LEON producing truncated output

Question

[intipedroso]

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.

[guillaume.rizk]

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

[John]

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.