Emily Van Syoc

Thanks for the quick reply! That ran with no errors, and in the 'results' folder there is this file: test_aln_q30_lenfilter.sorted.bam

I should mention that I'm working on an HPC cluster, not sure if that is part of the install problem as I've had issues with bowtie2 when installing metaphlan and...

Sorry for the delayed reply - I re-visited this after fixing the bowtie issue in other softwares but still having issues here. I'm running it locally right now in the...

In other news, I tried it on my local machine and am running into issues with the conda environment: $ conda env update --name eukdetect -f environment.yml Collecting package metadata...

I've done more troubleshooting on this: I ran each command in the eukdetect.rules file by hand and they ran successfully, so the problem is somewhere in the snakemake process? Here...

Here it is below (I'm using the test samples) $ cat config.yml #Default config file for eukdetect. Copy and edit for analysis #Directory where EukDetect output should be written output_dir:...

Good news, I've figured out a workaround and have a better idea of what's happening on the cluster... snakemake is not inheriting the conda environment in the shell I'm executing...

Hello - I'm running into a similar problem. Unfortunately, removing the extra column in the krakenUniq report is not sufficient to make kraken-biom work on krakenUniq reports, and my guess...

It looks like the developer has not been able to fix this bug as I am having the same issue...