Hi John,
I'm finding the exact same error while going through Jeremy's tutorial in a local instance of galaxy-dist. I was wonder if you found the solution.
I see cuffcompare wrapper outputs these files: cc_output.combined.gtf cc_output.input1.refmap cc_output.input1.tmap cc_output.loci cc_output.stats cc_output.tracking
and in the logs I'm seing this: galaxy.jobs DEBUG 2011-06-20 13:34:49,902 finish(): Could not move /home/galaxy/galaxy_dist/database/job_working_directory/47/cc_output to /home/galaxy/galaxy_dist/database/files/000/dataset_68.dat as directed by from_work_dir galaxy.jobs DEBUG 2011-06-20 13:34:49,917 finish(): Could not move /home/galaxy/galaxy_dist/database/job_working_directory/47/input1.tmap to /home/galaxy/galaxy_dist/database/files/000/dataset_69.dat as directed by from_work_dir galaxy.jobs DEBUG 2011-06-20 13:34:49,932 finish(): Could not move /home/galaxy/galaxy_dist/database/job_working_directory/47/input1.refmap to /home/galaxy/galaxy_dist/database/files/000/dataset_70.dat as directed by from_work_dir galaxy.jobs DEBUG 2011-06-20 13:34:49,948 finish(): Moved /home/galaxy/galaxy_dist/database/job_working_directory/47/cc_output.combined.gtf to /home/galaxy/galaxy_dist/database/files/000/dataset_71.dat as directed by from_work_dir
Only cc_output.combined.gtf is correctly being moved, the rest aren't being call by the correct filenames.
Thanks, -- Carlos Borroto Baltimore, MD
2011/6/10 吳正華 johnwu@ibms.sinica.edu.tw:
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_output 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_output.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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