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hdf5 issue - unable to open file #19
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Hi Thomas, I'm not sure about this one. Can you make sure that the input files do exist and that the Rayan |
My experience is that such errors are the result of specifying paths for input or output files. minia doesn't deal well with that. If I start in my project root and call, for instance |
hi Sven, yes in fact, gatb-pipeline is even less robust than minia (as it accumulates the bugs of both :) ). Sorry about that, it's indeed a more sure thing to specify full paths rather than relative paths. And regarding output, it's a byproduct of the fact that I always run analyses in current folders (e.g. |
I'm going to close this one, feel free to reopen in case the problem occurs again. |
I understand that I am incredibly late to the party but I ran into this problem again and remembered that this ticket exists. Thank you @rchikhi and @svenrahmann for commenting on this and providing valuable hints! For the gatb-minia-pipeline in particular specifying the absolute path for the output folder (parameter -o) solved the issue. Bonus: specifying the absolute path for the input files only does not help. It looks like it does at first but, due to the required solution above, the run breaks after the first iteration. |
Hi,
I previously ran the gatb-minia-pipeline successfully on CentOS Linux 7.6 but when I switched to an Ubuntu 16.04 LTS, I ran into some trouble:
Has this been seen/solved before?
Thanks.
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