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")?
-John On Mon, Feb 10, 2014 at 7:00 AM, graham etherington (TSL) <graham.ethering...@sainsbury-laboratory.ac.uk> wrote: > Hi Philippe, > 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 > format?) > > Cheers, > Graham > > > Dr. Graham Etherington > Bioinformatics Support Officer, > The Sainsbury Laboratory, > Norwich Research Park, > Norwich NR4 7UH. > UK > Tel: +44 (0)1603 450601 > > From: Philippe Moncuquet <philippe.m...@gmail.com> > Date: Monday, 10 February 2014 03:50 > To: Galaxy Dev <galaxy-dev@lists.bx.psu.edu> > Subject: [galaxy-dev] Error introduced with Fastq Groomer > > Hi, > > Some unexpected symbols were introduced while grooming my fastq file > > Before > > @DJTPB5M1:327:C3PC4ACXX:6:1104:9355:84986 1:N:0:GTCCGC > GAGCCTTGCTAGGAGAGGGAAGGTGGAAGATCATCATTTCCAGGAGAGCACTGCTAGCAGGAAGCCACGTCTGCATTACACGCTTCATTAGGGACTTCCC > + > @@@FFFFFFFHHHE@=FDEGCCG2A7CDFHE>F<:B?BDEGGHGICHC9B@FGEHEGG;F=GHI==CE:;BBC>C>>@CC>;8=?=CA;AA>AA<AC<C< > > > After > > @DJTPB5M1:327:C3PC4ACXX:6:1104:9355:84986 1:N:0:GTCCGC > GAGCCTTGCTAGGAGAGGGAAGGTGGAAGATCATCATTTCCAGGAGAGCACTGCTAGCAGGAAGCCACG+1�CATTACACGCTTCATTAGGGACTTCCC > + > @@@FFFFFFFHHHE@=FDEGCCG2A7CDFHE>F<:B?BDEGGHGICHC9B@FGEHEGG;F=GHI==CE:;BBC>C>>@CC>;8=?=CA;AA>AA<AC<C< > > > 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 ? > > > Regards, > > Philip > > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
