Cuffcompare Error In Galaxy

Question: Cuffcompare Error In Galaxy

7.5 years ago by

吳正華 • 60 wrote:

Dear galaxy team: I was testing local galaxy of our lab by analyzing RNA-seq data in JeremyĄŚs 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/c c_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/i nput1. 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/i nput1. 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/c c_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 IĄŚve 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 errorĄK Thanks in advance for your help! Best John Wu

rna-seq cufflinks • 1.2k views

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modified 7.4 years ago by Carlos Borroto • 390 • written 7.5 years ago by 吳正華 • 60

7.4 years ago by

Carlos Borroto • 390

Washington Metropolitan Area

Carlos Borroto • 390 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.refm ap 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.c ombined.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>:

ADD COMMENT • link written 7.4 years ago by Carlos Borroto • 390

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

ADD REPLY • link written 7.4 years ago by Carlos Borroto • 390

Hi Carlos, We're expecting to release a stable distribution this week, but you are always free to pull changes from the central repository. The suggested method would be to just pull all changesets up to the one you want, or up to the tip changeset. It's not trivial to pull single changesets, you have to export them from central, import them to your local repository, and then you'll have to merge when we release a new stable distribution. --nate

ADD REPLY • link written 7.4 years ago by Nate Coraor ♦ 3.2k

Thanks Nate, For now I downloaded: https://bitbucket.org/galaxy/galaxy- central/raw/e74e89a4c03a/tools/ngs_rna/cuffcompare_wrapper.py https://bitbucket.org/galaxy/galaxy- central/raw/d1f2d2e5246a/tools/ngs_rna/cuffcompare_wrapper.xml I saved to current versions of these files, so I'll make sure to replace them before updating to the next stable version to avoid merging errors. Thanks again, -- Carlos Borroto Baltimore, MD

ADD REPLY • link written 7.4 years ago by Carlos Borroto • 390

Hi Carlos: After I replaced cuffcompare_wrapper.py & cuffcompare_wrapper.xml with code provided by Jeremy, now I can execute cuffcompare on my local galaxy. You can check following link: https://bitbucket.org/galaxy/galaxy-central/changeset/f4b98c453389 hope this helps. Best John Wu 1. Re: cuffcompare error in galaxy (Carlos Javier Borroto) Message: 1 Date: Mon, 20 Jun 2011 14:01:15 -0400 To: ??? <johnwu@ibms.sinica.edu.tw> Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] cuffcompare error in galaxy Message-ID: <banlkti=jtr88l_x5-szpgnu4=ovqao=epq@mail.gmail.com> Content-Type: text/plain; charset=UTF-8 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.refm ap 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.c ombine d.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 ??? <johnwu@ibms.sinica.edu.tw>: 'cc_output' finished: output. _______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user End of galaxy-user Digest, Vol 60, Issue 21 *******************************************

ADD REPLY • link written 7.4 years ago by 吳正華 • 60

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