I'm having the same issue (though with interlacer). I suspect that
it's an issue with the way the forward and reverse are read. Mine look
like yours, where forward is 1:N and reverse is 2:N instead of the /1
and /2 that the tool says that it expects. Our data are Illumina
pipeline 1.9 (HiSeq), so maybe that's the problem? I don't actually
know, however, or how to fix this. Just interesting to have run into
this problem today and then seen your email.

-Lucinda

On Tue, Nov 8, 2011 at 2:19 PM, Matthew Herron <xprinc...@gmail.com> wrote:
> Hi,
> I am trying to join two groomed fastq files from a paired-end Illumina
> read using the fastq joiner tool. The drop-down menus correctly
> identify the groomed fastq files, but after cranking for a few minutes
> the tool produces empty output:
>
> "FASTQ joiner on data 5 and data 4emptyformat: fastqsanger, database:
> ?Info: There were 3497909 known sequence reads not utilized.Joined 0
> of 3497909 read pairs (0.00%)."
>
> The files have the same number of reads (3497909), reads have the same
> number of bases (102), and the joiner tool doesn't have any options
> (other than choosing the two files to join). I have tried this with
> Sanger and with Illumina 1.3+ quality scores, and in both (left-right)
> orientations. I've pasted the beginnings of the two files below my
> signature in case this is useful for diagnosing the problem.
> Can anyone tell me what I'm doing wrong?  Thanks,
> --
> Matthew D. Herron, PhD
> Department of Zoology
> University of British Columbia
> x.princ...@gmail.com
> http://www.eebweb.arizona.edu/grads/mherron/
>
> Sample of read 1:
> @HWI-ST765:83:D091AACXX:1:1101:1202:2130 1:N:0:ACTTGA
> TTATTCCGTTTACCTTCACGCTGTTATGGCTCTCGGTGTTCGGCAATAGCGCGCTGTATGAAATTATCCACGGCGGCGCGGCATTTGCCGAGGAAGCGATG
> +
> CCCFFFFFHHHHHJJJJJJJJJJJJIJIJJJIEHII?FGIIJJJJJJJIJJJHFFDDEEEDEDDDDEDDDDDDDDDDDDDDDDDDD@CCD3<BDD@DDDBD
>
> Sample of read 2:
> @HWI-ST765:83:D091AACXX:1:1101:1202:2130 2:N:0:ACTTGA
> ATTCCCCAGCACCAGCGCCCCGGAGTCCGCCGAGGTCACATAAAACAGCAGGCCAGTAATGGTGGCGACGGAGGCGCTAAAGGTAAACGCCGGATACTGCG
> +
> CCCFFFFFFGHHHJJJJJJJJJIJIFHIIJJJJIG:BEFFFFEEEDDCBDDDDDDD@CDDDCACDDDBDDDDDDBDDDDDDDC>@CCC@@DDDDDDDDEDB
> ___________________________________________________________
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-- 
Lucinda Lawson
Postdoctoral Research Computational Biologist
USDA-ARS
Gainesville, FL

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