---------- Forwarded message ---------- From: XiaoTao Jiang <biofuture.ji...@gmail.com> Date: 2013/9/2 Subject: About empty no peek problem To: galaxy-user-requ...@lists.bx.psu.edu
Dear all Today I embed one of my R script into local galaxy, I have encountered a strange problem. The script can successfully in local. However, when I run it online in galaxy, the output file is empty and in history panel, it display empty and no peek. I searched the mailing list, but still can not find solutions to solve it. The command display in sever is : *key part * galaxy.jobs.runners.local DEBUG 2013-09-02 17:29:49,297 *executing:* R CMD BATCH --slave "--args /Users/jiangxiaotao/Programe/galaxy-galaxy-dist-a4113cc1cb5e/database/files/000/dataset_44.dat /Users/jiangxiaotao/Programe/galaxy-galaxy-dist-a4113cc1cb5e/database/files/000/dataset_64.dat" barchart.r galaxy.jobs.runners.local DEBUG 2013-09-02 17:29:49,493 *execution finished: * R CMD BATCH --slave "--args /Users/jiangxiaotao/Programe/galaxy-galaxy-dist-a4113cc1cb5e/database/files/000/dataset_44.dat /Users/jiangxiaotao/Programe/galaxy-galaxy-dist-a4113cc1cb5e/database/files/000/dataset_64.dat" barchart.r galaxy.jobs DEBUG 2013-09-02 17:29:49,538 Tool did not define exit code or stdio handling; checking stderr for success galaxy.tools DEBUG 2013-09-02 17:29:49,697 Error opening galaxy.json file: [Errno 2] No such file or directory: '/Users/jiangxiaotao/Programe/galaxy-galaxy-dist-a4113cc1cb5e/database/job_working_directory/000/71/galaxy.json' galaxy.jobs DEBUG 2013-09-02 17:29:49,759 job 71 ended I check the generated output file /Users/jiangxiaotao/Programe/galaxy-galaxy-dist-a4113cc1cb5e/database/files/000/dataset_64.dat It is empty zero in size and then I run the command in local command R CMD BATCH --slave "--args /Users/jiangxiaotao/Programe/galaxy-galaxy-dist-a4113cc1cb5e/database/files/000/dataset_44.dat /Users/jiangxiaotao/Programe/galaxy-galaxy-dist-a4113cc1cb5e/database/files/000/dataset_64.dat" barchart.r The output is correct. Any suggestions will be appreciated !! Xiaotao JIANG Regards, The University of HongKong Department of Civil Engineering
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