[Olalla]

Thanks a lot to all for your suggestions. Finally I got the program running, by deleting the bloody white spaces in the read names and then setting -NW:mrnl=80 in MIRA, after that all worked perfectly

[maubp]

If you had several lines starting GIMXFMA02G21Y1 but the descriptions were different, something strange has happened. I suspect you still have a problem in your data, and all you have done by editing the read names is avoid MIRA's sanity test without fixing the real problem.

[maubp]

So, the read names in my fastq files appear as follows:
GIMXFMA02G21Y1 length=60 xy=2788_0299 region=2 run=R_2010_06_09_09_17_36_ that is, long names with spaces. So I think that what MIRA is doing is juts taking the first 14 characters as the read name (e.g. GIMXFMA02G21Y1),

Yes, that is the identifier - everything after the space is an optional description in FASTQ.

which in fact are repeated among many of the files that I do have (I have found common lines when comparing files including only these names in the lines). However, when I search for common lines in files including all information in headers (like GIMXFMA02G21Y1 length=60 xy=2788_0299 region=2 run=R_2010_06_09_09_17_36_), the output of the search is that there are no common lines between any of the files, so I think that I should first eliminate spaces, maybe replacing them by ":".

Something is wrong, GIMXFMA02G21Y1 should be unique. What does this give?

grep GIMXFMA02G21Y1 your_file.fastq