Sam Lambrechts

So is this limited to 16 threads or not? Because I also get this warning

When I run `echo $0` outside of Snakemake I get `-bash` conda and mamba are available in that shell, but I'm not sure how I can find out whether they...

I also noticed this, and wonder why? Wouldn't complex metagenomes benefit from a higher `--min-count` setting? Or is this not as straightforward, because complex metagenomes might contain both organisms that...

Ok great, thank you. Is there an option to only use the custom databases you specify, without rerunning the standard databases?

Ok thank you. The reason I ask, is because I'm running out of time on our HPC. Maximum runtime for a job is 72 hours, and it's not enough with...

Hi, Disabling the standard databases to only get output from custom databases worked for me, so thanks for that! > If you disable too many, you would lose the utility...

Hi Francisco, Ok interesting. I added the log parameter to both the binRefine and metabatCross rules, which produces the log files, but they are all empty. Best, Sam

Ok when I manually put in the commands for a specific sample, I get an error at the following step: ``` (metawrap) [vsc42339@gligar08 UT_6]$ mv $(basename /scratch/gent/vo/000/gvo00043/vsc42339/MICROBIAN/metaGEM/concoct/UT_6/UT_6.concoct-bins) $(echo $(basename /scratch/gent/vo/000/gvo00043/vsc42339/MICROBIAN/metaGEM/concoct/UT_6/UT_6.concoct-bins)|sed...

Yes, I did: ``` (base) [vsc42339@gligar08 metaGEM]$ set +u;source activate envs/metawrap;set -u; (metawrap) [vsc42339@gligar08 metaGEM]$ mkdir -p /scratch/gent/vo/000/gvo00043/vsc42339/MICROBIAN/metaGEM/refined_bins/UT_6 (metawrap) [vsc42339@gligar08 metaGEM]$ fsampleID=$(echo $(basename $(dirname /scratch/gent/vo/000/gvo00043/vsc42339/MICROBIAN/metaGEM/concoct/UT_6/UT_6.concoct-bins))) (metawrap) [vsc42339@gligar08 metaGEM]$ mkdir -p...

Ok sorry I forgot the dot at the end of `cp -r /scratch/gent/vo/000/gvo00043/vsc42339/MICROBIAN/metaGEM/concoct/UT_6/UT_6.concoct-bins /scratch/gent/vo/000/gvo00043/vsc42339/MICROBIAN/metaGEM/metabat/UT_6/UT_6.metabat-bins /scratch/gent/vo/000/gvo00043/vsc42339/MICROBIAN/metaGEM/maxbin/UT_6/UT_6.maxbin-bins .` to specify the location where they need to be copied. So anyway, this command...