Matthew,
yes we have seen such kind of long runs before (depending on server load). 
Happy most of our reads are now in 1.8+ format.
You can parallelise the process by splitting the file in 4 or 6 and submit for 
grooming and afterwards merge them again...
Alex


________________________________________
Van: galaxy-user-boun...@lists.bx.psu.edu 
[galaxy-user-boun...@lists.bx.psu.edu] namens Matthew McCormack 
[mccorm...@molbio.mgh.harvard.edu]
Verzonden: maandag 27 februari 2012 21:13
To: galaxy-user@lists.bx.psu.edu
Onderwerp: [galaxy-user] FASTQ groomer processing time

I used FASTQ groomer on a 29 Gb Illumina 1.5+ FASTQ file to go from
Illumina 1.3-1.7+ to Sanger and it is still processing after over 30
hrs. Is this a normal time frame for a FASTQ file this size ?

Matthew


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