-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_13/scaffold_13_8816508-9085923

-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_13-snap.1620-T1
Valid prediction for Augustus_model.g21991.t1
Valid prediction for GeneMark_model.55943_t
Valid prediction for GlimmerHMM_glimmerT_32793-T1
Valid prediction for GeneMark_model.55937_t
Couldn't classify 20254, 20510
Sorry, prediction pasa_asmbl_11134.p1 fails validation.
(ATG)	 TA	18657-18872	GT	AGG
(GAG)	 AG	18990-19085	GT	AGG
(GAC)	 AG	19193-19426	GT	AGG
(TTG)	 AG	19857-19876	GT	TGG
(GGC)	 AG	20010-20134	GT	AGG
(GAG)	 AG	20254-20510	AG	GCA
-recovered pasa_asmbl_11134.p1, initial, 18657, 18872
-recovered pasa_asmbl_11134.p1, internal, 18990, 19085
-recovered pasa_asmbl_11134.p1, internal, 19193, 19426
-recovered pasa_asmbl_11134.p1, internal, 19857, 19876
-recovered pasa_asmbl_11134.p1, internal, 20010, 20134
Valid prediction for GlimmerHMM_glimmerT_32775-T1
Valid prediction for GeneMark_model.55953_t
Valid prediction for GlimmerHMM_glimmerT_32776-T1
Valid prediction for snap_scaffold_13-snap.1616-T1
Valid prediction for GlimmerHMM_glimmerT_32783-T1
Valid prediction for GeneMark_model.55954_t
Valid prediction for snap_scaffold_13-snap.1631-T1
Valid prediction for GlimmerHMM_glimmerT_32788-T1
Valid prediction for GeneMark_model.55941_t
Valid prediction for GlimmerHMM_glimmerT_32778-T1
Valid prediction for pasa_asmbl_11152.p1
Valid prediction for Augustus_model.g21999.t1
Valid prediction for pasa_asmbl_11146.p1
Valid prediction for GlimmerHMM_glimmerT_32789-T1
Valid prediction for GeneMark_model.55927_t
Valid prediction for snap_scaffold_13-snap.1630-T1
Valid prediction for GeneMark_model.55934_t
Valid prediction for Augustus_model.g21994.t1
Valid prediction for snap_scaffold_13-snap.1606-T1
Valid prediction for GlimmerHMM_glimmerT_32781-T1
Valid prediction for snap_scaffold_13-snap.1615-T1
Couldn't classify 92605, 92760
Sorry, prediction pasa_asmbl_11141.p1 fails validation.
(GTG)	 CA	92605-92760	GT	CCG
(ATT)	 AG	95561-95841	GT	AGG
(GAA)	 AG	95926-95983	GT	TGG
(TTC)	 AG	96073-96249	GT	TTG
(GTG)	 AG	96489-96617	TG	AGT
-recovered pasa_asmbl_11141.p1, terminal, 96489, 96617
-recovered pasa_asmbl_11141.p1, internal, 95561, 95841
-recovered pasa_asmbl_11141.p1, internal, 95926, 95983
-recovered pasa_asmbl_11141.p1, internal, 96073, 96249
Valid prediction for Augustus_model.g21995.t1
Valid prediction for snap_scaffold_13-snap.1628-T1
Valid prediction for CodingQuarry_transcript_13149-T1
Valid prediction for GeneMark_model.55933_t
Valid prediction for GeneMark_model.55951_t
Valid prediction for snap_scaffold_13-snap.1619-T1
Valid prediction for snap_scaffold_13-snap.1613-T1
Valid prediction for GeneMark_model.55947_t
Valid prediction for snap_scaffold_13-snap.1607-T1
Valid prediction for Augustus_model.g22000.t1
Valid prediction for GeneMark_model.55956_t
Couldn't classify 74348, 74399
Sorry, prediction pasa_asmbl_11137.p1 fails validation.
(CGC)	 CA	74348-74399	GT	AGG
(GCC)	 AG	74672-74813	GT	GGG
(AAT)	 AG	75030-75162	GT	AGG
(ACT)	 AG	75404-75601	GT	AGG
(AAA)	 AG	75759-75999	GT	AGG
(ATT)	 AG	76315-76443	GT	AAG
(GCG)	 AG	76556-76719	GT	CTG
(ATG)	 AG	76911-77064	GT	AGG
(GTA)	 AG	77174-77245	GT	AGG
(AAA)	 AG	77342-77493	TG	GAT
-recovered pasa_asmbl_11137.p1, initial, 76911, 77064
-recovered pasa_asmbl_11137.p1, terminal, 77342, 77493
-recovered pasa_asmbl_11137.p1, internal, 74672, 74813
-recovered pasa_asmbl_11137.p1, internal, 75030, 75162
-recovered pasa_asmbl_11137.p1, internal, 75404, 75601
-recovered pasa_asmbl_11137.p1, internal, 75759, 75999
-recovered pasa_asmbl_11137.p1, internal, 76315, 76443
-recovered pasa_asmbl_11137.p1, internal, 76556, 76719
-recovered pasa_asmbl_11137.p1, internal, 76911, 77064
-recovered pasa_asmbl_11137.p1, internal, 77174, 77245
Valid prediction for Augustus_model.g21997.t1
Valid prediction for GlimmerHMM_glimmerT_32791-T1
Valid prediction for GlimmerHMM_glimmerT_32785-T1
Valid prediction for HiQ_model.g22006.t1
Valid prediction for snap_scaffold_13-snap.1621-T1
Valid prediction for GeneMark_model.55945_t
Valid prediction for GlimmerHMM_glimmerT_32779-T1
Valid prediction for snap_scaffold_13-snap.1604-T1
Valid prediction for snap_scaffold_13-snap.1632-T1
Valid prediction for GeneMark_model.55939_t
Valid prediction for Augustus_model.g22002.t1
Valid prediction for GlimmerHMM_glimmerT_32768-T1
Valid prediction for GeneMark_model.55931_t
Valid prediction for snap_scaffold_13-snap.1626-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_32772-T1
Valid prediction for Augustus_model.g21996.t1
Valid prediction for CodingQuarry_transcript_13151-T1
Valid prediction for HiQ_model.g22009.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.55936_t
Valid prediction for GlimmerHMM_glimmerT_32774-T1
Valid prediction for pasa_asmbl_9950.p1
Valid prediction for GeneMark_model.55930_t
Valid prediction for GeneMark_model.55949_t
Valid prediction for GeneMark_model.55955_t
Valid prediction for CodingQuarry_transcript_13147-T1
Valid prediction for GeneMark_model.55925_t
Valid prediction for GeneMark_model.55928_t
Valid prediction for Augustus_model.g22007.t1
Valid prediction for Augustus_model.g21993.t1
Valid prediction for snap_scaffold_13-snap.1622-T1
Valid prediction for snap_scaffold_13-snap.1608-T1
Valid prediction for snap_scaffold_13-snap.1617-T1
Valid prediction for CodingQuarry_transcript_13150-T1
Valid prediction for GlimmerHMM_glimmerT_32773-T1
Valid prediction for GlimmerHMM_glimmerT_32787-T1
Valid prediction for HiQ_model.g22008.t1
Valid prediction for GeneMark_model.55938_t
Valid prediction for Augustus_model.g21992.t1
Valid prediction for GeneMark_model.55958_t
Valid prediction for GeneMark_model.55948_t
Valid prediction for Augustus_model.g22005.t1
Valid prediction for snap_scaffold_13-snap.1623-T1
Valid prediction for GlimmerHMM_glimmerT_32790-T1
Valid prediction for GeneMark_model.55950_t
Valid prediction for snap_scaffold_13-snap.1625-T1
Valid prediction for snap_scaffold_13-snap.1618-T1
Valid prediction for snap_scaffold_13-snap.1610-T1
Valid prediction for snap_scaffold_13-snap.1629-T1
Valid prediction for pasa_asmbl_9952.p1
Valid prediction for GlimmerHMM_glimmerT_32769-T1
Valid prediction for GlimmerHMM_glimmerT_32792-T1
Valid prediction for GeneMark_model.55932_t
Valid prediction for GeneMark_model.55944_t
Valid prediction for GeneMark_model.55935_t
Valid prediction for GeneMark_model.55952_t
Valid prediction for GeneMark_model.55940_t
Valid prediction for HiQ_model.g21989.t1
Valid prediction for GlimmerHMM_glimmerT_32786-T1
Valid prediction for GlimmerHMM_glimmerT_32782-T1
Valid prediction for GeneMark_model.55929_t
Valid prediction for snap_scaffold_13-snap.1614-T1
Valid prediction for CodingQuarry_transcript_13146-T1
Valid prediction for snap_scaffold_13-snap.1605-T1
Couldn't classify 189257, 189424
Couldn't classify 189855, 189881
Sorry, prediction pasa_asmbl_9953.p1 fails validation.
(TTT)	 AT	189257-189424	GT	TGG
(GCT)	 AG	189519-189701	GT	AGG
(GAT)	 AG	189855-189881	AG	CCA
-recovered pasa_asmbl_9953.p1, internal, 189519, 189701
Valid prediction for snap_scaffold_13-snap.1627-T1
Valid prediction for Augustus_model.g22003.t1
Valid prediction for Augustus_model.g22001.t1
Valid prediction for snap_scaffold_13-snap.1603-T1
Valid prediction for GeneMark_model.55957_t
Valid prediction for pasa_asmbl_9954.p1
Valid prediction for GeneMark_model.55926_t
Valid prediction for snap_scaffold_13-snap.1611-T1
Valid prediction for GlimmerHMM_glimmerT_32777-T1
Valid prediction for CodingQuarry_transcript_13148-T1
Valid prediction for GlimmerHMM_glimmerT_32771-T1
Valid prediction for snap_scaffold_13-snap.1609-T1
Valid prediction for pasa_asmbl_9963.p1
Valid prediction for Augustus_model.g22010.t1
Valid prediction for GlimmerHMM_glimmerT_32784-T1
Valid prediction for Augustus_model.g21990.t1
Valid prediction for Augustus_model.g21998.t1
Valid prediction for snap_scaffold_13-snap.1612-T1
Valid prediction for GeneMark_model.55942_t
Valid prediction for GeneMark_model.55946_t
Valid prediction for pasa_asmbl_9960.p1
Valid prediction for snap_scaffold_13-snap.1624-T1
Valid prediction for Augustus_model.g22004.t1
Valid prediction for pasa_asmbl_9959.p1
Valid prediction for GlimmerHMM_glimmerT_32780-T1
Valid prediction for GlimmerHMM_glimmerT_32770-T1
Valid prediction for snap_scaffold_13-snap.1602-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 39904, rend_intergenic: 33026  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66619, rend_intergenic: 59160  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 269416
-exon list size: 478


building trellis

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9.0    
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22.9    
23.1    
23.3    
23.5    
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25.8    
26.0    
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26.9    
27.1    
27.3    
27.5    
27.7    
27.9    
28.1    
28.3    
28.5    
28.7    
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29.2    
29.4    
29.6    
29.8    
30.0    
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30.4    
30.6    
30.8    
31.0    
31.2    
31.5    
31.7    
31.9    
32.1    
32.3    
32.5    
32.7    
32.9    
33.1    
33.3    
33.5    
33.8    
34.0    
34.2    
34.4    
34.6    
34.8    
35.0    
35.2    
35.4    
35.6    
35.8    
36.0    
36.2    
36.5    
36.7    
36.9    
37.1    
37.3    
37.5    
37.7    
37.9    
38.1    
38.3    
38.5    
38.8    
39.0    
39.2    
39.4    
39.6    
39.8    
40.0    
40.2    
40.4    
40.6    
40.8    
41.0    
41.2    
41.5    
41.7    
41.9    
42.1    
42.3    
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42.7    
42.9    
43.1    
43.3    
43.5    
43.8    
44.0    
44.2    
44.4    
44.6    
44.8    
45.0    
45.2    
45.4    
45.6    
45.8    
46.0    
46.2    
46.5    
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47.1    
47.3    
47.5    
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48.1    
48.3    
48.5    
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49.2    
49.4    
49.6    
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50.0    
50.2    
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50.8    
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51.2    
51.5    
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52.3    
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53.3    
53.5    
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54.0    
54.2    
54.4    
54.6    
54.8    
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55.6    
55.8    
56.0    
56.2    
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57.1    
57.3    
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57.9    
58.1    
58.3    
58.5    
58.8    
59.0    
59.2    
59.4    
59.6    
59.8    
60.0    
60.2    
60.4    
60.6    
60.8    
61.0    
61.3    
61.5    
61.7    
61.9    
62.1    
62.3    
62.5    
62.7    
62.9    
63.1    
63.3    
63.5    
63.7    
64.0    
64.2    
64.4    
64.6    
64.8    
65.0    
65.2    
65.4    
65.6    
65.8    
66.0    
66.2    
66.5    
66.7    
66.9    
67.1    
67.3    
67.5    
67.7    
67.9    
68.1    
68.3    
68.5    
68.8    
69.0    
69.2    
69.4    
69.6    
69.8    
70.0    
70.2    
70.4    
70.6    
70.8    
71.0    
71.2    
71.5    
71.7    
71.9    
72.1    
72.3    
72.5    
72.7    
72.9    
73.1    
73.3    
73.5    
73.8    
74.0    
74.2    
74.4    
74.6    
74.8    
75.0    
75.2    
75.4    
75.6    
75.8    
76.0    
76.2    
76.5    
76.7    
76.9    
77.1    
77.3    
77.5    
77.7    
77.9    
78.1    
78.3    
78.5    
78.8    
79.0    
79.2    
79.4    
79.6    
79.8    
80.0    
80.2    
80.4    
80.6    
80.8    
81.0    
81.2    
81.5    
81.7    
81.9    
82.1    
82.3    
82.5    
82.7    
82.9    
83.1    
83.3    
83.5    
83.8    
84.0    
84.2    
84.4    
84.6    
84.8    
85.0    
85.2    
85.4    
85.6    
85.8    
86.0    
86.2    
86.5    
86.7    
86.9    
87.1    
87.3    
87.5    
87.7    
87.9    
88.1    
88.3    
88.5    
88.8    
89.0    
89.2    
89.4    
89.6    
89.8    
90.0    
90.2    
90.4    
90.6    
90.8    
91.0    
91.2    
91.5    
91.7    
91.9    
92.1    
92.3    
92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.8    
94.0    
94.2    
94.4    
94.6    
94.8    
95.0    
95.2    
95.4    
95.6    
95.8    
96.0    
96.2    
96.5    
96.7    
96.9    
97.1    
97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 39904, rend_intergenic: 33026  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66619, rend_intergenic: 59160  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support