Hello,
I have seen some previous issues on this but I still dont really understand if this is a bug of this version or I am missing something.
My dRep run exits normally. I have run 3 different binners and then binette (refinement tool) which also produces some qaulity reports based on checkM2. This is what I use as input for dRep run so it does not run checkM2 again. My goal is to extract medium and high quality MAGs so my first question is should I filter them first before dRep? Then I would like to have a file with quality metrics of the final dreplicated genomes but my widb.csv has NAs. I mean I can do this manually but still it would be helpful to have this output with the run. I attach the relevant output datatables
genomeInformation.csv
Widb.csv
log_text.txt
This is my code
dRep dereplicate "$DREP_OUT" \
--genomes "$STAGING"/*.fa \
--genomeInfo "$GENOME_INFO" \
--processors "$SLURM_CPUS_PER_TASK" \
--completeness 50 \
--contamination 10 \
--S_algorithm fastANI \
--P_ani 0.9 \
--S_ani 0.99 \
--cov_thresh 0.1 \
--clusterAlg average
Thanks loads!
Hello,
I have seen some previous issues on this but I still dont really understand if this is a bug of this version or I am missing something.
My dRep run exits normally. I have run 3 different binners and then binette (refinement tool) which also produces some qaulity reports based on checkM2. This is what I use as input for dRep run so it does not run checkM2 again. My goal is to extract medium and high quality MAGs so my first question is should I filter them first before dRep? Then I would like to have a file with quality metrics of the final dreplicated genomes but my widb.csv has NAs. I mean I can do this manually but still it would be helpful to have this output with the run. I attach the relevant output datatables
genomeInformation.csv
Widb.csv
log_text.txt
This is my code
Thanks loads!