drep

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Unknown AssertionError

4

Hey @MrOlm, I'm running `dRep` via snakemake with the following: ``` Job 0: Running dRep on all NOMIS MAGs Reason: Forced execution (date && dRep dereplicate $(dirname /scratch/users/sbusi/nomis_mags/results/Bins/dRep/dereplicated_genomes) \ -p...

susheelbhanu

dRep facing error while installing by conda

4

conda config --add channels bioconda; conda install drep Warning: 'bioconda' already in 'channels' list, moving to the top Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve....

poddarharsh15

dRep taking much longer than estimated using FastANI

2

Hi, I am dereplicating about 5,000 MAGs using dRep 3.3.0 with the new default FastANI genome comparison algorithm. dRep initially estimated a pairwise alignment phase of about 160 minutes, but...

jdwinkler-lanzatech

mash pre-cluster sketch size?

5

Dear dRep team, This is confusing to me when using mash sketch size 1000: def run_mash_on_genome_chunks(genome_chunks, mash_exe, sketch_folder, MASH_folder, logdir, **kwargs): dry = kwargs.get('dry', False) p = kwargs.get('processors', 6) MASH_s...

jianshu93

Support for long genome name

2

- Feature request Recent years, `DASTool` is being popular. However, `DASTool` always put bins to `_DASTool_bins/`, so when I compare Bins from different folder, an `duplicate genome basenames` exception will...

Hocnonsense

drep to consider rRNA genes?

2

Hi Thanks for a great tool. Have you considered a scoring scheme taking the presence of e.g. rRNA genes into account to prioritize bins meeting more of the MiMAG requirements?...

Kirk3gaard

Advice on handling memory errors

4

Hi @MrOlm I ran into a memory error while attempting to dereplicate a dataset of ~300k prokaryotic genomes Do you have any advice on how to best get around this?...

cazzlewazzle89

Why the value of # scaffolds, # contigs, and Predicted genes are same?

2

Hi Matt, The column of **# Schaffolds** in my Chdb.csv file and my **Predicted genes** are the same. What went wrong there according to your experience? Best, Bing

B-1991-ing

Drep doesn't detect mash even if it's installed.

3

Hello, We encountered the following problem. https://github.com/metagenome-atlas/atlas/issues/547#issuecomment-1230550503 Drep doesn't detect mash even though it is installed.

SilasK

UnicodeEncodeError: 'ascii' codec can't encode character '\u21b5' in position 4397: ordinal not in range(128)

3

Hi, thanks for your tools! I am running dRep v3.4.0 for dereplicating the genome, and I have installed the checkm, here is the err. Why does this happen? *************************************************** ..::...

yuemo98