eukdetect gets stuck on taxonomize

[umerijaz]

Hi Abigail,

For some reason eukdetect gets stuck at the taxonomize stage, i.e., snakemake sleeps and is forever stuck. I thought it was an error with ete3, and even regenerated the taxa.sqlite and taxa.sqlite.traverse.pkl for taxdump_1_14_2020.tar.gz that is available at figshare.

I think the problem is with these python files count_primary_and_secondary.py
Perhaps there is a setting for snakemake which can prevent it from sleeping?

For the test data both aln and filtering are produced as follows:
[ ~/test/tests/output2]$ ls
aln filtering
[ ~/test/tests/output2]$ ls aln
test_aln_q30_lenfilter.sorted.bam
[ ~/test/tests/output2]$ ls filtering
test_aln_q30_lenfilter_complexityfilter_dupfilter.sorted.bam test_aln_q30_lenfilter_complexityfilter_dupfilter.sorted.bam.bai test_read_counts_and_mismatches.txt

Thanks!
Umer