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Sydney-Informatics-Hub / Scalable-DIA-NN

Scalable workflow to run https://github.com/vdemichev/DiaNN on NCI Gadi HPC
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Add to the README a note about 'ln: file exists' error when running setup #12

Open calizilla opened 8 months ago

calizilla commented 8 months ago

If the inputs contain a filename clash (ie there are subdirectories containing the raw input data, and one or more of the files among these directories have identical basenames) the setup script will print a warning message such as: 

ln: failed to create symbolic link 'Raw_data/ZenoTof_LS_MM_D_60_1.wiff': File exists
ln: failed to create symbolic link 'Raw_data/ZenoTof_LS_MM_D_60_1.wiff.scan': File exists
ln: failed to create symbolic link 'Raw_data/ZenoTof_LS_MM_A_38_3.wiff': File exists
ln: failed to create symbolic link 'Raw_data/ZenoTof_LS_MM_A_38_3.wiff.scan': File exists

The setup script will run to completion, but only one of the files for each identical name will be linked. User will need to check these files and either rename the affected files to avoid clashes, or delete any unintended duplicates from the source directory. Then unlink the linked files and rerun setup to ensure the Raw_data dir is clean.

calizilla commented 3 months ago

Check that this resolution https://github.com/Sydney-Informatics-Hub/Scalable-DIA-NN/issues/26 does not prevent identification of such affected files