solve ERROR:vcontact2: Error in contig clustering ERROR:vcontact2: No columns to parse from file

Issue #97 new
Former user created an issue

I run successfully.

install: mamba create --name vContact2 python=3.7; conda activate vContact2; mamba install -y -c conda-forge pytables biopython networkx numpy pandas scipy scikit-learn psutil pyparsing mamba install -y -c bioconda mcl blast diamond; wget https://bitbucket.org/MAVERICLab/vcontact2/get/master.tar.gz; tar xvf MAVERICLab-vcontact2-c0413a6c92e8; cd MAVERICLab-vcontact2-c0413a6c92e8 && python3 -m pip install ; wget -c http://www.paccanarolab.org/static_content/clusterone/cluster_one-1.0.jar; mv cluster_one-1.0.jar /nfs3/public2/User/name/miniconda3/bin/; cd /nfs3/public2/User/name/miniconda3/bin/; chmod 755 cluster_one-1.0.jar

run: conda activate vContact2; vcontact2 --raw-proteins ./test.fasta --rel-mode 'Diamond' --proteins-fp gene2genome.csv --db 'ProkaryoticViralRefSeq211-Merged' --pcs-mode MCL --vcs-mode ClusterONE --output-dir ./vcontact2out -t 20

Comments (1)

  1. k6logc

    Yes! 🎉 This one worked for me, thank you! Only minor tweak is from [python3 -m pip install] to [python3 -m pip install .]

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