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