---------- Forwarded message ---------- From: XiaoTao Jiang biofuture.jiang@gmail.com Date: 2013/9/2 Subject: About empty no peek problem To: galaxy-user-request@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