-
from code added in 2b78b96, this:
```shell
srun -p high2 --time=5:00:00 --nodes=1 --cpus-per-task 32 --mem 50GB --pty /bin/bash
snakemake -j 32 --snakefile benchmarking.snakefile
csvtk concat b…
-
@luizirber and I chatted a bit over slack about the new [mastiff](https://github.com/sourmash-bio/mastiff) service he built, which allows ~realtime search of the SRA public metagenomes (!!)
This, i…
-
Hi there,
I just re-ran a subset of my data through METABOLIC-C. The last time I ran the program, I pointed the call to the entire list of transcriptome bams and I received molecular weight scores p…
-
Hi there,
I am aiming to make plots with coverage data for several bam files. I get .depth files and .csv files (as well as ORF_calls and HMM_results. However, there are no plots. Here is my input a…
-
Hi Stephen,
I was wondering if you have the sample-specific metagenomes that you assembled available. These would be of great use to me in addition to the representative genomes.
Thank you,
Mat…
-
If I were to bin 2 metagenomes that both contain an E. coli clonal population (along with other stuff). Both metagenomes would return a genome named Escherichia coli clonal population. It may be use…
-
relevant to #309
I've been working on annotating catlases. In this use case, I built a "metapangenome" graph. I did a genome query (_R. gnavus_) in 605 gut microbiome metagenomes, and then combined…
-
Hi,
I am using this pipeline to reanalyze some data from Illumina Novaseq PE250bp.
And I have noticed that in this paper , they sequenced at Hiseq PE250bp (McNichol, J., Berube, P., Biller, S.…
-
Hi,
I had to reinstall fama on a new server and I used the same 'recipe' that you sent me last year. However, I get an error:
Writing /gpfs/fs3c/aafc/aafc_shp/can0002/deep-metagenomes/fama/Gorzelak/…
-
Hi I am getting the following error:
sample1.fastq.gz is either empty or contains multiple entries with the same identifier. Please check your input FASTA file and execute genomad annotate again. …