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MGXlab / CAT_pack

CAT/BAT/RAT: tools for taxonomic classification of contigs and metagenome-assembled genomes (MAGs) and for taxonomic profiling of metagenomes
MIT License
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Help updating taxonomy #43

Open mihinduk opened 4 years ago

mihinduk commented 4 years ago

Hi, I just updated my databases and need to update my annotations following these instructions: Alternatively, if you already have a predicted proteins fasta file and/or an alignment table for example from previous runs, you can supply them to CAT, which will then skip the steps that have already been done and start from there:

$ CAT contigs -c {contigs fasta} -d {database folder} -t {taxonomy folder} -p {predicted proteins fasta} -a {alignment file}

Can you please tell me the name of the predicted proteins fasta and alignment file to use?

Thank you, Kathie Mihindukulasuriya

bastiaanvonmeijenfeldt commented 4 years ago

Hi Kathie,

If I understand correctly you already ran CAT on your contigs once, updated some database files, and want to run CAT again while skipping some of the earlier steps.

Which databases did you update? If you only updated your taxonomy files you can skip the DIAMOND alignment. If you updated NR you'll have to run DIAMOND again. In any case protein predictions can be skipped!

The {predicted proteins fasta} file from earlier runs is called out.CAT.predicted_proteins.faa. The {alignment file} is called out.CAT.alignment.diamond.

Hope this helps!