Re: [galaxy-user] Cuffcompare error
Hello Alessia, This appears to be a known bug in Cuffcompare that can be worked around by reordering the input files: http://seqanswers.com/forums/showthread.php?t=5809 If you have questions about this, it would probably be worth asking the tool authors for input/advice at tophat.cuffli...@gmail.com. Best wishes for your project, Jen Galaxy team On 11/7/11 5:50 PM, Alessia D wrote: Hi, I am trying to run Cuffcompare on a set of 6 Cufflinks-generated datasets (3 replicates of 2 conditions). I am consistently getting the following error: Error running cuffcompare. Warning: Your version of Cufflinks is not up-to-date. It is recommended that you upgrade to Cufflinks v1.1.0 to benefit from the most recent features and bug fixes (http://cufflinks.cbcb.umd.edu). Error: no XLocus created for transcript CUFF.34072.1 (file ./input3) [2, 2], on chrY+:274296-277218 However, if I run Cuffcompare on the 2 conditions separately (3x Cufflinks datasets), everything works fine. Does anyone know why this is? Thanks Alessia ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] cuffcompare error in galaxy (Carlos Javier Borroto)
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 From: Carlos Javier Borroto To: ??? Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] cuffcompare error in galaxy Message-ID: 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.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.combine 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 ??? : > 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/c > c_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/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_output.combined.gtf to > /home/galaxy/software/galaxy_dist/database/files/000/dataset_402.dat &
Re: [galaxy-user] cuffcompare error in galaxy
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 On Mon, Jun 20, 2011 at 3:30 PM, Nate Coraor wrote: > 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 > > Carlos Javier Borroto wrote: >> 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 >> 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 : >> >> 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/s
Re: [galaxy-user] cuffcompare error in galaxy
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 Carlos Javier Borroto wrote: > 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 > 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 : > >> 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/softwa
Re: [galaxy-user] cuffcompare error in galaxy
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 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 : >> 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_
Re: [galaxy-user] cuffcompare error in galaxy
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 : > 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 > > > > > > > > > > ___ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > T
