Nothing happens after building phylogeny

nothing seems to be happening after building Phylogeny step:
Hi @f.asnicar!
.tre file is generated but there is no data in it, all steps ran smoothly upto the concatenation of alignments is done and then it says building phylogeny and then nothing is happening it seems…command is still running but I do not see any output getting generated.

Screenshot of the tmp directory:

Do you have any idea why this is happening?



In the second screenshot, you shouldn’t lookt at the tmp folder, but at its parent. In your case (from the first screenshot), should be: /luster/rsharma/PHYLO_ANALYSIS/OUT3/ALL_phylophlan/. This would be the output folder.

Although, if PhyloPhlAn says Building phylogeny [..], then it means that RAxML/FastTree (or whichever tool you specified) is still running.


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