-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_10/scaffold_10_8512725-8669539

-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 snap_scaffold_10-snap.1685-T1
Couldn't classify 129239, 129301
Sorry, prediction pasa_asmbl_4606.p1 fails validation.
(GAG)	 AG	129239-129301	GT	CGG
(GTG)	 AG	129875-130061	GT	AGG
(GGA)	 AG	130907-131075	GT	AGG
(GGA)	 AG	131249-131405	GC	AGG
(GAG)	 AG	131534-131617	GT	AAG
(AAT)	 AG	131753-131890	GT	AGG
(GTG)	 AG	132338-132574	GT	TGG
(GAG)	 AG	132938-133009	GT	TGG
(ACC)	 AG	133152-133175	CC	GAC
-recovered pasa_asmbl_4606.p1, terminal, 133152, 133175
-recovered pasa_asmbl_4606.p1, internal, 129239, 129301
-recovered pasa_asmbl_4606.p1, internal, 129875, 130061
-recovered pasa_asmbl_4606.p1, internal, 130907, 131075
-recovered pasa_asmbl_4606.p1, internal, 131249, 131405
-recovered pasa_asmbl_4606.p1, internal, 131534, 131617
-recovered pasa_asmbl_4606.p1, internal, 131753, 131890
-recovered pasa_asmbl_4606.p1, internal, 132338, 132574
-recovered pasa_asmbl_4606.p1, internal, 132938, 133009
Couldn't classify 128025, 128112
Sorry, prediction pasa_asmbl_4605.p1 fails validation.
(ATG)	 AC	124787-124810	GT	AGG
(GGA)	 AG	125018-125104	GT	TGG
(GGC)	 AG	125376-125518	GT	AAG
(ATT)	 AG	127469-127605	GT	TGG
(GTT)	 AG	127786-127879	GT	AGG
(TAA)	 AG	128025-128112	GA	GTG
-recovered pasa_asmbl_4605.p1, initial, 124787, 124810
-recovered pasa_asmbl_4605.p1, internal, 125018, 125104
-recovered pasa_asmbl_4605.p1, internal, 125376, 125518
-recovered pasa_asmbl_4605.p1, internal, 127469, 127605
-recovered pasa_asmbl_4605.p1, internal, 127786, 127879
Valid prediction for GeneMark_model.43750_t
Valid prediction for GeneMark_model.43738_t
Valid prediction for snap_scaffold_10-snap.1684-T1
Valid prediction for GlimmerHMM_glimmerT_25613-T1
Valid prediction for GeneMark_model.43747_t
Valid prediction for GlimmerHMM_glimmerT_25605-T1
Valid prediction for snap_scaffold_10-snap.1675-T1
Valid prediction for GlimmerHMM_glimmerT_25617-T1
Valid prediction for GeneMark_model.43756_t
Valid prediction for GeneMark_model.43751_t
Valid prediction for GeneMark_model.43740_t
Valid prediction for GlimmerHMM_glimmerT_25616-T1
Valid prediction for Augustus_model.g17183.t1
Valid prediction for GeneMark_model.43743_t
Valid prediction for pasa_asmbl_4604.p1
Valid prediction for snap_scaffold_10-snap.1676-T1
Valid prediction for CodingQuarry_transcript_5488-T1
Valid prediction for snap_scaffold_10-snap.1671-T1
Valid prediction for GeneMark_model.43752_t
Valid prediction for snap_scaffold_10-snap.1688-T1
Valid prediction for GeneMark_model.43737_t
Valid prediction for HiQ_model.g17187.t1
Valid prediction for GeneMark_model.43744_t
Valid prediction for snap_scaffold_10-snap.1690-T1
Valid prediction for snap_scaffold_10-snap.1677-T1
Valid prediction for snap_scaffold_10-snap.1679-T1
Valid prediction for snap_scaffold_10-snap.1681-T1
Valid prediction for GeneMark_model.43760_t
Valid prediction for Augustus_model.g17188.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 GeneMark_model.43758_t
Valid prediction for pasa_asmbl_3509.p1
Valid prediction for GlimmerHMM_glimmerT_25618-T1
Valid prediction for snap_scaffold_10-snap.1691-T1
Valid prediction for GlimmerHMM_glimmerT_25611-T1
Valid prediction for GlimmerHMM_glimmerT_25614-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.43736_t
Valid prediction for GeneMark_model.43754_t
Valid prediction for GeneMark_model.43761_t
Valid prediction for snap_scaffold_10-snap.1689-T1
Valid prediction for GlimmerHMM_glimmerT_25609-T1
Valid prediction for CodingQuarry_transcript_5489-T1
Valid prediction for GeneMark_model.43748_t
Valid prediction for GlimmerHMM_glimmerT_25615-T1
Valid prediction for GlimmerHMM_glimmerT_25610-T1
Valid prediction for snap_scaffold_10-snap.1668-T1
Valid prediction for GeneMark_model.43755_t
Valid prediction for GeneMark_model.43759_t
Valid prediction for GeneMark_model.43745_t
Valid prediction for CodingQuarry_transcript_5487-T1
Valid prediction for snap_scaffold_10-snap.1669-T1
Valid prediction for GeneMark_model.43753_t
Valid prediction for CodingQuarry_transcript_5485-T1
Valid prediction for snap_scaffold_10-snap.1674-T1
Valid prediction for HiQ_model.g17184.t1
Valid prediction for GeneMark_model.43746_t
Valid prediction for Augustus_model.g17189.t1
Valid prediction for GeneMark_model.43739_t
Valid prediction for GlimmerHMM_glimmerT_25619-T1
Valid prediction for GlimmerHMM_glimmerT_25608-T1
Valid prediction for Augustus_model.g17185.t1
Valid prediction for snap_scaffold_10-snap.1686-T1
Sorry, intron length (4) is less than minimum required (10)
Couldn't classify 53523, 54065
Sorry, prediction pasa_asmbl_3518.p1 fails validation.
(CTG)	 TA	53523-54065	GA	CAG
Valid prediction for snap_scaffold_10-snap.1680-T1
Valid prediction for snap_scaffold_10-snap.1670-T1
Valid prediction for GeneMark_model.43741_t
Valid prediction for GeneMark_model.43757_t
Valid prediction for snap_scaffold_10-snap.1682-T1
Valid prediction for snap_scaffold_10-snap.1683-T1
Valid prediction for Augustus_model.g17186.t1
Valid prediction for GlimmerHMM_glimmerT_25606-T1
Valid prediction for GeneMark_model.43749_t
Couldn't classify 107376, 108766
Couldn't classify 116587, 116695
Sorry, prediction pasa_asmbl_3513.p1 fails validation.
(GGA)	 GG	107376-108766	GT	AGG
(ACC)	 AG	108917-109096	GT	TGG
(GGT)	 AG	110680-110839	GT	AGG
(GTG)	 AG	112258-112465	GT	ATG
(ACA)	 AG	113228-113444	GT	AGG
(GGT)	 AG	113573-113687	GT	GGG
(ATC)	 AG	115161-115400	GT	AGG
(GTC)	 AG	116188-116405	GT	AGG
(ATC)	 AG	116587-116695	AC	GCA
add_exon() Sorry, pasa_asmbl_3513.p1 113228-113444-terminal-3 is invalid.
-recovered pasa_asmbl_3513.p1, terminal, 113228, 113444
-recovered pasa_asmbl_3513.p1, internal, 108917, 109096
-recovered pasa_asmbl_3513.p1, internal, 110680, 110839
-recovered pasa_asmbl_3513.p1, internal, 112258, 112465
-recovered pasa_asmbl_3513.p1, internal, 113228, 113444
-recovered pasa_asmbl_3513.p1, internal, 113573, 113687
-recovered pasa_asmbl_3513.p1, internal, 115161, 115400
-recovered pasa_asmbl_3513.p1, internal, 116188, 116405
Valid prediction for GeneMark_model.43742_t
Valid prediction for snap_scaffold_10-snap.1673-T1
Valid prediction for snap_scaffold_10-snap.1672-T1
Couldn't classify 14609, 14648
Sorry, prediction pasa_asmbl_4105.p1 fails validation.
(GAG)	 AG	14609-14648	GT	AGG
(CCC)	 AG	15969-16077	GT	AGG
(CTT)	 AG	16571-16679	GT	AGG
(TGT)	 AG	16792-16900	GT	AGG
(TGT)	 AG	17099-17212	GT	CAG
(AGT)	 AG	17436-17651	GT	AGG
(ATT)	 AG	17745-17807	GT	AGG
(GTC)	 AG	18350-18487	GT	TGG
(GTG)	 AG	18585-18754	TC	AAT
-recovered pasa_asmbl_4105.p1, terminal, 17745, 17807
-recovered pasa_asmbl_4105.p1, terminal, 18585, 18754
-recovered pasa_asmbl_4105.p1, internal, 14609, 14648
-recovered pasa_asmbl_4105.p1, internal, 15969, 16077
-recovered pasa_asmbl_4105.p1, internal, 16571, 16679
-recovered pasa_asmbl_4105.p1, internal, 16792, 16900
-recovered pasa_asmbl_4105.p1, internal, 17099, 17212
-recovered pasa_asmbl_4105.p1, internal, 17436, 17651
-recovered pasa_asmbl_4105.p1, internal, 17745, 17807
-recovered pasa_asmbl_4105.p1, internal, 18350, 18487
Couldn't classify 127146, 127364
Couldn't classify 127613, 127726
Sorry, prediction CodingQuarry_transcript_5486-T1 fails validation.
(ATG)	 AG	125070-125159	GT	TGG
(ATA)	 AG	126769-126975	GT	AGG
(AAG)	 AG	127146-127364	GG	AAG
(AGT)	 AC	127613-127726	GT	AGG
(GCT)	 AG	127851-127862	GC	GAG
-recovered CodingQuarry_transcript_5486-T1, initial, 125070, 125159
-recovered CodingQuarry_transcript_5486-T1, terminal, 127851, 127862
-recovered CodingQuarry_transcript_5486-T1, internal, 125070, 125159
-recovered CodingQuarry_transcript_5486-T1, internal, 126769, 126975
-recovered CodingQuarry_transcript_5486-T1, internal, 127851, 127862
Valid prediction for snap_scaffold_10-snap.1687-T1
Valid prediction for GlimmerHMM_glimmerT_25612-T1
Valid prediction for snap_scaffold_10-snap.1678-T1
Valid prediction for GlimmerHMM_glimmerT_25607-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 23271, rend_intergenic: 19428  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58108, rend_intergenic: 45161  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77797, rend_intergenic: 75443  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80163, rend_intergenic: 78015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151628, rend_intergenic: 138449  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 156815
-exon list size: 315


building trellis

0.3    
0.6    
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1.3    
1.6    
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2.2    
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5.0    
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6.9    
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10.7    
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21.5    
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22.7    
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23.3    
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25.6    
25.9    
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27.1    
27.4    
27.8    
28.1    
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28.7    
29.0    
29.3    
29.7    
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30.3    
30.6    
30.9    
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31.5    
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33.1    
33.4    
33.8    
34.1    
34.4    
34.7    
35.0    
35.3    
35.6    
36.0    
36.3    
36.6    
36.9    
37.2    
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37.9    
38.2    
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38.8    
39.1    
39.4    
39.7    
40.1    
40.4    
40.7    
41.0    
41.3    
41.6    
42.0    
42.3    
42.6    
42.9    
43.2    
43.5    
43.8    
44.2    
44.5    
44.8    
45.1    
45.4    
45.7    
46.1    
46.4    
46.7    
47.0    
47.3    
47.6    
47.9    
48.3    
48.6    
48.9    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.1    
51.4    
51.7    
52.1    
52.4    
52.7    
53.0    
53.3    
53.6    
53.9    
54.3    
54.6    
54.9    
55.2    
55.5    
55.8    
56.2    
56.5    
56.8    
57.1    
57.4    
57.7    
58.0    
58.4    
58.7    
59.0    
59.3    
59.6    
59.9    
60.3    
60.6    
60.9    
61.2    
61.5    
61.8    
62.1    
62.5    
62.8    
63.1    
63.4    
63.7    
64.0    
64.4    
64.7    
65.0    
65.3    
65.6    
65.9    
66.2    
66.6    
66.9    
67.2    
67.5    
67.8    
68.1    
68.5    
68.8    
69.1    
69.4    
69.7    
70.0    
70.3    
70.7    
71.0    
71.3    
71.6    
71.9    
72.2    
72.6    
72.9    
73.2    
73.5    
73.8    
74.1    
74.4    
74.8    
75.1    
75.4    
75.7    
76.0    
76.3    
76.7    
77.0    
77.3    
77.6    
77.9    
78.2    
78.5    
78.9    
79.2    
79.5    
79.8    
80.1    
80.4    
80.8    
81.1    
81.4    
81.7    
82.0    
82.3    
82.6    
83.0    
83.3    
83.6    
83.9    
84.2    
84.5    
84.9    
85.2    
85.5    
85.8    
86.1    
86.4    
86.8    
87.1    
87.4    
87.7    
88.0    
88.3    
88.6    
89.0    
89.3    
89.6    
89.9    
90.2    
90.5    
90.9    
91.2    
91.5    
91.8    
92.1    
92.4    
92.7    
93.1    
93.4    
93.7    
94.0    
94.3    
94.6    
95.0    
95.3    
95.6    
95.9    
96.2    
96.5    
96.8    
97.2    
97.5    
97.8    
98.1    
98.4    
98.7    
99.1    
99.4    
99.7    
-found 11 predictions from path traversal
Error with prediction: snap lend_intergenic: 23271, rend_intergenic: 19428  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58108, rend_intergenic: 45161  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77797, rend_intergenic: 75443  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80163, rend_intergenic: 78015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151628, rend_intergenic: 138449  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 9 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 15402
-exon list size: 20


building trellis

4.5    
9.1    
13.6    
18.2    
22.7    
27.3    
31.8    
36.4    
40.9    
45.5    
50.0    
54.5    
59.1    
63.6    
68.2    
72.7    
77.3    
81.8    
86.4    
90.9    
95.5    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 10857
-exon list size: 14


building trellis

6.2    
12.5    
18.8    
25.0    
31.2    
37.5    
43.8    
50.0    
56.2    
62.5    
68.8    
75.0    
81.2    
87.5    
93.8    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support