Hi Matthew,

Are you by chance using sequences with the newer CASAVA 1.8+ formatting? For example:


If so, this tool is known to not work correctly (it skips over the IDs). We do consider it a priority to update the tool. You can track our progress by following the bitbucket ticket here:


Thank you for your patience,

Galaxy team

On 11/3/11 5:45 PM, Matthew Herron wrote:
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 4
format: 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). Can anyone tell me what
I'm doing wrong?

Jennifer Jackson
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