Hi there, 
I'm using bowtie2 to align some fastq files downloaded from [ENA][1]

I've first run a quality check to see if there is something annoying, but in general terms it is fine. 
Then, I've run bowtie-2 as follow: 
 

    bowtie2 -x human_index_bowtie/human_index_bwt -U SRR11557616.fastq.gz -S 5h.sam

But I got this error message: 

    Error: Read SRR11557616.1 ugc_599_6_F3_0002_0/1 has more quality values than read characters.
    terminate called after throwing an instance of 'int'
    Aborted (core dumped)
    (ERR): bowtie2-align exited with value 134

the head of the file is a bit weird: 

    head -n 8

    @SRR11557614.1 ugc_599_3_F3_0001_0 length=74
    T3.0321.1000.133...11...011..20...11...21...10...11...31....0....2....1....
    +SRR11557614.1 ugc_599_3_F3_0001_0 length=74
    !aB_aaaBa^aQBWaYBBBaYBBBOa_BBWSBBBKaBBBNWBBBWOBBBS^BBBN`BBBBSBBBBPBBBBaBBBB
    @SRR11557614.2 ugc_599_3_F3_0001_1 length=74
    T2.3313.1031.030...30...231..10...22...00...02...22...13....0....2....2....
    +SRR11557614.2 ugc_599_3_F3_0001_1 length=74
    !aBaaaaBaa_]BPa^BBBbaBBBaaaBBaaBBB\`BBBa\BBBaaBBBaaBBBWPBBBBaBBBBaBBBBaBBBB

Any ideas how to solve the problem? or I should select a different file?

Thanks! 


  [1]: https://www.ebi.ac.uk/ena/browser/home
The problem is that this is a colorspace file (like ABI SOLiD system, not Illumina), and `bowtie2` does not support colorspace alignment. `bowtie` (aka `bowtie1`) used to support it, but support got dropped in recent versions afaik. 

See: http://bowtie-bio.sourceforge.net/news.shtml

Colorspace support was dropped in versions 1.3.0 and later so you would need to download a version prior to that, then build an index `bowtie-build` with the `-C` option to enable colorspace, and then align your data. See manual for details, I never used colorspace myself.