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 <joh...@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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___________________________________________________________
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