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LyonsLab / coge

CoGe (Comparative Genomics) Platform

Home Page:http://genomevolution.org

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spaces in iRODS folder names causing failures

elyons opened this issue · comments

commented

If there are spaces in iRODS folder names, CoGe's workflow will fail:

Fetching /iplant/home/arabiflora/coge_data/Concatenated AFG data/A02concat_R1.fastq
Job: mkdir -p /scratch/coge/tmp/uploads/arabiflora/FCFBB44EEBD611EAA59889A743376945/irods/iplant/home/arabiflora/coge_data/Concatenated AFG data && export irodsEnvFile='/opt/apache2/coge/irodsEnv' && iget -fT '/iplant/home/arabiflora/coge_data/Concatenated AFG data/A02concat_R1.fastq' '/scratch/coge/tmp/uploads/arabiflora/FCFBB44EEBD611EAA59889A743376945/irods/iplant/home/arabiflora/coge_data/Concatenated AFG data' && touch /scratch/coge/tmp/uploads/arabiflora/FCFBB44EEBD611EAA59889A743376945/irods/iplant/home/arabiflora/coge_data/Concatenated AFG data/A02concat_R1.fastq.done
Submitted at: 31/08/20 at 03:13:44PM
Completed at: 31/08/20 at 03:13:58PM
Execution time: 12.550773 sec
Assigned to task: 14389
Return status: 0
Expected outputs: /scratch/coge/tmp/uploads/arabiflora/FCFBB44EEBD611EAA59889A743376945/irods/iplant/home/arabiflora/coge_data/Concatenated AFG data/A02concat_R1.fastq, /scratch/coge/tmp/uploads/arabiflora/FCFBB44EEBD611EAA59889A743376945/irods/iplant/home/arabiflora/coge_data/Concatenated AFG data/A02concat_R1.fastq.done
Command Output: