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
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:
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@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@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
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:
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 carlos.borroto@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@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
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:
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:
Thanks Nate,
For now I downloaded: https://bitbucket.org/galaxy/galaxy-central/raw/e74e89a4c03a/tools/ngs_rna/c... https://bitbucket.org/galaxy/galaxy-central/raw/d1f2d2e5246a/tools/ngs_rna/c...
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 nate@bx.psu.edu 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 carlos.borroto@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@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
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:
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:
galaxy-user@lists.galaxyproject.org
-
Carlos Javier Borroto -
Nate Coraor