The groomer was recently migrated to the tool shed - this has not been
released as part of a galaxy-dist though so I assume you are still
running a version of the fastq groomer bundled with Galaxy? If yes,
what version of Galaxy are you running (i.e. can you attach the output
of "hg summary")?
On Mon, Feb 10, 2014 at 7:00 AM, graham etherington (TSL)
I’m unable to suggest a reason as to why this has happened, other than some
sort of corruption whilst the job was running, but I would point out two
things to you.
1. I don’t think you need to run the fastq groomer on your data anyway as
it’s in Illumina 1.8+ format, which should already be in fastqsanger format.
2. It appears that the fastq groomer hasn’t worked as the quality scores
haven’t changed format. (A general question to anyone here – will fastq
groomer change the quality format of reads that are already in fastqsanger
Dr. Graham Etherington
Bioinformatics Support Officer,
The Sainsbury Laboratory,
Norwich Research Park,
Norwich NR4 7UH.
Tel: +44 (0)1603 450601
From: Philippe Moncuquet <philippe.mcqt(a)gmail.com>
Date: Monday, 10 February 2014 03:50
To: Galaxy Dev <galaxy-dev(a)lists.bx.psu.edu>
Subject: [galaxy-dev] Error introduced with Fastq Groomer
Some unexpected symbols were introduced while grooming my fastq file
I relaunch this step without being able to reproduce the bug. Any ideas
about this problem ? Have you guys came across the same problem before ?
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