-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_19/scaffold_19_8367095-8624663

-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 GlimmerHMM_glimmerT_45521-T1
Valid prediction for snap_scaffold_19-snap.1664-T1
Valid prediction for snap_scaffold_19-snap.1641-T1
Valid prediction for snap_scaffold_19-snap.1651-T1
Valid prediction for GeneMark_model.79483_t
Valid prediction for GlimmerHMM_glimmerT_45522-T1
Valid prediction for GeneMark_model.79496_t
Valid prediction for snap_scaffold_19-snap.1661-T1
Valid prediction for GeneMark_model.79478_t
Valid prediction for snap_scaffold_19-snap.1643-T1
Valid prediction for pasa_asmbl_22330.p1
Valid prediction for GeneMark_model.79499_t
Valid prediction for GeneMark_model.79493_t
Valid prediction for GlimmerHMM_glimmerT_45524-T1
Couldn't classify 95189, 95197
Couldn't classify 96257, 96439
Sorry, prediction pasa_asmbl_22333.p1 fails validation.
(GAC)	 CA	95189-95197	GT	ATG
(CAA)	 AG	95315-95481	GT	AGG
(CGG)	 AG	95601-95669	GT	AGG
(GAA)	 AG	95978-96047	GT	AGG
(AGT)	 AG	96257-96439	CA	AGC
-recovered pasa_asmbl_22333.p1, internal, 95315, 95481
-recovered pasa_asmbl_22333.p1, internal, 95601, 95669
-recovered pasa_asmbl_22333.p1, internal, 95978, 96047
Valid prediction for snap_scaffold_19-snap.1663-T1
Valid prediction for GeneMark_model.79475_t
Couldn't classify 104744, 104873
Sorry, prediction pasa_asmbl_22717.p1 fails validation.
(AAG)	 AG	104744-104873	GT	AGG
(CTG)	 AG	105012-105142	GT	GGG
(GAG)	 AG	105285-105353	GT	TGG
(TTC)	 AG	105820-105909	GT	CGG
(ATC)	 AG	106000-106082	GT	AGG
(CTC)	 AG	106473-106585	GT	CAG
(AAT)	 AG	107360-107523	GT	AGG
(AAC)	 AG	108551-108658	GT	AGG
(GAT)	 AG	108782-108933	GT	AGG
(ATG)	 AG	109038-109113	TG	AGT
-recovered pasa_asmbl_22717.p1, terminal, 109038, 109113
-recovered pasa_asmbl_22717.p1, internal, 104744, 104873
-recovered pasa_asmbl_22717.p1, internal, 105012, 105142
-recovered pasa_asmbl_22717.p1, internal, 105285, 105353
-recovered pasa_asmbl_22717.p1, internal, 105820, 105909
-recovered pasa_asmbl_22717.p1, internal, 106000, 106082
-recovered pasa_asmbl_22717.p1, internal, 106473, 106585
-recovered pasa_asmbl_22717.p1, internal, 107360, 107523
-recovered pasa_asmbl_22717.p1, internal, 108551, 108658
-recovered pasa_asmbl_22717.p1, internal, 108782, 108933
Couldn't classify 92615, 92714
Couldn't classify 95102, 95164
Sorry, prediction pasa_asmbl_22332.p1 fails validation.
(AGG)	 CC	92615-92714	GT	GTG
(CTG)	 AG	93317-93431	GT	GTG
(GGG)	 AG	94389-94536	GT	AGG
(GGC)	 AG	95102-95164	AG	AGA
-recovered pasa_asmbl_22332.p1, internal, 93317, 93431
-recovered pasa_asmbl_22332.p1, internal, 94389, 94536
Couldn't classify 28409, 28438
Sorry, prediction pasa_asmbl_22327.p2 fails validation.
(ATG)	 GA	22634-22750	GT	GGG
(GTG)	 AG	24801-24917	GT	AGG
(ATC)	 AG	27352-27441	GT	AGG
(TGT)	 AG	28409-28438	GT	ATG
-recovered pasa_asmbl_22327.p2, initial, 22634, 22750
-recovered pasa_asmbl_22327.p2, internal, 24801, 24917
-recovered pasa_asmbl_22327.p2, internal, 27352, 27441
-recovered pasa_asmbl_22327.p2, internal, 28409, 28438
Valid prediction for snap_scaffold_19-snap.1659-T1
Valid prediction for snap_scaffold_19-snap.1648-T1
Valid prediction for GlimmerHMM_glimmerT_45527-T1
Valid prediction for GlimmerHMM_glimmerT_45523-T1
Valid prediction for GlimmerHMM_glimmerT_45534-T1
Valid prediction for Augustus_model.g30371.t1
Valid prediction for snap_scaffold_19-snap.1646-T1
Valid prediction for GeneMark_model.79485_t
Valid prediction for GeneMark_model.79489_t
Valid prediction for GeneMark_model.79466_t
Valid prediction for GeneMark_model.79474_t
Couldn't classify 41052, 41166
Sorry, prediction pasa_asmbl_22331.p1 fails validation.
(AAC)	 AG	41052-41166	GT	TGG
(ATG)	 AG	41270-41336	GT	GAG
(AGT)	 AG	41430-41477	GT	AGG
(GAG)	 AG	42248-42384	GT	CAG
(CAT)	 AG	42569-42684	GT	AGG
(ACC)	 AG	42962-43099	GT	AGG
(TTC)	 AG	43347-43529	GT	AGG
(GTG)	 AG	43686-43799	GT	AAG
(CAC)	 AG	43926-44141	GT	AGG
(GCA)	 AG	44337-44394	GT	AGG
(GTA)	 AG	45459-45565	GT	AGG
(GAG)	 AG	46427-46549	GT	AGG
(AAA)	 AG	46876-46989	GT	AGG
(GGC)	 AG	48529-48675	GT	GGG
(GTG)	 AG	48937-49147	GT	CAG
(CCA)	 AG	49749-49939	GT	AGG
(GTG)	 AG	51142-51242	GT	AGG
(GCA)	 AG	51477-51615	GT	AGG
(ATC)	 AG	51931-52056	TT	GAT
-recovered pasa_asmbl_22331.p1, initial, 41270, 41336
-recovered pasa_asmbl_22331.p1, terminal, 51931, 52056
-recovered pasa_asmbl_22331.p1, internal, 41052, 41166
-recovered pasa_asmbl_22331.p1, internal, 41270, 41336
-recovered pasa_asmbl_22331.p1, internal, 41430, 41477
-recovered pasa_asmbl_22331.p1, internal, 42248, 42384
-recovered pasa_asmbl_22331.p1, internal, 42569, 42684
-recovered pasa_asmbl_22331.p1, internal, 42962, 43099
-recovered pasa_asmbl_22331.p1, internal, 43347, 43529
-recovered pasa_asmbl_22331.p1, internal, 43686, 43799
-recovered pasa_asmbl_22331.p1, internal, 43926, 44141
-recovered pasa_asmbl_22331.p1, internal, 44337, 44394
-recovered pasa_asmbl_22331.p1, internal, 45459, 45565
-recovered pasa_asmbl_22331.p1, internal, 46427, 46549
-recovered pasa_asmbl_22331.p1, internal, 46876, 46989
-recovered pasa_asmbl_22331.p1, internal, 48529, 48675
-recovered pasa_asmbl_22331.p1, internal, 48937, 49147
-recovered pasa_asmbl_22331.p1, internal, 49749, 49939
-recovered pasa_asmbl_22331.p1, internal, 51142, 51242
-recovered pasa_asmbl_22331.p1, internal, 51477, 51615
Valid prediction for GeneMark_model.79472_t
Valid prediction for snap_scaffold_19-snap.1662-T1
Valid prediction for snap_scaffold_19-snap.1649-T1
Valid prediction for snap_scaffold_19-snap.1638-T1
Valid prediction for Augustus_model.g30365.t1
Valid prediction for GeneMark_model.79468_t
Valid prediction for GlimmerHMM_glimmerT_45538-T1
Valid prediction for Augustus_model.g30363.t1
Valid prediction for snap_scaffold_19-snap.1657-T1
Valid prediction for Augustus_model.g30366.t1
Valid prediction for snap_scaffold_19-snap.1650-T1
Valid prediction for Augustus_model.g30361.t1
Couldn't classify 33261, 33353
Couldn't classify 38827, 38832
Sorry, prediction pasa_asmbl_22328.p1 fails validation.
(GAG)	 CT	33261-33353	GT	AGG
(GTG)	 AG	33478-33560	GT	AGG
(GCC)	 AG	33819-33941	GT	AAG
(ACC)	 AG	34497-34576	GT	CAG
(ATT)	 AG	34697-34884	GT	AGG
(GCA)	 AG	35184-35249	GT	AGG
(TGC)	 AG	35441-35533	GT	AGG
(ATT)	 AG	35649-35760	GT	AGG
(TGG)	 AG	35884-36002	GT	AGG
(CAC)	 AG	36450-36536	GT	AGG
(GAT)	 AG	36706-36795	GT	AGG
(AGT)	 AG	36918-37033	GT	AGG
(GGT)	 AG	37548-37617	GT	AGG
(TTT)	 AG	37846-37971	GT	AGG
(TAC)	 AG	38058-38129	GT	AGG
(CTG)	 AG	38299-38445	GT	AGG
(CGC)	 AG	38585-38668	GT	AGG
(ACG)	 AG	38827-38832	TA	TGT
-recovered pasa_asmbl_22328.p1, internal, 33478, 33560
-recovered pasa_asmbl_22328.p1, internal, 33819, 33941
-recovered pasa_asmbl_22328.p1, internal, 34497, 34576
-recovered pasa_asmbl_22328.p1, internal, 34697, 34884
-recovered pasa_asmbl_22328.p1, internal, 35184, 35249
-recovered pasa_asmbl_22328.p1, internal, 35441, 35533
-recovered pasa_asmbl_22328.p1, internal, 35649, 35760
-recovered pasa_asmbl_22328.p1, internal, 35884, 36002
-recovered pasa_asmbl_22328.p1, internal, 36450, 36536
-recovered pasa_asmbl_22328.p1, internal, 36706, 36795
-recovered pasa_asmbl_22328.p1, internal, 36918, 37033
-recovered pasa_asmbl_22328.p1, internal, 37548, 37617
-recovered pasa_asmbl_22328.p1, internal, 37846, 37971
-recovered pasa_asmbl_22328.p1, internal, 38058, 38129
-recovered pasa_asmbl_22328.p1, internal, 38299, 38445
-recovered pasa_asmbl_22328.p1, internal, 38585, 38668
Valid prediction for Augustus_model.g30370.t1
Valid prediction for Augustus_model.g30362.t1
Valid prediction for GeneMark_model.79481_t
Valid prediction for snap_scaffold_19-snap.1660-T1
Couldn't classify 30812, 30880
Couldn't classify 32057, 32098
Sorry, prediction pasa_asmbl_22697.p1 fails validation.
(AAG)	 AC	30812-30880	GT	AGG
(AAC)	 AG	30990-31164	GT	CGG
(ATG)	 AG	31488-31543	GT	AGG
(ACT)	 AG	32057-32098	CT	GCC
add_exon() Sorry, pasa_asmbl_22697.p1 31488-31543-initial-1 is invalid.
-recovered pasa_asmbl_22697.p1, initial, 31488, 31543
-recovered pasa_asmbl_22697.p1, internal, 30990, 31164
-recovered pasa_asmbl_22697.p1, internal, 31488, 31543
Valid prediction for snap_scaffold_19-snap.1636-T1
Valid prediction for GeneMark_model.79498_t
Couldn't classify 39142, 39228
Couldn't classify 39887, 39972
Sorry, prediction pasa_asmbl_22329.p1 fails validation.
(GAG)	 AG	39142-39228	GT	AGG
(AGT)	 AG	39429-39545	GT	ATG
(AAT)	 AG	39635-39746	GT	AGG
(CCT)	 AG	39887-39972	CT	GCC
-recovered pasa_asmbl_22329.p1, internal, 39142, 39228
-recovered pasa_asmbl_22329.p1, internal, 39429, 39545
-recovered pasa_asmbl_22329.p1, internal, 39635, 39746
Valid prediction for GlimmerHMM_glimmerT_45536-T1
Valid prediction for GlimmerHMM_glimmerT_45533-T1
Valid prediction for snap_scaffold_19-snap.1639-T1
Valid prediction for Augustus_model.g30367.t1
Valid prediction for GlimmerHMM_glimmerT_45529-T1
Valid prediction for GlimmerHMM_glimmerT_45531-T1
Couldn't classify 101425, 101622
Couldn't classify 104188, 104218
Sorry, prediction pasa_asmbl_22335.p2 fails validation.
(GGT)	 CA	101425-101622	GT	AGG
(AAG)	 AG	102271-102360	GT	TGG
(TCC)	 AG	103230-103363	GT	TGG
(GGA)	 AG	104188-104218	GA	GAG
-recovered pasa_asmbl_22335.p2, internal, 102271, 102360
-recovered pasa_asmbl_22335.p2, internal, 103230, 103363
Valid prediction for snap_scaffold_19-snap.1656-T1
Valid prediction for snap_scaffold_19-snap.1632-T1
Valid prediction for GlimmerHMM_glimmerT_45539-T1
Valid prediction for GeneMark_model.79476_t
Valid prediction for GlimmerHMM_glimmerT_45520-T1
Valid prediction for GlimmerHMM_glimmerT_45535-T1
Valid prediction for CodingQuarry_transcript_25683-T1
Valid prediction for snap_scaffold_19-snap.1635-T1
Valid prediction for GeneMark_model.79487_t
Valid prediction for GeneMark_model.79490_t
Valid prediction for snap_scaffold_19-snap.1653-T1
Valid prediction for GeneMark_model.79471_t
Valid prediction for GeneMark_model.79469_t
Valid prediction for snap_scaffold_19-snap.1652-T1
Valid prediction for GlimmerHMM_glimmerT_45528-T1
Valid prediction for GlimmerHMM_glimmerT_45540-T1
Valid prediction for GeneMark_model.79500_t
Valid prediction for GeneMark_model.79492_t

-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 GlimmerHMM_glimmerT_45537-T1
Valid prediction for GeneMark_model.79479_t
Valid prediction for GeneMark_model.79491_t
Valid prediction for pasa_asmbl_21506.p1
Valid prediction for GeneMark_model.79484_t
Valid prediction for GlimmerHMM_glimmerT_45525-T1
Valid prediction for GeneMark_model.79494_t
Valid prediction for snap_scaffold_19-snap.1633-T1
Valid prediction for snap_scaffold_19-snap.1634-T1
Valid prediction for GlimmerHMM_glimmerT_45526-T1
Valid prediction for GeneMark_model.79473_t
Valid prediction for GeneMark_model.79495_t
Valid prediction for HiQ_model.g30368.t1
Valid prediction for HiQ_model.g30364.t1
Valid prediction for GeneMark_model.79467_t
Valid prediction for GeneMark_model.79488_t
Valid prediction for GeneMark_model.79480_t
Valid prediction for snap_scaffold_19-snap.1645-T1
Valid prediction for snap_scaffold_19-snap.1647-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for GeneMark_model.79482_t
Valid prediction for snap_scaffold_19-snap.1658-T1
Valid prediction for CodingQuarry_transcript_25684-T1
Valid prediction for snap_scaffold_19-snap.1644-T1
Valid prediction for snap_scaffold_19-snap.1642-T1
Couldn't classify 146171, 146266
Sorry, prediction pasa_asmbl_21508.p1 fails validation.
(GAG)	 GC	146171-146266	GT	TGG
(ATG)	 AG	146589-147071	CA	AAC
-recovered pasa_asmbl_21508.p1, terminal, 146589, 147071
Valid prediction for snap_scaffold_19-snap.1655-T1
Valid prediction for GlimmerHMM_glimmerT_45530-T1
Valid prediction for Augustus_model.g30369.t1
Valid prediction for GeneMark_model.79470_t
Valid prediction for GeneMark_model.79497_t
Valid prediction for GeneMark_model.79501_t
Valid prediction for GlimmerHMM_glimmerT_45532-T1
Valid prediction for snap_scaffold_19-snap.1654-T1
Valid prediction for snap_scaffold_19-snap.1640-T1
Valid prediction for GeneMark_model.79477_t
Valid prediction for snap_scaffold_19-snap.1637-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 22809, rend_intergenic: 18725  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52056, rend_intergenic: 39849  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97552, rend_intergenic: 86754  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106146, rend_intergenic: 101834  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162264, rend_intergenic: 156922  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 257569
-exon list size: 499


building trellis

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81.2    
81.4    
81.6    
81.8    
82.0    
82.2    
82.4    
82.6    
82.8    
83.0    
83.2    
83.4    
83.6    
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    
86.4    
86.6    
86.8    
87.0    
87.2    
87.4    
87.6    
87.8    
88.0    
88.2    
88.4    
88.6    
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    
91.4    
91.6    
91.8    
92.0    
92.2    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
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    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.8    
98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 18 predictions from path traversal
Error with prediction: snap lend_intergenic: 22809, rend_intergenic: 18725  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52056, rend_intergenic: 39849  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97552, rend_intergenic: 86754  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106146, rend_intergenic: 101834  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162264, rend_intergenic: 156922  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 12 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 18724
-exon list size: 37


building trellis

2.6    
5.1    
7.7    
10.3    
12.8    
15.4    
17.9    
20.5    
23.1    
25.6    
28.2    
30.8    
33.3    
35.9    
38.5    
41.0    
43.6    
46.2    
48.7    
51.3    
53.8    
56.4    
59.0    
61.5    
64.1    
66.7    
69.2    
71.8    
74.4    
76.9    
79.5    
82.1    
84.6    
87.2    
89.7    
92.3    
94.9    
97.4    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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

-building DP trellis

-building trellis in range 8382 - 18724
-exon list size: 11


building trellis

7.7    
15.4    
23.1    
30.8    
38.5    
46.2    
53.8    
61.5    
69.2    
76.9    
84.6    
92.3    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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

-building DP trellis

-building trellis in range 8609 - 18724
-exon list size: 9


building trellis

9.1    
18.2    
27.3    
36.4    
45.5    
54.5    
63.6    
72.7    
81.8    
90.9    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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

-building DP trellis

-building trellis in range 8609 - 18677
-exon list size: 8


building trellis

10.0    
20.0    
30.0    
40.0    
50.0    
60.0    
70.0    
80.0    
90.0    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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