![]() Tail fiber proteins in the same PC, that could be indicative of something pretty interesting! Or perhaps (more The output files you can find how many keywords were found in the same VC or PC. However, vConTACT will aggregate these gene keywords and in Note: These keywords have no effect on the calculations. (Multiple keywords must be separated using " ":) Protein_id,contig_id,keywords ref|NP_039777.1|,Sulfolobus spindle-shaped virus 1,ORF B-251 ref|NP_039778.1|,Sulfolobus spindle-shaped virus 1,ORF D-335 ref|NP_039779.1|,Sulfolobus spindle-shaped virus 1,ORF E-54 ref|NP_039780.1|,Sulfolobus spindle-shaped virus 1,ORF F-92 ref|NP_039781.1|,Sulfolobus spindle-shaped virus 1,ORF D-244 ref|NP_039782.1|,Sulfolobus spindle-shaped virus 1,ORF E-178 ref|NP_039783.1|,Sulfolobus spindle-shaped virus 1,ORF F-93 ref|NP_039784.1|,Sulfolobus spindle-shaped virus 1,ORF E-51 ref|NP_039785.1|,Sulfolobus spindle-shaped virus 1,ORF E-96 That said, if there is an issue and you're trying to troubleshoot,Īlways re-run and specify a new output directory. Recovery and re-start of any interrupted analysis. Generally speaking, if a user provides an intermediaryįile, vConTACT2 will skip the steps it would of taken to get to that file. Providing files at various points along the processing pipeline. ![]() Provide a more seamless "pipeline" to go from raw data to a finished network. VConTACT2 tries to alleviate some of the challenges created by the complex file format of the original vConTACT and "-c1-bin" must point to the jarfile, not to the directory it's in. Vcontact -raw-proteins -rel-mode ‘Diamond’ -proteins-fp -db 'ProkaryoticViralRefSeq94-Merged' -pcs-mode MCL -vcs-mode ClusterONE -c1-bin -output-dir Please use this file to create and bootstrap the vConTACT container. A little moreĭetail is provided at our iVirus website, and if you're really adventurous, check outĪ singularity definitions file (containing all the "instructions" to download and install everything) is providedĪccompanying this documentation. Singularity is a containerization solution that allows users/developers to package anĮntire operating systems' worth of files into a single file so that they can run a program on any system. While Windows is not officially supported, users have been able to run vConTACT on these machines (usually Installing vConTACT dependencies may seem daunting, but the instructions below should work for the vast majority of vConTACT will use any user-provided paths before searching through system PATHs. Installation (below) should make this a mostly Generally you want these tools to be in your system or user PATHs. ClusterONE (only if using for PC or VC construction).DIAMOND (only if using DIAMOND for PC construction).BLASTP (only if using BLASTP for PC construction).VConTACT also requires several executables, depending on use. VConTACT requires numerous python packages to function correctly, and each must be properly installed and working for To cluster and provide taxonomic context of metagenomic sequencing data. VConTACT2 is a tool to perform guilt-by-contig-association classification of viral genomic sequence data. Installations, running, FAQs, among others! ![]() Welcome to the vConTACT2 wiki! Here you can find detailed descriptions and other helpful information for requirements,
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