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-bounces@lists.bx.psu.edu [galaxy-user-bounces@lists.bx.psu.edu] namens Matthew McCormack [mccormack@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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