File path in *.ds file
JinyuanSun opened this issue · 3 comments
JinyuanSun commented
Hi,
It seems the file name in *.ds file does not support an absolute path like /home/user/dataset/*.pdb.
I have a .ds file:
/home/jsun/gpse_v2/test/structure_dataset/A0A1Q8LK65_AF.pdb
/home/jsun/gpse_v2/test/structure_dataset/W7ISS8_AF.pdb
/home/jsun/gpse_v2/test/structure_dataset/A5EDZ7_AF.pdb
/home/jsun/gpse_v2/test/structure_dataset/A0A3G7HEQ2_AF.pdb
/home/jsun/gpse_v2/test/structure_dataset/A0A6J4VWF3_AF.pdb
/home/jsun/gpse_v2/test/structure_dataset/A0A1R4K1N1_AF.pdb
/home/jsun/gpse_v2/test/structure_dataset/A0A7W8E001_AF.pdb
and in the error log:
[INFO] Console - ----------------------------------------------------------------------------------------------
[INFO] Console - P2Rank 2.4
[INFO] Console - ----------------------------------------------------------------------------------------------
[INFO] Console -
[INFO] Main - loading default config from [/home/jsun/gpse_v2/p2rank_2.4/config/default.groovy]
[INFO] Main - looking for dataset in dataset_base_dir [/home/jsun/gpse_v2/GPSE/filtered.ds]...
[INFO] Dataset - loading dataset [/home/jsun/gpse_v2/GPSE/filtered.ds]
[ERROR] Dataset - protein file doesn't exist: .//home/jsun/gpse_v2/test/structure_dataset/A0A7W8E001_AF.pdb
[ERROR] Dataset - protein file doesn't exist: .//home/jsun/gpse_v2/test/structure_dataset/W7ISS8_AF.pdb
[ERROR] Dataset - protein file doesn't exist: .//home/jsun/gpse_v2/test/structure_dataset/A0A1Q8LK65_AF.pdb
[ERROR] Dataset - protein file doesn't exist: .//home/jsun/gpse_v2/test/structure_dataset/A5EDZ7_AF.pdb
[ERROR] Dataset - protein file doesn't exist: .//home/jsun/gpse_v2/test/structure_dataset/A0A1M4DY30_AF.pdb
[ERROR] Dataset - protein file doesn't exist: .//home/jsun/gpse_v2/test/structure_dataset/A0A447WAH0_AF.pdb
[ERROR] Dataset - protein file doesn't exist: .//home/jsun/gpse_v2/test/structure_dataset/A0A1R4K1N1_AF.pdb
How can I modify the setting to avoid this? Thanks a lot! 🙏
rdk commented
Thanks for the bug report. This is a bug and unfortunately there is no workaround or setting that would fix it.
It fill be fixed in the next release. It's already fixed in develop branch so you can make your own build.
rdk commented
Fix will be included in the next release.