-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_9/scaffold_9_7772685-8060761

-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.g14968.t1
Valid prediction for Augustus_model.g14977.t1
Valid prediction for CodingQuarry_transcript_62231-T1
Valid prediction for GlimmerHMM_glimmerT_22527-T1
Valid prediction for Augustus_model.g14974.t1
Valid prediction for snap_scaffold_9-snap.1634-T1
Valid prediction for GlimmerHMM_glimmerT_22540-T1
Valid prediction for GlimmerHMM_glimmerT_22528-T1
Valid prediction for snap_scaffold_9-snap.1657-T1
Valid prediction for GlimmerHMM_glimmerT_22525-T1
Valid prediction for snap_scaffold_9-snap.1670-T1
Valid prediction for snap_scaffold_9-snap.1668-T1
Valid prediction for snap_scaffold_9-snap.1660-T1
Valid prediction for snap_scaffold_9-snap.1644-T1
Valid prediction for GlimmerHMM_glimmerT_22535-T1
Valid prediction for Augustus_model.g14980.t1
Valid prediction for snap_scaffold_9-snap.1632-T1
Valid prediction for GlimmerHMM_glimmerT_22538-T1
Valid prediction for GlimmerHMM_glimmerT_22544-T1
Valid prediction for GlimmerHMM_glimmerT_22522-T1
Valid prediction for snap_scaffold_9-snap.1636-T1
Valid prediction for snap_scaffold_9-snap.1665-T1
Valid prediction for GlimmerHMM_glimmerT_22519-T1
Valid prediction for GlimmerHMM_glimmerT_22542-T1
Valid prediction for GlimmerHMM_glimmerT_22537-T1
Valid prediction for GlimmerHMM_glimmerT_22526-T1
Valid prediction for GlimmerHMM_glimmerT_22523-T1
Valid prediction for snap_scaffold_9-snap.1658-T1
Valid prediction for pasa_asmbl_54142.p1
Valid prediction for GlimmerHMM_glimmerT_22532-T1
Valid prediction for snap_scaffold_9-snap.1643-T1
Valid prediction for snap_scaffold_9-snap.1659-T1
Valid prediction for Augustus_model.g14982.t1
Valid prediction for snap_scaffold_9-snap.1649-T1
Valid prediction for pasa_asmbl_54140.p1
Valid prediction for Augustus_model.g14983.t1
Valid prediction for snap_scaffold_9-snap.1647-T1
Valid prediction for snap_scaffold_9-snap.1672-T1
Valid prediction for snap_scaffold_9-snap.1635-T1
Valid prediction for GlimmerHMM_glimmerT_22517-T1
Valid prediction for Augustus_model.g14973.t1
Valid prediction for snap_scaffold_9-snap.1631-T1
Valid prediction for Augustus_model.g14972.t1
Couldn't classify 22575, 22865
Sorry, prediction pasa_asmbl_54141.p1 fails validation.
(GTC)	 CT	22575-22865	GT	TTG
(ATT)	 AG	23834-23971	GT	GGG
(CTG)	 AG	24761-24921	GT	AGG
(TCT)	 AG	25134-25341	GT	AGG
(AAT)	 AG	25668-25817	GT	CAG
(ATC)	 AG	25908-26006	GT	CTG
(TGG)	 AG	26089-26172	GT	AGG
(CAA)	 AG	27313-27423	GT	AGG
(CTA)	 AG	27618-27904	GT	AGG
(GAG)	 AG	28011-28272	CA	GAC
-recovered pasa_asmbl_54141.p1, terminal, 28011, 28272
-recovered pasa_asmbl_54141.p1, internal, 23834, 23971
-recovered pasa_asmbl_54141.p1, internal, 24761, 24921
-recovered pasa_asmbl_54141.p1, internal, 25134, 25341
-recovered pasa_asmbl_54141.p1, internal, 25668, 25817
-recovered pasa_asmbl_54141.p1, internal, 25908, 26006
-recovered pasa_asmbl_54141.p1, internal, 26089, 26172
-recovered pasa_asmbl_54141.p1, internal, 27313, 27423
-recovered pasa_asmbl_54141.p1, internal, 27618, 27904
Valid prediction for snap_scaffold_9-snap.1652-T1
Valid prediction for GlimmerHMM_glimmerT_22536-T1
Valid prediction for snap_scaffold_9-snap.1646-T1
Valid prediction for Augustus_model.g14971.t1
Couldn't classify 98233, 98468
Couldn't classify 99117, 99140
Sorry, prediction pasa_asmbl_54144.p1 fails validation.
(AAT)	 AG	98233-98468	GT	CGG
(CTT)	 AG	98592-98762	GT	TGG
(GTC)	 AG	98847-99006	GT	AGG
(GTG)	 AG	99117-99140	GT	GAG
-recovered pasa_asmbl_54144.p1, internal, 98233, 98468
-recovered pasa_asmbl_54144.p1, internal, 98592, 98762
-recovered pasa_asmbl_54144.p1, internal, 98847, 99006
-recovered pasa_asmbl_54144.p1, internal, 99117, 99140
Couldn't classify 22656, 22865
Sorry, prediction CodingQuarry_transcript_62229-T1 fails validation.
(ATG)	 GG	9615-9714	GT	AGG
(TGC)	 AG	9842-10002	GT	AGG
(GCT)	 AG	10781-10891	GT	GGG
(GTG)	 AG	11467-11621	GT	AGG
(AAA)	 AG	12021-12120	GT	AGG
(ATC)	 AG	12213-12384	GT	AGG
(AGG)	 AG	12708-12961	GT	AGG
(TAT)	 AG	13047-13190	GT	ACG
(ATT)	 AG	13289-13457	GT	AGG
(GCA)	 AG	13550-13640	GT	AGG
(ACG)	 AG	13734-13816	GT	GAG
(GTG)	 AG	14102-14252	GT	AGG
(GTG)	 AG	14706-14809	GT	GGG
(GTA)	 AG	14900-15085	GT	AGG
(GAG)	 AG	15821-16022	GT	AGG
(GGG)	 AG	16323-16444	GT	AGG
(ACT)	 AG	16530-16717	GT	AGG
(GGT)	 AG	16814-16908	GT	AGG
(GGC)	 AG	17018-17610	GT	AGG
(GGT)	 AG	17819-17916	GT	AGG
(GTT)	 AG	18042-18212	GT	AGG
(CTG)	 AG	18349-18489	GT	AGG
(ACG)	 AG	19248-19427	GT	AGG
(ACC)	 AG	20361-20525	GT	AGG
(AAG)	 AG	20855-20929	GT	CGG
(GTG)	 AG	21032-21202	GT	AGG
(GTG)	 CT	22656-22865	GT	TTG
(ATT)	 AG	23834-23971	GT	GGG
(CTG)	 AG	24761-24921	GT	AGG
(TCT)	 AG	25134-25341	GT	AGG
(AAT)	 AG	25668-25817	GT	CAG
(ATC)	 AG	25908-26006	GT	CTG
(TGG)	 AG	26089-26172	GT	AGG
(CAA)	 AG	27313-27423	GT	AGG
(CTA)	 AG	27618-27904	GT	AGG
(GAG)	 AG	28011-28272	CA	GAC
-recovered CodingQuarry_transcript_62229-T1, initial, 9615, 9714
add_exon() Sorry, CodingQuarry_transcript_62229-T1 14102-14252-terminal-3 is invalid.
-recovered CodingQuarry_transcript_62229-T1, terminal, 14102, 14252
add_exon() Sorry, CodingQuarry_transcript_62229-T1 17018-17610-terminal-2 is invalid.
-recovered CodingQuarry_transcript_62229-T1, terminal, 17018, 17610
-recovered CodingQuarry_transcript_62229-T1, terminal, 28011, 28272
-recovered CodingQuarry_transcript_62229-T1, internal, 9842, 10002
-recovered CodingQuarry_transcript_62229-T1, internal, 10781, 10891
-recovered CodingQuarry_transcript_62229-T1, internal, 11467, 11621
-recovered CodingQuarry_transcript_62229-T1, internal, 12021, 12120
-recovered CodingQuarry_transcript_62229-T1, internal, 12213, 12384
-recovered CodingQuarry_transcript_62229-T1, internal, 12708, 12961
-recovered CodingQuarry_transcript_62229-T1, internal, 13047, 13190
-recovered CodingQuarry_transcript_62229-T1, internal, 13289, 13457
-recovered CodingQuarry_transcript_62229-T1, internal, 13550, 13640
-recovered CodingQuarry_transcript_62229-T1, internal, 13734, 13816
-recovered CodingQuarry_transcript_62229-T1, internal, 14102, 14252
-recovered CodingQuarry_transcript_62229-T1, internal, 14706, 14809
-recovered CodingQuarry_transcript_62229-T1, internal, 14900, 15085
-recovered CodingQuarry_transcript_62229-T1, internal, 15821, 16022
-recovered CodingQuarry_transcript_62229-T1, internal, 16323, 16444
-recovered CodingQuarry_transcript_62229-T1, internal, 16530, 16717
-recovered CodingQuarry_transcript_62229-T1, internal, 16814, 16908
-recovered CodingQuarry_transcript_62229-T1, internal, 17018, 17610
-recovered CodingQuarry_transcript_62229-T1, internal, 17819, 17916
-recovered CodingQuarry_transcript_62229-T1, internal, 18042, 18212
-recovered CodingQuarry_transcript_62229-T1, internal, 18349, 18489
-recovered CodingQuarry_transcript_62229-T1, internal, 19248, 19427
-recovered CodingQuarry_transcript_62229-T1, internal, 20361, 20525
-recovered CodingQuarry_transcript_62229-T1, internal, 20855, 20929
-recovered CodingQuarry_transcript_62229-T1, internal, 21032, 21202
-recovered CodingQuarry_transcript_62229-T1, internal, 23834, 23971
-recovered CodingQuarry_transcript_62229-T1, internal, 24761, 24921
-recovered CodingQuarry_transcript_62229-T1, internal, 25134, 25341
-recovered CodingQuarry_transcript_62229-T1, internal, 25668, 25817
-recovered CodingQuarry_transcript_62229-T1, internal, 25908, 26006
-recovered CodingQuarry_transcript_62229-T1, internal, 26089, 26172
-recovered CodingQuarry_transcript_62229-T1, internal, 27313, 27423
-recovered CodingQuarry_transcript_62229-T1, internal, 27618, 27904
Valid prediction for snap_scaffold_9-snap.1656-T1
Valid prediction for GlimmerHMM_glimmerT_22518-T1
Valid prediction for snap_scaffold_9-snap.1661-T1
Valid prediction for GlimmerHMM_glimmerT_22533-T1
Valid prediction for GlimmerHMM_glimmerT_22529-T1
Valid prediction for Augustus_model.g14975.t1
Valid prediction for Augustus_model.g14966.t1
Valid prediction for snap_scaffold_9-snap.1637-T1
Valid prediction for GlimmerHMM_glimmerT_22521-T1
Valid prediction for snap_scaffold_9-snap.1639-T1
Valid prediction for snap_scaffold_9-snap.1666-T1
Valid prediction for Augustus_model.g14978.t1
Valid prediction for Augustus_model.g14967.t1
Valid prediction for snap_scaffold_9-snap.1641-T1
Valid prediction for snap_scaffold_9-snap.1633-T1
Valid prediction for Augustus_model.g14981.t1
Valid prediction for snap_scaffold_9-snap.1650-T1
Valid prediction for Augustus_model.g14976.t1
Valid prediction for snap_scaffold_9-snap.1630-T1
Valid prediction for snap_scaffold_9-snap.1640-T1
Valid prediction for snap_scaffold_9-snap.1667-T1
Valid prediction for snap_scaffold_9-snap.1645-T1
Valid prediction for GlimmerHMM_glimmerT_22534-T1
Valid prediction for CodingQuarry_transcript_62230-T1
Valid prediction for GlimmerHMM_glimmerT_22520-T1
Couldn't classify 99449, 99636
Sorry, prediction pasa_asmbl_54145.p1 fails validation.
(GCC)	 AG	99449-99636	GT	AGG
(GGC)	 AG	100060-100174	GT	AGG
(ATC)	 AG	100284-100505	GT	AGG
(GTA)	 AG	100672-100889	GT	AGG
(GAC)	 AG	101012-101188	GT	AAG
(AGG)	 AG	101342-101459	CA	GAC
-recovered pasa_asmbl_54145.p1, terminal, 101342, 101459
-recovered pasa_asmbl_54145.p1, internal, 99449, 99636
-recovered pasa_asmbl_54145.p1, internal, 100060, 100174
-recovered pasa_asmbl_54145.p1, internal, 100284, 100505
-recovered pasa_asmbl_54145.p1, internal, 100672, 100889
-recovered pasa_asmbl_54145.p1, internal, 101012, 101188
Valid prediction for snap_scaffold_9-snap.1662-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 9059, 9201
Sorry, prediction pasa_asmbl_55118.p1 fails validation.
(TTA)	 TG	9059-9201	GT	GGG
(ACC)	 AG	9589-9687	GT	GCG
(GAC)	 AG	11397-11461	GT	AGG
(TGG)	 AG	11669-11826	GT	AGG
(ACA)	 AG	11902-12066	GC	GGG
(GTG)	 AG	12160-12306	GT	GTG
(GCT)	 AG	12421-12562	GT	AGG
(CAC)	 AG	13491-13703	GT	TGG
(CCA)	 AG	13824-13958	GT	TGG
(ATG)	 AG	14127-14275	GT	CTG
(GCT)	 AG	14725-14861	GT	AAG
(GAT)	 AG	14948-15078	GT	GGG
(GAG)	 AG	15213-15343	GT	CTG
(GCA)	 AG	15477-15579	GT	AGG
(ACC)	 AG	15748-15815	GT	AGG
(TAT)	 AG	16531-16576	GT	GAG
(GGA)	 AG	16688-16714	GT	AGG
(GGC)	 AG	17013-17360	GT	AGG
(GAA)	 AG	17505-17591	GT	AGG
(AGG)	 AG	17905-17943	GT	AGG
(CTG)	 AG	18060-18103	TC	GAT
add_exon() Sorry, pasa_asmbl_55118.p1 14127-14275-initial-1 is invalid.
-recovered pasa_asmbl_55118.p1, initial, 14127, 14275
add_exon() Sorry, pasa_asmbl_55118.p1 16531-16576-terminal-3 is invalid.
-recovered pasa_asmbl_55118.p1, terminal, 16531, 16576
-recovered pasa_asmbl_55118.p1, terminal, 18060, 18103
-recovered pasa_asmbl_55118.p1, internal, 9589, 9687
-recovered pasa_asmbl_55118.p1, internal, 11397, 11461
-recovered pasa_asmbl_55118.p1, internal, 11669, 11826
-recovered pasa_asmbl_55118.p1, internal, 11902, 12066
-recovered pasa_asmbl_55118.p1, internal, 12160, 12306
-recovered pasa_asmbl_55118.p1, internal, 12421, 12562
-recovered pasa_asmbl_55118.p1, internal, 13491, 13703
-recovered pasa_asmbl_55118.p1, internal, 13824, 13958
-recovered pasa_asmbl_55118.p1, internal, 14127, 14275
-recovered pasa_asmbl_55118.p1, internal, 14725, 14861
-recovered pasa_asmbl_55118.p1, internal, 14948, 15078
-recovered pasa_asmbl_55118.p1, internal, 15213, 15343
-recovered pasa_asmbl_55118.p1, internal, 15477, 15579
-recovered pasa_asmbl_55118.p1, internal, 15748, 15815
-recovered pasa_asmbl_55118.p1, internal, 16531, 16576
-recovered pasa_asmbl_55118.p1, internal, 16688, 16714
-recovered pasa_asmbl_55118.p1, internal, 17013, 17360
-recovered pasa_asmbl_55118.p1, internal, 17505, 17591
-recovered pasa_asmbl_55118.p1, internal, 17905, 17943
Valid prediction for GlimmerHMM_glimmerT_22541-T1
Valid prediction for snap_scaffold_9-snap.1673-T1
Valid prediction for CodingQuarry_transcript_62233-T1
Valid prediction for GlimmerHMM_glimmerT_22547-T1
Valid prediction for GlimmerHMM_glimmerT_22524-T1
Valid prediction for snap_scaffold_9-snap.1680-T1
Valid prediction for GlimmerHMM_glimmerT_22543-T1
Valid prediction for snap_scaffold_9-snap.1642-T1
Valid prediction for Augustus_model.g14986.t1
Valid prediction for GlimmerHMM_glimmerT_22531-T1
Valid prediction for snap_scaffold_9-snap.1675-T1
Valid prediction for pasa_asmbl_55111.p2
Valid prediction for snap_scaffold_9-snap.1654-T1
Valid prediction for GlimmerHMM_glimmerT_22545-T1
Valid prediction for snap_scaffold_9-snap.1648-T1
Valid prediction for Augustus_model.g14969.t1
Valid prediction for snap_scaffold_9-snap.1681-T1
Valid prediction for HiQ_model.g14985.t1
Valid prediction for GlimmerHMM_glimmerT_22539-T1
Valid prediction for Augustus_model.g14979.t1
Valid prediction for GlimmerHMM_glimmerT_22530-T1
Valid prediction for HiQ_model.g14970.t1
Valid prediction for GlimmerHMM_glimmerT_22548-T1
Valid prediction for snap_scaffold_9-snap.1669-T1
Valid prediction for Augustus_model.g14984.t1
Valid prediction for snap_scaffold_9-snap.1653-T1
Valid prediction for snap_scaffold_9-snap.1677-T1
Valid prediction for GlimmerHMM_glimmerT_22546-T1
Valid prediction for snap_scaffold_9-snap.1674-T1
Valid prediction for snap_scaffold_9-snap.1676-T1
Valid prediction for snap_scaffold_9-snap.1664-T1
Valid prediction for snap_scaffold_9-snap.1638-T1
Valid prediction for snap_scaffold_9-snap.1679-T1
Valid prediction for snap_scaffold_9-snap.1655-T1
Valid prediction for CodingQuarry_transcript_62232-T1
Valid prediction for snap_scaffold_9-snap.1651-T1
Valid prediction for snap_scaffold_9-snap.1671-T1
Valid prediction for pasa_asmbl_55115.p1
Valid prediction for GlimmerHMM_glimmerT_22549-T1
Valid prediction for CodingQuarry_transcript_62234-T1
Valid prediction for snap_scaffold_9-snap.1678-T1
Valid prediction for snap_scaffold_9-snap.1663-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 121198, rend_intergenic: 119078  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152778, rend_intergenic: 135069  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187003, rend_intergenic: 182560  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 225463, rend_intergenic: 222468  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 231296, rend_intergenic: 229376  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 235134, rend_intergenic: 232157  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 288077
-exon list size: 527


building trellis

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54.1    
54.3    
54.4    
54.6    
54.8    
55.0    
55.2    
55.4    
55.6    
55.8    
56.0    
56.1    
56.3    
56.5    
56.7    
56.9    
57.1    
57.3    
57.5    
57.7    
57.8    
58.0    
58.2    
58.4    
58.6    
58.8    
59.0    
59.2    
59.4    
59.5    
59.7    
59.9    
60.1    
60.3    
60.5    
60.7    
60.9    
61.1    
61.2    
61.4    
61.6    
61.8    
62.0    
62.2    
62.4    
62.6    
62.8    
62.9    
63.1    
63.3    
63.5    
63.7    
63.9    
64.1    
64.3    
64.5    
64.7    
64.8    
65.0    
65.2    
65.4    
65.6    
65.8    
66.0    
66.2    
66.4    
66.5    
66.7    
66.9    
67.1    
67.3    
67.5    
67.7    
67.9    
68.1    
68.2    
68.4    
68.6    
68.8    
69.0    
69.2    
69.4    
69.6    
69.8    
69.9    
70.1    
70.3    
70.5    
70.7    
70.9    
71.1    
71.3    
71.5    
71.6    
71.8    
72.0    
72.2    
72.4    
72.6    
72.8    
73.0    
73.2    
73.3    
73.5    
73.7    
73.9    
74.1    
74.3    
74.5    
74.7    
74.9    
75.0    
75.2    
75.4    
75.6    
75.8    
76.0    
76.2    
76.4    
76.6    
76.7    
76.9    
77.1    
77.3    
77.5    
77.7    
77.9    
78.1    
78.3    
78.4    
78.6    
78.8    
79.0    
79.2    
79.4    
79.6    
79.8    
80.0    
80.2    
80.3    
80.5    
80.7    
80.9    
81.1    
81.3    
81.5    
81.7    
81.9    
82.0    
82.2    
82.4    
82.6    
82.8    
83.0    
83.2    
83.4    
83.6    
83.7    
83.9    
84.1    
84.3    
84.5    
84.7    
84.9    
85.1    
85.3    
85.4    
85.6    
85.8    
86.0    
86.2    
86.4    
86.6    
86.8    
87.0    
87.1    
87.3    
87.5    
87.7    
87.9    
88.1    
88.3    
88.5    
88.7    
88.8    
89.0    
89.2    
89.4    
89.6    
89.8    
90.0    
90.2    
90.4    
90.5    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
91.9    
92.1    
92.2    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
94.0    
94.1    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.2    
99.4    
99.6    
99.8    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 121198, rend_intergenic: 119078  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152778, rend_intergenic: 135069  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187003, rend_intergenic: 182560  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 225463, rend_intergenic: 222468  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 231296, rend_intergenic: 229376  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 235134, rend_intergenic: 232157  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 29 predictions persist after filtering for low support