Question: LEON producing truncated output
1
gravatar for intipedroso
17 months ago by
intipedroso10
Chile
intipedroso10 wrote:

Hi,

 

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

leon

```

 

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 • 443 views
ADD COMMENTlink modified 17 months ago • written 17 months ago by intipedroso10

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

 

 

 

ADD REPLYlink written 17 months ago by guillaume.rizk0

I got all the exact same issues just now on https://www.encodeproject.org/files/ENCFF001LCY/@@download/ENCFF001LCY.fastq.gz

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 7 months ago by John11k
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