Some fastq.gz files cause cutadapt.fastq.gz to have unexpected EOF error

[GoogleCodeExporter]

I am running cutadapt 1.2.1, and have used it with no problem for a while now 
on both fastq and fastq.gz files as input. 

Occasionally when using fastq.gz files as input, cutadapt completes fine (no 
error messages, stat report looks normal), but when I use the post-custadapt 
fastq.gz (which I call cutadapt.fastq.gz) I run into problems. In particular, 
gzip (and gunzip) return an error when decompressing the cutadapt.fastq.gz, 
with message "unexpected end of file".

If the same .fastq (not compressed) file is run through cutadapt, the resulting 
cutadapt.fastq appears fine.

Of course, this doesn't always happen. Out of 66 files I ran recently, this 
occurred for 4 of them. I was wondering if you had any thoughts.

Thanks

Original issue reported on code.google.com by jwad...@gmail.com on 24 May 2013 at 6:01

[GoogleCodeExporter]

I have never encountered that problem. Which Python version are you using?

Is the problem reproducible? That is, does it always occur with specific files? 
Or does the problem occur randomly?

If you do not use any of the options that discard reads, you can count the 
number of lines with
'zcat trimmed-file.fastq.gz | wc -l'
and divide by four to get the number of reads. How many reads are in the input 
file and how many are in the output file before the corruption?

Original comment by marcel.m...@tu-dortmund.de on 29 May 2013 at 3:55

[GoogleCodeExporter]

Thanks for the report, but since I haven't received a reply and cannot 
reproduce it, my only choice is to close it. Please re-open if you have more 
information.

Original comment by marcel.m...@tu-dortmund.de on 11 Jul 2013 at 2:34

• Changed state: WontFix