63.4    
63.6    
63.9    
64.2    
64.4    
64.7    
65.0    
65.2    
65.5    
65.8    
66.0    
66.3    
66.6    
66.8    
67.1    
67.4    
67.6    
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68.2    
68.4    
68.7    
69.0    
69.3    
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70.1    
70.3    
70.6    
70.9    
71.1    
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73.0    
73.3    
73.5    
73.8    
74.1    
74.3    
74.6    
74.9    
75.1    
75.4    
75.7    
75.9    
76.2    
76.5    
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77.0    
77.3    
77.5    
77.8    
78.1    
78.3    
78.6    
78.9    
79.1    
79.4    
79.7    
79.9    
80.2    
80.5    
80.7    
81.0    
81.3    
81.6    
81.8    
82.1    
82.4    
82.6    
82.9    
83.2    
83.4    
83.7    
84.0    
84.2    
84.5    
84.8    
85.0    
85.3    
85.6    
85.8    
86.1    
86.4    
86.6    
86.9    
87.2    
87.4    
87.7    
88.0    
88.2    
88.5    
88.8    
89.0    
89.3    
89.6    
89.8    
90.1    
90.4    
90.6    
90.9    
91.2    
91.4    
91.7    
92.0    
92.2    
92.5    
92.8    
93.0    
93.3    
93.6    
93.9    
94.1    
94.4    
94.7    
94.9    
95.2    
95.5    
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96.0    
96.3    
96.5    
96.8    
97.1    
97.3    
97.6    
97.9    
98.1    
98.4    
98.7    
98.9    
99.2    
99.5    
99.7    
-found 38 predictions from path traversal
Error with prediction: snap lend_intergenic: 7249, rend_intergenic: 3260  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18810, rend_intergenic: 16838  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32991, rend_intergenic: 30173  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50793, rend_intergenic: 43773  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66557, rend_intergenic: 64706  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114881, rend_intergenic: 113712  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116988, rend_intergenic: 115321  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138075, rend_intergenic: 136377  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142098, rend_intergenic: 140687  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144605, rend_intergenic: 143406  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 30 predictions persist after filtering for low support