>>>> ConvertEnsembl <<<<
Parameters:
Project directory: convert/ensembl/rice
Processing convert/ensembl/rice/Oryza_sativa.IRGSP-1.0.dna_sm.toplevel.fa.gz
Chr01   1                43,270,923
Chr02   2                35,937,250
Chr03   3                36,413,819
Chr04   4                35,502,694
Chr05   5                29,958,434
Chr06   6                31,248,787
Chr07   7                29,697,621
Chr08   8                28,443,022
Chr09   9                23,012,720
Chr10   10               23,207,287
Chr11   11               29,021,106
Chr12   12               27,531,856
Finish writing /genomic.fa
Finish writing /genomic.fa
A  53,531,299  a  51,759,567
T  53,502,765  t  51,785,165
C  41,674,471  c  39,588,481
G  41,698,371  g  39,588,746
N         199  n     116,455
Gaps >= 30000: 0 (using N and n)
Processing convert/ensembl/rice/Oryza_sativa.IRGSP-1.0.54.gff3.gz
   Use Genes 35,666 from 37,960
   Use mRNAs 35,666 from 44,754
   Use Exons 153,846 from 198,053
Finish writing /anno.gff

>>Sequences
     12 Chromosomes of     373,245,519 total length
      2 Mt/Pt       of         625,045 total length -- not written to file
     49 Scaffolds   of       1,178,721 total length (12<10,000bp) -- not written to file

>>All Type (col 3)
   CDS                     165,271
   RNase_MRP_RNA                 1
   SRP_RNA                       2
   biological_region           546
   chromosome                   14
   exon                    198,053 *
   five_prime_UTR           45,615
   gene                     37,960 *
   lnc_RNA                      95
   mRNA                     44,754 *
   ncRNA_gene                1,011
   pre_miRNA                    97
   pseudogene                    7
   pseudogenic_transcript        7
   rRNA                        275
   scaffold                     49
   snRNA                        83
   snoRNA                      216
   tRNA                        242
   three_prime_UTR          51,073
>>All Gene Source (col 2)
   DDBJ                         53 *
   EMBL                         58 *
   RAP2018-11-26            37,849 *
>>All gene biotype=
   nontranslating_CDS        2,185
   protein_coding           35,775 *
>>Written to file
   Genes                  35,666
   mRNA                   35,666
   Exons                 153,846
>>Chromosome gene count 35,666
   Chr01      1                       4,967
   Chr02      2                       3,981
   Chr03      3                       4,272
   Chr04      4                       3,157
   Chr05      5                       2,861
   Chr06      6                       2,971
   Chr07      7                       2,730
   Chr08      8                       2,439
   Chr09      9                       1,992
   Chr10      10                      1,980
   Chr11      11                      2,273
   Chr12      12                      2,043
   Genes not on Chromosome      109
ConvertEnsembl completed