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You should have the following two directories share/phylosift/markers and /share/phylosift/ncbiThat's where phylosift will look for the databases by default.
On Tue, May 22, 2018 at 6:30 PM, kyle catalan <kyleca...@gmail.com> wrote:
Hi all,I have recently downloaded Phylosift from the following link:And I've tried executing the workflow for the tutorial. However, when I input the command:./phylosift all -f --paired tutorial_data/HMP_1.fastq.gz tutorial_data/HMP_2.fastq.gzI get the error: NCBI taxonomy data not found and unable to connect to update server.On another post here, someone had a similar problem and the solution for that was to download the ncbi directory from figshare. So, I've downloaded it in my home directory in the folder "share" but when I try to execute the command for the tutorial, the same error comes up. I've also tried to download the markers for phylosift, but the same error also comes up. How should I proceed?Thank you for any help.Regards,Kyle
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alignDir run_info.txt sequence_taxa.txt
blastDir sequence_taxa.1.txt taxa_90pct_HPD.txt
HMP_1.fastq.gz.html sequence_taxa_summary.1.txt taxasummary.txt
marker_summary.txt sequence_taxa_summary.txt treeDir