Dear galaxy team:
I was testing local galaxy of our lab by analyzing RNA-seq data in Jeremy’s RNA-seq tutorial. http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise I could run TopHat, cufflinks, and cuffdiff and got results correctly, but when I executed cuffcompare through galaxy, the following error occurred: Tool execution generated the following error message: Error running cuffcompare. [Errno 2] No such file or directory: 'cc_output' The tool produced the following additional output: cuffcompare v1.0.3 (2403) cuffcompare -o cc_output -s /home/galaxy/data/galaxy_data/sam_index/hg19.fasta ./input1 and error messages in log file (galaxy.log) are: galaxy.jobs INFO 2011-06-10 14:02:15,161 job 130 dispatched galaxy.jobs.runners.local DEBUG 2011-06-10 14:02:15,466 executing: python /home/galaxy/software/galaxy_dist/tools/ngs_rna/cuffcompare_wrapper.py -s --ref_file="None" --dbkey=hg19 --index_dir=/home/galaxy/software/galaxy_dist/tool-data /home/galaxy/software/galaxy_dist/database/files/000/dataset_398.dat galaxy.jobs.runners.local DEBUG 2011-06-10 14:02:27,834 execution finished: python /home/galaxy/software/galaxy_dist/tools/ngs_rna/cuffcompare_wrapper.py -s --ref_file="None" --dbkey=hg19 --index_dir=/home/galaxy/software/galaxy_dist/tool-data /home/galaxy/software/galaxy_dist/database/files/000/dataset_398.dat galaxy.jobs DEBUG 2011-06-10 14:02:27,943 finish(): Could not move /home/galaxy/software/galaxy_dist/database/job_working_directory/130/cc_outp ut to /home/galaxy/software/galaxy_dist/database/files/000/dataset_399.dat as directed by from_work_dir galaxy.jobs DEBUG 2011-06-10 14:02:27,971 finish(): Could not move /home/galaxy/software/galaxy_dist/database/job_working_directory/130/input1. tmap to /home/galaxy/software/galaxy_dist/database/files/000/dataset_400.dat as directed by from_work_dir galaxy.jobs DEBUG 2011-06-10 14:02:27,999 finish(): Could not move /home/galaxy/software/galaxy_dist/database/job_working_directory/130/input1. refmap to /home/galaxy/software/galaxy_dist/database/files/000/dataset_401.dat as directed by from_work_dir galaxy.jobs DEBUG 2011-06-10 14:02:28,027 finish(): Moved /home/galaxy/software/galaxy_dist/database/job_working_directory/130/cc_outp ut.combined.gtf to /home/galaxy/software/galaxy_dist/database/files/000/dataset_402.dat as directed by from_work_dir galaxy.jobs DEBUG 2011-06-10 14:02:28,174 job 130 ended I’ve tried to manually execute cuffcompare to analyze dataset_398.dat (which is the output of tophat) and I could get correct cuffcompare output. $ cuffcompare -o cc_output -s /home/galaxy/data/galaxy_data/sam_index/hg19. fasta dataset_398.dat It seems that the coffcompare_wrapper might have something to do with this error… Thanks in advance for your help! Best John Wu
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