Question: LEON producing truncated output
gravatar for intipedroso
3.7 years ago by
intipedroso10 wrote:



I am using LEON V 1.0.0. I have compressed a fastq file and when I decompress it the output is truncated.



$/home/shared/app/leon-1.0.0-Source/leon -file foo.fastq.gz.leon -d


Start decompression

        Input filename: foo.fastq.gz.leon

        Qual filename: ./foo.fastq.qual

        Output format: Fastq

        Kmer size: 31


        Input File was compressed with leon version 1.0.0

        Block count: 105


[Decompressing all streams]  99   %   elapsed:   0 min 7  sec    estimated remaining:   0 min 0  sec


        Output filename: ./foo.fastq.d

        Time: 11.90s

        Speed: 0.00 mo/s




If i look at the size of the files


$ ls -lh foo.fastq.*

-rw-rw-r-- 1 ipedroso ipedroso  14K dic  1 14:43 foo.fastq.d

-rw-rw-r-- 1 ipedroso ipedroso  69M dic  1 14:43 foo.fastq.gz.leon

-rw-rw-r-- 1 ipedroso ipedroso 138M dic  1 14:43 foo.fastq.gz.qual


the original compress file was about 400M.


No idea why LEON generates a file with a ".d" extension as well.


Help much appreciated.

gatb fastq leon • 1.2k views
ADD COMMENTlink modified 3.7 years ago • written 3.7 years ago by intipedroso10

Hi,  could you also post the command used to compress the file ?




ADD REPLYlink written 3.7 years ago by guillaume.rizk20

I got all the exact same issues just now on

Also the final file size of the compressed file is much smaller than the file size stated in the program's final compression report. I think it forgot to write some data to disk. Also the reported compression ratios are not particularly good - although I appreciate the point of this publication/tool was to show that you can compress DNA in graphs. It's a shame that it just turns out to be slow and bigger than just storing the DNA in a table.

Finally, the .d file for me is in FASTA format not FASTQ, which is probably a relevant issue if the author chooses to debug this.

ADD REPLYlink written 2.9 years ago by John12k
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