Closed mgalardini closed 3 years ago
Hi Marco,
Thanks for the detailed report. Really this should work with the options you've used, so we will try and fix. What is in out/poppunk
after running the first command?
$ ls out/poppunk/
poppunk_distanceDistribution.png poppunk.dists.npy poppunk.dists.pkl poppunk.h5 poppunk_qcreport.txt
Hi Marco - I'm looking at a fix on our most recent branch (refine_fix
), but I can't replicate in the test
directory with:
../poppunk-runner.py --create-db --r-files references.txt --output out/poppunk --qc-filter continue
../poppunk-runner.py --fit-model dbscan --ref-db out/poppunk
Does this work for you? Also, there are two --output
flags in your first command, in case that's causing any problems.
I updated poppunk to version 2.4.0 to fix #171 and it seems that the issue is not there anymore. However if I use version 2.3.0 the issue reappears, even after removing the extra --output
argument in the first command.
I changed some of the file parsing behaviour in the upgrade to v2.4, hopefully that's fixed the behaviour, please let us know if this issue reappears.
Fantastic, will certainly do. Thanks for the great software
Versions
Command used and output returned
Describe the bug
When creating the sketches, the output database can be indicated as being nested inside an existing directory, but not when fitting the model. I believe the problem is here when the code is looking at the base directory. I am fine just placing the db in the same directory in which I am running poppunk but maybe you have an interest in fixing this.