Sequences with "*" are not written to the new FASTA file.

------ ConvertEnsembl ./data/seq/cabbE ------
./data/seq/cabbE/sequence exists - clear existing  .fna and .fa  files
./data/seq/cabbE/annotation exists - clear existing  .gff and .gff3 files
Log file to  ./data/seq/cabbE/xConvertENS.log
Parameters:
   Project Directory: ./data/seq/cabbE
   Verbose
Processing ./data/seq/cabbE/Brassica_oleracea.BOL.dna_sm.toplevel.fa.gz
C1      C1               43,764,888
C2      C2               52,886,895
C3      C3               64,984,695
C4      C4               53,719,093
C5      C5               46,902,585
C6      C6               39,822,476
C7      C7               48,366,697
C8      C8               41,758,685
C9      C9               54,679,868
Scaf    Scaffold00285       550,871  *
Scaf    Scaffold00418       360,705  *
Scaf    Scaffold00434       343,593  *
Scaf    Scaffold00452       324,463  *
Scaf    Scaffold00534       246,008  *
Scaf    Scaffold00576       215,938  *
Scaf    Scaffold00578       215,108  *
Scaf    Scaffold00579       214,022  *
Scaf    Scaffold00580       213,535  *
Scaf    Scaffold00581       213,381  *
Scaf    Scaffold00613       193,719  *
Scaf    Scaffold00615       192,988  *
Scaf    Scaffold00616       192,287  *
Scaf    Scaffold00626       187,934  *
Scaf    Scaffold00629       187,313  *
Scaf    Scaffold00640       176,243  *
Scaf    Scaffold00641       174,647  *
Scaf    Scaffold00667       159,200  *
Scaf    Scaffold00671       156,667  *
Scaf    Scaffold00673       154,937  *
Suppressing further scaffold outputs
Sequences not output: 32,919  (*)
Finish writing ./data/seq/cabbE/sequence/genomic.fna

A  69,247,430  a  61,229,198
T  69,276,626  t  61,218,908
C  40,952,680  c  32,332,328
G  40,973,403  g  32,310,317
N         305  n  39,344,687

Gaps >= 30000: 39 (using N and n)
Finish writing ./data/seq/cabbE/annotation/gap.gff

Processing ./data/seq/cabbE/Brassica_oleracea.BOL.59.gff3.gz
   Use Gene 59,225 from 59,225
   Use mRNA 54,761 from 59,225
   Use Exon 256,428 from 269,978
Finish writing ./data/seq/cabbE/annotation/anno.gff

>>Sequences
       9 Output 9      Chromosomes      446,885,882
  32,919 Output 0      Scaffolds         41,736,625 (32,327 < 10,000bp)

>>All Types  (col 3)  (+ are processed keywords)
   CDS                     268,591
   RNase_MRP_RNA                 3
   SRP_RNA                      29
   chromosome                    9
   exon                    269,978 +
   gene                     59,225 +
   lnc_RNA                      22
   mRNA                     59,225 +
   ncRNA_gene                1,361
   pre_miRNA                   121
   rRNA                        220
   scaffold                 32,919
   snRNA                       174
   snoRNA                      282
   tRNA                        510
>>All Gene Source (col 2)
   brad                     59,225
>>All gene biotype= (col 8)
   nontranslating_CDS            5
   protein_coding           59,220 +
>>Written to file
   Genes                    59,225
   mRNA                     54,761
   Exons                   256,428
>>Chromosome gene count 54,761
   C1         C1                      5,401
   C2         C2                      5,842
   C3         C3                      8,489
   C4         C4                      6,426
   C5         C5                      5,849
   C6         C6                      4,762
   C7         C7                      5,751
   C8         C8                      5,599
   C9         C9                      6,642
   Genes not on Chromosome    4,459

------ Finish ConvertEnsembl ./data/seq/cabbE -------