[galaxy-user] cuffcompare error in galaxy

[Carlos Javier Borroto]

I see there is this changeset:
https://bitbucket.org/galaxy/galaxy-central/changeset/f4b98c453389

As I have cufflinks 1.0.3, I wonder if this is the cause of the error.
Maybe I should move to galaxy-central if I want to use cufflinks. Is
there any clean way to backport a changeset from -central to -dist?

Thanks,
--
Carlos Borroto
Baltimore, MD



On Mon, Jun 20, 2011 at 2:01 PM, Carlos Javier Borroto
<carlos.borroto at gmail.com> wrote:
> 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 at 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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