brokit.get_clusters_from_fasta_filepath failing to remove output files

[charudatta-navare]

@wasade @gregcaporaso

I need to make uclust calls a large number of times in my script, and I get 'OSError: Too many open files' when the dataset size exceeds a certain limit, when I am using brokit.get_clusters_from_fasta_filepath function. However, when I use qiime_system_call instead to call uclust, I don't get an error. I think get_clusters_from_fasta_filepath may not be removing some output files, and I am not sure whether this is related to scikit-bio or brokit. I tried changing suppress_stdout of Uclust class to true, but that did not solve the problem.

Thanks!

[josenavas]

The issue is not the fact of not removing files, but keeping files open.