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snayfach / MAGpurify

Improvement of metagenome-assembled genomes
GNU General Public License v3.0
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Analysis automation #20

Open Philippemetagenomica opened 2 years ago

Philippemetagenomica commented 2 years ago

Hello everybody. I have a question about this software. I have 5 directories with at least 40 bins in each. I need to analyze at least 4 modules. Do I have to do this for each bin? The software does not accept to put the directory and do for all the bins at once?

Philippemetagenomica commented 2 years ago

I've tried to run this comand: $magpurify phylo-markers be_30_BY_bins.* magpurify_teste but agpurify: error: unrecognized arguments: be_30_BY_bins.002.fasta.fna be_30_BY_bins.003.fasta.fna be_30_BY_bins.004.fasta.fna be_30_BY_bins.005.fasta.fna be_30_BY_bins.006.fasta.fna be_30_BY_bins.007.fasta.fna be_30_BY_bins.008.fasta.fna be_30_BY_bins.009.fasta.fna be_30_BY_bins.010.fasta.fna be_30_BY_bins.011.fasta.fna be_30_BY_bins.012.fasta.fna be_30_BY_bins.013.fasta.fna be_30_BY_bins.014.fasta.fna be_30_BY_bins.015.fasta.fna be_30_BY_bins.016.fasta.fna be_30_BY_bins.017.fasta.fna be_30_BY_bins.018.fasta.fna be_30_BY_bins.019.fasta.fna be_30_BY_bins.020.fasta.fna be_30_BY_bins.021.fasta.fna be_30_BY_bins.022.fasta.fna be_30_BY_bins.023.fasta.fna be_30_BY_bins.024.fasta.fna be_30_BY_bins.025.fasta.fna be_30_BY_bins.026.fasta.fna be_30_BY_bins.027.fasta.fna be_30_BY_bins.028.fasta.fna be_30_BY_bins.029.fasta.fna be_30_BY_bins.030.fasta.fna be_30_BY_bins.031.fasta.fna be_30_BY_bins.032.fasta.fna be_30_BY_bins.033.fasta.fna be_30_BY_bins.034.fasta.fna be_30_BY_bins.035.fasta.fna be_30_BY_bins.036.fasta.fna be_30_BY_bins.037.fasta.fna be_30_BY_bins.038.fasta.fna be_30_BY_bins.039.fasta.fna be_30_BY_bins.040.fasta.fna be_30_BY_bins.041.fasta.fna be_30_BY_bins.042.fasta.fna be_30_BY_bins.043.fasta.fna be_30_BY_bins.044.fasta.fna be_30_BY_bins.abund1 be_30_BY_bins.log be_30_BY_bins.marker be_30_BY_bins.marker_of_each_bin.tar.gz be_30_BY_bins.noclass be_30_BY_bins.summary be_30_BY_bins.tooshort magpurify_teste

magpurify_teste is my directory.

Why the extension is .fasta.fna I don't know The official one is.fasta Is the output from Maxbin. But I've tried to change for fna to run CheckM and here we have .fasta.fna so didn't work very well.

So, if someone could help I will thank you for the rest of my Ph.D

Thank you!!!!

TomasaSbaffi commented 2 years ago

Hello, did you solve your issue? I am a beginner and trying to find the best solution to this issue myself, for now I find looping as a best solution but also I am wondering if there is an altenative included in the package that I could not find. Also, I see authors applying MAGpurify after dereplication with (i.e.) DAS tool so to have a lower "unique" set of bins to clean up.

Anyone any idea?