I’m trying to build a phylogenetic tree from a custom database of MAGs.
When running phylophlan with the following settings:
–verbose 2>&1 | tee phylophlan.log
I successfully run the script all the way through generating the output_tol/bins_concatenated.aln. At the last step in iqtree, I receive the error:
[e] Command ‘[’/miniconda3/bin/iqtree’, ‘-quiet’, ‘-nt’, ‘AUTO’, ‘-m’, ‘LG’, ‘-s’, ‘output_tol/bins_concatenated.aln’, ‘-pre’, ‘/output_tol/bins.tre’]’ returned non-zero exit status 2.
I can see that iqtree seems to be the right version and functioning properly (/miniconda3/bin/iqtree --help generates the help list).
When I try to run the command by itself I get the error “Sequence XXX contains too many characters”, and it appears that my sequence alignment file contain gaps, but all samples do not have the same lengths.
Is there a parameter I missed in the phytophlan function call to remedy this error?