Hi Michael, which version of the FASTQC wrapper are you running? Can you point us to the exact build and toolshed version?
Thanks, Bjoern Am 02.01.2015 um 21:22 schrieb Waldron, Michael H: > Having a problem with directing FastQC output in Galaxy. User is running a > job whose command line looks like this: > > # FastQC cl = > /nas02/apps/galaxy-prod/galaxy-dist/tool-data/shared/jars/FastQC/fastqc > --outdir=/proj/galaxy/job_working_directory/010/10467/dataset_13836_files > /proj/galaxy/job_working_directory/010/10467/dataset_13836_files/SRR016862.fastq > > Job output looks like this: > > ## odpath=None: No output found in None. Output for the run was: > # FastQC cl = > /nas02/apps/galaxy-prod/galaxy-dist/tool-data/shared/jars/FastQC/fastqc > --outdir=/proj/galaxy/job_working_directory/010/10467/dataset_13827_files > /proj/galaxy/job_working_directory/010/10467/dataset_13827_files/SRR016862.fastq > Started analysis of SRR016862.fastq > Approx 5% complete for SRR016862.fastq > Approx 10% complete for SRR016862.fastq > Approx 15% complete for SRR016862.fastq > Approx 20% complete for SRR016862.fastq > Approx 25% complete for SRR016862.fastq > Approx 30% complete for SRR016862.fastq > Approx 35% complete for SRR016862.fastq > Approx 40% complete for SRR016862.fastq > Approx 45% complete for SRR016862.fastq > Approx 50% complete for SRR016862.fastq > Approx 55% complete for SRR016862.fastq > Approx 60% complete for SRR016862.fastq > Approx 65% complete for SRR016862.fastq > Approx 70% complete for SRR016862.fastq > Approx 75% complete for SRR016862.fastq > Approx 80% complete for SRR016862.fastq > Approx 85% complete for SRR016862.fastq > Approx 90% complete for SRR016862.fastq > Approx 95% complete for SRR016862.fastq > Analysis complete for SRR016862.fastq > > The job_working_directory/010/10467 directory is created, however it is > empty. It appears this "odpath" needs to be set somehow? > > Does anyone know a solution for this? > > Mike Waldron > Systems Specialist > ITS - Research Computing Center > University of North Carolina at Chapel Hill > > > > > ___________________________________________________________ > 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: > https://lists.galaxyproject.org/ > > 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
